From f35a640c1c9efef8c066463def2f1c47e193dada Mon Sep 17 00:00:00 2001 From: Valentina Date: Thu, 15 Oct 2026 16:01:15 +0200 Subject: [PATCH 01/21] fix(viewer): select literals per property with language fallback --- lode/viewer/base_viewer.py | 208 ++++++++++++++++++++----------------- lode/viewer/owl_viewer.py | 14 ++- lode/viewer/rdf_viewer.py | 25 ++--- lode/viewer/skos_viewer.py | 28 +++-- tests/test_owl_viewer.py | 55 ++++++++++ 5 files changed, 203 insertions(+), 127 deletions(-) diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 2593ecc..548898d 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -1,4 +1,8 @@ -# base_viewer.py +"""Generic viewer: turns model instances into the dictionaries the HTML templates render. + +Format-specific viewers (OWL, RDF, SKOS) extend it with their table of contents +and display names. It also serializes the provenance of each entity. +""" import hashlib import re from typing import Dict, List, Optional, Tuple @@ -6,7 +10,6 @@ import urllib.parse from rdflib import Graph, URIRef, BNode, Literal as RDFlibLiteral -from rdflib.namespace import RDF, OWL from lode.reader.provenance_graph import ProvenanceGraph from lode.helpers.rdf import iri_local_name @@ -25,18 +28,28 @@ ] def formats_for(graph): + """Return the serialization formats available for a graph. + + Quad formats are offered only for a ProvenanceGraph, because only it keeps + the named graph of each triple. + """ return QUAD_SERIALIZATION_FORMATS if isinstance(graph, ProvenanceGraph) else SERIALIZATION_FORMATS class BaseViewer: - """Base viewer per visualizzare istanze estratte dal Reader.""" - + """Base viewer to display the instances extracted by the Reader.""" + def __init__(self, reader): + """Bind the viewer to a Reader and share its instance cache.""" self.reader = reader self._cache = reader._instance_cache # it uses self._internal_iris = None self._ontology_ns = None def _get_ontology_ns(self) -> str: + """Return the namespace of the documented ontology (its IRI ending in '/' or '#'), or ''. + + Computed once from the first Model instance and then cached. + """ if self._ontology_ns is None: self._ontology_ns = '' for inst in self.get_all_instances(): @@ -48,15 +61,17 @@ def _get_ontology_ns(self) -> str: return self._ontology_ns def _has_local_triples(self, uri) -> bool: + """Return True if the graph has at least one triple whose subject is this IRI.""" if not uri: return False return (URIRef(str(uri)), None, None) in self.reader._graph def _formats(self): + """Return the serialization formats available for the loaded graph.""" return formats_for(self.reader._graph) def _with_provenance(self, sub): - """Con moduli attivi: ricolloca le triple di `sub` nei named graph d'origine.""" + """With modules active, put the triples of `sub` back into their original named graphs.""" ds = self.reader._graph if not isinstance(ds, ProvenanceGraph): return sub @@ -69,6 +84,10 @@ def _with_provenance(self, sub): return out def _is_internal(self, uri) -> bool: + """Return True if the IRI belongs to a browsable entity of this documentation. + + The set of IRIs is built once, on first use. + """ if not uri: return False if self._internal_iris is None: @@ -80,7 +99,7 @@ def _is_internal(self, uri) -> bool: return str(uri) in self._internal_iris def get_all_instances(self) -> List: - """Ottiene tutte le istanze (esclusi literal).""" + """Return all the instances in the cache, literals excluded.""" instances = [] for uri_id, instance_set in self._cache.items(): @@ -91,53 +110,49 @@ def get_all_instances(self) -> List: instances.extend(instance_list) return instances - + def get_instances_from_single_resource(self, resource_uri: str) -> Optional[set]: - """Ottiene istanze per un URI specifico dalla cache.""" - # Cerca l'URI nella cache + """Return the cached instances registered under an IRI, or None when it is unknown.""" + # Look the IRI up in the cache for uri_id in self._cache.keys(): if str(uri_id) == resource_uri: return self._cache[uri_id] return None + def _select_by_language(self, values: List, language: Optional[str] = None) -> List: + """Keep the values of one property in the best available language. + + The choice is made per property, not per literal: only with all the + siblings in view can a fallback exist. Tags follow BCP 47, so they are + compared case-insensitively. Order of preference (RFC 4647 lookup): the + exact tag, the tag truncated from the right (en-GB, then en), 'en', + untagged literals, then every literal sorted by tag (nothing disappears). + Non-literal values always pass, and the input order is kept. + """ + lits = [v for v in values if isinstance(v, Literal)] + parts = (language or "en").strip().lower().split("-") + # shortcut: no skipping of singleton subtags (zh-x-private), upgrade if such tags matter + chain = ["-".join(parts[:i]) for i in range(len(parts), 0, -1)] + ["en"] + + def tagged(wanted: str) -> List: + """Literals whose tag is exactly `wanted`, ignoring case.""" + return [l for l in lits if (l.get_has_language() or "").lower() == wanted] + + chosen = (next((m for m in map(tagged, chain) if m), None) + or [l for l in lits if not l.get_has_language()] + or sorted(lits, key=lambda l: str(l.get_has_language() or ""))) + keep = {id(l) for l in chosen} + return [v for v in values if not isinstance(v, Literal) or id(v) in keep] + def _get_best_label(self, resource, language: Optional[str] = None) -> Optional[str]: """Gets the best label to display: language > preferred_label > label > identifier.""" - # 1. Force 'en' as the absolute default if no language makes it this far - target_lang = language.strip().lower() if language else "en" - - # Check Preferred Labels for the target language - labels = resource.get_has_preferred_label() - for label in labels: - if hasattr(label, 'get_has_language') and label.get_has_language(): - if label.get_has_language().lower().startswith(target_lang): - # RETURN RAW LABEL - return label.get_has_value() - - # Check Normal Labels for the target language - labels = resource.get_has_label() - for label in labels: - if hasattr(label, 'get_has_language') and label.get_has_language(): - if label.get_has_language().lower().startswith(target_lang): - # RETURN RAW LABEL - return label.get_has_value() - - # --- DETERMINISTIC FALLBACKS --- - # If we reach here, no English label exists. - # We sort them by language tag. - - labels = resource.get_has_preferred_label() - if labels: - sorted_labels = sorted(labels, key=lambda x: str(x.get_has_language() or "")) - # RETURN RAW LABEL - return sorted_labels[0].get_has_value() - - labels = resource.get_has_label() - if labels: - sorted_labels = sorted(labels, key=lambda x: str(x.get_has_language() or "")) - # RETURN RAW LABEL - return sorted_labels[0].get_has_value() + # Preferred labels come first, so they win within the same language + labels = list(resource.get_has_preferred_label()) + list(resource.get_has_label()) + selected = self._select_by_language(labels, language) + if selected: + return selected[0].get_has_value() # Final Fallback: The URI Identifier resource_id = resource.get_has_identifier() @@ -182,6 +197,7 @@ def _is_toc_entity(self, instance) -> bool: return self._has_local_triples(instance.get_has_identifier()) def get_toc_instances(self) -> List: + """Return the instances that get their own card and link (the browsable entities).""" return [i for i in self.get_all_instances() if self._is_toc_entity(i)] def _handle_single_resource(self, resource_uri: str, language: Optional[str] = None) -> Dict: @@ -269,8 +285,8 @@ def _format_entities(self, instances: List, language: Optional[str] = None) -> L # We use the helper to get clean text for each item formatted_values = [] if isinstance(value, list): - for v in value: - # Nested list (es. has_property_chain: lista di catene) + for v in self._select_by_language(value, language): + # Nested list (e.g. has_property_chain: list of chains) if isinstance(v, list): chain_dict = self._resolve_chain_value(v, language) if chain_dict and chain_dict['text']: @@ -414,7 +430,7 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None # 6. Extract the actual text values extracted_values = [] - for val in values: + for val in self._select_by_language(values, language): entry = self._resolve_resource_value(val, language) if entry['text']: # 7. Check if the link if an visualizable ontology or not @@ -440,7 +456,7 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None # 9. Statements data.update(self._format_statement(all_instances, ontology_model, language)) - # Ordine alfabetico su tutti i metadati (uri/label in testa) + # Alphabetical order on all the metadata (uri/label first) pinned = ['uri', 'label'] rest = sorted(k for k in data if k not in pinned) data = {k: data[k] for k in pinned if k in data} | {k: data[k] for k in rest} @@ -448,8 +464,11 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None return data def _resolve_chain_value(self, chain, language=None) -> dict: - """Renderizza una property chain ordinata (lista di Relation) come un - unico valore con parti cliccabili unite dall'operatore di composizione.""" + """Render an ordered property chain (a list of Relations) as a single value. + + The clickable parts are joined by the composition operator. Returns None + when no member has a displayable text. + """ members = [] for m in chain: md = self._resolve_resource_value(m, language) @@ -523,17 +542,6 @@ def _resolve_resource_value(self, obj, language=None) -> dict: lit_lang = obj.get_has_language() - # If a language is requested (e.g., 'pt') - if language: - target_lang = language.strip().lower() - - # If the literal has a tag, and it DOES NOT match 'pt', destroy it. - if lit_lang and not lit_lang.lower().startswith(target_lang): - return handler_dic - - # if not lit_lang: - # return handler_dic - handler_dic['text'] = obj.get_has_value() handler_dic['lan'] = lit_lang handler_dic['type'] = obj_type @@ -566,7 +574,7 @@ def _resolve_resource_value(self, obj, language=None) -> dict: if attr.startswith('_') or attr in skip or not value: continue values = value if isinstance(value, list) else [value] - for v in values: + for v in self._select_by_language(values, language): resolved = self._resolve_resource_value(v, language) if resolved.get('text') or resolved.get('nested'): siblings.append({ @@ -614,38 +622,41 @@ def _format_statement(self, instances, target_instance, language=None) -> Dict: if target_instance is None: return statements + # 2. Group the objects by predicate: the language is chosen per property + grouped = {} for instance in instances: - if isinstance(instance, Statement): - subj = instance.get_has_subject() - - # 2. Identity comparison (handles punning: same URI, different Python instances) - if subj is not target_instance: - continue - - predicate = instance.get_has_predicate() - obj = instance.get_has_object() - - if obj: - obj_data = self._resolve_resource_value(obj, language) - - # 3. Predicate Resolution - pred_label = self._get_best_label(predicate, language) if predicate else "Annotation" - - if pred_label not in statements: - statements[pred_label] = [] - - # 4. Resolve Object and Prevent Duplicates - if obj: - obj_data = self._resolve_resource_value(obj, language) - - - if obj_data not in statements[pred_label]: - statements[pred_label].append(obj_data) + if not isinstance(instance, Statement): + continue + # Identity comparison (handles punning: same URI, different Python instances) + if instance.get_has_subject() is not target_instance: + continue + obj = instance.get_has_object() + if not obj: + continue + predicate = instance.get_has_predicate() + pred_label = self._get_best_label(predicate, language) if predicate else "Annotation" + grouped.setdefault(pred_label, []).append(obj) + + # 3. Pick the language per property, resolve, drop empties and duplicates + for pred_label, objs in grouped.items(): + values = [] + for obj in self._select_by_language(objs, language): + obj_data = self._resolve_resource_value(obj, language) + if obj_data['text'] and obj_data not in values: + values.append(obj_data) + if values: + statements[pred_label] = values return statements @staticmethod def _clean_name(self, name: str) -> str: + """Turn an attribute or getter name into a display label. + + Drops the has_/get_ prefix, splits camelCase, replaces underscores with + spaces and lowercases. It is a staticmethod that still takes `self` as its + first argument, so callers pass it explicitly. + """ if not name: return "" name = re.sub(r'^(get_has_|get_|has_)', '', name) @@ -697,6 +708,7 @@ def _parse_restriction(self, obj, language=None, _seen=None) -> list: # Helper to safely call getter methods (e.g., get_applies_on_property) def _get(instance, prop_name, default=None): + """Read a property through its getter, or directly as an attribute, with a default for None.""" getter = f"get_{prop_name}" if hasattr(instance, getter): res = getattr(instance, getter)() @@ -829,6 +841,7 @@ def _is_likely_ontology(self, url: str) -> bool: host = parsed.hostname or '' def _host_is(domain: str) -> bool: + """True if the URL host is the domain or one of its subdomains.""" return host == domain or host.endswith('.' + domain) # 4. Common Ontology Registries & Permanent URLs @@ -856,21 +869,21 @@ def _host_is(domain: str) -> bool: return False - # Mappa class_key -> nome del getter del parent (None = no hierarchy) + # Map class_key -> name of the parent getter (missing = no hierarchy) _HIERARCHY_PARENT_GETTERS = { 'Concept': 'get_is_sub_concept_of', 'Relation': 'get_is_sub_property_of', 'Attribute': 'get_is_sub_property_of', 'Property': 'get_is_sub_property_of', - # Annotation, Individual: nessuna gerarchia -> non in mappa + # Annotation, Individual: no hierarchy -> not in the map } _FULL_IRI_ATTRS = {'is_defined_by'} def _build_hierarchy(self, instances, parent_getter_name, language=None): """ - Costruisce un albero (forest) di dict. - anchor_id usa lo stesso formato di _format_entities: id_{md5}_{ClassName} + Build a forest (list of trees) of dicts from the parent relation. + anchor_id uses the same format as _format_entities: id_{md5}_{ClassName} """ import hashlib @@ -897,6 +910,7 @@ def _build_hierarchy(self, instances, parent_getter_name, language=None): roots = [uri for uri in by_uri if uri not in has_internal_parent] def node_dict(uri, visited): + """Build the tree node of an entity with its children, stopping on cycles.""" if uri in visited: return None visited = visited | {uri} @@ -925,6 +939,10 @@ def node_dict(uri, visited): # ========== PROVENANCE: subgraph serialisation for each card ========== def _build_provenance_subgraph(self, instance) -> List[Dict[str, str]]: + """Serialize the triples an instance comes from, once per available format. + + Returns an empty list when the instance has no provenance. + """ sub = self.reader.get_provenance_subgraph(instance) if not any(True for _ in sub): return [] @@ -936,13 +954,17 @@ def _build_provenance_subgraph(self, instance) -> List[Dict[str, str]]: @staticmethod def _safe_serialize(g, fmt: str) -> str: + """Serialize a graph, returning a comment with the error instead of raising. + + One format that fails must not break the page that shows all of them. + """ try: return g.serialize(format=fmt) except Exception as e: return f"# serialization error ({fmt}): {e}" def export_resource(self, resource_uri: str, fmt: str = "turtle") -> str: - """Serializza il subgraph della singola risorsa (unione su punning).""" + """Serialize the subgraph of a single resource (the union of its punned instances).""" g = Graph() for prefix, ns in self.reader._graph.namespaces(): g.bind(prefix, ns) @@ -950,6 +972,6 @@ def export_resource(self, resource_uri: str, fmt: str = "turtle") -> str: if instances: inst_iter = instances if isinstance(instances, set) else [instances] for inst in inst_iter: - for t in self.reader.get_provenance_subgraph(inst): # giΓ  esiste + for t in self.reader.get_provenance_subgraph(inst): # already exists g.add(t) return self._safe_serialize(self._with_provenance(g), fmt) \ No newline at end of file diff --git a/lode/viewer/owl_viewer.py b/lode/viewer/owl_viewer.py index 320fd2d..db01eed 100644 --- a/lode/viewer/owl_viewer.py +++ b/lode/viewer/owl_viewer.py @@ -1,9 +1,9 @@ -# viewer/owl_viewer.py +"""Viewer for OWL artefacts.""" from typing import Dict, Optional from lode.viewer.base_viewer import BaseViewer class OwlViewer(BaseViewer): - """Viewer OWL""" + """OWL viewer""" TYPE_MAP = { 'concept': {'singular': 'Class', 'plural': 'Classes', 'abb': 'c'}, @@ -14,6 +14,7 @@ class OwlViewer(BaseViewer): } def get_toc_config(self): + """Return the table of contents: (class name, section id, TYPE_MAP key) in display order.""" return [ ('Concept', 'concepts', 'Concept'), ('Relation', 'relations', 'Relation'), @@ -24,8 +25,15 @@ def get_toc_config(self): def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: + """Build the template data for one resource, or for the whole ontology grouped by entity type. + + Both views also carry the ontology metadata and the TYPE_MAP of display names. + """ + + anguage = language.strip() if language else "en" + all_instances = self.get_all_instances() - metadata_dict = self._find_and_format_metadata(all_instances) + metadata_dict = self._find_and_format_metadata(all_instances, language) if resource_uri: data = super().get_view_data(resource_uri, language) diff --git a/lode/viewer/rdf_viewer.py b/lode/viewer/rdf_viewer.py index 7ddc7fa..34840a0 100644 --- a/lode/viewer/rdf_viewer.py +++ b/lode/viewer/rdf_viewer.py @@ -1,4 +1,4 @@ -# viewer/rdf_viewer.py +"""Viewer for RDF/RDFS artefacts.""" from typing import Dict, Optional from lode.viewer.base_viewer import BaseViewer @@ -15,6 +15,13 @@ class RdfViewer(BaseViewer): } def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: + """Build the template data for one resource, or for the vocabulary grouped by concepts, properties and containers. + + Both views also carry the vocabulary metadata and the TYPE_MAP of display names. + """ + + language = language.strip() if language else "en" + all_instances = self.get_all_instances() metadata_dict = self._find_and_format_metadata(all_instances, language) @@ -24,7 +31,7 @@ def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[s data['type_map'] = self.TYPE_MAP return data - # title in SINGOLARE per matchare le chiavi di TYPE_MAP + # title in SINGULAR to match the TYPE_MAP keys toc_config = [ ('Concept', 'concepts', 'Concept'), ('Property', 'properties', 'Property'), @@ -35,18 +42,4 @@ def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[s data['metadata'] = metadata_dict data['type_map'] = self.TYPE_MAP - # DEBUG β€” togliere dopo - print("=" * 60) - print(f"DEBUG RDF VIEWER") - print(f" grouped_view = {data.get('grouped_view')}") - print(f" sections count = {len(data.get('sections') or [])}") - for s in data.get('sections') or []: - print(f" [{s['id']}] title={s['title']!r} entities={len(s['entities'])}") - print(f" type_map keys = {list(data['type_map'].keys())}") - # Conta i tipi reali nel cache - from collections import Counter - types = Counter(type(i).__name__ for i in self.get_all_instances()) - print(f" instances by type = {dict(types)}") - print("=" * 60) - return data \ No newline at end of file diff --git a/lode/viewer/skos_viewer.py b/lode/viewer/skos_viewer.py index 5061635..f434aca 100644 --- a/lode/viewer/skos_viewer.py +++ b/lode/viewer/skos_viewer.py @@ -1,13 +1,14 @@ -# viewer/skos.py +"""Viewer for SKOS artefacts.""" import hashlib from typing import Dict, Optional, List from lode.viewer.base_viewer import BaseViewer from lode.helpers.rdf import iri_local_name class SkosViewer(BaseViewer): - """Viewer SKOS con visualizzazione LODE-style.""" + """SKOS viewer with LODE-style rendering.""" def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: + """Build the template data for one resource, or for the scheme grouped by collections and concepts.""" # 1. Single resource detail view if resource_uri: return super().get_view_data(resource_uri, language) @@ -22,7 +23,7 @@ def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[s return self._build_skos_grouped_view(toc_config, language) def _build_skos_grouped_view(self, group_definitions: List, language: Optional[str] = None) -> Dict: - """Costruisce la vista raggruppata con formattazione SKOS-style.""" + """Build the grouped view with SKOS-style formatting.""" all_instances = self.get_all_instances() sections = [] @@ -45,7 +46,7 @@ def _build_skos_grouped_view(self, group_definitions: List, language: Optional[s } def _format_skos_entities(self, instances: List, language: Optional[str] = None) -> List[Dict]: - """Formatta le entitΓ  SKOS in stile LODE.""" + """Format the SKOS entities in LODE style, sorted by label (or IRI when there is none).""" entities = [] for instance in instances: @@ -159,7 +160,7 @@ def _format_skos_entities(self, instances: List, language: Optional[str] = None) return entities def _format_concept_list(self, concepts, language: Optional[str]) -> List[Dict]: - """Formatta una lista di concetti con label e URI.""" + """Format a list of concepts with label and IRI; plain string IRIs are marked as external.""" items = [] concept_list = concepts if isinstance(concepts, (list, set)) else [concepts] @@ -182,22 +183,19 @@ def _format_concept_list(self, concepts, language: Optional[str]) -> List[Dict]: return items def _get_definition(self, instance, language: Optional[str]) -> Optional[str]: - """Estrae la definizione.""" + """Extract the definition text in the given language, or None when there is none.""" if hasattr(instance, 'has_definition') and instance.has_definition: return self._get_literal_value(instance.has_definition, language) return None def _get_literal_value(self, value, language: Optional[str]) -> Optional[str]: - """Estrae il valore stringa da un Literal o lista di Literal.""" + """Extract the string value of a Literal or of a list of Literals. + + The first literal in the best available language wins (see `_select_by_language`). + """ if isinstance(value, (set, list)): - if language: - for v in value: - if hasattr(v, 'get_has_language') and v.get_has_language() == language: - return v.get_has_value() if hasattr(v, 'get_has_value') else str(v) - for v in value: - if hasattr(v, 'get_has_value'): - return v.get_has_value() - return str(v) + for v in self._select_by_language(list(value), language): + return v.get_has_value() if hasattr(v, 'get_has_value') else str(v) elif hasattr(value, 'get_has_value'): return value.get_has_value() elif value: diff --git a/tests/test_owl_viewer.py b/tests/test_owl_viewer.py index c4925e0..b82aefd 100644 --- a/tests/test_owl_viewer.py +++ b/tests/test_owl_viewer.py @@ -292,6 +292,61 @@ def test_each_section_entity_is_toc_kind(self): assert ent["type"] in toc_keys +# --------------------------------------------------------------------------- +# Language selection: per property, with fallback +# --------------------------------------------------------------------------- + +def _lit(text, lang=None): + """Build a model Literal with an optional language tag.""" + lit = Literal() + lit.set_has_value(text) + if lang: + lit.set_has_language(lang) + return lit + + +class TestLanguageSelection: + """The language is chosen per property: requested, then 'en', then untagged, then all.""" + + @pytest.mark.parametrize("tags, requested, expected", [ + (["da", "en", "it"], "it", ["it"]), + (["da", "en"], "cs", ["en"]), + (["da", None], "cs", [None]), + (["da", "es"], "cs", ["da", "es"]), + (["en", None], "en", ["en"]), + (["en-GB", "en"], "en", ["en"]), + (["en", "en-GB"], "en-GB", ["en-GB"]), + (["en", "da"], "en-GB", ["en"]), + (["EN", "da"], "en", ["EN"]), + (["en-GB", "da"], "en", ["en-GB", "da"]), + ]) + def test_select_by_language(self, tags, requested, expected): + v = _viewer() + lits = [_lit(str(t), t) for t in tags] + picked = v._select_by_language(lits, requested) + assert [l.get_has_language() for l in picked] == expected + + def test_label_falls_back_to_en_not_alphabetical(self): + c = _entity(Concept, C) + for text, lang in (("Datatjeneste", "da"), ("Data service", "en"), ("Servizio", "it")): + c.set_has_label(_lit(text, lang)) + assert _viewer(c)._get_best_label(c, "cs") == "Data service" + + def test_metadata_has_only_requested_language_and_no_none(self): + onto = _entity(Model, ONTO) + title = _entity(Annotation, "http://purl.org/dc/terms/title", "title") + stmts = [] + for text, lang in (("Title", "en"), ("Titolo", "it")): + st = Statement() + st.set_has_subject(onto) + st.set_has_predicate(title) + st.set_has_object(_lit(text, lang)) + stmts.append(st) + v = _viewer(onto, title, *stmts) + texts = [e["text"] for e in v.get_view_data(language="en")["metadata"]["title"]] + assert texts == ["Title"] + + # =========================================================================== # Integration: real corpus, same loader pattern as test_owl_integrity. # =========================================================================== From 26b6678868f929f3c06f3d15bb6d93104f6621a3 Mon Sep 17 00:00:00 2001 From: Valentina Date: Thu, 15 Oct 2026 16:02:43 +0200 Subject: [PATCH 02/21] fix(publication): added docstrings in eng + replaced astro with mkdocs material --- .dockerignore | 4 +- .github/workflows/deploy-docs.yml | 17 +- .github/workflows/release.yml | 2 +- .gitignore | 8 +- Dockerfile | 2 +- LICENSE.md | 2 +- README.md | 21 +- docs/.gitignore | 21 - docs/AGENTS.md | 22 - docs/CLAUDE.md | 22 - docs/README.md | 49 - docs/{src/content/docs => }/api/endpoints.md | 5 +- docs/astro.config.mjs | 41 - .../{src/content/docs => }/getting_started.md | 18 +- docs/index.md | 24 + docs/package-lock.json | 5567 ----------------- docs/package.json | 17 - docs/public/favicon.svg | 1 - docs/src/assets/houston.webp | Bin 98506 -> 0 bytes docs/src/content.config.ts | 7 - docs/src/content/docs/guides/example.md | 11 - docs/src/content/docs/index.mdx | 34 - docs/src/content/docs/reference/example.md | 11 - docs/tsconfig.json | 5 - docs/{src/content/docs => }/usage/cli.md | 11 +- docs/{src/content/docs => }/usage/docker.md | 35 +- docs/{src/content/docs => }/usage/web_form.md | 7 +- lode/__init__.py | 3 +- lode/api.py | 77 +- lode/builder.py | 48 +- lode/cli.py | 28 +- lode/exceptions.py | 29 +- lode/helpers/__init__.py | 2 +- lode/helpers/html_utils.py | 1 + lode/models/__init__.py | 5 + lode/models/annotation.py | 3 + lode/models/atom.py | 22 +- lode/models/attribute.py | 5 +- lode/models/cardinality.py | 13 +- lode/models/collection.py | 11 +- lode/models/concept.py | 78 +- lode/models/container.py | 12 +- lode/models/datatype.py | 3 + lode/models/datatypeRestriction.py | 7 + lode/models/individual.py | 16 +- lode/models/literal.py | 17 +- lode/models/model.py | 33 +- lode/models/oneOf.py | 7 +- lode/models/property.py | 37 +- lode/models/propertyConceptRestriction.py | 16 +- lode/models/propertySelfRestriction.py | 5 + lode/models/quantifier.py | 12 +- lode/models/relation.py | 47 +- lode/models/resource.py | 143 +- lode/models/restriction.py | 3 + lode/models/rule.py | 22 +- lode/models/statement.py | 19 +- lode/models/truthFunction.py | 11 +- lode/models/value.py | 9 +- lode/models/variable.py | 4 + lode/reader/config/old_base.yaml | 599 -- lode/reader/config_manager.py | 94 +- lode/reader/loader.py | 47 +- lode/reader/logic/base_logic.py | 175 +- lode/reader/logic/owl_logic.py | 162 +- lode/reader/logic/rdf_logic.py | 21 +- lode/reader/logic/skos_logic.py | 44 +- lode/reader/modules.py | 69 +- lode/reader/provenance_graph.py | 29 +- lode/reader/reader.py | 243 +- lode/reader/warnings/owl_warnings.py | 13 + lode/viewer/__init__.py | 7 +- mkdocs.yml | 40 + pyproject.toml | 23 +- tests/data/provenance/main.ttl | 3 + tests/test_modules.py | 52 +- uv.lock | 97 +- 77 files changed, 1313 insertions(+), 7117 deletions(-) delete mode 100644 docs/.gitignore delete mode 100644 docs/AGENTS.md delete mode 100644 docs/CLAUDE.md delete mode 100644 docs/README.md rename docs/{src/content/docs => }/api/endpoints.md (95%) delete mode 100644 docs/astro.config.mjs rename docs/{src/content/docs => }/getting_started.md (61%) create mode 100644 docs/index.md delete mode 100644 docs/package-lock.json delete mode 100644 docs/package.json delete mode 100644 docs/public/favicon.svg delete mode 100644 docs/src/assets/houston.webp delete mode 100644 docs/src/content.config.ts delete mode 100644 docs/src/content/docs/guides/example.md delete mode 100644 docs/src/content/docs/index.mdx delete mode 100644 docs/src/content/docs/reference/example.md delete mode 100644 docs/tsconfig.json rename docs/{src/content/docs => }/usage/cli.md (82%) rename docs/{src/content/docs => }/usage/docker.md (66%) rename docs/{src/content/docs => }/usage/web_form.md (86%) delete mode 100644 lode/reader/config/old_base.yaml create mode 100644 mkdocs.yml diff --git a/.dockerignore b/.dockerignore index 5509ba4..4d5b6c5 100644 --- a/.dockerignore +++ b/.dockerignore @@ -24,9 +24,7 @@ htmlcov/ .idea/ # Docs site build artifacts -docs/node_modules/ -docs/.astro/ -docs/dist/ +site/ # Runtime spool cache **/spool/ diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index cddd0ed..9ab55cb 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -5,6 +5,7 @@ on: branches: [main] paths: - 'docs/**' + - 'mkdocs.yml' workflow_run: workflows: ["Run tests"] types: [completed] @@ -30,7 +31,7 @@ jobs: uses: actions/download-artifact@v4 with: name: coverage-report - path: docs/public/coverage + path: docs/coverage github-token: ${{ secrets.GITHUB_TOKEN }} run-id: ${{ github.event.workflow_run.id }} @@ -39,13 +40,21 @@ jobs: uses: actions/download-artifact@v4 with: name: coverage-badge - path: docs/public/coverage + path: docs/coverage github-token: ${{ secrets.GITHUB_TOKEN }} run-id: ${{ github.event.workflow_run.id }} - - uses: withastro/action@v5 + - uses: actions/setup-python@v5 with: - path: ./docs + python-version: "3.13" + + - run: pip install mkdocs-material "mkdocs<2" + + - run: mkdocs build --strict + + - uses: actions/upload-pages-artifact@v3 + with: + path: site deploy: needs: build diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0e8d7b6..aa4d359 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -54,4 +54,4 @@ jobs: UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }} run: | uv build - uv publish --token $UV_PUBLISH_TOKEN + uv publish --check-url https://pypi.org/simple/ --token $UV_PUBLISH_TOKEN diff --git a/.gitignore b/.gitignore index 2b28c9e..793c3eb 100644 --- a/.gitignore +++ b/.gitignore @@ -19,9 +19,11 @@ htmlcov/ .idea/ # Starlight/Astro -docs/node_modules/ -docs/.astro/ -docs/dist/ +site/ # saved files spool/ + +# claude +CLAUDE.md +.claude/ \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index af5ab1d..9bc2345 100644 --- a/Dockerfile +++ b/Dockerfile @@ -29,7 +29,7 @@ USER appuser # Install dependencies first for better layer caching (frozen = exact lockfile) COPY --chown=appuser:appuser pyproject.toml uv.lock README.md ./ -RUN uv sync --frozen --no-dev --no-install-project +RUN uv sync --frozen --no-dev --no-install-project --extra server # Application code COPY --chown=appuser:appuser . . diff --git a/LICENSE.md b/LICENSE.md index d764181..8e3cb7f 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ ISC License -Copyright (c) 2025 Valentina Pasqual, Sivio Peroni +Copyright (c) 2025 Valentina Pasqual, Silvio Peroni Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above diff --git a/README.md b/README.md index 917f824..4915a17 100644 --- a/README.md +++ b/README.md @@ -9,19 +9,22 @@ LODE 2.0 is an open source service that automatically extracts entities from sem ## Installation ```bash -pip install lode -``` - -## Usage - -```python -from lode import example_function +pip install oc-lode -result = example_function() -print(result) +# with the web service (`lode serve`) +pip install "oc-lode[server]" ``` + ## Usage + +```bash +# Build static documentation from an ontology URL or a local file +lode build --url --read-as [--out ./docs] [--lang en] [--imported] [--closure] +lode build --file --read-as [--out ./docs] +# Run the web service (requires the [server] extra) +lode serve --port 8000 +``` ## Documentation diff --git a/docs/.gitignore b/docs/.gitignore deleted file mode 100644 index 6240da8..0000000 --- a/docs/.gitignore +++ /dev/null @@ -1,21 +0,0 @@ -# build output -dist/ -# generated types -.astro/ - -# dependencies -node_modules/ - -# logs -npm-debug.log* -yarn-debug.log* -yarn-error.log* -pnpm-debug.log* - - -# environment variables -.env -.env.production - -# macOS-specific files -.DS_Store diff --git a/docs/AGENTS.md b/docs/AGENTS.md deleted file mode 100644 index c5ff429..0000000 --- a/docs/AGENTS.md +++ /dev/null @@ -1,22 +0,0 @@ -## Development - -When starting the dev server, use background mode: - -``` -astro dev --background -``` - -Manage the background server with `astro dev stop`, `astro dev status`, and `astro dev logs`. - -## Documentation - -Full documentation: https://docs.astro.build - -Consult these guides before working on related tasks: - -- [Adding pages, dynamic routes, or middleware](https://docs.astro.build/en/guides/routing/) -- [Working with Astro components](https://docs.astro.build/en/basics/astro-components/) -- [Using React, Vue, Svelte, or other framework components](https://docs.astro.build/en/guides/framework-components/) -- [Adding or managing content](https://docs.astro.build/en/guides/content-collections/) -- [Adding styles or using Tailwind](https://docs.astro.build/en/guides/styling/) -- [Supporting multiple languages](https://docs.astro.build/en/guides/internationalization/) diff --git a/docs/CLAUDE.md b/docs/CLAUDE.md deleted file mode 100644 index c5ff429..0000000 --- a/docs/CLAUDE.md +++ /dev/null @@ -1,22 +0,0 @@ -## Development - -When starting the dev server, use background mode: - -``` -astro dev --background -``` - -Manage the background server with `astro dev stop`, `astro dev status`, and `astro dev logs`. - -## Documentation - -Full documentation: https://docs.astro.build - -Consult these guides before working on related tasks: - -- [Adding pages, dynamic routes, or middleware](https://docs.astro.build/en/guides/routing/) -- [Working with Astro components](https://docs.astro.build/en/basics/astro-components/) -- [Using React, Vue, Svelte, or other framework components](https://docs.astro.build/en/guides/framework-components/) -- [Adding or managing content](https://docs.astro.build/en/guides/content-collections/) -- [Adding styles or using Tailwind](https://docs.astro.build/en/guides/styling/) -- [Supporting multiple languages](https://docs.astro.build/en/guides/internationalization/) diff --git a/docs/README.md b/docs/README.md deleted file mode 100644 index 1b7f5c3..0000000 --- a/docs/README.md +++ /dev/null @@ -1,49 +0,0 @@ -# Starlight Starter Kit: Basics - -[![Built with Starlight](https://astro.badg.es/v2/built-with-starlight/tiny.svg)](https://starlight.astro.build) - -``` -npm create astro@latest -- --template starlight -``` - -> πŸ§‘β€πŸš€ **Seasoned astronaut?** Delete this file. Have fun! - -## πŸš€ Project Structure - -Inside of your Astro + Starlight project, you'll see the following folders and files: - -``` -. -β”œβ”€β”€ public/ -β”œβ”€β”€ src/ -β”‚ β”œβ”€β”€ assets/ -β”‚ β”œβ”€β”€ content/ -β”‚ β”‚ └── docs/ -β”‚ └── content.config.ts -β”œβ”€β”€ astro.config.mjs -β”œβ”€β”€ package.json -└── tsconfig.json -``` - -Starlight looks for `.md` or `.mdx` files in the `src/content/docs/` directory. Each file is exposed as a route based on its file name. - -Images can be added to `src/assets/` and embedded in Markdown with a relative link. - -Static assets, like favicons, can be placed in the `public/` directory. - -## 🧞 Commands - -All commands are run from the root of the project, from a terminal: - -| Command | Action | -| :------------------------ | :----------------------------------------------- | -| `npm install` | Installs dependencies | -| `npm run dev` | Starts local dev server at `localhost:4321` | -| `npm run build` | Build your production site to `./dist/` | -| `npm run preview` | Preview your build locally, before deploying | -| `npm run astro ...` | Run CLI commands like `astro add`, `astro check` | -| `npm run astro -- --help` | Get help using the Astro CLI | - -## πŸ‘€ Want to learn more? - -Check out [Starlight’s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build), or jump into the [Astro Discord server](https://astro.build/chat). diff --git a/docs/src/content/docs/api/endpoints.md b/docs/api/endpoints.md similarity index 95% rename from docs/src/content/docs/api/endpoints.md rename to docs/api/endpoints.md index 36bc33f..44baec1 100644 --- a/docs/src/content/docs/api/endpoints.md +++ b/docs/api/endpoints.md @@ -1,7 +1,4 @@ ---- -title: API Endpoints -description: LODE REST API reference ---- +# API endpoints Interactive docs available at `/docs` (Swagger) and `/redoc` (ReDoc) when the server is running. diff --git a/docs/astro.config.mjs b/docs/astro.config.mjs deleted file mode 100644 index a59d492..0000000 --- a/docs/astro.config.mjs +++ /dev/null @@ -1,41 +0,0 @@ -import { defineConfig } from 'astro/config'; -import starlight from '@astrojs/starlight'; - -export default defineConfig({ - site: 'https://opencitations.github.io', - base: '/lode', - - integrations: [ - starlight({ - title: 'LODE 2.0', - description: 'Live OWL Documentation Environment β€” extract and document RDF/OWL/SKOS semantic artefacts as browsable HTML.', - - social: [ - { icon: 'github', label: 'GitHub', href: 'https://github.com/opencitations/lode' }, - ], - - sidebar: [ - { - label: 'Getting Started', - items: [ - { label: 'Installation', slug: 'getting_started' }, - ], - }, - { - label: 'Usage', - items: [ - { label: 'Web Form', slug: 'usage/web_form' }, - { label: 'CLI', slug: 'usage/cli' }, - { label: 'Docker', slug: 'usage/docker' }, - ], - }, - { - label: 'API Reference', - items: [ - { label: 'Endpoints', slug: 'api/endpoints' }, - ], - }, - ], - }), - ], -}); \ No newline at end of file diff --git a/docs/src/content/docs/getting_started.md b/docs/getting_started.md similarity index 61% rename from docs/src/content/docs/getting_started.md rename to docs/getting_started.md index 673ef03..8f38258 100644 --- a/docs/src/content/docs/getting_started.md +++ b/docs/getting_started.md @@ -1,7 +1,4 @@ ---- -title: Getting Started -description: Install and run LODE 2.0 ---- +# Getting started ## Requirements @@ -11,12 +8,15 @@ description: Install and run LODE 2.0 ## Installation ```bash -pip install lode2 +pip install oc-lode + +# with the web service (`lode serve`) +pip install "oc-lode[server]" ``` ## First run -Start the web server: +Start the web server (requires the `[server]` extra): ```bash lode serve --port 8000 @@ -27,7 +27,7 @@ Open `http://localhost:8000` in your browser, paste an ontology URL and click ** Or generate a static site from a local file: ```bash -lode build --file my_ontology.ttl --read-as owl --out ./docs +lode build --file my_ontology.ttl --read-as owl --out ./site ``` ## Development install @@ -36,5 +36,5 @@ lode build --file my_ontology.ttl --read-as owl --out ./docs git clone https://github.com/opencitations/lode.git cd lode uv sync --all-extras --dev -uvicorn lode.api:app --reload --port 8000 -``` \ No newline at end of file +uv run python main.py +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..040258b --- /dev/null +++ b/docs/index.md @@ -0,0 +1,24 @@ +# LODE 2.0 + +Live OWL Documentation Environment β€” extract and document semantic artefacts as browsable, interlinked HTML. Maintained by [OpenCitations](https://opencitations.net). + +[Get started](getting_started.md){ .md-button .md-button--primary } +[View on GitHub](https://github.com/opencitations/lode){ .md-button } + +## Features + +- Extracts and documents OWL classes, properties, individuals, restrictions and more +- Renders browsable HTML with embedded navigation links +- Serves a dynamic web interface and REST API +- Generates self-contained static sites from the CLI +- Content negotiation: returns RDF serializations on request +- Docker-ready with configurable storage via environment variables + +## Quick start + +```bash +pip install "oc-lode[server]" +lode serve --port 8000 +``` + +Open `http://localhost:8000` to use the web form, or `http://localhost:8000/docs` for the interactive API. diff --git a/docs/package-lock.json b/docs/package-lock.json deleted file mode 100644 index fb4256a..0000000 --- a/docs/package-lock.json +++ /dev/null @@ -1,5567 +0,0 @@ -{ - "name": "docs", - "version": 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{ defineCollection } from 'astro:content'; -import { docsLoader } from '@astrojs/starlight/loaders'; -import { docsSchema } from '@astrojs/starlight/schema'; - -export const collections = { - docs: defineCollection({ loader: docsLoader(), schema: docsSchema() }), -}; diff --git a/docs/src/content/docs/guides/example.md b/docs/src/content/docs/guides/example.md deleted file mode 100644 index ebd0f3b..0000000 --- a/docs/src/content/docs/guides/example.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: Example Guide -description: A guide in my new Starlight docs site. ---- - -Guides lead a user through a specific task they want to accomplish, often with a sequence of steps. -Writing a good guide requires thinking about what your users are trying to do. - -## Further reading - -- Read [about how-to guides](https://diataxis.fr/how-to-guides/) in the DiΓ‘taxis framework diff --git a/docs/src/content/docs/index.mdx b/docs/src/content/docs/index.mdx deleted file mode 100644 index 61eb820..0000000 --- a/docs/src/content/docs/index.mdx +++ /dev/null @@ -1,34 +0,0 @@ ---- -title: LODE 2.0 -description: Live OWL Documentation Environment β€” extract and document RDF/OWL/SKOS semantic artefacts as browsable HTML. -template: splash -hero: - title: LODE 2.0 - tagline: Live OWL Documentation Environment β€” extract and document semantic artefacts as browsable, interlinked HTML. - actions: - - text: Get started - link: /lode/getting_started/ - icon: right-arrow - - text: View on GitHub - link: https://github.com/opencitations/lode - icon: external - variant: minimal ---- - -## Features - -- Extracts and documents OWL classes, properties, individuals, restrictions and more -- Renders browsable HTML with embedded navigation links -- Serves a dynamic web interface and REST API -- Generates self-contained static sites from the CLI -- Content negotiation: returns RDF serializations on request -- Docker-ready with configurable storage via environment variables - -## Quick start - -```bash -pip install lode2 -lode serve --port 8000 -``` - -Open `http://localhost:8000` to use the web form, or `http://localhost:8000/docs` for the interactive API. \ No newline at end of file diff --git a/docs/src/content/docs/reference/example.md b/docs/src/content/docs/reference/example.md deleted file mode 100644 index 0224f09..0000000 --- a/docs/src/content/docs/reference/example.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: Example Reference -description: A reference page in my new Starlight docs site. ---- - -Reference pages are ideal for outlining how things work in terse and clear terms. -Less concerned with telling a story or addressing a specific use case, they should give a comprehensive outline of what you're documenting. - -## Further reading - -- Read [about reference](https://diataxis.fr/reference/) in the DiΓ‘taxis framework diff --git a/docs/tsconfig.json b/docs/tsconfig.json deleted file mode 100644 index 8bf91d3..0000000 --- a/docs/tsconfig.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "extends": "astro/tsconfigs/strict", - "include": [".astro/types.d.ts", "**/*"], - "exclude": ["dist"] -} diff --git a/docs/src/content/docs/usage/cli.md b/docs/usage/cli.md similarity index 82% rename from docs/src/content/docs/usage/cli.md rename to docs/usage/cli.md index 56b32a0..2f154a6 100644 --- a/docs/src/content/docs/usage/cli.md +++ b/docs/usage/cli.md @@ -1,13 +1,10 @@ ---- -title: CLI Reference -description: LODE command line interface ---- +# CLI reference ## Commands ### `lode serve` -Start the web server. +Start the web server (requires the `[server]` extra). ```bash lode serve [--port PORT] @@ -34,6 +31,7 @@ lode build (--url URL | --file FILE) --read-as FORMAT [OPTIONS] | `--lang` | no | Language tag for labels (default `en`) | | `--imported` | no | Load `owl:imports` at depth 1 | | `--closure` | no | Load the full `owl:imports` closure | +| `--partial-import` | no | Load only the imported entities that are actually used | ## Examples @@ -42,7 +40,7 @@ lode build (--url URL | --file FILE) --read-as FORMAT [OPTIONS] lode build --url http://purl.org/spar/fabio --read-as owl --out ./fabio # from a local file -lode build --file ontology.ttl --read-as owl --out ./docs +lode build --file ontology.ttl --read-as owl --out ./site # with Italian labels and imports lode build --url http://purl.org/spar/fabio --read-as owl --lang it --imported --out ./fabio @@ -54,4 +52,5 @@ lode build --url http://purl.org/spar/fabio --read-as owl --lang it --imported - |----------|---------|-------------| | `LODE_SPOOL_DIR` | `$TMPDIR/lode-spool` | Cache for fetched URLs and uploads | | `LODE_BUILD_DIR` | `$TMPDIR/lode-builds` | Workspace for ZIP build jobs | +| `LODE_LOG_LEVEL` | `WARNING` | Log verbosity (`DEBUG`, `INFO`, `WARNING`, ...) | | `LODE_DEBUG` | `false` | Show full tracebacks in error pages | diff --git a/docs/src/content/docs/usage/docker.md b/docs/usage/docker.md similarity index 66% rename from docs/src/content/docs/usage/docker.md rename to docs/usage/docker.md index 2f62898..ff7442e 100644 --- a/docs/src/content/docs/usage/docker.md +++ b/docs/usage/docker.md @@ -1,45 +1,44 @@ ---- -title: Docker -description: Deploy LODE with Docker ---- +# Docker + +The image listens on port `8080`. ## Quick start ```bash docker build -t lode . -docker run -p 8000:8000 lode +docker run -p 8080:8080 lode +``` + +Open `http://localhost:8080`. + +## From Docker Hub + +```bash +docker run -p 8080:8080 opencitations/lode:latest ``` -Open `http://localhost:8000`. +Replace `latest` with the desired version tag. ## With persistent storage ```bash -docker run -p 8000:8000 \ +docker run -p 8080:8080 \ -v lode-data:/data \ -e LODE_SPOOL_DIR=/data/spool \ -e LODE_BUILD_DIR=/data/builds \ - lode + opencitations/lode:latest ``` ## Production (read-only filesystem) ```bash -docker run -p 8000:8000 \ +docker run -p 8080:8080 \ --read-only \ --tmpfs /tmp \ -v lode-data:/data \ -e LODE_SPOOL_DIR=/data/spool \ -e LODE_BUILD_DIR=/data/builds \ - lode -``` - -## From the registry - -Once published: - -```bash -docker run -p 8000:8000 ghcr.io/opencitations/lode:latest + opencitations/lode:latest ``` ## Environment variables diff --git a/docs/src/content/docs/usage/web_form.md b/docs/usage/web_form.md similarity index 86% rename from docs/src/content/docs/usage/web_form.md rename to docs/usage/web_form.md index c4cffa2..902270c 100644 --- a/docs/src/content/docs/usage/web_form.md +++ b/docs/usage/web_form.md @@ -1,7 +1,4 @@ ---- -title: Web Form -description: How to use the LODE web interface ---- +# Web form Start the server and open `http://localhost:8000`. @@ -11,7 +8,7 @@ Start the server and open `http://localhost:8000`. |-------|-------------| | **URL** | Public http(s) URL of the artefact | | **File** | Upload a local `.ttl`, `.rdf`, `.owl`, `.n3`, `.jsonld` file | -| **Format** | Artefact type (`owl` is currently available) | +| **Format** | Artefact type (`owl`, `rdf`, `skos`) | | **Language** | Preferred language for labels (e.g. `en`, `it`) | | **Load imports** | Also fetch `owl:imports` at depth 1 | | **Load closure** | Fetch the full `owl:imports` closure | diff --git a/lode/__init__.py b/lode/__init__.py index 8d1c8b6..5d99a7a 100644 --- a/lode/__init__.py +++ b/lode/__init__.py @@ -1 +1,2 @@ - +"""LODE: Live OWL Documentation Environment, maintained by OpenCitations.""" + diff --git a/lode/api.py b/lode/api.py index 077ec31..0bbff78 100644 --- a/lode/api.py +++ b/lode/api.py @@ -13,12 +13,9 @@ # ========================================================================== # 1. IMPORTS # ========================================================================== -from enum import Enum -from functools import lru_cache from pathlib import Path from typing import Optional from urllib.parse import urlencode -from uuid import uuid4 import hashlib import logging import os @@ -57,10 +54,15 @@ # ========================================================================== # 2. APP SETUP # ========================================================================== +LOG_LEVEL = os.getenv("LODE_LOG_LEVEL", "WARNING").strip().upper() + logging.basicConfig( - level=logging.DEBUG, + level=LOG_LEVEL, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", ) +# Third-party loggers: silence per-request HTTP noise and URI warnings. +logging.getLogger("urllib3").setLevel(logging.WARNING) +logging.getLogger("rdflib").setLevel(logging.ERROR) logger = logging.getLogger(__name__) # When enabled, error pages include the full traceback (development only). @@ -127,7 +129,7 @@ def _prune_builds() -> int: if st.st_mtime < cutoff: shutil.rmtree(p, ignore_errors=True) continue - for root, _dirs, files in os.walk(p): + for root, _, files in os.walk(p): for f in files: try: total += os.path.getsize(os.path.join(root, f)) @@ -141,6 +143,11 @@ def _prune_builds() -> int: # ========================================================================== def _nav_qs(read_as: str, url, upload_id, lang, imported, closure, partial_import) -> str: + """Build the query string that keeps the current view parameters in navigation links. + + Exactly one of `upload_id` and `url` is emitted, so a link never mixes the two + sources. Boolean options are included only when enabled. + """ p = {"read_as": read_as, "lang": lang or ""} p["upload_id" if upload_id else "url"] = upload_id or (url or "") if imported: @@ -154,6 +161,11 @@ def _nav_qs(read_as: str, url, upload_id, lang, imported, closure, partial_impor def _render_view(request, reader, *, resource, lang, source_url, upload_id, read_as, imported=None, closure=None, partial_import=None): + """Render one resource (or the whole artefact) as the minified viewer page. + + The body is minified after rendering, so Content-Length is recomputed: + keeping the old value would truncate the response. + """ viewer = reader.get_viewer() data = viewer.get_view_data(resource_uri=resource, language=lang) data["warnings"] = reader.get_warnings() @@ -172,11 +184,22 @@ def _render_view(request, reader, *, resource, lang, source_url, upload_id, read # 7. READER RESOLUTION # ========================================================================== def _url_token(url, read_as, imported, closure, partial_import) -> str: - key = f"{url}|{read_as}|{imported}|{closure}|{partial_import}".encode() + """Return the stable cache key for a URL and its load options. + + Every option that changes the loaded graph is part of the key, so two + requests share a cached copy only if they would produce the same result. + """ + key =f"{url}|{read_as}|{imported}|{closure}|{partial_import}".encode() return "url_" + hashlib.sha256(key).hexdigest()[:32] def _load_url(url, read_as, imported, closure, partial_import, warnings, use_cache=True): + """Load an artefact from a URL, through the disk cache when allowed. + + The URL is validated first (SSRF protection). Only the main document is + cached: modules (imports, closure) are re-applied on every hit, so the cache + never goes stale on remote ontologies. Blocking: network and disk I/O. + """ # Enforce http(s)://host up front: a non-URL value (local path, file://, ...) # must never reach the loader and be opened as a local file. security.check_url_safe(url) @@ -184,7 +207,7 @@ def _load_url(url, read_as, imported, closure, partial_import, warnings, use_cac token = _url_token(url, read_as, imported, closure, partial_import) path = spool.get_path(token) if use_cache and os.path.exists(path): - # cache hit: ricostruisci dal Turtle salvato + # cache hit: rebuild from the saved Turtle reader = Reader() reader.load_instances(path, read_as, imported=imported, closure=closure, partial_import=partial_import, warnings=warnings) @@ -195,11 +218,11 @@ def _load_url(url, read_as, imported, closure, partial_import, warnings, use_cac os.unlink(path) except OSError: pass - # cache miss (or forced refresh): scarica e processa dalla URL + # cache miss (or forced refresh): fetch and process the URL reader = Reader() reader.load_instances(url, read_as, imported=imported, closure=closure, partial_import=partial_import, warnings=warnings) - # persisti SOLO il documento principale: i moduli vengono riapplicati a ogni hit, + # persist ONLY the main document: modules are re-applied on every hit. try: g = reader._graph main = g.graph(reader._ontology_iri) if isinstance(g, ProvenanceGraph) else g @@ -211,6 +234,11 @@ def _load_url(url, read_as, imported, closure, partial_import, warnings, use_cac def _resolve_reader(read_as: str, url, upload_id, imported, closure, partial_import, warnings, use_cache=True): + """Build a Reader from an uploaded file or from a URL. + + Raises ArtefactValidationError when the upload has expired or when neither + source is given. Uploads win over URLs and are never re-fetched. + """ if upload_id: # Uploads are not re-fetched, so the cache flag does not apply to them. path = spool.get_path(upload_id) @@ -259,7 +287,7 @@ def _zip_response(reader, slug: str, lang: Optional[str] = None) -> FileResponse Blocking and disk-heavy: callers must keep it off the event loop. """ - from lode.builder import build_html # lazy: evita l'import circolare + from lode.builder import build_html # lazy: avoids a circular import if not _BUILD_SLOTS.acquire(timeout=_BUILD_WAIT): raise HTTPException(503, "Server busy: too many concurrent builds", @@ -303,6 +331,11 @@ def _zip_response(reader, slug: str, lang: Optional[str] = None) -> FileResponse # 9. ERROR RENDERING # ========================================================================== def _error_payload(exc: Exception) -> dict: + """Build the dict used by error.html for any exception. + + The traceback is included only for non-LODE errors and only when LODE_DEBUG + is set: it is always logged server-side and never shown to users otherwise. + """ is_lode = isinstance(exc, LODEError) return { "type": type(exc).__name__, @@ -317,6 +350,7 @@ def _error_payload(exc: Exception) -> dict: @app.exception_handler(LODEError) async def lode_error_handler(request: Request, exc: LODEError): + """Show a domain error (LODEError) as an HTML page with HTTP 400.""" logger.error(f"{type(exc).__name__}: {exc}") return templates.TemplateResponse( "error.html", {"request": request, "error": _error_payload(exc)}, status_code=400 @@ -325,6 +359,10 @@ async def lode_error_handler(request: Request, exc: LODEError): @app.exception_handler(Exception) async def unexpected_error_handler(request: Request, exc: Exception): + """Show an unhandled exception as an HTML page with HTTP 500. + + The full traceback goes to the server log; the page shows it only in debug mode. + """ logger.exception("Unexpected error") return templates.TemplateResponse( "error.html", {"request": request, "error": _error_payload(exc)}, status_code=500 @@ -358,9 +396,8 @@ async def limit_upload_size(request: Request, call_next): # ========================================================================== @app.get("/", response_class=HTMLResponse, tags=["ops"], summary="Web input form") async def input_web_interface(request: Request): - """Interfaccia web per l'API""" - return templates.TemplateResponse("index.html", { - "request": request, + """Serve the HTML input form, the entry point of the web interface.""" + return templates.TemplateResponse(request, "index.html", { "formats": [format.value for format in ReadAsFormat], "enabled_formats": sorted(ENABLED_FORMATS), }) @@ -385,7 +422,7 @@ def extract_get( lang: Optional[str] = Query(None, description="Language tag for labels, e.g. 'en', 'it'"), imported: Optional[bool] = Query(None, description="Also load owl:imports (depth 1)"), closure: Optional[bool] = Query(None, description="Load the full owl:imports closure"), - partial_import: Optional[bool] = Query(None, description="Additiornally load only explicitly mentioned entities from other ontologies"), + partial_import: Optional[bool] = Query(None, description="Additionally load only explicitly mentioned entities from other ontologies"), format: Optional[str] = Query(None, description="Force a serialization (ttl, rdf, jsonld…) instead of HTML"), warnings: bool = Query(False, description="Collect and show reader warnings"), cache: bool = Query(True, description="Use the disk cache for fetched URLs"), @@ -397,11 +434,7 @@ def extract_get( reader = _resolve_reader(read_as.value, url, upload_id, imported, closure, partial_import, warnings, use_cache=cache) - # Content negotiation - accept = request.headers.get("accept", "text/html") - serial = None - - # Content negotiation: i formati disponibili dipendono dal grafo (quadruple solo con moduli) + # Content negotiation: the available formats depend on the graph (quads only with modules) accept = request.headers.get("accept", "text/html") available = formats_for(reader._graph) serial = None @@ -443,7 +476,7 @@ async def extract_post( resource: Optional[str] = Form(None, description="IRI of a single resource; omit for the whole ontology"), lang: Optional[str] = Form(None, description="Language tag for labels, e.g. 'en', 'it'"), imported: Optional[bool] = Form(None, description="Also load owl:imports (depth 1)"), - partial_import: Optional[bool] = Form(None, description="Additiornally load only explicitly mentioned entities from other ontologies"), + partial_import: Optional[bool] = Form(None, description="Additionally load only explicitly mentioned entities from other ontologies"), closure: Optional[bool] = Form(None, description="Load the full owl:imports closure"), warnings: bool = Form(False, description="Collect and show reader warnings"), ): @@ -477,7 +510,7 @@ def build_get( lang: Optional[str] = Query(None, description="Language tag for labels, e.g. 'en', 'it'"), imported: Optional[bool] = Query(None, description="Also load owl:imports (depth 1)"), closure: Optional[bool] = Query(None, description="Load the full owl:imports closure"), - partial_import: Optional[bool] = Query(None, description="Additiornally load only explicitly mentioned entities from other ontologies"), + partial_import: Optional[bool] = Query(None, description="Additionally load only explicitly mentioned entities from other ontologies"), warnings: bool = Query(False, description="Collect and show reader warnings"), cache: bool = Query(True, description="Use the disk cache for fetched URLs"), ): @@ -496,7 +529,7 @@ async def build_post( lang: Optional[str] = Form(None, description="Language tag for labels, e.g. 'en', 'it'"), imported: Optional[bool] = Form(None, description="Also load owl:imports (depth 1)"), closure: Optional[bool] = Form(None, description="Load the full owl:imports closure"), - partial_import: Optional[bool] = Form(None, description="Additiornally load only explicitly mentioned entities from other ontologies"), + partial_import: Optional[bool] = Form(None, description="Additionally load only explicitly mentioned entities from other ontologies"), warnings: bool = Form(False, description="Collect and show reader warnings"), ): """Build the static site from an uploaded file instead of a URL.""" diff --git a/lode/builder.py b/lode/builder.py index 248e9c0..eaf76fc 100644 --- a/lode/builder.py +++ b/lode/builder.py @@ -1,4 +1,8 @@ -# lode/builder.py +"""Static-site builder: renders an artefact as a folder of plain HTML pages. + +Produces an index page, one page per documented resource and the serializations +of the whole artefact and of each resource, ready to publish on any static host. +""" import re import shutil from pathlib import Path @@ -17,6 +21,12 @@ _SER = [(f["fmt"], f["ext"]) for f in SERIALIZATION_FORMATS] def _get_template_env(static_path: str = "static") -> Environment: + """Create the Jinja2 environment used to render the static pages. + + `static_path` is the relative path from the page to the static folder, so it + differs between the index and the resource pages. The web app's url_for does + not exist here, hence the minimal replacement registered below. + """ try: pkg_path = importlib.resources.files("lode").joinpath("templates") template_dir = str(pkg_path) @@ -29,6 +39,7 @@ def _get_template_env(static_path: str = "static") -> Environment: ) def url_for(name: str, path: str = "") -> str: + """Resolve static files relative to the page; every other route goes to the root.""" if name == "static": return f"{static_path}/{path}" return "/" @@ -37,6 +48,7 @@ def url_for(name: str, path: str = "") -> str: return env def _prefix_map(graph): + """Map each namespace IRI of the graph to its prefix ('default' for the empty one).""" return {str(ns): (p or 'default') for p, ns in graph.namespaces()} def _safe_segment(seg: str) -> str: @@ -54,21 +66,37 @@ def _safe_segment(seg: str) -> str: def _rel_slug(uri, graph): + """Return the 'prefix/local' path of a resource, with both parts made filesystem-safe. + + The local part is empty for a bare namespace IRI: callers skip those. + """ prefix, ns, local = graph.namespace_manager.compute_qname(URIRef(str(uri)), generate=True) prefix = _safe_segment(prefix or "default") or "default" return f"{prefix}/{_safe_segment(local)}" def _local_name(uri: str) -> str: + """Return the part of an IRI after '#', or its last path segment.""" return uri.split('#', 1)[1] if '#' in uri else uri.rstrip('/').rsplit('/', 1)[-1] def _copy_static(out_dir: Path) -> None: + """Copy the package's static assets into the output folder, once. + + An existing static folder is left untouched, so rebuilding does not overwrite it. + """ static_src = Path(__file__).parent / "static" static_dst = out_dir / "static" if static_src.exists() and not static_dst.exists(): shutil.copytree(static_src, static_dst) def build_html(viewer, out_dir: Path, lang: str = "en", reader=None) -> None: + """Write the whole static site for a viewer into `out_dir`. + + Writes index.html, the serializations of the artefact and, under resources/, + one page plus serializations for each resource that belongs to the ontology + namespace or has local triples. Blocking and disk-heavy; existing files are + overwritten. A page is never written outside resources/, whatever the IRI. + """ from collections import defaultdict out_dir.mkdir(parents=True, exist_ok=True) @@ -97,9 +125,11 @@ def build_html(viewer, out_dir: Path, lang: str = "en", reader=None) -> None: materialized.add(str(u)) def _keep(uri): + """Tell whether a resource gets its own page, and so can be linked to.""" return str(uri) in materialized def resource_url_resource(uri, section=None): + """Link to a resource from a resource page; unpublished IRIs stay absolute.""" if not _keep(uri): return uri rel = _rel_slug(uri, graph) @@ -108,6 +138,7 @@ def resource_url_resource(uri, section=None): return f"../{rel}.html" def resource_url_index(uri, section=None): + """Link to a resource from the index page; unpublished IRIs stay absolute.""" if not _keep(uri): return uri rel = _rel_slug(uri, graph) @@ -145,7 +176,6 @@ def resource_url_index(uri, section=None): res_dir = out_dir / "resources" res_dir.mkdir(parents=True, exist_ok=True) - count = 0 for class_key, section_id, _ in toc_config: for inst in grouped.get(class_key, []): uri = inst.get_has_identifier() @@ -178,26 +208,36 @@ def resource_url_index(uri, section=None): data_r["resource_url"] = resource_url_resource data_r["export_base"] = _local_name(uri) page.write_text(_minify(template_resource.render(**data_r)), encoding="utf-8") - count += 1 class _FakeRequest: + """Minimal stand-in for a web request, so the viewer templates render without a web app.""" + def __init__(self, path: str): + """Build a GET request for `path` with no query parameters.""" self.url = _FakeURL(path) self.method = "GET" self.query_params = _FakeQueryParams() self.is_static = True class _FakeQueryParams: + """Query parameters that are always empty: a static page has no query string.""" + def get(self, key: str, default: str = "") -> str: + """Return the default for any key.""" return default - # Accesso diretto tipo request.query_params.read_as + # Direct access such as request.query_params.read_as def __getattr__(self, key: str) -> str: + """Return an empty string for any attribute.""" return "" class _FakeURL: + """Minimal URL object exposing only the path, as the templates need.""" + def __init__(self, path: str): + """Store the page path.""" self.path = path def __str__(self) -> str: + """Return the page path.""" return self.path \ No newline at end of file diff --git a/lode/cli.py b/lode/cli.py index 7f5c8a5..c061a72 100644 --- a/lode/cli.py +++ b/lode/cli.py @@ -10,11 +10,26 @@ from pathlib import Path def cmd_serve(args): - import uvicorn + """Start the FastAPI web service with uvicorn. + + uvicorn is imported lazily because it belongs to the optional [server] + extra: the build command must keep working without it. Blocks until the + server is stopped; binds to all interfaces so it works inside Docker. + """ + try: + import uvicorn + except ImportError: + sys.exit("Server dependencies missing: pip install oc-lode[server]") uvicorn.run("lode.api:app", host="0.0.0.0", port=args.port, reload=False) def cmd_build(args): + """Generate the static HTML documentation for one artefact. + + Reader and builder are imported lazily so that `lode serve` and `--help` + do not pay their import cost. Creates the output directory if missing and + overwrites existing pages in it. Prints the output path on success. + """ from lode.reader import Reader from lode.builder import build_html from lode.helpers.formats import check_format_enabled, ReadAsFormat @@ -37,15 +52,20 @@ def cmd_build(args): def main(): - parser = argparse.ArgumentParser(prog="lode") + """Parse the command line and dispatch to the chosen subcommand. + + Entry point of the `lode` script declared in pyproject.toml. Adds no logic + of its own: serve and build are thin adapters over the core. + """ + parser =argparse.ArgumentParser(prog="lode") sub = parser.add_subparsers(dest="cmd", required=True) # --- serve --- - p_serve = sub.add_parser("serve", help="Avvia il server FastAPI") + p_serve = sub.add_parser("serve", help="Start the FastAPI web service") p_serve.add_argument("--port", type=int, default=8000) # --- build --- - p_build = sub.add_parser("build", help="Genera HTML statici") + p_build = sub.add_parser("build", help="Generate static HTML documentation") src = p_build.add_mutually_exclusive_group(required=True) src.add_argument("--url") src.add_argument("--file") diff --git a/lode/exceptions.py b/lode/exceptions.py index 7ff77dc..32058f1 100644 --- a/lode/exceptions.py +++ b/lode/exceptions.py @@ -1,28 +1,43 @@ +"""Domain exceptions of LODE. + +Every error the user can cause (bad URL, unreachable or malformed artefact, +rejected upload) is a LODEError subclass, so the web layer can tell it apart +from an unexpected failure and show a clear message instead of a traceback. +""" from datetime import datetime, timezone +from typing import Optional import uuid class LODEError(Exception): - """Base exception. All LODE errors inherit this exception""" + """Base exception. All LODE errors inherit this exception. + + Carries a `context` dict (which file, which URL, which limit), a UTC + `timestamp` and a unique `request_id` so a message shown to the user can be + matched with the server log. + """ - def __init__(self, message: str, context: dict = None): + def __init__(self, message: str, context: Optional[dict] = None): + """Store the message together with its context, timestamp and request id.""" super().__init__(message) self.context = context or {} self.timestamp = datetime.now(timezone.utc).isoformat() self.request_id = str(uuid.uuid4()) class ArtefactLoadError(LODEError): - """Artefatto raggiunto ma non parsabile in nessun formato RDF.""" + """The artefact was reached but cannot be parsed in any RDF format.""" pass class ArtefactNotFoundError(LODEError): - """Artefatto risponde 404 o errore di rete.""" + """The artefact answers 404 or the request fails with a network error.""" pass class ArtefactUnavailableError(LODEError): - """Host remoto raggiunto ma in errore server (5xx): l'artefatto puo' esistere, - e' il servizio a essere temporaneamente non disponibile.""" + """The remote host was reached but answers with a server error (5xx). + + The artefact may well exist: it is the service that is temporarily unavailable. + """ pass class ArtefactValidationError(LODEError): - """Artefatto rifiutato dai security check (size, estensione, scheme/SSRF, non testo).""" + """The artefact was rejected by a security check (size, extension, URL scheme/SSRF, non-text).""" pass \ No newline at end of file diff --git a/lode/helpers/__init__.py b/lode/helpers/__init__.py index 66a3934..83014cf 100644 --- a/lode/helpers/__init__.py +++ b/lode/helpers/__init__.py @@ -1 +1 @@ -# helpers/__init__.py \ No newline at end of file +"""Small helpers shared by the reader, the viewer, the builder and the API.""" \ No newline at end of file diff --git a/lode/helpers/html_utils.py b/lode/helpers/html_utils.py index 22ab17b..e17ca4e 100644 --- a/lode/helpers/html_utils.py +++ b/lode/helpers/html_utils.py @@ -18,6 +18,7 @@ def minify(html: str) -> str: stash: list[str] = [] def _hold(m: re.Match) -> str: + """Replace a protected block with a numbered placeholder and remember the block.""" stash.append(m.group(0)) return f"\x00MD{len(stash)-1}\x00" diff --git a/lode/models/__init__.py b/lode/models/__init__.py index d1a9463..f940e21 100644 --- a/lode/models/__init__.py +++ b/lode/models/__init__.py @@ -1,3 +1,8 @@ +"""Internal representation of the entities extracted from an ontology (the Model layer). + +The Reader fills these classes and the Viewer renders them: neither depends on +how the other works. +""" from .resource import Resource from .property import Property from .relation import Relation diff --git a/lode/models/annotation.py b/lode/models/annotation.py index b20908f..5f223a8 100644 --- a/lode/models/annotation.py +++ b/lode/models/annotation.py @@ -1,6 +1,9 @@ +"""Annotation: an owl:AnnotationProperty.""" from .property import Property class Annotation(Property): + """An annotation property: it carries documentation, not logical meaning.""" def __init__(self, **kwargs): + """Create an annotation property; all state comes from Property.""" super().__init__(**kwargs) \ No newline at end of file diff --git a/lode/models/atom.py b/lode/models/atom.py index 76d7595..3aa50b4 100644 --- a/lode/models/atom.py +++ b/lode/models/atom.py @@ -1,14 +1,28 @@ +"""Atom: an atom of a SWRL rule.""" from .resource import Resource class Atom(Resource): + """A SWRL atom: a predicate applied to a list of arguments.""" + def __init__(self, **kwargs): + """Create an atom with no arguments and no predicate.""" super().__init__(**kwargs) self.has_arguments = [] # Variable or Resource [1...n] self.has_predicate = None # Concept (classPredicate) or Property (propertyPredicate) [1] - def get_has_arguments(self): return list(self.has_arguments) - def set_has_arguments(self, v): self.has_arguments.append(v) + def get_has_arguments(self): + """Return a copy of has_arguments.""" + return list(self.has_arguments) + + def set_has_arguments(self, v): + """Add an argument (a variable or a resource) to has_arguments.""" + self.has_arguments.append(v) + + def get_has_predicate(self): + """Return has_predicate (a concept or a property).""" + return self.has_predicate - def get_has_predicate(self): return self.has_predicate - def set_has_predicate(self, v): self.has_predicate = v \ No newline at end of file + def set_has_predicate(self, v): + """Set has_predicate.""" + self.has_predicate = v \ No newline at end of file diff --git a/lode/models/attribute.py b/lode/models/attribute.py index f48096f..36d2166 100644 --- a/lode/models/attribute.py +++ b/lode/models/attribute.py @@ -1,10 +1,13 @@ +"""Attribute: an owl:DatatypeProperty.""" from .property import Property class Attribute(Property): + """A datatype property: it relates a resource to literals.""" def __init__(self, **kwargs): + """Create an attribute with empty has_range and has_type.""" super().__init__(**kwargs) # Relation with Literal - self.has_range = [] # GIΓ  definita in parent class, card 1..* + self.has_range = [] # Already defined in the parent class, card 1..* self.has_type = [] # [1..*] \ No newline at end of file diff --git a/lode/models/cardinality.py b/lode/models/cardinality.py index 7aa9a79..61cfdb6 100644 --- a/lode/models/cardinality.py +++ b/lode/models/cardinality.py @@ -1,26 +1,29 @@ +"""Cardinality: an OWL cardinality restriction (exactly, min or max).""" from .propertyConceptRestriction import PropertyConceptRestriction class Cardinality(PropertyConceptRestriction): - + """A restriction on how many values a property can take on a concept.""" + def __init__(self, **kwargs): + """Create a cardinality restriction with no number and no type set.""" super().__init__(**kwargs) self.has_cardinality = None # int[1] self.has_cardinality_type = None # str[1] def get_has_cardinality(self): - """Restituisce il valore has_cardinality""" + """Return has_cardinality, the number of values.""" return self.has_cardinality def set_has_cardinality(self, var): - """Aggiunge un integer a has_cardinality""" + """Set has_cardinality, converting the value to int.""" self.has_cardinality = int(var) def get_has_cardinality_type(self): - """Restituisce il valore has_cardinality_type""" + """Return has_cardinality_type ("exactly", "min" or "max").""" return self.has_cardinality_type def set_has_cardinality_type(self, string): - """Aggiunge una string a has_cardinality_type""" + """Set has_cardinality_type ("exactly", "min" or "max").""" self.has_cardinality_type = string diff --git a/lode/models/collection.py b/lode/models/collection.py index 3f9ba9a..af59184 100644 --- a/lode/models/collection.py +++ b/lode/models/collection.py @@ -1,26 +1,29 @@ +"""Collection: a SKOS collection of concepts.""" from .resource import Resource class Collection(Resource): + """A SKOS collection: a labelled group of concepts or other collections.""" def __init__(self, **kwargs): + """Create an unordered collection with no members.""" super().__init__(**kwargs) self.is_ordered= False # bool[1] self.has_member= [] # [0..*] def get_is_ordered(self): - """Restituisce il valore is_ordered bool[1]""" + """Return is_ordered.""" return self.is_ordered def set_is_ordered(self, bool): - """Setta il valore di is_ordered bool [1]""" + """Set is_ordered.""" self.is_ordered = bool def get_has_member(self): - """Restituisce il valore has_member [0..*]""" + """Return a copy of has_member.""" return list(self.has_member) def set_has_member(self, concept_or_collection): - """Setta il valore di has_member [0..*]""" + """Add a concept or a collection to has_member.""" self.has_member.append(concept_or_collection) \ No newline at end of file diff --git a/lode/models/concept.py b/lode/models/concept.py index cfb9b40..fc576a9 100644 --- a/lode/models/concept.py +++ b/lode/models/concept.py @@ -1,8 +1,15 @@ +"""Concept: an OWL class or SKOS concept, with its hierarchy and matching relations.""" from .resource import Resource class Concept(Resource): + """An OWL class or a SKOS concept. + + Holds the relations between concepts (sub/super, disjoint, equivalent, SKOS + matches) and the inverse links to the properties and individuals that refer to it. + """ def __init__(self, **kwargs): + """Create a concept with every relation list empty.""" super().__init__(**kwargs) @@ -18,121 +25,132 @@ def __init__(self, **kwargs): self.has_exact_match = [] # 0..* self.has_close_match = [] # 0..* self.has_key = [] # 0..* - self.individuals_with_this_type = [] # 0..* (inverso di Individual.has_type) + self.individuals_with_this_type = [] # 0..* (inverse of Individual.has_type) self.is_in_domain_of = [] # 0..* def set_has_key(self, prop): + """Add a property to has_key (owl:hasKey).""" self.has_key.append(prop) def get_has_key(self): + """Return the has_key list (not a copy).""" return self.has_key - # Setter e Getter per is_sub_concept_of + # Setter and getter foris_sub_concept_of def set_is_sub_concept_of(self, concept): + """Add a super concept to is_sub_concept_of and register self as its sub concept. + + The inverse link is set only when the target supports it (a Restriction or + TruthFunction may not have the attribute). + """ if concept not in self.is_sub_concept_of: self.is_sub_concept_of.append(concept) - # inverso: solo se il target supporta la relazione (es. Restriction/TruthFunction potrebbero non averlo) + # inverse: only if the target supports the relation inv = getattr(concept, 'is_super_concept_of', None) if inv is not None and self not in inv: inv.append(self) def set_is_super_concept_of(self, concept): + """Add a concept to is_super_concept_of, ignoring duplicates.""" if concept not in self.is_super_concept_of: self.is_super_concept_of.append(concept) def get_is_super_concept_of(self): + """Return the is_super_concept_of list (not a copy).""" return self.is_super_concept_of def get_is_sub_concept_of(self): - """Restituisce la lista is_sub_concept_of""" + """Return the is_sub_concept_of list (not a copy).""" return self.is_sub_concept_of - # Setter e Getter per is_disjoint_with + # Setter and getter foris_disjoint_with def set_is_disjoint_with(self, concept): - """Aggiunge un Concept a is_disjoint_with""" + """Add a concept to is_disjoint_with.""" self.is_disjoint_with.append(concept) def get_is_disjoint_with(self): - """Restituisce la lista is_disjoint_with""" + """Return the is_disjoint_with list (not a copy).""" return self.is_disjoint_with - # Setter e Getter per is_equivalent_to + # Setter and getter foris_equivalent_to def set_is_equivalent_to(self, concept): - """Aggiunge un Concept a is_equivalent_to""" + """Add a concept to is_equivalent_to.""" self.is_equivalent_to.append(concept) def get_is_equivalent_to(self): - """Restituisce la lista is_equivalent_to""" + """Return the is_equivalent_to list (not a copy).""" return self.is_equivalent_to - # Setter e Getter per is_related_to + # Setter and getter foris_related_to def set_is_related_to(self, concept): - """Aggiunge un Concept a is_related_to""" + """Add a concept to is_related_to.""" self.is_related_to.append(concept) def get_is_related_to(self): - """Restituisce la lista is_related_to""" + """Return the is_related_to list (not a copy).""" return self.is_related_to - # Setter e Getter per has_broad_match + # Setter and getter forhas_broad_match def set_has_broad_match(self, concept): - """Aggiunge un Concept a has_broad_match""" + """Add a concept to has_broad_match.""" self.has_broad_match.append(concept) def get_has_broad_match(self): - """Restituisce la lista has_broad_match""" + """Return the has_broad_match list (not a copy).""" return self.has_broad_match - # Setter e Getter per has_narrow_match + # Setter and getter forhas_narrow_match def set_has_narrow_match(self, concept): - """Aggiunge un Concept a has_narrow_match""" + """Add a concept to has_narrow_match.""" self.has_narrow_match.append(concept) def get_has_narrow_match(self): - """Restituisce la lista has_narrow_match""" + """Return the has_narrow_match list (not a copy).""" return self.has_narrow_match - # Setter e Getter per has_related_match + # Setter and getter forhas_related_match def set_has_related_match(self, concept): - """Aggiunge un Concept a has_related_match""" + """Add a concept to has_related_match.""" self.has_related_match.append(concept) def get_has_related_match(self): - """Restituisce la lista has_related_match""" + """Return the has_related_match list (not a copy).""" return self.has_related_match - # Setter e Getter per has_exact_match + # Setter and getter forhas_exact_match def set_has_exact_match(self, concept): - """Aggiunge un Concept a has_exact_match""" + """Add a concept to has_exact_match.""" self.has_exact_match.append(concept) def get_has_exact_match(self): - """Restituisce la lista has_exact_match""" + """Return the has_exact_match list (not a copy).""" return self.has_exact_match - # Setter e Getter per has_close_match + # Setter and getter forhas_close_match def set_has_close_match(self, concept): - """Aggiunge un Concept a has_close_match""" + """Add a concept to has_close_match.""" self.has_close_match.append(concept) def get_has_close_match(self): - """Restituisce la lista has_close_match""" + """Return the has_close_match list (not a copy).""" return self.has_close_match def set_individuals_with_this_type(self, individual): - """Aggiunge un Individual a individuals_with_this_type (inverso di rdf:type).""" + """Add an individual to individuals_with_this_type (inverse of rdf:type), ignoring duplicates.""" if individual not in self.individuals_with_this_type: self.individuals_with_this_type.append(individual) def get_individuals_with_this_type(self): - """Restituisce la lista individuals_with_this_type.""" + """Return a copy of individuals_with_this_type.""" return list(self.individuals_with_this_type) def set_is_in_domain_of(self, prop): + """Add a property to is_in_domain_of, ignoring duplicates.""" if prop not in self.is_in_domain_of: self.is_in_domain_of.append(prop) def get_is_in_domain_of(self): + """Return a copy of is_in_domain_of.""" return list(self.is_in_domain_of) \ No newline at end of file diff --git a/lode/models/container.py b/lode/models/container.py index 765da66..c13489e 100644 --- a/lode/models/container.py +++ b/lode/models/container.py @@ -1,21 +1,23 @@ +"""Container: an RDF container or list.""" from .resource import Resource class Container(Resource): """RDF Container (Bag, Seq, Alt, List)""" - + def __init__(self): + """Create a container with no members.""" super().__init__() self.members = [] def set_has_member(self, member): - """Aggiunge un singolo membro""" + """Add a single member, ignoring duplicates.""" if member not in self.members: self.members.append(member) def set_has_members(self, members: list): - """Imposta tutti i membri in una volta""" - self._members = members.copy() + """Set all the members at once, from a copy of `members`.""" + self.members = members.copy() def get_has_members(self): - """Ritorna la lista dei membri""" + """Return a copy of the members list.""" return self.members.copy() diff --git a/lode/models/datatype.py b/lode/models/datatype.py index df9bdc5..20ab961 100644 --- a/lode/models/datatype.py +++ b/lode/models/datatype.py @@ -1,6 +1,9 @@ +"""Datatype: an RDFS/OWL datatype such as xsd:string.""" from .concept import Concept class Datatype(Concept): + """A datatype: the kind of value a literal can have.""" def __init__(self, **kwargs): + """Create a datatype; all state comes from Concept.""" super().__init__(**kwargs) diff --git a/lode/models/datatypeRestriction.py b/lode/models/datatypeRestriction.py index 7b66c44..5f04de2 100644 --- a/lode/models/datatypeRestriction.py +++ b/lode/models/datatypeRestriction.py @@ -1,21 +1,28 @@ +"""DatatypeRestriction: an owl:DatatypeRestriction (a datatype narrowed by facets).""" from .restriction import Restriction class DatatypeRestriction(Restriction): + """A datatype narrowed by an XSD facet, such as a pattern or a minimum value.""" def __init__(self, **kwargs): + """Create a datatype restriction with no datatype and no facet value.""" super().__init__(**kwargs) self.applies_on_concept = None # Datatype (from owl:onDatatype) string (xsd:pattern, xsd:minInclusive, ...) self.has_restriction_value = None # Literal (the corresponding value e.g. 0.0) def get_applies_on_concept(self): + """Return applies_on_concept (the datatype, or the facet string).""" return self.applies_on_concept def set_applies_on_concept(self, datatype): + """Set applies_on_concept (the datatype, or the facet string).""" self.applies_on_concept = datatype def set_has_restriction_value(self, string): + """Set has_restriction_value (the literal value of the facet).""" self.has_restriction_value = string def get_has_restriction_value(self): + """Return has_restriction_value (the literal value of the facet).""" return self.has_restriction_value \ No newline at end of file diff --git a/lode/models/individual.py b/lode/models/individual.py index 006de5b..f096396 100644 --- a/lode/models/individual.py +++ b/lode/models/individual.py @@ -1,18 +1,20 @@ +"""Individual: an OWL named individual.""" from .resource import Resource class Individual(Resource): """ - Rappresenta un'istanza individuale di una classe (owl:NamedIndividual). - Estende Resource con relazioni specifiche per individui OWL. + Represents an individual instance of a class (owl:NamedIndividual). + Extends Resource with the relations specific to OWL individuals. """ def __init__(self, **kwargs): + """Create an individual with empty is_same_as and is_different_from lists.""" super().__init__(**kwargs) # Relations with Individual self.is_same_as = [] # 0..* self.is_different_from = [] # 0..* - # Relations with Concept (ereditato ma qui esplicitato, perchΓ¨ cambia la cardinalitΓ ) + # Relations with Concept (inherited but made explicit here, because the cardinality changes) # self.has_type = [] # 1..* # def get_has_type(self): @@ -22,17 +24,17 @@ def __init__(self, **kwargs): # self.has_type.append(concept) def get_is_same_as(self): - """Restituisce la lista is_same_as [0..*]""" + """Return a copy of is_same_as [0..*].""" return list(self.is_same_as) def set_is_same_as(self, individual): - """Aggiunge un Individual a is_same_as [0..*]""" + """Add an individual to is_same_as [0..*].""" self.is_same_as.append(individual) def get_is_different_from(self): - """Restituisce la lista is_different_from [0..*]""" + """Return a copy of is_different_from [0..*].""" return list(self.is_different_from) def set_is_different_from(self, individual): - """Aggiunge un Individual a is_different_from [0..*]""" + """Add an individual to is_different_from [0..*].""" self.is_different_from.append(individual) diff --git a/lode/models/literal.py b/lode/models/literal.py index 369c970..8dfaf08 100644 --- a/lode/models/literal.py +++ b/lode/models/literal.py @@ -1,9 +1,12 @@ +"""Literal: an RDF literal with its value, language and datatype.""" from .resource import Resource -class Literal(Resource): +class Literal(Resource): + """An RDF literal: a lexical value with an optional language tag and datatype.""" def __init__(self, **kwargs): - + """Create an empty literal: no value, language or datatype.""" + super().__init__(**kwargs) # Attributes @@ -13,23 +16,25 @@ def __init__(self, **kwargs): self.has_type = None def set_has_language(self, literal): - """Imposta has_language""" + """Set has_language.""" self.has_language = literal def get_has_language(self): - """Restituisce has_language""" + """Return has_language.""" return self.has_language def set_has_value(self, literal): - """Imposta has_value""" + """Set has_value.""" self.has_value = literal def get_has_value(self): - """Restituisce has_value""" + """Return has_value.""" return self.has_value def set_has_type(self, datatype): + """Set has_type, the datatype of the literal.""" self.has_type = datatype def get_has_type(self): + """Return has_type, the datatype of the literal.""" return self.has_type diff --git a/lode/models/model.py b/lode/models/model.py index a94dec9..b5c2a90 100644 --- a/lode/models/model.py +++ b/lode/models/model.py @@ -1,70 +1,73 @@ +"""Model: the documented ontology (or vocabulary) itself, with its versions and imports.""" from .resource import Resource class Model(Resource): + """An ontology or vocabulary: versioning, compatibility, imports and namespaces.""" def __init__(self, **kwargs): + """Create a model with no versions, imports or namespaces.""" super().__init__(**kwargs) self.has_version = [] # 0..* self.is_backward_compatible_with = [] # 0..* self.imports = [] # 0..* self.is_incompatible_with = [] # 0..* - self.has_top_concept = [] # 0..1 + self.has_top_concept = None # 0..1 self.has_prior_version = None # 0..1 self.has_namespaces = {} # 1 (prefix -> URI) def get_has_version(self): - """Restituisce la lista has_version""" + """Return a copy of has_version.""" return list(self.has_version) def set_has_version(self, model): - """Aggiunge un Model a has_version """ + """Add a model to has_version.""" self.has_version.append(model) def get_is_backward_compatible_with(self): - """Restituisce la lista is_backward_compatible_with""" + """Return a copy of is_backward_compatible_with.""" return list(self.is_backward_compatible_with) def set_is_backward_compatible_with(self, model): - """Aggiunge un Model a is_backward_compatible_with""" + """Add a model to is_backward_compatible_with.""" self.is_backward_compatible_with.append(model) def get_imports(self): - """Restituisce la lista imports""" + """Return a copy of imports.""" return list(self.imports) def set_imports(self, model): - """Aggiunge un Model a imports""" + """Add a model to imports.""" self.imports.append(model) def get_is_incompatible_with(self): - """Restituisce la lista is_incompatible_with""" + """Return a copy of is_incompatible_with.""" return list(self.is_incompatible_with) def set_is_incompatible_with(self, model): - """Aggiunge un Model a is_incompatible_with""" + """Add a model to is_incompatible_with.""" self.is_incompatible_with.append(model) def get_has_top_concept(self): - """Restituisce la lista has_top_concept""" + """Return has_top_concept (a single concept, or None).""" return self.has_top_concept def set_has_top_concept(self, concept): - """Aggiunge un Concept a has_top_concept""" + """Set has_top_concept, replacing any previous value.""" self.has_top_concept = concept def get_has_prior_version(self): - """Restituisce la lista has_prior_version""" + """Return has_prior_version (a single model, or None).""" return self.has_prior_version def set_has_prior_version(self, model): - """Aggiunge un Model a has_prior_version""" + """Set has_prior_version, replacing any previous value.""" self.has_prior_version = model def get_has_namespaces(self): - """Restituisce il dizionario prefix -> URI""" + """Return a copy of the prefix -> URI dictionary.""" return dict(self.has_namespaces) def set_has_namespaces(self, namespaces: dict): - """Imposta il dizionario dei namespace (prefix -> URI)""" + """Set the prefix -> URI dictionary of the namespaces.""" self.has_namespaces = namespaces \ No newline at end of file diff --git a/lode/models/oneOf.py b/lode/models/oneOf.py index b983d2c..47ce034 100644 --- a/lode/models/oneOf.py +++ b/lode/models/oneOf.py @@ -1,17 +1,20 @@ +"""OneOf: an owl:oneOf enumeration.""" from .restriction import Restriction class OneOf(Restriction): + """A class defined by listing its members (owl:oneOf).""" def __init__(self, **kwargs): + """Create an enumeration with no resources.""" super().__init__(**kwargs) self.applies_on_resource = [] # 1..* def get_applies_on_resource(self): - """Restituisce la lista applies on resource""" + """Return a copy of applies_on_resource.""" return list(self.applies_on_resource) def set_applies_on_resource(self, resource): - """Aggiunge un Resource a applies_on_resource """ + """Add a resource to applies_on_resource.""" self.applies_on_resource.append(resource) diff --git a/lode/models/property.py b/lode/models/property.py index be764ef..032f973 100644 --- a/lode/models/property.py +++ b/lode/models/property.py @@ -1,10 +1,12 @@ +"""Property: the base class of RDF/OWL properties.""" from .resource import Resource class Property(Resource): """Represents an RDF Property""" def __init__(self, **kwargs): - + """Create a property that is not functional, with empty hierarchy, domain and range.""" + super().__init__(**kwargs) # Attributes @@ -22,17 +24,21 @@ def __init__(self, **kwargs): # Relations with Concept (1..*) self.has_domain = [] - # Metodi per is_functional + # Methods foris_functional def set_is_functional(self, bool): - """Imposta is_functional""" + """Set is_functional.""" self.is_functional = bool def get_is_functional(self): - """Restituisce is_functional""" + """Return is_functional.""" return self.is_functional - # Metodi per is_sub_property_of / is_super_property_of + # Methods foris_sub_property_of / is_super_property_of def set_is_sub_property_of(self, property_obj): + """Add a super property to is_sub_property_of and register self as its sub property. + + The inverse link is set only when the target supports it. + """ if property_obj not in self.is_sub_property_of: self.is_sub_property_of.append(property_obj) inv = getattr(property_obj, 'is_super_property_of', None) @@ -40,46 +46,51 @@ def set_is_sub_property_of(self, property_obj): inv.append(self) def get_is_sub_property_of(self): + """Return a copy of is_sub_property_of.""" return list(self.is_sub_property_of) def set_is_super_property_of(self, property_obj): + """Add a property to is_super_property_of, ignoring duplicates.""" if property_obj not in self.is_super_property_of: self.is_super_property_of.append(property_obj) def get_is_super_property_of(self): + """Return a copy of is_super_property_of.""" return list(self.is_super_property_of) - # Metodi per is_disjoint_with + # Methods foris_disjoint_with def set_is_disjoint_with(self, property_obj): - """Aggiunge una property a is_disjoint_with""" + """Add a property to is_disjoint_with.""" self.is_disjoint_with.append(property_obj) def get_is_disjoint_with(self): - """Restituisce una copia della lista is_disjoint_with""" + """Return a de-duplicated copy of is_disjoint_with (order is not preserved).""" return list(set(self.is_disjoint_with)) def set_is_equivalent_to(self, property_obj): - """Aggiunge una property a is_equivalent_to""" + """Add a property to is_equivalent_to.""" self.is_equivalent_to.append(property_obj) def get_is_equivalent_to(self): - """Restituisce una copia della lista is_equivalent_to""" + """Return a de-duplicated copy of is_equivalent_to (order is not preserved).""" return list(set(self.is_equivalent_to)) - # Metodi per has_range + # Methods forhas_range def set_has_range(self, resource): + """Add a resource to has_range, ignoring duplicates.""" if resource not in self.has_range: self.has_range.append(resource) def get_has_range(self): - """Restituisce una copia della lista has_range""" + """Return a copy of has_range.""" return list(self.has_range) def set_has_domain(self, concept): + """Add a concept to has_domain, ignoring duplicates.""" if concept not in self.has_domain: self.has_domain.append(concept) def get_has_domain(self): - """Restituisce una copia della lista has_domain""" + """Return a copy of has_domain.""" return list(self.has_domain) diff --git a/lode/models/propertyConceptRestriction.py b/lode/models/propertyConceptRestriction.py index 29ffff7..f9cd3e3 100644 --- a/lode/models/propertyConceptRestriction.py +++ b/lode/models/propertyConceptRestriction.py @@ -1,7 +1,11 @@ +"""PropertyConceptRestriction: a restriction that links a property to a concept.""" from .restriction import Restriction class PropertyConceptRestriction(Restriction): + """Base of the restrictions that apply a property to a concept (quantifiers, cardinalities).""" + def __init__(self, **kwargs): + """Create a restriction with no property, no concept, and is_inverse False.""" super().__init__(**kwargs) self.applies_on_property = None # 1 @@ -9,25 +13,25 @@ def __init__(self, **kwargs): self.is_inverse = False #bool 1 def get_applies_on_property(self): - """Restituisce il valore applies on property""" + """Return applies_on_property.""" return self.applies_on_property def set_applies_on_property(self, property): - """Aggiunge un Property a applies_on_property """ + """Set applies_on_property.""" self.applies_on_property = property def get_applies_on_concept(self): - """Restituisce la lista applies on concept""" + """Return applies_on_concept.""" return self.applies_on_concept def set_applies_on_concept(self, concept): - """Aggiunge un Concept a applies_on_concept """ + """Set applies_on_concept.""" self.applies_on_concept = concept def get_is_inverse(self): - """Restituisce la lista applies on concept""" + """Return is_inverse.""" return self.is_inverse def set_is_inverse(self, boolean): - """Sets if the restriction is inverse""" + """Set is_inverse: whether the restriction is on the inverse of the property.""" self.is_inverse = boolean diff --git a/lode/models/propertySelfRestriction.py b/lode/models/propertySelfRestriction.py index ce673aa..03a7a9c 100644 --- a/lode/models/propertySelfRestriction.py +++ b/lode/models/propertySelfRestriction.py @@ -1,15 +1,20 @@ +"""PropertySelfRestriction: an owl:hasSelf restriction.""" from .restriction import Restriction class PropertySelfRestriction(Restriction): + """A restriction on the individuals related to themselves by a property (owl:hasSelf).""" def __init__(self, **kwargs): + """Create a self restriction with no property.""" super().__init__(**kwargs) self.applies_on_property = None # [1] def get_applies_on_property(self): + """Return applies_on_property.""" return self.applies_on_property def set_applies_on_property(self, relation): + """Set applies_on_property.""" self.applies_on_property = relation diff --git a/lode/models/quantifier.py b/lode/models/quantifier.py index 577bb2d..b5ce1f1 100644 --- a/lode/models/quantifier.py +++ b/lode/models/quantifier.py @@ -1,16 +1,22 @@ +"""Quantifier: an existential or universal property restriction.""" from .propertyConceptRestriction import PropertyConceptRestriction class Quantifier(PropertyConceptRestriction): - + """A quantified restriction of a property on a concept. + + The type is "some" (owl:someValuesFrom) or "only" (owl:allValuesFrom). + """ + def __init__(self, **kwargs): + """Create a quantifier with no type set.""" super().__init__(**kwargs) self.has_quantifier_type = None # str[1] def get_has_quantifier_type(self): - """Restituisce il valore has_quantifier_type""" + """Return has_quantifier_type ("some" or "only").""" return self.has_quantifier_type def set_has_quantifier_type(self, string): - """Aggiunge una string a has_quantifier_type""" + """Set has_quantifier_type ("some" or "only").""" self.has_quantifier_type = string \ No newline at end of file diff --git a/lode/models/relation.py b/lode/models/relation.py index 6ec5cc5..88518f7 100644 --- a/lode/models/relation.py +++ b/lode/models/relation.py @@ -1,10 +1,11 @@ +"""Relation: an owl:ObjectProperty and its logical characteristics.""" from .property import Property class Relation(Property): - """Rappresenta una Object Property RDF""" + """Represents an RDF Object Property""" def __init__(self, **kwargs): - # Chiama il costruttore della classe padre + """Create a relation with every characteristic set to False and no inverses or chains.""" super().__init__(**kwargs) # Attributes @@ -22,73 +23,75 @@ def __init__(self, **kwargs): # Relation with Concept self.has_range = [] # 1..* - # Metodi per is_asymmetric + # Methods foris_asymmetric def set_is_asymmetric(self, value): - """Imposta is_asymmetric""" + """Set is_asymmetric.""" self.is_asymmetric = value def get_is_asymmetric(self): - """Restituisce is_asymmetric""" + """Return is_asymmetric.""" return self.is_asymmetric - # Metodi per is_inverse_functional + # Methods foris_inverse_functional def set_is_inverse_functional(self, value): - """Imposta is_inverse_functional""" + """Set is_inverse_functional.""" self.is_inverse_functional = value def get_is_inverse_functional(self): - """Restituisce is_inverse_functional""" + """Return is_inverse_functional.""" return self.is_inverse_functional - # Metodi per is_irreflexive + # Methods foris_irreflexive def set_is_irreflexive(self, value): - """Imposta is_irreflexive""" + """Set is_irreflexive.""" self.is_irreflexive = value def get_is_irreflexive(self): - """Restituisce is_irreflexive""" + """Return is_irreflexive.""" return self.is_irreflexive - # Metodi per is_reflexive + # Methods foris_reflexive def set_is_reflexive(self, value): - """Imposta is_reflexive""" + """Set is_reflexive.""" self.is_reflexive = value def get_is_reflexive(self): - """Restituisce is_reflexive""" + """Return is_reflexive.""" return self.is_reflexive - # Metodi per is_symmetric + # Methods foris_symmetric def set_is_symmetric(self, value): - """Imposta is_symmetric""" + """Set is_symmetric.""" self.is_symmetric = value def get_is_symmetric(self): - """Restituisce is_symmetric""" + """Return is_symmetric.""" return self.is_symmetric - # Metodi per is_transitive + # Methods foris_transitive def set_is_transitive(self, value): - """Imposta is_transitive""" + """Set is_transitive.""" self.is_transitive = value def get_is_transitive(self): - """Restituisce is_transitive""" + """Return is_transitive.""" return self.is_transitive def get_is_inverse_of(self): - """Returns the list of inverse of""" + """Return a de-duplicated copy of is_inverse_of (order is not preserved).""" return list(set(self.is_inverse_of)) def set_is_inverse_of(self, relation): - """Adds a inverse relation""" + """Add a relation to is_inverse_of.""" self.is_inverse_of.append(relation) def set_has_property_chain(self, relation): + """Add a relation to has_property_chain, ignoring duplicates.""" if relation not in self.has_property_chain: self.has_property_chain.append(relation) def get_has_property_chain(self): + """Return a copy of has_property_chain.""" return list(self.has_property_chain) # def set_has_range(self, concept): diff --git a/lode/models/resource.py b/lode/models/resource.py index eb6a535..7ae5bda 100644 --- a/lode/models/resource.py +++ b/lode/models/resource.py @@ -1,7 +1,16 @@ +"""Root of the LODE model: the RDF resource every other entity extends.""" + + class Resource(): - """Rappresenta una Risorsa RDF""" + """An RDF resource, with its annotations (labels, notes, ...) and links to other resources. + + Cardinalities are noted next to each field in __init__. Multi-valued fields + are plain lists filled by the setters; most getters return a copy so callers + cannot alter the model by accident. + """ def __init__(self): + """Create an empty resource: no identifier, not deprecated, all lists empty.""" # Init Attributes self.has_identifier = None self.is_deprecated = False @@ -20,8 +29,6 @@ def __init__(self): self.has_example = [] self.has_history_note = [] self.has_scope_note = [] - self.has_contributor = [] - self.has_creator = [] # Relations with Resources (0..*) self.see_also = [] @@ -39,187 +46,179 @@ def __init__(self): self.is_in_range_of = [] def set_has_identifier(self, value): - """Imposta has_identifier""" + """Set has_identifier.""" self.has_identifier = value def get_has_identifier(self): - """Restituisce has_identifier""" + """Return has_identifier.""" return self.has_identifier def set_is_deprecated(self, value): - """Imposta is_deprecated""" + """Set is_deprecated.""" self.is_deprecated = value def get_is_deprecated(self): - """Restituisce is_deprecated""" + """Return is_deprecated.""" return self.is_deprecated def set_has_comment(self, literal): - """Aggiunge un literal a has_comment""" + """Add a literal to has_comment.""" self.has_comment.append(literal) def get_has_comment(self): - """Restituisce una copia della lista has_comment""" - return list(set(self.has_comment)) + """Return a de-duplicated copy of has_comment, in insertion order.""" + return list(dict.fromkeys(self.has_comment)) def set_has_label(self, literal): - """Aggiunge un literal a has_label""" + """Add a literal to has_label.""" self.has_label.append(literal) def get_has_label(self): - """Restituisce una copia della lista has_label""" - return list(set(self.has_label)) + """Return a de-duplicated copy of has_label, in insertion order.""" + return list(dict.fromkeys(self.has_label)) def set_has_preferred_label(self, literal): - """Aggiunge un literal a has_preferred_label""" + """Add a literal to has_preferred_label.""" self.has_preferred_label.append(literal) def get_has_preferred_label(self): - """Restituisce una copia della lista has_preferred_label""" - return list(set(self.has_preferred_label)) + """Return a de-duplicated copy of has_preferred_label, in insertion order.""" + return list(dict.fromkeys(self.has_preferred_label)) def set_has_alternative_label(self, literal): - """Aggiunge un literal a has_alternative_label""" + """Add a literal to has_alternative_label.""" self.has_alternative_label.append(literal) def get_has_alternative_label(self): - """Restituisce una copia della lista has_alternative_label""" - return list(set(self.has_alternative_label)) + """Return a de-duplicated copy of has_alternative_label, in insertion order.""" + return list(dict.fromkeys(self.has_alternative_label)) def set_has_hidden_label(self, literal): - """Aggiunge un literal a has_hidden_label""" + """Add a literal to has_hidden_label.""" self.has_hidden_label.append(literal) def get_has_hidden_label(self): - """Restituisce una copia della lista has_hidden_label""" - return list(set(self.has_hidden_label)) + """Return a de-duplicated copy of has_hidden_label, in insertion order.""" + return list(dict.fromkeys(self.has_hidden_label)) def set_has_notation(self, literal): - """Aggiunge un literal a has_notation""" + """Add a literal to has_notation.""" self.has_notation.append(literal) def get_has_notation(self): - """Restituisce una copia della lista has_notation""" - return list(set(self.has_notation)) + """Return a de-duplicated copy of has_notation, in insertion order.""" + return list(dict.fromkeys(self.has_notation)) def set_has_note(self, literal): - """Aggiunge un literal a has_note""" + """Add a literal to has_note.""" self.has_note.append(literal) def get_has_note(self): - """Restituisce una copia della lista has_note""" - return list(set(self.has_note)) + """Return a de-duplicated copy of has_note, in insertion order.""" + return list(dict.fromkeys(self.has_note)) def set_has_change_note(self, literal): - """Aggiunge un literal a has_change_note""" + """Add a literal to has_change_note.""" self.has_change_note.append(literal) def get_has_change_note(self): - """Restituisce una copia della lista has_change_note""" - return list(set(self._has_change_note)) + """Return a de-duplicated copy of has_change_note, in insertion order.""" + return list(dict.fromkeys(self.has_change_note)) def set_has_definition(self, literal): - """Aggiunge un literal a has_definition""" + """Add a literal to has_definition.""" self.has_definition.append(literal) def get_has_definition(self): - """Restituisce una copia della lista has_definition""" - return list(set(self.has_definition)) + """Return a de-duplicated copy of has_definition, in insertion order.""" + return list(dict.fromkeys(self.has_definition)) def set_has_editorial_note(self, literal): - """Aggiunge un literal a has_editorial_note""" + """Add a literal to has_editorial_note.""" self.has_editorial_note.append(literal) def get_has_editorial_note(self): - """Restituisce una copia della lista has_editorial_note""" - return list(set(self.has_editorial_note)) + """Return a de-duplicated copy of has_editorial_note, in insertion order.""" + return list(dict.fromkeys(self.has_editorial_note)) def set_has_example(self, literal): - """Aggiunge un literal a has_example""" + """Add a literal to has_example.""" self.has_example.append(literal) def get_has_example(self): - """Restituisce una copia della lista has_example""" - return list(set(self.has_example)) + """Return a de-duplicated copy of has_example, in insertion order.""" + return list(dict.fromkeys(self.has_example)) def set_has_history_note(self, literal): - """Aggiunge un literal a has_history_note""" + """Add a literal to has_history_note.""" self.has_history_note.append(literal) def get_has_history_note(self): - """Restituisce una copia della lista has_history_note""" - return list(set(self.has_history_note)) + """Return a de-duplicated copy of has_history_note, in insertion order.""" + return list(dict.fromkeys(self.has_history_note)) def set_has_scope_note(self, literal): - """Aggiunge un literal a has_scope_note""" + """Add a literal to has_scope_note.""" self.has_scope_note.append(literal) def get_has_scope_note(self): - """Restituisce una copia della lista has_scope_note""" - return list(set(self.has_scope_note)) + """Return a de-duplicated copy of has_scope_note, in insertion order.""" + return list(dict.fromkeys(self.has_scope_note)) def set_see_also(self, resource): - """Aggiunge una risorsa a see_also""" + """Add a resource to see_also.""" self.see_also.append(resource) def get_see_also(self): - """Restituisce una copia della lista see_also""" - return list(set(self.see_also)) + """Return a de-duplicated copy of see_also, in insertion order.""" + return list(dict.fromkeys(self.see_also)) def set_is_defined_by(self, resource): - """Aggiunge una risorsa a is_defined_by""" + """Add a resource to is_defined_by.""" self.is_defined_by.append(resource) def get_is_defined_by(self): - """Restituisce una copia della lista is_defined_by""" - return list(set(self.is_defined_by)) + """Return a de-duplicated copy of is_defined_by, in insertion order.""" + return list(dict.fromkeys(self.is_defined_by)) def set_has_version_info(self, resource): - """Aggiunge una risorsa a has_version_info""" + """Add a resource to has_version_info.""" self.has_version_info.append(resource) def get_has_version_info(self): - """Restituisce una copia della lista has_version_info""" - return list(set(self.has_version_info)) + """Return a de-duplicated copy of has_version_info, in insertion order.""" + return list(dict.fromkeys(self.has_version_info)) def set_has_type(self, concept): + """Add a concept to has_type, ignoring duplicates.""" if concept not in self.has_type: self.has_type.append(concept) def get_has_type(self): + """Return a copy of has_type.""" return list(self.has_type) def set_is_included_in(self, model): - """Aggiunge un model a is_included_in""" + """Add a model to is_included_in.""" self.is_included_in.append(model) def get_is_included_in(self): - """Restituisce una copia della lista is_included_in""" - return list(set(self.is_included_in)) - - def set_has_contributor(self, literal): - self.has_contributor.append(literal) - - def get_has_contributor(self): - return list(set(self.has_contributor)) - - def set_has_creator(self, literal): - self.has_creator.append(literal) - - def get_has_creator(self): - return list(set(self.has_creator)) + """Return a de-duplicated copy of is_included_in, in insertion order.""" + return list(dict.fromkeys(self.is_included_in)) def get_also_defined_as(self): - """Returns the list of also defined as""" + """Return a copy of also_defined_as.""" return list(self.also_defined_as) def set_also_defined_as(self, resource): - """Aggiunge un Resource alla lista di also_defined_as""" + """Add a resource to also_defined_as.""" self.also_defined_as.append(resource) def set_is_in_range_of(self, prop): + """Add a property to is_in_range_of, ignoring duplicates.""" if prop not in self.is_in_range_of: self.is_in_range_of.append(prop) def get_is_in_range_of(self): + """Return a copy of is_in_range_of.""" return list(self.is_in_range_of) \ No newline at end of file diff --git a/lode/models/restriction.py b/lode/models/restriction.py index 5d7f518..53c1a90 100644 --- a/lode/models/restriction.py +++ b/lode/models/restriction.py @@ -1,7 +1,10 @@ +"""Restriction: base class of OWL restrictions and anonymous class expressions.""" from .concept import Concept class Restriction(Concept): + """Base of the anonymous classes built by restrictions and logical operators.""" def __init__(self, **kwargs): + """Create a restriction; all state comes from Concept.""" super().__init__(**kwargs) diff --git a/lode/models/rule.py b/lode/models/rule.py index 07e308a..357d5d8 100644 --- a/lode/models/rule.py +++ b/lode/models/rule.py @@ -1,13 +1,27 @@ +"""Rule: a SWRL rule.""" from .resource import Resource class Rule(Resource): + """A SWRL rule: when every antecedent atom holds, the consequent atoms hold.""" + def __init__(self, **kwargs): + """Create a rule with no antecedent and no consequent.""" super().__init__(**kwargs) self.has_antecedent = [] # Atom [1..*] self.has_consequent = [] # Atom [1..*] - def get_has_antecedent(self): return list(self.has_antecedent) - def set_has_antecedent(self, atom): self.has_antecedent.append(atom) + def get_has_antecedent(self): + """Return a copy of has_antecedent.""" + return list(self.has_antecedent) + + def set_has_antecedent(self, atom): + """Add an atom to has_antecedent.""" + self.has_antecedent.append(atom) + + def get_has_consequent(self): + """Return a copy of has_consequent.""" + return list(self.has_consequent) - def get_has_consequent(self): return list(self.has_consequent) - def set_has_consequent(self, atom): self.has_consequent.append(atom) \ No newline at end of file + def set_has_consequent(self, atom): + """Add an atom to has_consequent.""" + self.has_consequent.append(atom) \ No newline at end of file diff --git a/lode/models/statement.py b/lode/models/statement.py index 8462c01..246faa3 100644 --- a/lode/models/statement.py +++ b/lode/models/statement.py @@ -1,8 +1,11 @@ +"""Statement: a reified RDF triple.""" from .resource import Resource class Statement(Resource): + """An RDF triple (subject, predicate, object) described as a resource, so it can be documented.""" def __init__(self, **kwargs): + """Create a positive statement with no subject, predicate or object.""" super().__init__(**kwargs) self.is_positive_statement = True # bool [1] @@ -12,35 +15,35 @@ def __init__(self, **kwargs): # Attributes def get_is_positive_statement(self): - """Restituisce il valore is_positive_statement [1]""" + """Return is_positive_statement.""" return self.is_positive_statement def set_is_positive_statement(self, statement): - """Setta il valore di a is_positive_statement [1]""" + """Set is_positive_statement.""" self.is_positive_statement = statement # Relations with Resource def get_has_subject(self): - """Restituisce il valore has_subject [1]""" + """Return has_subject.""" return self.has_subject def set_has_subject(self, statement): - """Setta il valore di a has_subject [1]""" + """Set has_subject.""" self.has_subject = statement def get_has_object(self): - """Restituisce il valore has_object [1]""" + """Return has_object.""" return self.has_object def set_has_object(self, statement): - """Setta il valore di a has_object [1]""" + """Set has_object.""" self.has_object = statement # Relation with Property def get_has_predicate(self): - """Restituisce il valore has_predicate [1]""" + """Return has_predicate.""" return self.has_predicate def set_has_predicate(self, statement): - """Setta il valore di a has_predicate [1]""" + """Set has_predicate.""" self.has_predicate = statement diff --git a/lode/models/truthFunction.py b/lode/models/truthFunction.py index 2e1b69a..99ab47e 100644 --- a/lode/models/truthFunction.py +++ b/lode/models/truthFunction.py @@ -1,29 +1,32 @@ +"""TruthFunction: a class expression built with a logical operator (and, or, not).""" from .restriction import Restriction class TruthFunction(Restriction): + """A class expression combining concepts with a logical operator (and, or, not).""" # the has_cardinality_type can have one of three values: "max", "min", and "exact". Any other string will be interpreted as "exact". # fallback = exact def __init__(self, **kwargs): + """Create a truth function with no operator and no concepts.""" super().__init__(**kwargs) self.has_logical_operator = None # string[1] self.applies_on_concept = [] # 1..* def get_has_logical_operator(self): - """Restituisce la stringa per has_logical_operator""" + """Return has_logical_operator.""" return self.has_logical_operator def set_has_logical_operator(self, literal): - """Aggiunge una str a as_logical_operator""" + """Set has_logical_operator.""" self.has_logical_operator = literal def get_applies_on_concept(self): - """Restituisce la lista applies on concept""" + """Return a copy of applies_on_concept.""" return list(self.applies_on_concept) def set_applies_on_concept(self, concept): - """Aggiunge un Concept a applies_on_concept """ + """Add a concept to applies_on_concept.""" self.applies_on_concept.append(concept) diff --git a/lode/models/value.py b/lode/models/value.py index cd75ffc..262722c 100644 --- a/lode/models/value.py +++ b/lode/models/value.py @@ -1,23 +1,28 @@ +"""Value: an owl:hasValue restriction.""" from .restriction import Restriction class Value(Restriction): + """A restriction requiring a property to take one specific resource as value (owl:hasValue).""" def __init__(self, **kwargs): + """Create a value restriction with no resource and no property.""" super().__init__(**kwargs) self.applies_on_resource = None # 1 self.applies_on_property = None # 1 def get_applies_on_resource(self): - """Restituisce la lista applies on resource""" + """Return applies_on_resource.""" return self.applies_on_resource def set_applies_on_resource(self, resource): - """Aggiunge un Resource a applies_on_resource """ + """Set applies_on_resource.""" self.applies_on_resource = resource def get_applies_on_property(self): + """Return applies_on_property.""" return self.applies_on_property def set_applies_on_property(self, prop): + """Set applies_on_property.""" self.applies_on_property = prop \ No newline at end of file diff --git a/lode/models/variable.py b/lode/models/variable.py index 26a3294..8777eca 100644 --- a/lode/models/variable.py +++ b/lode/models/variable.py @@ -1,5 +1,9 @@ +"""Variable: a variable of a SWRL rule.""" from .resource import Resource class Variable(Resource): + """A SWRL variable, used as an argument of an atom.""" + def __init__(self, **kwargs): + """Create a variable; all state comes from Resource.""" super().__init__(**kwargs) \ No newline at end of file diff --git a/lode/reader/config/old_base.yaml b/lode/reader/config/old_base.yaml deleted file mode 100644 index ca61cd6..0000000 --- a/lode/reader/config/old_base.yaml +++ /dev/null @@ -1,599 +0,0 @@ -name: BASE - -# ====================== -# MAPPER -# ====================== -mapper: - # ========== Classification, no behavior ========== - - rdfs:Literal: - is: class - target_class: Literal - - # All definitions belonging to reasoning are excluded - # such as owl:bottomObjectPorperty owl:topObjectProperty, owl:bottomObjectProperty, owl:topDataProperty, owl:bottomDataProperty, owl:Thing, owl:Nothing - - - # rdfs:Container, rdfs:ContainerMembershipProperty, rdfs:member - # skos:memberList, skos:narrower [!!], skos:inScheme [!!!], skos:narrowerTransitive, skos:semanticRelation, skos:broaderTransitive, skos:mappingRelation - - rdfs:Datatype: - is: class - target_class: Datatype - - owl:ObjectProperty: - is: class - target_class: Relation - - rdf:Property: - is: class - target_class: Property - - owl:DatatypeProperty: - is: class - target_class: Attribute - - owl:AnnotationProperty: - is: class - target_class: Annotation - - owl:OntologyProperty: - is: class - target_class: Property - - owl:DeprecatedProperty: - is: class - target_class: Relation - - owl:Thing: - is: class - target_class: Individual - - # ========== Property characteristics (with behavior) ========== - owl:AsymmetricProperty: - is: class - target_class: Relation - setters: - - set_is_asymmetric: True - - owl:SymmetricProperty: - is: class - target_class: Relation - setters: [set_is_symmetric: True] - - owl:FunctionalProperty: - is: class - target_class: Property - setters: - - set_is_functional: True - - owl:InverseFunctionalProperty: - is: class - target_class: Relation - setters: [set_is_inverse_functional: True] - - owl:TransitiveProperty: - is: class - target_class: Relation - setters: [set_is_transitive: True] - - owl:IrreflexiveProperty: - is: class - target_class: Relation - setters: [set_is_irreflexive: True] - - owl:ReflexiveProperty: - is: class - target_class: Relation - setters: [set_is_reflexive: True] - - owl:NegativePropertyAssertion: - is: class - target_class: Statement - setters: [set_is_positive_statement: False] - - # ========== Datatypes ========== - owl:DataRange: - is: class - target_class: Datatype - - # ========== Model ========== - owl:Ontology: - is: class - target_class: Model - - skos:ConceptScheme: - is: class - target_class: Model - - # ========== Individuals ========== - owl:NamedIndividual: - is: class - target_class: Individual - - # ========== Statements ========== - owl:Annotation: - is: class - target_class: Statement - - owl:sourceIndividual: - is: predicate - target_classes: [Statement] - setters: [set_has_subject: Individual] - - owl:targetIndividual: - is: predicate - target_classes: [Statement] - setters: [set_has_object: Individual] - - owl:targetValue: - is: predicate - target_classes: [Statement] - setters: [set_has_object: Literal] - - # ========== Property ========== - rdfs:domain: - is: predicate - target_classes: [Property] - setters: [set_has_domain: Concept] - - rdfs:range: - is: predicate - target_classes: [Property] - # handler: handle_range - setters: [set_has_range: Resource] - - rdfs:subPropertyOf: - is: predicate - target_classes: [Property] - setters: [set_is_sub_property_of: Property] - - owl:propertyDisjointWith: - is: predicate - target_classes: [Property] - setters: [set_is_disjoint_with: Property] - - owl:equivalentProperty: - is: predicate - target_classes: [Property] - setters: [set_is_equivalent_to: Property] - - # ========== Concept ========== - rdfs:subClassOf: - is: predicate - target_classes: [Concept] - setters: [set_is_sub_concept_of: Concept] - - owl:disjointWith: - is: predicate - target_classes: [Concept] - setters: [set_is_disjoint_with: Concept] - - owl:equivalentClass: - is: predicate - target_classes: [Concept] - setters: [set_is_equivalent_to: Concept] - - # ========== Model ========== - owl:imports: - is: predicate - target_classes: [Model] - setters: [set_imports: Model] - - owl:versionIRI: - is: predicate - target_classes: [Model] - setters: [set_has_version: Model] - - owl:priorVersion: - is: predicate - target_classes: [Model] - setters: [set_has_prior_version: Model] - - owl:backwardCompatibleWith: - is: predicate - target_classes: [Model] - setters: [set_is_backward_compatible_with: Model] - - owl:incompatibleWith: - is: predicate - target_classes: [Model] - setters: [set_is_incompatible_with: Model] - - skos:hasTopConcept: - is: predicate - target_classes: [Model] - setters: [set_has_top_concept: Concept] - - # inverse skos:hasTopConcept - skos:isTopConceptOf: - is: predicate - target_classes: [Concept] - setter: [set_has_top_concept: Model] - - skos:inScheme: - is: predicate - target_classes: [Resource] - setters: [set_is_defined_by: Resource] - - # ========== Statement/Annotation ========== - - owl:annotatedProperty: - is: predicate - target_classes: [Statement] - setters: [set_has_predicate: Property] - - owl:annotatedSource: - is: predicate - target_classes: [Statement] - setters: [set_has_subject: Resource] - - owl:annotatedTarget: - is: predicate - target_classes: [Statement] - setters: [set_has_object: Resource] - - owl:assertionProperty: - is: predicate - target_classes: [Statement] - setters: [set_has_predicate: Property] - - # ========== Concepts ========== - - skos:Concept: - is: class - target_class: Concept - - owl:Class: - is: class - target_class: Concept - - rdfs:Class: - is: class - target_class: Concept - - owl:DeprecatedClass: - is: class - target_class: Concept - setters: [set_is_deprecated: True] - - # owl:Thing: - # is: class - # target_class: Individual - - # owl:Nothing: - # is: class - # target_class: Individual - - # ========== SKOS Concept Relations ========== - skos:broader: - is: predicate - target_classes: [Concept] - setters: [set_is_sub_concept_of: Concept] - - skos:narrower: - is: predicate - target_classes: [Concept] - handler: handle_narrower - - skos:related: - is: predicate - target_classes: [Concept] - setters: [set_is_related_to: Concept] - - skos:broadMatch: - is: predicate - target_classes: [Concept] - setters: [set_has_broad_match: Concept] - - skos:narrowMatch: - is: predicate - target_classes: [Concept] - setters: [set_has_narrow_match: Concept] - - skos:relatedMatch: - is: predicate - target_classes: [Concept] - setters: [set_has_related_match: Concept] - - skos:exactMatch: - is: predicate - target_classes: [Concept] - setters: [set_has_exact_match: Concept] - - skos:closeMatch: - is: predicate - target_classes: [Concept] - setters: [set_has_close_match: Concept] - - # ========== Collection ========== - - skos:Collection: - is: class - target_class: Collection - - skos:OrderedCollection: - is: class - target_class: Collection - setter: [is_ordered: True] - - skos:member: - is: predicate - target_classes: [Collection] - handler: handle_membership - - - # ========== Resource ========== - - rdfs:Resource: - is: class - target_class: Resource - - rdfs:label: - is: predicate - target_classes: [Resource] - setters: [set_has_label: Literal] - - rdfs:comment: - is: predicate - target_classes: [Resource] - setters: [set_has_comment: Literal] - - # ========== SKOS Resource to Literals ========== - skos:prefLabel: - is: predicate - target_classes: [Resource] - setters: [set_has_preferred_label: Literal] - - skos:altLabel: - is: predicate - target_classes: [Resource] - setters: [set_has_alternative_label: Literal] - - skos:hiddenLabel: - is: predicate - target_classes: [Resource] - setters: [set_has_hidden_label: Literal] - - skos:definition: - is: predicate - target_classes: [Resource] - setters: [set_has_definition: Literal] - - skos:example: - is: predicate - target_classes: [Resource] - setters: [set_has_example: Literal] - - skos:note: - is: predicate - target_classes: [Resource] - setters: [set_has_note: Literal] - - skos:scopeNote: - is: predicate - target_classes: [Resource] - setters: [set_has_scope_note: Literal] - - skos:historyNote: - is: predicate - target_classes: [Resource] - setters: [set_has_history_note: Literal] - - skos:editorialNote: - is: predicate - target_classes: [Resource] - setters: [set_has_editorial_note: Literal] - - skos:changeNote: - is: predicate - target_classes: [Resource] - setters: [set_has_change_note: Literal] - - skos:notation: - is: predicate - target_classes: [Resource] - setters: [set_has_notation: Literal] - - # ========== Resource Object Properties ========== - rdfs:seeAlso: - is: predicate - target_classes: [Resource] - setters: [set_see_also: Resource] - - rdfs:isDefinedBy: - is: predicate - target_classes: [Model, Resource] - setters: [set_is_defined_by: Resource] - - owl:versionInfo: - is: predicate - target_classes: [Resource] - setters: [set_has_version_info: Resource] - - # ========== Boolean Properties ========== - owl:deprecated: - is: predicate - target_classes: [Resource] - setters: [set_is_deprecated: True] - - # ========== Concepts - Differenza da base ========== - owl:Axiom: - is: class - target_class: Restriction - - owl:Restriction: - is: class - target_class: Restriction - - # ========== Relation - Solo in OWL ========== - owl:inverseOf: - is: predicate - target_classes: [Relation] - setters: [set_is_inverse_of: Relation] - - owl:propertyChainAxiom: - is: predicate - target_classes: [Relation] - handler: handle_property_chain - - # ========== TRUTH FUNCTIONS - Con handlers (looks for different subjects concepts or truth function)========== - owl:intersectionOf: - is: predicate - inferred_class: TruthFunction - target_classes: [TruthFunction, Concept] - handler: handle_intersection - - owl:unionOf: - is: predicate - inferred_class: TruthFunction - target_classes: [TruthFunction, Concept] - handler: handle_union - - owl:complementOf: - is: predicate - inferred_class: TruthFunction - target_classes: [TruthFunction, Concept] - handler: handle_complement - - # ========== VALUE - with setter ========== - owl:hasValue: - is: predicate - inferred_class: Value - target_classes: [Value] - setters: - [set_applies_on_resource: Resource] - - # ========== ONE OF - with setter ========== - owl:oneOf: - is: predicate - inferred_class: OneOf - target_classes: [OneOf, Concept] - handler: handle_one_of - - # ========== QUANTIFIERS - Con handlers ========== - # owl:someValuesFrom: - # is: predicate - # inferred_class: Quantifier - # target_classes: [Quantifier] - # handler: handle_quantifier_exist - - # owl:allValuesFrom: - # is: predicate - # inferred_class: Quantifier - # target_classes: [Quantifier] - # handler: handle_quantifier_all - - owl:someValuesFrom: - is: predicate - inferred_class: Quantifier - target_classes: [Quantifier] - setters: - - set_has_quantifier_type: "some" - # needed as it is inferred, not explicitly declared - - set_applies_on_concept: Concept - - owl:allValuesFrom: - is: predicate - inferred_class: Quantifier - target_classes: [Quantifier] - setters: - - set_has_quantifier_type: "only" - # needed as it is inferred, not explicitly declared - - set_applies_on_concept: Concept - - # ========== CARDINALITY - Con handlers ========== - owl:cardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - # needs an handler since it defaults set_applies_on_concept to OWL.Thing - handler: handle_cardinality_exactly - - owl:minCardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - # needs an handler since it defaults set_applies_on_concept to OWL.Thing - handler: handle_cardinality_min - - owl:maxCardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - # needs an handler since it defaults set_applies_on_concept to OWL.Thing - handler: handle_cardinality_min - - owl:qualifiedCardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - setters: - - set_has_cardinality_type: "exactly" - # need set_applies_on_concept as it is inferred, not explicitly declared - - set_applies_on_concept: Concept - - owl:minQualifiedCardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - setters: - - set_has_cardinality_type: "min" - # need set_applies_on_concept as it is inferred, not explicitly declared - - set_applies_on_concept: Concept - - owl:maxQualifiedCardinality: - is: predicate - inferred_class: Cardinality - target_classes: [Cardinality] - setters: - - set_has_cardinality_type: "max" - # need set_applies_on_concept as it is inferred, not explicitly declared - - set_applies_on_concept: Concept - - # ========== Restrictions - Target diverso ========== - owl:onProperty: - is: predicate - target_classes: [Restriction] - setters: [set_applies_on_property: Property] - - owl:onClass: - is: predicate - target_classes: [Restriction] - setters: [set_applies_on_concept: Concept] - - owl:onDatatype: - is: predicate - target_classes: [Restriction] - setters: [set_applies_on_concept: Datatype] - - owl:onDataRange: - is: predicate - target_classes: [Restriction] - setters: [set_applies_on_concept: Datatype] - - # ========== Individual - Target diverso ========== - owl:sameAs: - is: predicate - target_classes: [Individual] - setters: [set_is_same_as: Individual] - - owl:differentFrom: - is: predicate - target_classes: [Individual] - setters: [set_is_different_from: Individual] - - rdf:type: - is: predicate - target_classes: [Individual, Resource] - setters: [set_has_type: Concept] - -# ====================== -# ENRICHER -# ====================== -enricher: - owl:AllDisjointClasses: process_all_disjoint_classes - owl:AllDifferent: process_all_different - owl:AllDisjointProperties: process_all_disjoint_properties - rdfs:range: infer_range - rdfs:domain: infer_domain \ No newline at end of file diff --git a/lode/reader/config_manager.py b/lode/reader/config_manager.py index b553ea8..7702771 100644 --- a/lode/reader/config_manager.py +++ b/lode/reader/config_manager.py @@ -1,4 +1,9 @@ -# config_magarer.py - STRATEGIE CON CONFIG UNIFICATA +"""Configuration managers: bind each artefact type to its YAML mapper, logic and viewer. + +The mapping from RDF/OWL/SKOS constructs to the model lives in the YAML files +under reader/config, not in Python: a manager loads base.yaml, merges the +type-specific file on top and exposes the result to the logic classes. +""" import yaml from pathlib import Path @@ -7,25 +12,34 @@ from lode.models import * class ConfigManager(ABC): - """Strategia basata su config YAML unico""" - + """Strategy driven by a single merged YAML configuration. + + Subclasses only say which config file they use and how to build their + logic and viewer; parsing and caching of the mappings is shared here. + """ + def __init__(self): + """Load and merge the YAML configuration; mappings are parsed lazily.""" self.config = self._load_config() self._type_mapping_cache = None self._property_mapping_cache = None @abstractmethod def create_logic(self, graph: Graph, cache: dict): - """Factory method per creare Logic specifica""" + """Factory method: build the logic specific to this artefact type.""" pass @property @abstractmethod def config_name(self) -> str: - """Nome del file config specifico: 'owl' | 'skos' | 'rdfs'""" + """Name of the type-specific config file: 'owl' | 'skos' | 'rdf'.""" pass def _load_config(self) -> dict: + """Read base.yaml and the type-specific YAML, and return them deep-merged. + + Files are looked up next to this module so the config ships inside the wheel. + """ config_dir = Path(__file__).parent / 'config' with open(config_dir / 'base.yaml') as f: @@ -37,6 +51,10 @@ def _load_config(self) -> dict: return self._deep_merge(base, specific) def _deep_merge(self, base: dict, override: dict) -> dict: + """Merge `override` into a copy of `base`, recursing into nested dicts. + + The 'name' and 'inherits' keys only describe the file and are not merged. + """ result = base.copy() for key, value in override.items(): if key in ('name', 'inherits'): @@ -47,18 +65,9 @@ def _deep_merge(self, base: dict, override: dict) -> dict: result[key] = value return result - # def _load_config(self) -> dict: - # """Carica config da file YAML unico""" - # config_path = Path(__file__).parent / 'config' / 'base.yaml' - - # with open(config_path, 'r') as f: - # config = yaml.safe_load(f) - - # return config - @abstractmethod def create_viewer(self, reader): - """Factory method per creare Viewer specifico""" + """Factory method: build the viewer specific to this artefact type.""" pass # ========== NAMESPACE MAP ========== @@ -80,6 +89,10 @@ def _parse_uri(self, uri_str: str) -> URIRef: return URIRef(self.NAMESPACES[prefix] + local) def _parse_class(self, class_name: str): + """Resolve a model class name from the YAML into the class itself. + + Raises KeyError for an unknown name, so a typo in the config fails loudly. + """ import lode.models as _models cls = getattr(_models, class_name, None) if cls is None: @@ -87,6 +100,10 @@ def _parse_class(self, class_name: str): return cls def _parse_value(self, value): + """Convert a setter argument from the YAML: model class names become classes. + + 'Literal', booleans and strings that are not model classes are kept as they are. + """ if value == 'Literal': return 'Literal' elif value is True or value is False: @@ -121,7 +138,7 @@ def get_property_mapping(self) -> dict[URIRef, dict]: return self._property_mapping_cache def _parse_config(self, cfg: dict) -> dict: - """Parse un blocco di config""" + """Parse one mapper entry: resolve class names (and setter arguments) into classes.""" parsed = cfg.copy() if 'target_class' in parsed: @@ -152,6 +169,10 @@ def get_group_axioms(self) -> dict[URIRef, str]: } def get_fallback_class(self) -> type | None: + """Return the class given to resources no mapping recognised, or None if unset. + + An unknown class name in the config falls back to Statement. + """ fallback = self.config.get('mapper', {}).get('fallback_class') if fallback: import lode.models as _models @@ -161,21 +182,21 @@ def get_fallback_class(self) -> type | None: # ========== HELPER METHODS ========== def get_classifier_predicates(self) -> set[URIRef]: - """Predicati con 'inferred_class'""" + """Predicates whose config declares an 'inferred_class'.""" return { pred for pred, cfg in self.get_property_mapping().items() if 'inferred_class' in cfg } def classify_by_predicate(self, uri: Node, graph: Graph) -> type | None: - """Classifica guardando predicati. - - inferred_class: tipo del soggetto (BNode restrictions, quantifiers, etc.) -> priorita' massima - Se piu' predicati hanno inferred_class, vince la classe piu' specifica (issubclass). - - target_classes con 1 elemento, nessun inferred_class, classify != false: - tipo implicito del soggetto (fallback) - - target_classes con 2+ elementi: ambiguo, gestito dall'handler -> None - - classify: false nel config: il predicato non classifica il soggetto, - serve solo per i setters in phase3 (es. facet XSD) + """Classify a subject by looking at the mapped predicates it uses. + - inferred_class: type of the subject (BNode restrictions, quantifiers, etc.) -> highest priority. + If several predicates have an inferred_class, the most specific class wins (issubclass). + - target_classes with 1 element, no inferred_class, classify != false: + implicit type of the subject (fallback) + - target_classes with 2+ elements: ambiguous, left to the handler -> None + - classify: false in the config: the predicate does not classify the subject, + it is only used by the setters in phase3 (e.g. XSD facets) """ fallback = None inferred = None @@ -191,50 +212,65 @@ def classify_by_predicate(self, uri: Node, graph: Graph) -> type | None: return inferred if inferred else fallback def get_punning_priority(self): + """Return the classes in the order that decides which one wins on a punned IRI.""" names = self.config.get('punning_priority', []) return [self._parse_class(n) for n in names] -# config_manager.py - aggiungi nei concrete managers +# ========== CONCRETE MANAGERS ========== class OwlConfigManager(ConfigManager): + """Configuration for OWL artefacts.""" @property def config_name(self) -> str: + """Use owl.yaml on top of base.yaml.""" return 'owl' - + def create_logic(self, graph: Graph, cache: dict): + """Build the OWL logic.""" from lode.reader.logic import OwlLogic return OwlLogic(graph, cache, self) def create_viewer(self, reader): + """Build the OWL viewer.""" from lode.viewer import OwlViewer return OwlViewer(reader) class RdfConfigManager(ConfigManager): + """Configuration for RDF/RDFS artefacts.""" + @property def config_name(self) -> str: + """Use rdf.yaml on top of base.yaml.""" return 'rdf' def create_logic(self, graph: Graph, cache: dict): + """Build the RDF logic.""" from lode.reader.logic import RdfLogic return RdfLogic(graph, cache, self) def create_viewer(self, reader): + """Build the RDF viewer.""" from lode.viewer import RdfViewer return RdfViewer(reader) class SkosConfigManager(ConfigManager): + """Configuration for SKOS artefacts.""" + @property def config_name(self) -> str: + """Use skos.yaml on top of base.yaml.""" return 'skos' def create_logic(self, graph: Graph, cache: dict): + """Build the SKOS logic.""" from lode.reader.logic import SkosLogic return SkosLogic(graph, cache, self) def create_viewer(self, reader): + """Build the SKOS viewer.""" from lode.viewer import SkosViewer return SkosViewer(reader) @@ -248,6 +284,10 @@ def create_viewer(self, reader): def get_configuration(configuration_name: str) -> ConfigManager: + """Return a new manager for the given artefact type (case-insensitive). + + Raises ValueError listing the available types when the name is unknown. + """ key = configuration_name.upper() if key not in CONFIGURATION_REGISTRY: available = ', '.join(CONFIGURATION_REGISTRY.keys()) diff --git a/lode/reader/loader.py b/lode/reader/loader.py index 7fac94f..8d25027 100644 --- a/lode/reader/loader.py +++ b/lode/reader/loader.py @@ -1,5 +1,7 @@ -""" -Reader - Caricamento e validazione file RDF +"""Loading and validation of RDF artefacts, from a local file or from a URL. + +Every security check on remote content (SSRF, size, text-only, XXE) runs here, +before the RDF parser sees any byte. """ import requests import os @@ -15,10 +17,19 @@ from lode.reader.provenance_graph import ProvenanceGraph class Loader: - """Gestisce il caricamento di file RDF""" + """Load an RDF artefact into a graph, optionally together with its imports. + + The loaded graph is a plain Graph, or a ProvenanceGraph (one named graph per + ontology) when imported, closure or partial_import is requested. + """ def __init__(self, file_path: Optional[str] = None, imported=None, closure=None, partial_import=None): - + """Prepare the loader and, when `file_path` is given, load it immediately. + + `imported`, `closure` and `partial_import` select the module applied + after loading (see lode.reader.modules); at most one of them is used. + """ + self.graph = Graph() self.ontology_iri = None self._imported = imported @@ -38,7 +49,6 @@ def load(self, source: str) -> None: if self._is_url(source): self._load_from_url_with_content_negotiation(source) - # ADD BY VALE TO FIX WINDOWS LOCAL BUG - COMMENTED FOR PRODUCTION elif os.path.isfile(source): self._load_from_local_file(source) else: @@ -69,6 +79,11 @@ def load(self, source: str) -> None: # ---------------------------------------------------------- def _apply_modules(self) -> None: + """Apply the requested import module to the loaded graph. + + Precedence: partial_import, then imported, then closure. Also records the + IRIs that were imported, so the viewer can keep the original model metadata. + """ if self._partial_import: self.graph, self.imported_uris = modules.apply_partial_import(self.graph) elif self._imported: @@ -112,6 +127,17 @@ def _load_from_url_with_content_negotiation(self, url: str) -> None: context={"url": url, "http_status": response.status_code} ) + # Reject HTML/XHTML pages before downloading: servers answer with a + # human-readable page when no RDF serialization is available. + content_type = response.headers.get("Content-Type", "").lower() + mime = content_type.split(";")[0].strip() + if mime in ("text/html", "application/xhtml+xml"): + response.close() + raise ArtefactLoadError( + "Resource is an HTML page, not an RDF serialization", + context={"url": url, "content_type": mime}, + ) + # SECURITY: reject by declared Content-Length before downloading the body declared = response.headers.get("Content-Length") if declared and declared.isdigit(): @@ -153,6 +179,11 @@ def _load_from_url_with_content_negotiation(self, url: str) -> None: # LOCAL FILE LOADING # ---------------------------------------------------------- def _load_from_local_file(self, path: str) -> None: + """Parse a local file, trying every known RDF format. + + Raises ArtefactLoadError if no format can parse it. The caller is expected + to have excluded URLs: this method opens `path` on the local disk. + """ with open(path, "rb") as f: raw = f.read() graph = parse_any(raw) @@ -165,12 +196,17 @@ def _load_from_local_file(self, path: str) -> None: # HELPERS # ---------------------------------------------------------- def _is_url(self, s: str) -> bool: + """Return True only for http(s) URLs; other schemes are not treated as URLs.""" try: return urlparse(s).scheme in ("http", "https") except Exception: return False def _guess_format_from_content_type(self, content_type: str) -> Optional[str]: + """Map an HTTP Content-Type to an rdflib format name, or None when unknown. + + The result is only a hint: parse_any still falls back to the other formats. + """ if "text/turtle" in content_type or "application/x-turtle" in content_type: return "turtle" if "application/rdf+xml" in content_type: @@ -182,6 +218,7 @@ def _guess_format_from_content_type(self, content_type: str) -> Optional[str]: return None def get_graph(self) -> Graph: + """Return the loaded graph (a ProvenanceGraph when modules were applied).""" return self.graph def _fetch_following_redirects(self, url: str, headers: dict, max_redirects: int = security.MAX_REDIRECTS): diff --git a/lode/reader/logic/base_logic.py b/lode/reader/logic/base_logic.py index 6f74494..1224d35 100644 --- a/lode/reader/logic/base_logic.py +++ b/lode/reader/logic/base_logic.py @@ -1,4 +1,8 @@ -# base_logic.py +"""Format-independent core of the extraction logic. + +BaseLogic turns the triples of a graph into model instances in phases. What is +specific to OWL, RDF or SKOS lives in the subclasses and in the YAML mapper. +""" from abc import ABC, abstractmethod from rdflib import Graph, URIRef, Node, Literal as RDFlibLiteral, BNode from rdflib.namespace import RDF, RDFS, OWL, SKOS, XSD, Namespace @@ -9,12 +13,23 @@ from lode.models import * from lode.helpers.rdf import iri_local_name, iri_namespace +import logging +logger = logging.getLogger(__name__) + class BaseLogic(ABC): """ - Logica base comune per parsing RDF. + Common base logic for RDF parsing. + + Owns the instance cache, the triples-to-instance provenance map and the + generic machinery (get_or_create, populate_instance, SWRL, statements); + subclasses implement the phases that differ between formats. """ def __init__(self, graph: Graph, instance_cache: dict, strategy): + """Bind the logic to a graph, a shared instance cache and a config manager. + + Fails fast if the config names a handler this logic does not implement. + """ self.graph = graph self._instance_cache = instance_cache self._strategy = strategy @@ -28,10 +43,12 @@ def __init__(self, graph: Graph, instance_cache: dict, strategy): self._warnings = [] def add_warning(self, code, subject, message): + """Record a reader warning with a machine-readable code, its subject and a message.""" self._warnings.append({'code': code, 'subject': str(subject), 'message': message}) def get_warnings(self): - if not getattr(self, '_warnings_enabled', False): # self qui Γ¨ la LOGIC + """Return the collected warnings, or [] when they were not requested.""" + if not getattr(self, '_warnings_enabled', False): # self is the logic here return [] def save_warnings(self, filepath: str = None): @@ -49,6 +66,7 @@ def save_warnings(self, filepath: str = None): json.dump(self._warnings, f, indent=2, ensure_ascii=False) def _get_allowed_classes(self) -> set: + """Resolve the 'allowed_classes' names of the config into the model classes.""" class_names = self._strategy.config.get('allowed_classes', []) import lode.models as _models return {getattr(_models, name) for name in class_names if getattr(_models, name, None) is not None} @@ -66,25 +84,35 @@ def get_namespaces(self) -> dict: @abstractmethod def phase1_classify_from_predicates(self): + """Phase 1: create instances for subjects whose predicates reveal their class.""" pass @abstractmethod def phase2_create_from_types(self): + """Phase 2: create instances from the rdf:type declarations of the graph.""" pass @abstractmethod def phase3_populate_properties(self): + """Phase 3: fill every instance from its triples, through the property mapping.""" pass @abstractmethod def phase4_process_group_axioms(self): + """Phase 4: process axioms that involve several entities at once (e.g. AllDisjointClasses).""" pass @abstractmethod def phase5_fallback(self): + """Phase 5: give a class (and the format defaults) to whatever is still unclassified.""" pass def phase6_create_statements(self): + """Phase 6: reify every triple no earlier phase consumed as a Statement. + + Structural list triples and structural vocabulary subjects without a type + are skipped; triples already tracked by an instance are not duplicated. + """ for subj, pred, obj in self.graph: # if pred in self._property_mapping: # continue @@ -100,13 +128,13 @@ def phase6_create_statements(self): continue self._create_statement_for_triple(subj, pred, obj) - # ========== VALIDAZIONE CONFIG -> LOGIC ========== + # ========== CONFIG -> LOGIC VALIDATION ========== def _validate_handlers(self): """ - Fail-fast: verifica che tutti gli handler dichiarati nel config - esistano come metodi su questa istanza Logic. - Solleva AttributeError subito, prima di qualsiasi parsing. + Fail-fast: check that every handler declared in the config + exists as a method on this Logic instance. + Raises AttributeError immediately, before any parsing. """ errors = [] @@ -131,7 +159,7 @@ def _validate_handlers(self): + "\n".join(f" - {e}" for e in errors) ) - # ========== RISOLUZIONE CLASSI AMMESSE ========== + # ========== ALLOWED CLASS RESOLUTION ========== def _resolve_allowed_class(self, python_class: type, id: Node = None) -> type: """ @@ -145,7 +173,7 @@ def _resolve_allowed_class(self, python_class: type, id: Node = None) -> type: if python_class in self._allowed_classes: return python_class - # Hook per logica custom pre-MRO (es. OWL: controlla cache) + # Hook for custom pre-MRO logic (e.g. OWL: check the cache) resolved = self._pre_resolve_hook(python_class, id) if resolved: return resolved @@ -154,41 +182,41 @@ def _resolve_allowed_class(self, python_class: type, id: Node = None) -> type: if parent_class in self._allowed_classes: return parent_class - print(f" [WARN] {python_class.__name__} -> Resource (fallback finale)") + logger.warning("%s fell back to Resource", python_class.__name__) return Resource def _pre_resolve_hook(self, python_class: type, id: Node) -> type | None: """ - Hook opzionale per logica custom pre-MRO. - Le subclass possono override senza toccare _resolve_allowed_class. - Ritorna None per delegare al comportamento base. + Optional hook for custom pre-MRO logic. + Subclasses can override it without touching _resolve_allowed_class. + Returns None to delegate to the base behaviour. """ return None # ========== Namespaces resolution ========== def populate_namespaces(self): - """Attacca i prefissi del grafo a ogni Model in cache.""" + """Attach the graph prefixes to every cached Model.""" ns = {prefix: str(uri) for prefix, uri in self.graph.namespaces()} for instances in self._instance_cache.values(): for inst in instances: if isinstance(inst, Model): inst.set_has_namespaces(ns) - # ========== PROVENANCE ========== (nota: _triples_map viene scritto solo da questi tre metodi.) + # ========== PROVENANCE ========== (note: _triples_map is written only by these three methods.) def _track(self, instance, *triples): - """Attribuisce uno o piu' tripla alla provenance di `instance`.""" + """Attribute one or more triples to the provenance of `instance`.""" self._triples_map.setdefault(instance, set()).update(triples) def _untrack(self, instance, *triples): - """Rimuove tripla dalla provenance di `instance`.""" + """Remove triples from the provenance of `instance`.""" bucket = self._triples_map.get(instance) if bucket: bucket.difference_update(triples) def _move_tracking(self, old, new): - """Trasferisce la provenance quando un'istanza viene promossa/sostituita.""" + """Move the provenance from `old` to `new` when an instance is promoted or replaced.""" if old in self._triples_map: self._triples_map.setdefault(new, set()).update(self._triples_map.pop(old)) @@ -199,8 +227,8 @@ def _traverse_hierarchy( start: object, next_getter: str, direction: str = "up", # "up" | "down" | "both" - collect: callable = None, # (node) -> value | None β€” ferma e ritorna quando non None - visit_all: callable = None, # (node) -> None β€” visita ogni nodo senza fermarsi + collect: callable = None, # (node) -> value | None β€” stops and returns when not None + visit_all: callable = None, # (node) -> None β€” visits every node without stopping ) -> object | None: """ Generic BFS traversal along a property hierarchy. @@ -276,6 +304,11 @@ def _traverse_hierarchy( def _create_literal(self, rdflib_literal): + """Return the model Literal for an rdflib literal, one per distinct lexical form. + + The instance is cached under a LITERAL:: key; language and datatype are + copied over when present. + """ literal_key = f"LITERAL::{rdflib_literal}" if literal_key in self._instance_cache: return next(iter(self._instance_cache[literal_key])) @@ -295,9 +328,11 @@ def _create_literal(self, rdflib_literal): return literal def _is_rdf_collection(self, node: Node) -> bool: + """Return True if the node is the head of an RDF list (it has an rdf:first).""" return (node, RDF.first, None) in self.graph def _instance_matches_target(self, instance, target_classes: list) -> bool: + """Return True if the instance is of one of the target classes, or a subclass of one.""" instance_class = instance.__class__ if instance_class in target_classes: return True @@ -307,6 +342,14 @@ def _instance_matches_target(self, instance, target_classes: list) -> bool: return False def _apply_setters(self, instance, setters_config, obj): + """Call the setters declared in the config on `instance`, using `obj` as the value. + + Per entry: 'Literal' builds a Literal from obj; a bool or a string is passed + as a constant; a model class resolves obj to an instance of that class (the + punned instance of the same class if one is cached); anything else passes + obj as is. An entry with no value calls the setter with no argument. + Structural vocabulary URIs are never added to has_type. + """ for setter_item in setters_config: if isinstance(setter_item, dict): for setter_name, value_type in setter_item.items(): @@ -343,6 +386,10 @@ def _apply_setters(self, instance, setters_config, obj): getattr(instance, setter_item)() def _handle_collection_object(self, instance, predicate, collection_uri): + """Resolve an RDF list used as an object and pass its members to the first matching setter. + + Failures are logged and swallowed: one malformed list must not stop the read. + """ try: collection = RDFLibCollection(self.graph, collection_uri) items = [] @@ -361,15 +408,24 @@ def _handle_collection_object(self, instance, predicate, collection_uri): if hasattr(instance, setter_name): getattr(instance, setter_name)(items) break - except Exception as e: - print(f"Errore Collection: {e}") + except Exception: + logger.warning("Collection handling failed on %s (predicate %s)", + instance, predicate, exc_info=True) def clear_cache(self): + """Empty the shared instance cache.""" self._instance_cache.clear() # ========== LOGIC CORE ========== def get_or_create(self, id: Node, python_class: type = None, populate: bool = True): + """Return the model instance for a node, creating (and populating) it when needed. + + Literals go through _create_literal; built-in datatypes and undeclared XSD + terms are always Datatype. A cached instance is reused; a single cached + instance of a broader class is promoted to the requested one, so punning + keeps working. Returns None, after logging, when creation fails. + """ try: if isinstance(id, RDFlibLiteral): @@ -394,7 +450,7 @@ def get_or_create(self, id: Node, python_class: type = None, populate: bool = Tr # if uri_str.startswith(ns) and id not in (OWL.Thing, OWL.Nothing, RDFS.Literal): # return None - # Individual punning: non sovrascrivere tipi esistenti non-Individual + # Individual punning: do not override existing non-Individual types if python_class == Individual and id in self._instance_cache: is_named_individual = (id, RDF.type, OWL.NamedIndividual) in self.graph if not is_named_individual: @@ -433,17 +489,25 @@ def get_or_create(self, id: Node, python_class: type = None, populate: bool = Tr return instance - except Exception as e: - print(f"Cannot create {python_class.__name__ if python_class else 'Unknown'} for {id}: {e}") + except Exception: + logger.warning("Cannot create %s for %s", + python_class.__name__ if python_class else "Unknown", id, exc_info=True) return None def populate_instance(self, instance, uri: Node): + """Fill an instance from the triples of `uri`, following the property mapping. + + Only predicates in the allowed namespaces are read. A configured handler or + setters list runs for each predicate; failures are logged and skipped. Every + handled triple is recorded in the provenance map, except the rdf:type that + selected the instance's class. + """ if isinstance(uri, URIRef): instance.set_has_identifier(str(uri)) elif isinstance(uri, BNode): instance.has_identifier = str(uri) - is_subordinate = self._is_punning_subordinate(instance, uri) + # is_subordinate = self._is_punning_subordinate(instance, uri) for predicate, obj in self.graph.predicate_objects(uri): if iri_namespace(str(predicate)) not in self._allowed_namespaces: @@ -454,23 +518,26 @@ def populate_instance(self, instance, uri: Node): if config is not None: target_classes = config.get('target_classes', []) - if is_subordinate and target_classes and type(instance) not in target_classes: - continue + #if is_subordinate and target_classes and type(instance) not in target_classes: + # continue if target_classes and not self._instance_matches_target(instance, target_classes): continue if 'handler' in config: try: - getattr(self, config['handler'])(instance, uri, predicate, obj, None) - handled = True - except Exception as e: - print(f" Errore handler {config['handler']}: {e}") + # An explicit False means "not admissible for this instance". + result = getattr(self, config['handler'])(instance, uri, predicate, obj, None) + handled = result is not False + except Exception: + logger.warning("Handler %s failed on %s (predicate %s)", + config['handler'], uri, predicate, exc_info=True) elif 'setters' in config: try: self._apply_setters(instance, config['setters'], obj) handled = True - except Exception as e: - print(f" Errore setters: {e}") + except Exception: + logger.warning("Setters failed on %s (predicate %s)", + uri, predicate, exc_info=True) if not handled and config is None and self._is_rdf_collection(obj): self._handle_collection_object(instance, predicate, obj) @@ -482,6 +549,7 @@ def populate_instance(self, instance, uri: Node): # ========== HELPERS ========== def _is_triple_mapped(self, subj, pred, obj) -> bool: + """Return True if some instance already tracks this triple in its provenance.""" if subj not in self._instance_cache: return False instances = self._instance_cache[subj] @@ -493,6 +561,11 @@ def _is_triple_mapped(self, subj, pred, obj) -> bool: return False def _convert_collection_to_container(self, collection_uri): + """Return the Container that represents an RDF list, building and caching it once. + + The container is cached before its members are resolved, so a list that + contains itself cannot loop forever. + """ if collection_uri in self._instance_cache: for cached in self._instance_cache[collection_uri]: if isinstance(cached, Container): @@ -516,13 +589,18 @@ def _convert_collection_to_container(self, collection_uri): if member_instance: members.append(member_instance) container.set_has_members(members) - except Exception as e: - print(f"Errore Collection: {e}") + except Exception: + logger.warning("Collection to container conversion failed for %s", + collection_uri, exc_info=True) return container def _create_statement_for_triple(self, subj, pred, obj): - + """Reify one triple as a Statement, unless its predicate is already mapped. + + Lists in object position become Containers and literals become Literals. + """ + if pred in self._property_mapping: return @@ -636,6 +714,10 @@ def _create_nested_statement(self, node): return statement def _get_punning_dominant(self, uri): + """Return the instance that wins when an IRI is used as several things (punning). + + The winner follows the config's punning priority; with no match, any cached one. + """ if uri not in self._instance_cache: return None cached = self._instance_cache[uri] @@ -651,12 +733,14 @@ def _get_punning_dominant(self, uri): return next(iter(cached)) def _is_punning_subordinate(self, instance, uri): + """Return True if `instance` loses against another instance of the same IRI.""" dom = self._get_punning_dominant(uri) return dom is not None and dom is not instance # ========== SWRL ========== def handle_swrl_imp(self, uri): + """Build a Rule from a swrl:Imp, with its body atoms as antecedent and head atoms as consequent.""" # Force promotion to Rule if cached as something else if uri in self._instance_cache: existing = next(iter(self._instance_cache[uri])) @@ -681,8 +765,8 @@ def handle_swrl_imp(self, uri): atom = self._parse_swrl_atom(atom_node) if atom: rule.set_has_antecedent(atom) - except Exception as e: - print(f"Errore body AtomList: {e}") + except Exception: + logger.warning("SWRL body parsing failed for rule %s", uri, exc_info=True) head_node = self.graph.value(uri, SWRL_NS.head) if head_node: @@ -691,10 +775,11 @@ def handle_swrl_imp(self, uri): atom = self._parse_swrl_atom(atom_node) if atom: rule.set_has_consequent(atom) - except Exception as e: - print(f"Errore head AtomList: {e}") + except Exception: + logger.warning("SWRL head parsing failed for rule %s", uri, exc_info=True) def _parse_swrl_atom(self, atom_node): + """Build an Atom from a SWRL atom node: its predicate (by atom kind) and its arguments.""" atom = self.get_or_create(atom_node, Atom) if not atom: return None @@ -742,18 +827,20 @@ def _parse_swrl_atom(self, atom_node): if arg2: atom.set_has_arguments(self._resolve_swrl_arg(arg2)) - # arguments (BuiltinAtom β€” lista RDF) + # arguments (BuiltinAtom β€” RDF list) args_node = self.graph.value(atom_node, SWRL_NS.arguments) if args_node: try: for arg in RDFLibCollection(self.graph, args_node): atom.set_has_arguments(self._resolve_swrl_arg(arg)) - except Exception as e: - print(f"Errore builtin arguments: {e}") + except Exception: + logger.warning("SWRL builtin arguments failed for atom %s", + atom_node, exc_info=True) return atom def _resolve_swrl_arg(self, node): + """Resolve a SWRL argument: a Literal, a Variable or, by default, an Individual.""" if isinstance(node, RDFlibLiteral): return self._create_literal(node) if (node, RDF.type, SWRL_NS.Variable) in self.graph: diff --git a/lode/reader/logic/owl_logic.py b/lode/reader/logic/owl_logic.py index f8ba505..f80af02 100644 --- a/lode/reader/logic/owl_logic.py +++ b/lode/reader/logic/owl_logic.py @@ -1,4 +1,4 @@ -# owl_logic.py +"""Extraction logic for OWL artefacts.""" from rdflib import Graph, URIRef, Node, Literal as RDFlibLiteral, BNode from rdflib.namespace import RDF, RDFS, OWL, SKOS, XSD @@ -8,6 +8,8 @@ from lode.reader.logic.base_logic import BaseLogic from lode.reader.warnings import owl_warnings +import logging +logger = logging.getLogger(__name__) class OwlLogic(BaseLogic): """ @@ -21,9 +23,9 @@ class OwlLogic(BaseLogic): - Property type inference for properties not explicitly typed in the artefact """ - # _get_allowed_namespaces: ereditato da BaseLogic, legge config YAML + # _get_allowed_namespaces: inherited from BaseLogic, reads the YAML config - # ========== HOOK per resolve custom OWL ========== + # ========== HOOK for custom OWL resolution ========== def _pre_resolve_hook(self, python_class: type, id: Node) -> type | None: """ @@ -75,6 +77,12 @@ def phase1_classify_from_predicates(self): self.get_or_create(uri, py_class, populate=False) def phase2_create_from_types(self): + """Create instances from rdf:type declarations. + + Subjects typed with a mapped type get the mapped class and its static + setters; subjects whose type is not mapped become Individuals, except for + structural vocabulary types. + """ type_mapping = self._strategy.get_type_mapping() for rdf_type, config in type_mapping.items(): @@ -164,14 +172,38 @@ def phase5_fallback(self): self._enrich_or_apply_owl_defaults(instance, uri) def handle_domain(self, instance, uri, predicate, obj, setter=None): + """Handle rdfs:domain: link the property to its domain and the domain back to the property. + + A domain that cannot become a Concept (it is cached as something else) is + forced into one, because of OWL punning. + """ concept = self.get_or_create(obj, Concept) if concept is None: concept = self._force_as_concept(obj) instance.set_has_domain(concept) concept.set_is_in_domain_of(instance) + def _is_data_range(self, node) -> bool: + """True if node denotes a data range: XSD/RDF built-in datatypes, rdfs:Literal, + anything typed rdfs:Datatype, or a datatype restriction BNode.""" + if (node, RDF.type, RDFS.Datatype) in self.graph: + return True + if isinstance(node, BNode): + return (node, OWL.onDatatype, None) in self.graph + return str(node).startswith(str(XSD)) or node in ( + RDFS.Literal, RDF.PlainLiteral, RDF.XMLLiteral, RDF.langString, RDF.HTML) def handle_range(self, instance, uri, predicate, obj, setter=None): + """Handle rdfs:range: set the range of a property and link the target back to it. + + An Attribute accepts only data ranges and a Relation only class ranges: any + other triple returns False, so it is not tracked for that instance. + """ + # Punning: each instance takes only the ranges its class admits. + # Returning False marks the triple as not admissible (not tracked). + is_data = self._is_data_range(obj) + if isinstance(instance, Attribute) != is_data and isinstance(instance, (Attribute, Relation)): + return False if isinstance(instance, Attribute): resource = self.get_or_create(obj, Datatype) else: @@ -182,7 +214,7 @@ def handle_range(self, instance, uri, predicate, obj, setter=None): resource.set_is_in_range_of(instance) def handle_equivalent_class(self, instance, uri, predicate, obj, setter=None): - """Β§9.1.2 EquivalentClasses β€” simmetria garantita.""" + """Β§9.1.2 EquivalentClasses β€” symmetry guaranteed.""" # add WARNING if not isinstance(instance, Concept): @@ -199,7 +231,7 @@ def handle_equivalent_class(self, instance, uri, predicate, obj, setter=None): other.set_is_equivalent_to(instance) def handle_disjoint_with(self, instance, uri, predicate, obj, setter=None): - """Β§9.1.3 DisjointClasses β€” simmetria garantita.""" + """Β§9.1.3 DisjointClasses β€” symmetry guaranteed.""" other = self.get_or_create(obj, Concept) if other: if other not in instance.get_is_disjoint_with(): @@ -207,7 +239,8 @@ def handle_disjoint_with(self, instance, uri, predicate, obj, setter=None): if instance not in other.get_is_disjoint_with(): other.set_is_disjoint_with(instance) - def handle_equivalent_property(self, instance, uri, predicate, obj, setter=None): + def handle_equivalent_property(self, instance, uri, predicate, obj, setter=None): + """Handle owl:equivalentProperty: link the two properties to each other (symmetric).""" if obj in self._instance_cache: other = self.get_or_create(obj, Property) else: @@ -219,7 +252,7 @@ def handle_equivalent_property(self, instance, uri, predicate, obj, setter=None) other.set_is_equivalent_to(instance) def handle_property_disjoint_with(self, instance, uri, predicate, obj, setter=None): - """Β§9.2.3 DisjointObjectProperties β€” simmetria garantita.""" + """Β§9.2.3 DisjointObjectProperties β€” symmetry guaranteed.""" other = self.get_or_create(obj, Property) if other: if other not in instance.get_is_disjoint_with(): @@ -241,7 +274,7 @@ def _ensure_individual(self, node): return ind def handle_same_as(self, instance, uri, predicate, obj, setter=None): - """Β§9.6.1 SameIndividual β€” simmetria garantita.""" + """Β§9.6.1 SameIndividual β€” symmetry guaranteed.""" subj_ind = self._ensure_individual(uri) other = self._ensure_individual(obj) if subj_ind and other: @@ -251,7 +284,7 @@ def handle_same_as(self, instance, uri, predicate, obj, setter=None): other.set_is_same_as(subj_ind) def handle_different_from(self, instance, uri, predicate, obj, setter=None): - """Β§9.6.2 DifferentIndividuals β€” simmetria garantita.""" + """Β§9.6.2 DifferentIndividuals β€” symmetry guaranteed.""" subj_ind = self._ensure_individual(uri) other = self._ensure_individual(obj) if subj_ind and other: @@ -261,6 +294,11 @@ def handle_different_from(self, instance, uri, predicate, obj, setter=None): other.set_is_different_from(subj_ind) def handle_inverse_of(self, instance, uri, predicate, obj, setter=None): + """Handle owl:inverseOf. + + On a restriction it sets the property the restriction applies to; on a + relation it links the two relations to each other (symmetric). + """ if isinstance(instance, Restriction) and not isinstance(instance, Relation): prop = self.get_or_create(obj, Property) if prop: @@ -294,7 +332,10 @@ def handle_on_property(self, instance, uri, predicate, obj, setter=None): instance.set_applies_on_property(prop) def _force_as_concept(self, uri): - """Aggiunge Concept in cache per URI giΓ  classificato come Individual/Resource (punning OWL).""" + """Add a Concept to the cache for an IRI already classified as Individual or Resource (OWL punning). + + It copies the attributes of the first cached instance, when there is one. + """ cached = list(self._instance_cache.get(uri, set())) concept = Concept() if cached: @@ -307,7 +348,12 @@ def _force_as_concept(self, uri): def _enrich_or_apply_owl_defaults(self, instance, uri): """ Applies OWL-mandated defaults to instances lacking explicit declarations. - [...docstring invariata...] + A Relation or Attribute without a domain (or with only owl:Thing) inherits + it from its super properties or its inverses, falling back to owl:Thing. + The range falls back to owl:Thing for a Relation and to rdfs:Literal for + an Attribute. An Individual without a type gets owl:Thing. Instances that + share an IRI (punning) are cross-linked through also_defined_as, except + for punning subordinates. """ if uri not in self._instance_cache: @@ -317,6 +363,7 @@ def _enrich_or_apply_owl_defaults(self, instance, uri): rdfs_string = self.get_or_create(RDFS.Literal, Datatype) def _safe_inherited(instance, getter_name): + """Inherited values, with ranges filtered to the right kind: datatypes for an Attribute, concepts for a Relation.""" values = self._get_inherited_property_values(instance, getter_name) if isinstance(instance, Attribute): if getter_name == "get_has_range": @@ -327,6 +374,7 @@ def _safe_inherited(instance, getter_name): return values def _is_only_default(values, default_id): + """True if the list is not empty and holds nothing but the default value.""" return values and all(d.get_has_identifier() == default_id for d in values) # Type-specific defaults: always apply, even for punning subordinates @@ -395,7 +443,14 @@ def _is_only_default(values, default_id): def _get_inherited_property_values(self, property_instance, getter_name: str) -> list: + """Return the domain or range inherited by a property, or [] when nothing is found. + + For a Relation the inverse relations are tried first, with domain and range + swapped (the domain of a relation is the range of its inverse); then the + super properties are walked upwards. + """ def collect(node): + """Return the first non-empty value on an ancestor (or on its inverses, swapped), never on the property itself.""" if node is property_instance: return None getter = getattr(node, getter_name, None) @@ -474,6 +529,7 @@ def _infer_property_type(self, instance) -> type: # (2) UP THE HIERARCHY def collect_type(node): + """Return the node's class when it is already a concrete property type.""" if type(node) in CONCRETE: return type(node) return None @@ -583,8 +639,8 @@ def process_all_disjoint_classes(self, uri: Node): class_b = self.get_or_create(class_b_uri, Concept) class_a.set_is_disjoint_with(class_b) class_b.set_is_disjoint_with(class_a) - except Exception as e: - print(f"Errore AllDisjointClasses: {e}") + except Exception: + logger.warning("AllDisjointClasses failed for %s", uri, exc_info=True) def process_all_different(self, uri: Node): """ @@ -603,8 +659,8 @@ def process_all_different(self, uri: Node): ind_b = self.get_or_create(ind_b_uri, Individual) ind_a.set_is_different_from(ind_b) ind_b.set_is_different_from(ind_a) - except Exception as e: - print(f"Errore AllDifferent: {e}") + except Exception: + logger.warning("AllDifferent failed for %s", uri, exc_info=True) def process_all_disjoint_properties(self, uri: Node): """ @@ -623,8 +679,8 @@ def process_all_disjoint_properties(self, uri: Node): prop_b = self.get_or_create(prop_b_uri, Property) prop_a.set_is_disjoint_with(prop_b) prop_b.set_is_disjoint_with(prop_a) - except Exception as e: - print(f"Errore AllDisjointProperties: {e}") + except Exception: + logger.warning("AllDisjointProperties failed for %s", uri, exc_info=True) # ========== HANDLER CALLED BY PHASE 3 FOR POPULATING INSTANCES ========== @@ -641,13 +697,14 @@ def handle_property_chain(self, instance, uri, predicate, obj, setter=None): instance.set_has_property_chain(chain_instances) def handle_has_key(self, instance, uri, predicate, obj, setter=None): + """Handle owl:hasKey: add every property of the key list to the concept.""" try: for prop_uri in RDFLibCollection(self.graph, obj): prop = self.get_or_create(prop_uri, Property) if prop: instance.set_has_key(prop) - except Exception as e: - print(f"Errore handle_has_key: {e}") + except Exception: + logger.warning("handle_has_key failed for %s", uri, exc_info=True) # ========== RESTRICTIONS ================================================ @@ -680,10 +737,15 @@ def handle_disjoint_union(self, instance, uri, predicate, obj, setter=None): concept_a.set_is_disjoint_with(concept_b) concept_b.set_is_disjoint_with(concept_a) - except Exception as e: - print(f"Errore disjointUnion: {e}") + except Exception: + logger.warning("disjointUnion failed for %s", uri, exc_info=True) def handle_datatype_restriction(self, instance, uri, predicate, obj, setter=None): + """Handle owl:withRestrictions on a datatype: set the datatype and one facet value per facet. + + Facet nodes (e.g. xsd:minInclusive) are cached and tracked, so phase 6 + does not turn them into Statements. + """ on_datatype = self.graph.value(uri, OWL.onDatatype) if on_datatype: dt = self.get_or_create(on_datatype, Datatype) @@ -719,20 +781,23 @@ def handle_datatype_restriction(self, instance, uri, predicate, obj, setter=None self._instance_cache[facet_node].add(instance) self._track(instance, *((facet_node, fp, fv) for fp, fv in self.graph.predicate_objects(facet_node))) - except Exception as e: - print(f"Errore handle_datatype_restriction: {e}") + except Exception: + logger.warning("Datatype restriction failed for %s", uri, exc_info=True) def handle_cardinality_exactly(self, instance, uri, predicate, obj, setter=None): + """Handle an exact cardinality (plain or qualified): type "exactly", the number, and owl:Thing as the default concept.""" instance.set_has_cardinality_type("exactly") instance.set_has_cardinality(obj) instance.set_applies_on_concept(self.get_or_create(OWL.Thing, Concept)) def handle_cardinality_min(self, instance, uri, predicate, obj, setter=None): + """Handle a minimum cardinality (plain or qualified): type "min", the number, and owl:Thing as the default concept.""" instance.set_has_cardinality_type("min") instance.set_has_cardinality(obj) instance.set_applies_on_concept(self.get_or_create(OWL.Thing, Concept)) def handle_cardinality_max(self, instance, uri, predicate, obj, setter=None): + """Handle a maximum cardinality (plain or qualified): type "max", the number, and owl:Thing as the default concept.""" instance.set_has_cardinality_type("max") instance.set_has_cardinality(obj) instance.set_applies_on_concept(self.get_or_create(OWL.Thing, Concept)) @@ -752,8 +817,8 @@ def _build_truth_function(self, instance, obj, operator): """ try: items = list(RDFLibCollection(self.graph, obj)) - except Exception as e: - print(f"Errore build_truth_function: {e}") + except Exception: + logger.warning("Truth function list failed for %s", obj, exc_info=True) return None if len(items) == 0: @@ -789,6 +854,7 @@ def _build_truth_function(self, instance, obj, operator): return tf def handle_intersection(self, instance, uri, predicate, obj, setter=None): + """Handle owl:intersectionOf as an "and" truth function; on a Concept it becomes an equivalent class.""" if type(instance) not in (TruthFunction, Concept): return tf = self._build_truth_function(instance, obj, "and") @@ -796,6 +862,7 @@ def handle_intersection(self, instance, uri, predicate, obj, setter=None): instance.set_is_equivalent_to(tf) def handle_union(self, instance, uri, predicate, obj, setter=None): + """Handle owl:unionOf as an "or" truth function; on a Concept it becomes an equivalent class.""" if type(instance) not in (TruthFunction, Concept): return tf = self._build_truth_function(instance, obj, "or") @@ -803,6 +870,7 @@ def handle_union(self, instance, uri, predicate, obj, setter=None): instance.set_is_equivalent_to(tf) def handle_complement(self, instance, uri, predicate, obj, setter=None): + """Handle owl:complementOf as a "not" truth function over the target concept.""" if type(instance) not in (TruthFunction, Concept): return if type(instance) is TruthFunction: @@ -820,6 +888,10 @@ def handle_complement(self, instance, uri, predicate, obj, setter=None): instance.set_is_equivalent_to(tf) def handle_one_of(self, instance, uri, predicate, obj, setter=None): + """Handle owl:oneOf: add the listed individuals to an enumeration. + + On a Concept a OneOf is created and set as its equivalent class. + """ if type(instance) not in (OneOf, Concept): return if type(instance) is Concept: @@ -831,8 +903,8 @@ def handle_one_of(self, instance, uri, predicate, obj, setter=None): resource = self.get_or_create(item, Individual) if resource: one_of.set_applies_on_resource(resource) - except Exception as e: - print(f"Errore oneOf su Concept: {e}") + except Exception: + logger.warning("oneOf on Concept failed for %s", uri, exc_info=True) instance.set_is_equivalent_to(one_of) else: # type(instance) is OneOf try: @@ -841,10 +913,11 @@ def handle_one_of(self, instance, uri, predicate, obj, setter=None): resource = self.get_or_create(item, Individual) if resource: instance.set_applies_on_resource(resource) - except Exception as e: - print(f"Errore oneOf: {e}") + except Exception: + logger.warning("oneOf failed for %s", uri, exc_info=True) def handle_has_value(self, instance, uri, predicate, obj, setter=None): + """Handle owl:hasValue: set the resource and, when the restriction names one, its property.""" resource = self.get_or_create(obj, Resource) if resource: instance.set_applies_on_resource(resource) @@ -857,21 +930,20 @@ def handle_has_value(self, instance, uri, predicate, obj, setter=None): def handle_rdf_type(self, instance, uri, predicate, obj, setter=None): """ - Handler bidirezionale per rdf:type. + Bidirectional handler for rdf:type. - - subject.has_type += object (lato Individual/Resource) - - object.individuals_with_this_type += subject (lato Concept, solo se l'oggetto e' - effettivamente classificato come Concept e non e' un URI strutturale - del vocabolario) + - subject.has_type += object (Individual/Resource side) + - object.individuals_with_this_type += subject (Concept side, only if the object + is really classified as a Concept and is not a structural vocabulary URI) - Replica la filter logic di _apply_setters per set_has_type: scarta - oggetti nei namespace OWL/RDF/RDFS, eccetto owl:Thing, owl:Nothing, + Mirrors the filter logic of _apply_setters for set_has_type: it discards + objects in the OWL/RDF/RDFS namespaces, except owl:Thing, owl:Nothing, rdfs:Literal. """ if not isinstance(obj, URIRef) and not isinstance(obj, BNode): return - # Filtro URI strutturali (stessa logica di _apply_setters) + # Structural URI filter (same logic as _apply_setters) if isinstance(obj, URIRef): obj_str = str(obj) if any(obj_str.startswith(ns) for ns in self._allowed_namespaces) \ @@ -882,18 +954,18 @@ def handle_rdf_type(self, instance, uri, predicate, obj, setter=None): if concept is None: return - # Lato diretto + # Direct side if hasattr(instance, 'set_has_type'): instance.set_has_type(concept) - # Lato inverso: solo se l'oggetto e' realmente un Concept - # (get_or_create puo' promuovere; type() esatto evita di sporcare + # Inverse side: only if the object is really a Concept + # (get_or_create can promote; the exact type() check avoids polluting # TruthFunction/Restriction/OneOf/etc.) if type(concept) is Concept and isinstance(instance, Individual): concept.set_individuals_with_this_type(instance) - # ========== OVERRIDE Statement per OWL (typed subject/object) ========== + # ========== Statement OVERRIDE for OWL (typed subject/object) ========== def _create_statement_for_triple(self, subj, pred, obj): """ @@ -973,8 +1045,8 @@ def _create_statement_for_triple(self, subj, pred, obj): elif self._is_unmapped_structured_bnode(obj): obj_inst = self._create_nested_statement(obj) else: - # oggetto mai visto: Individual (fallback class β€” _resolve_statement_endpoint - # ritorna il dominante in cache se presente, altrimenti crea Individual) + # object never seen: Individual (fallback class β€” _resolve_statement_endpoint + # returns the cached dominant instance if any, otherwise creates one) obj_inst = self._resolve_statement_endpoint(obj, Resource) if obj_inst: @@ -989,6 +1061,10 @@ def _create_statement_for_triple(self, subj, pred, obj): self._enrich_or_apply_owl_defaults(obj_inst, obj) def _resolve_statement_endpoint(self, node, fallback_class): + """Return the instance to use as subject or object of a Statement. + + It is the punning-dominant cached instance, or a new one of `fallback_class`. + """ dom = self._get_punning_dominant(node) if dom is not None: return dom diff --git a/lode/reader/logic/rdf_logic.py b/lode/reader/logic/rdf_logic.py index 824360e..b7ef1a0 100644 --- a/lode/reader/logic/rdf_logic.py +++ b/lode/reader/logic/rdf_logic.py @@ -1,4 +1,4 @@ -# rdf_logic.py +"""Extraction logic for RDF/RDFS artefacts.""" from rdflib import URIRef, Node, Literal as RDFlibLiteral, BNode from rdflib.namespace import RDF, RDFS, OWL, SKOS, XSD @@ -7,6 +7,9 @@ from lode.models import * from lode.reader.logic.base_logic import BaseLogic +import logging +logger = logging.getLogger(__name__) + class RdfLogic(BaseLogic): """ @@ -54,6 +57,10 @@ def phase1_classify_from_predicates(self): self.get_or_create(uri, py_class, populate=False) def phase2_create_from_types(self): + """Create an instance for every subject typed with a mapped rdf:type. + + Static setters and the handler declared for the type are applied right away. + """ type_mapping = self._strategy.get_type_mapping() for rdf_type, config in type_mapping.items(): @@ -90,7 +97,7 @@ def phase5_fallback(self): """ exclude_predicates = {RDF.first, RDF.rest, RDF.nil} - # 1. predicati -> Property + # 1. predicates -> Property for pred in set(self.graph.predicates()): if pred in self._instance_cache or pred in exclude_predicates: continue @@ -98,7 +105,7 @@ def phase5_fallback(self): continue self.get_or_create(pred, Property, populate=False) - # 2. soggetti/oggetti URI -> Resource + # 2. URI subjects/objects -> Resource for subj in set(self.graph.subjects()): if isinstance(subj, URIRef) and subj not in self._instance_cache: if self._is_structural(subj) or self._is_rdf_collection(subj): @@ -111,7 +118,7 @@ def phase5_fallback(self): continue self.get_or_create(obj, Resource, populate=False) - # 3. defaults RDFS su Property + # 3. RDFS defaults on Property for uri, instances in list(self._instance_cache.items()): for instance in list(instances): if isinstance(instance, Property): @@ -166,6 +173,7 @@ def _get_inherited_property_values(self, property_instance, getter_name: str) -> of getter_name found on an ancestor. """ def collect(node): + """Return the first non-empty value found on an ancestor, never on the property itself.""" if node is property_instance: return None getter = getattr(node, getter_name, None) @@ -215,8 +223,8 @@ def create_python_container(self, instance, uri): if rest is not None: self._triples_map[instance].add((node, RDF.rest, rest)) node = rest - except Exception as e: - print(f"Errore create_python_container (List): {e}") + except Exception: + logger.warning("List container build failed for %s", uri, exc_info=True) return # rdf:Bag/Alt/Seq: rdf:_N indexed members @@ -239,6 +247,7 @@ def create_python_container(self, instance, uri): self._triples_map[instance].add((uri, pred, obj)) def _resolve_container_member(self, node): + """Resolve a container member: a Literal for literals, a Resource otherwise.""" if isinstance(node, RDFlibLiteral): return self._create_literal(node) return self.get_or_create(node, Resource) \ No newline at end of file diff --git a/lode/reader/logic/skos_logic.py b/lode/reader/logic/skos_logic.py index bf18ae1..39703ab 100644 --- a/lode/reader/logic/skos_logic.py +++ b/lode/reader/logic/skos_logic.py @@ -1,4 +1,4 @@ -# logic.py - LOGICHE SPECIFICHE PER FORMATO +"""Extraction logic for SKOS artefacts.""" from rdflib import Graph, URIRef, Node, Literal as RDFlibLiteral, BNode from rdflib.namespace import RDF, RDFS, OWL, SKOS, XSD from rdflib.collection import Collection as RDFLibCollection @@ -6,27 +6,30 @@ from lode.models import * from lode.reader.logic.base_logic import BaseLogic +import logging +logger = logging.getLogger(__name__) + class SkosLogic(BaseLogic): """ - Logica SKOS. - - Differenze: - - Focus su Concept/ConceptScheme - - Relazioni skos:broader/narrower + SKOS logic. + + Differences: + - Focus on Concept/ConceptScheme + - skos:broader/narrower relations - NO default domain/range - NO Restriction, Individual, CompositeClass, Datatype, Attribute """ def _get_allowed_namespaces(self) -> set: + """Return the RDF, RDFS and SKOS namespaces, ignoring the config 'namespaces' key.""" return {str(RDF), str(RDFS), str(SKOS)} def phase1_classify_from_predicates(self): - print("\n--- FASE 1: Classificazione SKOS ---") - print(" Skip (SKOS usa solo types)") + """Do nothing: in SKOS the class always comes from rdf:type.""" + logger.debug("Phase 1 (SKOS classification): skipped, SKOS uses only rdf:type") def phase2_create_from_types(self): - print("\n--- FASE 2: Types SKOS ---") - + """Create an unpopulated instance for every subject typed with a mapped SKOS type.""" type_mapping = self._strategy.get_type_mapping() created = 0 @@ -40,28 +43,27 @@ def phase2_create_from_types(self): self.get_or_create(uri, py_class, populate=False) created += 1 - print(f" Create: {created}") + logger.debug("Phase 2 (SKOS types): created %d instances", created) def phase3_populate_properties(self): - print("\n--- FASE 3: Popolamento SKOS ---") - + """Fill every cached instance from its triples.""" for uri in list(self._instance_cache.keys()): for instance in list(self._instance_cache[uri]): self.populate_instance(instance, uri) - print(f" Popolate: {len(self._instance_cache)}") + logger.debug("Phase 3 (SKOS population): populated %d cache entries", len(self._instance_cache)) def phase4_process_group_axioms(self): - print("\n--- FASE 4: Axioms SKOS ---") - print(" Nessun axiom SKOS") + """Do nothing: SKOS has no group axioms.""" + logger.debug("Phase 4 (SKOS axioms): no group axioms in SKOS") def phase5_fallback(self): - print("\n--- FASE 5: FALLBACK ---") - print("TO BE IMPLEMENTED SOON") + """Do nothing yet: the SKOS fallback is not implemented.""" + logger.debug("Phase 5 (SKOS fallback): not implemented yet") - # Handler specifici SKOS + # SKOS-specific handlers def handle_membership(self, instance, uri, predicate, obj, value): - """Gestisce skos:member""" + """Handle skos:member: add the cached members of a Collection.""" if not isinstance(instance, Collection): return @@ -75,7 +77,7 @@ def handle_membership(self, instance, uri, predicate, obj, value): instance.set_has_member(member_obj) def handle_narrower(self, instance, uri, predicate, obj, value): - """Gestisce skos:narrower (inverso)""" + """Handle skos:narrower (the inverse of broader): link the concept to its broader concepts.""" if not isinstance(instance, Concept): return diff --git a/lode/reader/modules.py b/lode/reader/modules.py index ee354ba..737a07b 100644 --- a/lode/reader/modules.py +++ b/lode/reader/modules.py @@ -36,6 +36,9 @@ from lode.helpers.rdf import iri_namespace, iri_stem from lode.reader.provenance_graph import ProvenanceGraph +import logging +logger = logging.getLogger(__name__) + # Core vocabularies: never treated as external terms to dereference. _SKIP_NS = (str(RDF), str(RDFS), str(OWL), str(XSD)) @@ -64,12 +67,12 @@ def _load_formal_import(graph: ProvenanceGraph, source: str, depth: int, from lode.reader.loader import Loader # local import: loader imports modules try: imported_loader = Loader(source) - except Exception: - print(f" [formal import] could not load {source}") + except Exception as e: + logger.warning("Formal import failed for %s: %s", source, e) return imported_graph = imported_loader.get_graph() - print(f" [formal import] {len(imported_graph)} triples from {source}") + logger.info("Formal import: %d triples from %s", len(imported_graph), source) # Context = ontology IRI declared in the document (fallback: source) graph.add_document(imported_graph, source) @@ -78,12 +81,13 @@ def _load_formal_import(graph: ProvenanceGraph, source: str, depth: int, def _load_informal_import(source: str, target: ProvenanceGraph, visited: set, failed: set, - homes: dict) -> None: + homes: dict, name: Optional[str] = None) -> None: """Load a single document reached by dereferencing an IRI (informal import) into its own named graph of `target`. Its owl:imports are not followed. Records the outcome: success -> visited + homes[source] (name of its named graph); error -> failed (never retried).""" + if source in visited or source in failed: return from lode.reader.loader import Loader # local import: loader imports modules @@ -91,11 +95,11 @@ def _load_informal_import(source: str, target: ProvenanceGraph, visited: set, fa g = Loader(source).get_graph() except Exception as e: failed.add(source) - print(f" [informal import] could not load {source}: {type(e).__name__}: {e}") + logger.warning("Informal import failed for %s: %s: %s", source, type(e).__name__, e) return visited.add(source) - print(f" [informal import] {len(g)} triples from {source}") - homes[source] = target.add_document(g, source) + logger.info("Informal import: %d triples from %s", len(g), source) + homes[source] = target.add_document(g, name or source) # ---------------------------------------------------------- # IMPORTED / CLOSURE MODULES (formal imports) @@ -123,10 +127,11 @@ def apply_closure(graph: ProvenanceGraph): # ---------------------------------------------------------- # # Boundary: an external term receives -# - what the documented ontology says about it (with priority, per predicate), and -# - the triples of its "home" graph, i.e. of the ontology that owns it. -# Redefinitions found in third-party ontologies (formally imported ones included) are -# NOT copied: they belong to the import closure, available through imported/closure. +# - what the documented ontology says about it, in the main graph, and +# - ALL the triples of its "home" graph (types included), in the home graph. +# No per-predicate priority here: both sources are kept with their provenance; +# conflicting types become punned instances in the Reader, and the Viewer decides +# what to show. Redefinitions in third-party ontologies are NOT copied. # If the home cannot be reached, the term receives no external definition. def _namespace(term) -> str: @@ -165,8 +170,9 @@ def _namespace_failed(term, failed: set) -> bool: def apply_partial_import(graph: ProvenanceGraph): - """Dereference (1 hop) the external IRIs mentioned and add ONLY their definition, - taken from their home ontology (not the redefinitions in other ontologies).""" + """Dereference (1 hop) the external IRIs described by the documented ontology and + add ONLY their definition, taken from their home ontology (not the redefinitions + in other ontologies). Terms that are merely used stay plain external links.""" # 1. External terms: IRIs mentioned in the graph, excluding the import IRIs, the # core vocabularies and the ontology's own terms. import_iris = set(graph.objects(None, OWL.imports)) @@ -175,48 +181,49 @@ def apply_partial_import(graph: ProvenanceGraph): external = {t for t in mentioned if not str(t).startswith(_SKIP_NS) and not (own and str(t).startswith(own))} - # 2. Load into a separate graph (one named graph per document). The owl:imports + # 2. Keep only terms the documented ontology describes (subject of at least one of + # its triples): terms it merely uses stay plain external links. + described = {s for s, _, _ in graph if s in external} + + # 3. Load into a separate graph (one named graph per document). The owl:imports # documents are loaded first, as informal imports (no recursion): they are often - # the home of the mentioned terms, so they are not downloaded again. Then one + # the home of the described terms, so they are not downloaded again. Then one # attempt per namespace not covered yet. fetched = ProvenanceGraph() visited, failed, homes = set(), set(), {} # homes: source -> loaded ontology IRI - for iri in import_iris: + for iri in (import_iris if described else ()): _load_informal_import(str(iri), fetched, visited, failed, homes) - for term in external: + for term in described: if _home(term, homes) is None and not _namespace_failed(term, failed): - _load_informal_import(urldefrag(str(term))[0], fetched, visited, failed, homes) - - # 3. Headers of external ontologies (owl:Ontology) are not terms to document. - external -= set(fetched.subjects(RDF.type, OWL.Ontology)) + doc, frag = urldefrag(str(term)) + # Slash IRIs dereference the term itself: name the graph after the + # namespace, not after the first term fetched (e.g. dcterms:created). + _load_informal_import(doc, fetched, visited, failed, homes, + name=doc if frag else iri_namespace(term)) - # 4. Priority to the documented ontology: predicates it already asserts on an - # external term (e.g. rdfs:label) are not copied again from the home. - base_pairs = {(s, p) for s, p, _ in graph if s in external} + # 4. Headers of external ontologies (owl:Ontology) are not terms to document. + described -= set(fetched.subjects(RDF.type, OWL.Ontology)) - # 5. Copy from the home graph only, into its own named graph. + # 5. Copy the whole home description, into the home's named graph. seen: set = set() - for term in external: + for term in described: home = _home(term, homes) if home is not None: # home unreachable: no external definition - _copy_description(fetched, term, graph, seen, skip=base_pairs, ctx=home) + _copy_description(fetched, term, graph, seen, ctx=home) return graph, visited def _copy_description(src: ProvenanceGraph, node, dst: ProvenanceGraph, seen: set, - skip=frozenset(), ctx=None) -> None: + ctx=None) -> None: """Copy into `dst` the triples of `src` whose subject is `node`, in the same named graph. ctx restricts the copy to a single graph (the home); None = all graphs. - skip (subject, predicate) pairs already populated in the base: not overwritten. Blank nodes (restrictions, lists) are copied in full and stay in their parent's context; `seen` prevents cycles and repeated copies.""" if node in seen: return seen.add(node) for _, p, o, c in src.quads((node, None, None, ctx)): - if (node, p) in skip: - continue dst.graph(c).add((node, p, o)) if isinstance(o, BNode): _copy_description(src, o, dst, seen, ctx=c) \ No newline at end of file diff --git a/lode/reader/provenance_graph.py b/lode/reader/provenance_graph.py index 47d89d5..ced5a3f 100644 --- a/lode/reader/provenance_graph.py +++ b/lode/reader/provenance_graph.py @@ -1,3 +1,9 @@ +"""Named-graph container that keeps track of which ontology each triple comes from. + +Used when imports or partial imports are enabled: every loaded document lives +in its own named graph, named after its ontology IRI, while the rest of the +pipeline keeps reading the union of all of them as if it were a single Graph. +""" import os from pathlib import Path from urllib.parse import urlparse, quote @@ -8,21 +14,40 @@ QUAD_FORMATS = frozenset({"trig", "nquads"}) class ProvenanceGraph(Dataset): - """Dataset a named graph (uno per ontologia sorgente) che si presenta al pipeline come un Graph.""" + """Dataset with one named graph per source ontology, presented to the pipeline as a Graph. + + default_union makes queries see the union of all named graphs, so readers + and viewers need no knowledge of the provenance; only the code that cares + about the origin of a triple asks for a specific named graph. + """ def __init__(self, **kw): + """Create an empty dataset whose default graph is the union of its named graphs.""" super().__init__(default_union=True, **kw) def __iter__(self): + """Iterate over the plain triples of the union, like a Graph does.""" return self.triples((None, None, None)) def add_document(self, g: Graph, fallback: str) -> URIRef: - ctx = self.ontology_iri(g, fallback) + """Copy the triples of `g` into the named graph of its ontology and return its IRI. + + The graph is named by `ontology_iri`; `fallback` (usually the source URL + or path) is used when the document declares no ontology. + """ + ctx =self.ontology_iri(g, fallback) self.graph(ctx).__iadd__(g) return ctx @staticmethod def ontology_iri(g: Graph, fallback: str) -> URIRef: + """Return the IRI that names the graph of a document. + + Uses the first owl:Ontology or skos:ConceptScheme subject with an IRI. + Without one, falls back to the source itself: http(s)/file URLs as they + are, local paths as file:// URIs (a one-letter scheme is a Windows + drive), anything else as a urn:lode:source: URN. + """ for t in _ONTOLOGY_TYPES: for s in g.subjects(RDF.type, t): if isinstance(s, URIRef): diff --git a/lode/reader/reader.py b/lode/reader/reader.py index 723e2af..8465f23 100644 --- a/lode/reader/reader.py +++ b/lode/reader/reader.py @@ -1,7 +1,27 @@ -# reader.py - ORCHESTRATOR GENERICO +"""Generic orchestrator that turns a loaded RDF graph into model instances. + +The Reader sits between the Loader (parsing) and the Viewer (rendering): it +picks the configuration for the artefact type and runs the logic phases, so +CLI, API and viewers never depend on parsing details. +""" from lode.reader.loader import Loader from lode.reader.config_manager import get_configuration from lode.models import * +from rdflib import URIRef +from lode.reader.provenance_graph import ProvenanceGraph + +import logging +logger = logging.getLogger(__name__) + +def _value_key(value) -> str: + """Comparable form of a model value: lexical form for literals, IRI otherwise.""" + get_value = getattr(value, "get_has_value", None) + if get_value is not None and get_value() is not None: + return str(get_value()) + get_id = getattr(value, "get_has_identifier", None) + if get_id is not None and get_id(): + return str(get_id()) + return str(value) class Reader: """ @@ -14,25 +34,52 @@ class Reader: """ def __init__(self): + """Create an empty Reader; call load_instances() to populate it.""" self._instance_cache = {} - self._logic = None # Logic specializzata (OWL, SKOS, RDF, RDFS) + self._logic = None # specialised logic (OWL, SKOS, RDF/RDFS) self._graph = None self._configuration = None self._imported_uris = set() # needed to get the model before imported/closure models self._ontology_iri = None def get_warnings(self) -> list: + """Return the warnings collected while reading, or [] when they were not requested.""" if not getattr(self, '_warnings_enabled', False): return [] if self._logic and hasattr(self._logic, '_warnings'): return self._logic._warnings return [] - + + def _prioritize_documented_values(self) -> None: + """Reorder every multi-valued field so that values asserted by the documented + ontology (main named graph) come before those from imported or home graphs. + + Needed because the graph does not preserve insertion order across named graphs. + The sort is stable: within each group the original order is kept.""" + main = self._graph.graph(self._ontology_iri) + for uri, instances in self._instance_cache.items(): + if not isinstance(uri, URIRef): + continue + local = {str(o) for o in main.objects(uri, None)} + + if not local: + continue + for instance in instances: + for value in vars(instance).values(): + if isinstance(value, list) and len(value) > 1: + value.sort(key=lambda v: _value_key(v) not in local) + + def load_instances(self, graph_path: str, read_as: str, imported=None, closure=None, partial_import=None, warnings=False): - """Carica e processa grafo RDF""" + """Load an artefact and extract its model instances. + + `read_as` selects the configuration (owl, rdf, skos). Imports, closure and + partial_import are forwarded to the Loader; `warnings` turns on the reader + warnings. Blocking: it may fetch remote documents. + """ self._warnings_enabled = warnings - # 1. Parse generico + # 1. Generic parsing loader = Loader(graph_path, imported=imported, closure=closure, partial_import=partial_import) self._graph = loader.get_graph() self._ontology_iri = loader.ontology_iri @@ -40,18 +87,26 @@ def load_instances(self, graph_path: str, read_as: str, imported=None, closure=N # 1.5 saves the imported/closure uris to be reused in viewer so the model metadata are not overwritten self._imported_uris = getattr(loader, "imported_uris", set()) - # 2. Seleziona strategia + # 2. Select the configuration for the artefact type self._configuration = get_configuration(read_as) - # 3. Crea Logic specializzata + # 3. Create the specialised logic self._logic = self._configuration.create_logic(self._graph, self._instance_cache) - # 4. Esecuzione fasi + # 4. Run the extraction phases self._extract_instances() + # 5. Documented ontology first (only when a module is active) + if isinstance(self._graph, ProvenanceGraph): + self._prioritize_documented_values() + def get_instance(self, uri: str, instance_type=None): - """Ottiene istanze per URI""" + """Return the instances registered under an IRI. + + With `instance_type`, only the first instance of that type (or None); + otherwise the whole set. Returns None when the IRI is unknown. + """ uri_identifier = None for identifier in self._instance_cache.keys(): @@ -74,7 +129,7 @@ def get_instance(self, uri: str, instance_type=None): return None def get_instances(self) -> dict: - """Raggruppa istanze per tipo""" + """Group all instances by model class name; literal cache entries are skipped.""" grouped = {} for uri_identifier, instances in self._instance_cache.items(): @@ -92,13 +147,13 @@ def get_instances(self) -> dict: return grouped def get_triples_for_instance(self, instance): - """Ottiene le triple RDF associate a un'istanza Python""" + """Return the RDF triples that produced a model instance (empty set if unknown).""" if self._logic and hasattr(self._logic, '_triples_map'): return self._logic._triples_map.get(instance, set()) return set() def get_all_triples_map(self) -> dict: - """Ottiene la mappa completa instance β†’ triple""" + """Return the full instance -> triples map (empty dict if no logic is loaded).""" if self._logic and hasattr(self._logic, '_triples_map'): return self._logic._triples_map return {} @@ -113,7 +168,10 @@ def get_provenance_subgraph(self, instance): # function reused by the api to push instances def to_dict(self, instance) -> dict: - """Serializza un'istanza Python in dict JSON, includendo le triple RDF""" + """Serialize a model instance into a JSON-friendly dict, including its RDF triples. + + Empty values are left out of "properties"; every value is converted to a string. + """ result = { "instance": str(instance), "type": type(instance).__name__, @@ -122,14 +180,14 @@ def to_dict(self, instance) -> dict: "rdf_triples": [] } - # Serializza le proprietΓ  dell'istanza + # Serialize the instance properties for attr_name in instance.__dict__.keys(): value = getattr(instance, attr_name) # removes empty values from the properties if value is not None and not (isinstance(value, (list, set)) and not value): result["properties"][attr_name] = str(value) - # Aggiungi le triple RDF associate + # Add the associated RDF triples triples = self.get_triples_for_instance(instance) for s, p, o in triples: triple_dict = { @@ -141,51 +199,51 @@ def to_dict(self, instance) -> dict: return result - def _serialize_value(self, value): - """Helper per serializzare diversi tipi di valori""" - if isinstance(value, (str, int, float, bool)): - return value - elif isinstance(value, (list, set)): - return [self._serialize_value(v) for v in value] - elif hasattr(value, 'uri'): - return str(value.uri) - else: - return str(value) + # def _serialize_value(self, value): + # """Convert a value into a JSON-friendly form, recursing into lists and sets.""" + # if isinstance(value, (str, int, float, bool)): + # return value + # elif isinstance(value, (list, set)): + # return [self._serialize_value(v) for v in value] + # elif hasattr(value, 'uri'): + # return str(value.uri) + # else: + # return str(value) def get_viewer(self): - """Ottiene il viewer appropriato per il formato corrente.""" + """Return the viewer matching the loaded artefact type. + + Raises ValueError if load_instances() has not been called yet. + """ if not self._configuration: raise ValueError("No configuration loaded. Call load_instances() first.") return self._configuration.create_viewer(self) def clear_cache(self): - """Pulisce la cache""" + """Drop every cached instance, in the Reader and in its logic.""" self._instance_cache.clear() if self._logic: self._logic.clear_cache() - # ==================== ESTRAZIONE (ORCHESTRAZIONE) ==================== + # ==================== EXTRACTION (ORCHESTRATION) ==================== def _extract_instances(self): - """Estrazione in 6 fasi orchestrate""" - # print("\n" + "="*60) - # print("ESTRAZIONE INSTANCES") - # print("="*60) - - # FASE 0: Pre-crea datatypes (comune a tutti) - # self._phase0_create_datatypes() - - # FASE 1-4: Delegate alla Logic specifica + """Run the extraction phases in order, delegating each one to the logic. + + Phases 1-4 depend on the artefact type; fallback, statements and + namespaces are shared. Post-pipeline warning checks run only when enabled. + """ + # PHASES 1-4: delegated to the specific logic self._logic.phase1_classify_from_predicates() self._logic.phase2_create_from_types() self._logic.phase3_populate_properties() self._logic.phase4_process_group_axioms() - # FASE 5: Fallback (comune) + # PHASE 5: fallback (shared) self._logic.phase5_fallback() - # FASE 6: Statements + # PHASE 6: statements self._logic.phase6_create_statements() # FASE 7: Namespaces @@ -197,50 +255,18 @@ def _extract_instances(self): owl_warnings.run_post_checks(self._logic) if self._logic._warnings: - print(f"WARNINGS ({len(self._logic._warnings)}):") + logger.warning("%d reader warnings", len(self._logic._warnings)) for w in self._logic._warnings: - print(f" [{w['code']}] {w['message']}") + logger.warning("[%s] %s", w['code'], w['message']) self._logic.save_warnings() - # def _phase0_create_datatypes(self): - # """Pre-crea tutti i Datatype (comune a tutti i formati)""" - # print("\n--- FASE 0: Datatypes ---") - - # created = 0 - - # # 1. URI XSD - # for s, p, o in self._graph: - # if isinstance(s, URIRef) and str(s).startswith(str(XSD)): - # if s not in self._instance_cache: - # self._logic.create_empty_instance(s, Datatype) - # created += 1 - - # if isinstance(o, URIRef) and str(o).startswith(str(XSD)): - # if o not in self._instance_cache: - # self._logic.create_empty_instance(o, Datatype) - # created += 1 - - # # 2. rdfs:Literal - # if RDFS.Literal not in self._instance_cache: - # self._logic.create_empty_instance(RDFS.Literal, Datatype) - # created += 1 - - # # 3. BNode Datatypes - # for bnode in self._graph.subjects(RDF.type, RDFS.Datatype): - # if isinstance(bnode, BNode) and bnode not in self._instance_cache: - # self._logic.create_empty_instance(bnode, Datatype) - # created += 1 - - # print(f" Creati {created} datatypes") - def _phase5_fallback(self): """Fallback per risorse non categorizzate (comune)""" - #print("\n--- FASE 5: Fallback ---") fallback_class = self._configuration.get_fallback_class() if not fallback_class: - print(" Nessun fallback configurato") + logger.warning("No fallback class configured") return all_subjects = set(self._graph.subjects()) @@ -249,71 +275,4 @@ def _phase5_fallback(self): for subj in all_subjects: if subj not in self._instance_cache: self._logic.get_or_create(subj, fallback_class) - fallback_count += 1 - - #print(f" Fallback: {fallback_count} risorse -> {fallback_class.__name__}") - - # def get_ontology_metadata(self) -> Model: - # """ - # Extracts metadata and returns a populated Model object. - # """ - # if self._graph is None: - # return Model() - - # # 1. Create the Model instance - # ontology_model = Model() - - # # 2. Find the owl:Ontology node - # ontology_node = self._graph.value(predicate=RDF.type, object=OWL.Ontology) - - # if ontology_node: - # # --- IDENTIFIER (IRI) --- - # ontology_model.set_has_identifier(str(ontology_node)) - - # # --- TITLE (Label) --- - # title = ( - # self._graph.value(ontology_node, DCTERMS.title) or - # self._graph.value(ontology_node, DC.title) or - # self._graph.value(ontology_node, RDFS.label) - # ) - # if title: - # ontology_model.set_has_label(str(title)) - - # # --- DESCRIPTION (Comment) --- - # comment = ( - # self._graph.value(ontology_node, DCTERMS.description) or - # self._graph.value(ontology_node, RDFS.comment) - # ) - # if comment: - # ontology_model.set_has_comment(str(comment)) - - # # --- VERSION INFO --- - # version_info = self._graph.value(ontology_node, OWL.versionInfo) - # if version_info: - # ontology_model.set_has_version_info(str(version_info)) - - # # --- VERSION IRI --- - # version_iri = self._graph.value(ontology_node, OWL.versionIRI) - # if version_iri: - # v_model = Model() - # v_model.set_has_identifier(str(version_iri)) - # ontology_model.set_has_version(v_model) - - # # --- IMPORTS --- - # for imported_iri in self._graph.objects(ontology_node, OWL.imports): - # imported_model = Model() - # imported_model.set_has_identifier(str(imported_iri)) - # ontology_model.set_imports(imported_model) - - # # --- CREATORS (Custom handling) --- - # for pred in [DCTERMS.creator, DC.creator]: - # for creator in self._graph.objects(ontology_node, pred): - # ontology_model.set_has_creator(creator) - - - # # --- CONTRIBUTORS (Custom handling) --- - # for pred in [DCTERMS.contributor, DC.contributor]: - # for contributor in self._graph.objects(ontology_node, pred): - # ontology_model.set_has_contributor(contributor) - - # return ontology_model \ No newline at end of file + fallback_count += 1 \ No newline at end of file diff --git a/lode/reader/warnings/owl_warnings.py b/lode/reader/warnings/owl_warnings.py index ae225d5..8fb1652 100644 --- a/lode/reader/warnings/owl_warnings.py +++ b/lode/reader/warnings/owl_warnings.py @@ -25,6 +25,10 @@ def has_warning(logic, code: str, subject=None) -> bool: # ==================================================================== def flag_malformed_restrictions(logic, classified): + """Warn about BNodes that mix several restriction axioms (not valid OWL 2 DL). + + Warnings are grouped by the parent resource that holds the malformed BNodes. + """ axiom_preds = { p for p, cfg in logic._property_mapping.items() if isinstance(cfg.get('inferred_class'), type) @@ -48,11 +52,13 @@ def flag_malformed_restrictions(logic, classified): f"OWL 2 DL: malformed restrictions on {parent} ({', '.join(names)})") def empty_truth_function(logic, instance, bnode, operator): + """Warn that a truth function has an empty operand list and was ignored.""" ident = instance.get_has_identifier() logic.add_warning('empty_truth_function', ident, f'Β§8.1.1: Truth Function ({ident}, {operator}) is empty β€” ignored (collection BNode: {bnode})') def singleton_truth_function(logic, instance, bnode, operator): + """Warn that a truth function has a single operand, which usually points to an ontology mistake.""" ident = instance.get_has_identifier() logic.add_warning('singleton_truth_function', ident, f'Β§8.1.1: TruthFunction ({ident}, {operator}) has a single element β€” ontology should be checked (collection BNode: {bnode})') @@ -78,6 +84,7 @@ def run_post_checks(logic): def _check_orphan_restriction(logic, instance, uri): + """Warn about a restriction with no property; an anonymous one without owl:onProperty is also removed.""" if not isinstance(instance, PropertyConceptRestriction): return if instance.get_applies_on_property() is not None: @@ -91,6 +98,7 @@ def _check_orphan_restriction(logic, instance, uri): f'{type(instance).__name__} has owl:onProperty but applies_on_property is None') def _check_inverse_multiplicity(logic, instance, uri): + """Warn about a relation declared inverse of more than one relation.""" if not isinstance(instance, Relation): return inv = instance.get_is_inverse_of() @@ -109,11 +117,13 @@ def _check_inverse_multiplicity(logic, instance, uri): # f'Β§6.1.1: Relation {uri} is inverse of itself') def _check_empty_truth_function_post(logic, instance, uri): + """Warn about a truth function that still has no concepts after the whole read.""" if isinstance(instance, TruthFunction) and len(instance.get_applies_on_concept()) == 0: logic.add_warning('empty_restriction', uri, f'{type(instance).__name__} has empty applies_on_concept') def _check_property_hierarchy(logic, instance, uri): + """Warn when a property is a sub property of a property of a different kind (relation, attribute, annotation).""" if not isinstance(instance, (Relation, Attribute, Annotation)): return for sup in (instance.get_is_sub_property_of() or []): @@ -123,6 +133,7 @@ def _check_property_hierarchy(logic, instance, uri): f'{type(sup).__name__} {sup.get_has_identifier()}') def _check_class_datatype_hierarchy(logic, instance, uri): + """Warn when a class is a subclass of a datatype, or the other way round.""" if not isinstance(instance, (Concept, Datatype)) or isinstance(instance, DatatypeRestriction): return for sup in (instance.get_is_sub_concept_of() or []): @@ -132,6 +143,7 @@ def _check_class_datatype_hierarchy(logic, instance, uri): f'{type(sup).__name__} {sup.get_has_identifier()}') def _check_punning_conflicts(logic, uri, instances): + """Warn about an IRI used as both class and datatype, or as several property kinds (illegal punning).""" types = {type(i) for i in instances} if Concept in types and Datatype in types: logic.add_warning('class_datatype_conflict', uri, @@ -142,6 +154,7 @@ def _check_punning_conflicts(logic, uri, instances): f'Β§5.8.1: {uri} has multiple property types: {sorted(t.__name__ for t in prop_types)}') def _check_config_mismatches(logic): + """Warn when the subject of a mapped predicate was not given one of the classes the config expects.""" for pred, cfg in logic._property_mapping.items(): target_classes = cfg.get('target_classes', []) if not target_classes: diff --git a/lode/viewer/__init__.py b/lode/viewer/__init__.py index 73fabd5..1511a1c 100644 --- a/lode/viewer/__init__.py +++ b/lode/viewer/__init__.py @@ -1,4 +1,4 @@ -# viewer/__init__.py +"""Viewer layer: renders the model as view data for the HTML templates.""" from .base_viewer import BaseViewer from .owl_viewer import OwlViewer @@ -14,7 +14,10 @@ def get_viewer(read_as: str, reader): - """Factory per il viewer corretto in base al formato.""" + """Return the viewer that matches the artefact format (owl, rdf/rdfs, skos). + + An unknown format falls back to the generic BaseViewer. + """ key = read_as.lower() if key == 'owl': return OwlViewer(reader) diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..726b4d8 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,40 @@ +site_name: LODE 2.0 +site_description: Live OWL Documentation Environment β€” extract and document RDF/OWL/SKOS semantic artefacts as browsable HTML. +site_url: https://opencitations.github.io/lode/ +repo_url: https://github.com/opencitations/lode +repo_name: opencitations/lode + +theme: + name: material + features: + - navigation.sections + - navigation.top + - content.code.copy + palette: + - scheme: default + toggle: + icon: material/weather-night + name: Switch to dark mode + - scheme: slate + toggle: + icon: material/weather-sunny + name: Switch to light mode + +markdown_extensions: + - admonition + - attr_list + - tables + - toc: + permalink: true + - pymdownx.highlight + - pymdownx.superfences + +nav: + - Home: index.md + - Getting started: getting_started.md + - Usage: + - Web form: usage/web_form.md + - CLI: usage/cli.md + - Docker: usage/docker.md + - API reference: + - Endpoints: api/endpoints.md diff --git a/pyproject.toml b/pyproject.toml index 4f9e035..a706a01 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [project] -name = "lode" +name = "oc-lode" version = "0.3.15" description = "New reengineered version of LODE, maintained by OpenCitations" authors = [{name = "Valentina Pasqual, Silvio Peroni", email = "valentina.pasqual2@unibo.it"}] @@ -18,18 +18,21 @@ classifiers = [ "Programming Language :: Python :: 3.13", ] dependencies = [ - "fastapi>=0.104.1", - "uvicorn[standard]>=0.24.0", - "gunicorn>=21.0.0", - "python-multipart>=0.0.6", "rdflib>=7.4.0", "jinja2>=3.1.2", "requests>=2.31.0", - "owlready2>=0.50", "minify-html>=0.18.1", + "pyyaml>=6.0", +] + +[project.optional-dependencies] +server = [ + "fastapi>=0.104.1", + "uvicorn[standard]>=0.24.0", + "gunicorn>=21.0.0", + "python-multipart>=0.0.6", ] -# AGGIUNTO [project.scripts] lode = "lode.cli:main" @@ -52,7 +55,5 @@ build-backend = "hatchling.build" [tool.hatch.build.targets.wheel] packages = ["lode"] -# include template e static nel wheel -# [tool.hatch.build.targets.wheel.shared-data] -# "lode/templates" = "lode/templates" -# "lode/static" = "lode/static" +[tool.hatch.build.targets.sdist] +include = ["lode", "tests"] diff --git a/tests/data/provenance/main.ttl b/tests/data/provenance/main.ttl index a2d8a98..d980735 100644 --- a/tests/data/provenance/main.ttl +++ b/tests/data/provenance/main.ttl @@ -8,3 +8,6 @@ a owl:Class ; rdfs:subClassOf , , . rdfs:label "T from main"@en . + + rdfs:comment "V described by main" . + rdfs:comment "X described by main" . diff --git a/tests/test_modules.py b/tests/test_modules.py index 3a24cb7..8031110 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -261,11 +261,6 @@ def test_home_definition_in_home_graph(self, ds): assert contexts(ds, (H.T, RDF.type, OWL.Class)) == {HOME} assert contexts(ds, (H.T, RDFS.comment, Literal("T defined by home"))) == {HOME} - def test_documented_ontology_has_priority(self, ds): - """main restates the label of home#T: main's label wins, home's is not copied.""" - assert set(ds.objects(H.T, RDFS.label)) == {Literal("T from main", lang="en")} - assert contexts(ds, (H.T, RDFS.label, Literal("T from main", lang="en"))) == {MAIN} - def test_third_party_redefinition_is_not_copied(self, ds): """imp redefines home#T, but imp is not home#T's home.""" assert (H.T, RDFS.comment, Literal("T redefined by imp")) not in ds @@ -278,6 +273,23 @@ def test_blank_nodes_follow_parent_context(self, ds): assert contexts(ds, t) == {HOME} assert set(ds.predicates(restr)) == {RDF.type, OWL.onProperty, OWL.someValuesFrom} + # -- priority of documented ontology over imported ontos -------------- + + def test_both_definitions_kept_with_provenance(self, ds): + """main restates the label of home#T: both labels kept, each in its own graph.""" + assert contexts(ds, (H.T, RDFS.label, Literal("T from main", lang="en"))) == {MAIN} + assert contexts(ds, (H.T, RDFS.label, Literal("T from home", lang="en"))) == {HOME} + + def test_documented_values_come_first(self, main_path): + """The Reader puts main's label of home#T before home's.""" + from lode.reader.reader import Reader + reader = Reader() + reader.load_instances(graph_path=main_path, read_as="owl", partial_import=True) + for inst in reader._instance_cache[H.T]: + labels = [l.get_has_value() for l in inst.get_has_label()] + if labels: + assert labels[0] == "T from main", labels + # -- finding the home ------------------------------------------------- def test_home_by_dereferenced_document_when_iri_differs(self, ds): @@ -285,9 +297,10 @@ def test_home_by_dereferenced_document_when_iri_differs(self, ds): assert contexts(ds, (V.V, RDF.type, OWL.Class)) == {VER} def test_unreachable_home_gets_no_external_definition(self, ds, offline_fetch): - """missing is not served: imp's redefinition of missing#X must not fill the gap.""" + """missing is not served: only main's own triple, imp's redefinition must not fill the gap.""" assert "http://ex.org/missing" in offline_fetch - assert set(ds.predicate_objects(X.X)) == set() + assert set(ds.predicate_objects(X.X)) == {(RDFS.comment, Literal("X described by main"))} + assert contexts(ds, (X.X, RDFS.comment, Literal("X described by main"))) == {MAIN} # -- fetching --------------------------------------------------------- @@ -307,6 +320,8 @@ def test_vocabulary_without_ontology_fetched_once(self, tmp_path, offline_fetch, path = write_ttl(tmp_path, "m.ttl", """ a owl:Ontology . rdfs:seeAlso , . + rdfs:comment "a described by m2" . + rdfs:comment "b described by m2" . """) ds = Loader(path, partial_import=True).get_graph() assert len([u for u in offline_fetch if u.startswith("http://ex.org/voc/")]) == 1 @@ -317,6 +332,9 @@ def test_failed_namespace_not_retried_per_term(self, tmp_path, offline_fetch): path = write_ttl(tmp_path, "m.ttl", """ a owl:Ontology . rdfs:seeAlso , , . + rdfs:comment "a" . + rdfs:comment "b" . + rdfs:comment "c" . """) Loader(path, partial_import=True) assert len([u for u in offline_fetch if u.startswith("http://ex.org/dead/")]) == 1 @@ -553,9 +571,20 @@ def ds(self, client): def test_graphs_are_main_and_homes_only(self, ds): assert graphs(ds) == {MAIN, HOME, VER} - def test_documented_ontology_has_priority(self, ds): - assert set(ds.objects(H.T, RDFS.label)) == {Literal("T from main", lang="en")} + def test_both_definitions_kept_with_provenance(self, ds): + """main restates the label of home#T: both labels kept, each in its own graph.""" assert contexts(ds, (H.T, RDFS.label, Literal("T from main", lang="en"))) == {MAIN} + assert contexts(ds, (H.T, RDFS.label, Literal("T from home", lang="en"))) == {HOME} + + def test_documented_values_come_first(self, main_path): + """The Reader puts main's label of home#T before home's.""" + from lode.reader.reader import Reader + reader = Reader() + reader.load_instances(graph_path=main_path, read_as="owl", partial_import=True) + for inst in reader._instance_cache[H.T]: + labels = [l.get_has_value() for l in inst.get_has_label()] + if labels: + assert labels[0] == "T from main", labels def test_home_definition_in_home_graph(self, ds): assert contexts(ds, (H.T, RDFS.comment, Literal("T defined by home"))) == {HOME} @@ -573,7 +602,7 @@ def test_versioned_home_found_via_dereferenced_document(self, ds): assert contexts(ds, (V.V, RDF.type, OWL.Class)) == {VER} def test_unreachable_home_gives_no_external_definition(self, ds): - assert set(ds.predicate_objects(X.X)) == set() + assert set(ds.predicate_objects(X.X)) == {(RDFS.comment, Literal("X described by main"))} def test_external_ontology_headers_absent(self, ds): assert set(ds.subjects(RDF.type, OWL.Ontology)) == {MAIN} @@ -701,4 +730,5 @@ def test_same_upload_reloaded_gives_same_quads(self, client, flag): b = as_dataset(get(client, token, "trig", **{flag: True}), "trig") assert graphs(a) == graphs(b) for g in graphs(a): - assert isomorphic(a.graph(g), b.graph(g)), g \ No newline at end of file + assert isomorphic(a.graph(g), b.graph(g)), g + \ No newline at end of file diff --git a/uv.lock b/uv.lock index 57c7d7c..9a44003 100644 --- a/uv.lock +++ b/uv.lock @@ -444,51 +444,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/62/a1/3d680cbfd5f4b8f15abc1d571870c5fc3e594bb582bc3b64ea099db13e56/jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67", size = 134899, upload-time = "2025-03-05T20:05:00.369Z" }, ] -[[package]] -name = "lode" -version = "0.3.15" -source = { editable = "." } -dependencies = [ - { name = "fastapi" }, - { name = "gunicorn" }, - { name = "jinja2" }, - { name = "minify-html" }, - { name = "owlready2" }, - { name = "python-multipart" }, - { name = "rdflib" }, - { name = "requests" }, - { name = "uvicorn", extra = ["standard"] }, -] - -[package.dev-dependencies] -dev = [ - { name = "genbadge", extra = ["coverage"] }, - { name = "httpx" }, - { name = "pytest" }, - { name = "pytest-cov" }, -] - -[package.metadata] -requires-dist = [ - { name = "fastapi", specifier = ">=0.104.1" }, - { name = "gunicorn", specifier = ">=21.0.0" }, - { name = "jinja2", specifier = ">=3.1.2" }, - { name = "minify-html", specifier = ">=0.18.1" }, - { name = "owlready2", specifier = ">=0.50" }, - { name = "python-multipart", specifier = ">=0.0.6" }, - { name = "rdflib", specifier = ">=7.4.0" }, - { name = "requests", specifier = ">=2.31.0" }, - { name = "uvicorn", extras = ["standard"], specifier = ">=0.24.0" }, -] - -[package.metadata.requires-dev] -dev = [ - { name = "genbadge", extras = ["coverage"], specifier = ">=1.1.3" }, - { name = "httpx", specifier = ">=0.28.1" }, - { name = "pytest", specifier = ">=8.0.0" }, - { name = "pytest-cov", specifier = ">=7.0.0" }, -] - [[package]] name = "markupsafe" version = "3.0.3" @@ -618,10 +573,54 @@ wheels = [ ] [[package]] -name = "owlready2" -version = "0.50" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/a4/67/6fb3a628889d97f8a3d3c64d4597f0637db61a1856c835fe7c65d8e89658/owlready2-0.50.tar.gz", hash = "sha256:7be74c53a35497df138c8223dddcf65510def9b38494ae1fac4aa2a61c4677eb", size = 27328931, upload-time = "2026-02-05T10:42:01.733Z" } +name = "oc-lode" +version = "0.3.15" +source = { editable = "." } +dependencies = [ + { name = "jinja2" }, + { name = "minify-html" }, + { name = "pyyaml" }, + { name = "rdflib" }, + { name = "requests" }, +] + +[package.optional-dependencies] +server = [ + { name = "fastapi" }, + { name = "gunicorn" }, + { name = "python-multipart" }, + { name = "uvicorn", extra = ["standard"] }, +] + +[package.dev-dependencies] +dev = [ + { name = "genbadge", extra = ["coverage"] }, + { name = "httpx" }, + { name = "pytest" }, + { name = "pytest-cov" }, +] + +[package.metadata] +requires-dist = [ + { name = "fastapi", marker = "extra == 'server'", specifier = ">=0.104.1" }, + { name = "gunicorn", marker = "extra == 'server'", specifier = ">=21.0.0" }, + { name = "jinja2", specifier = ">=3.1.2" }, + { name = "minify-html", specifier = ">=0.18.1" }, + { name = "python-multipart", marker = "extra == 'server'", specifier = ">=0.0.6" }, + { name = "pyyaml", specifier = ">=6.0" }, + { name = "rdflib", specifier = ">=7.4.0" }, + { name = "requests", specifier = ">=2.31.0" }, + { name = "uvicorn", extras = ["standard"], marker = "extra == 'server'", specifier = ">=0.24.0" }, +] +provides-extras = ["server"] + +[package.metadata.requires-dev] +dev = [ + { name = "genbadge", extras = ["coverage"], specifier = ">=1.1.3" }, + { name = "httpx", specifier = ">=0.28.1" }, + { name = "pytest", specifier = ">=8.0.0" }, + { name = "pytest-cov", specifier = ">=7.0.0" }, +] [[package]] name = "packaging" From 9f3a12f2cdd6afcf4b27a890e3a1325843740724 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 12:24:51 +0200 Subject: [PATCH 03/21] fix: nested statements rendering in ontology annotation --- lode/reader/logic/base_logic.py | 12 +++---- lode/templates/_entity_card.html | 56 +------------------------------ lode/templates/_value.html | 55 ++++++++++++++++++++++++++++++ lode/templates/viewer.html | 7 +++- lode/viewer/base_viewer.py | 10 ++++-- tests/test_owl_viewer.py | 57 ++++++++++++++++++++++++++++++++ 6 files changed, 133 insertions(+), 64 deletions(-) create mode 100644 lode/templates/_value.html diff --git a/lode/reader/logic/base_logic.py b/lode/reader/logic/base_logic.py index 1224d35..a718670 100644 --- a/lode/reader/logic/base_logic.py +++ b/lode/reader/logic/base_logic.py @@ -635,14 +635,15 @@ def _create_statement_for_triple(self, subj, pred, obj): def _is_unmapped_structured_bnode(self, node) -> bool: """A BNode is a structured Statement value if: - it's a BNode (not URIRef, not Literal) - - it's not already in the instance cache (not classified by any phase) + - it's not already classified by any phase (a bare Resource in the cache is + only a placeholder made by a mapped predicate such as rdfs:seeAlso) - it has at least one outgoing triple - none of its outgoing predicates carry a useful rdf:type for our model (i.e. it's not declaring itself as a typed entity) """ if not isinstance(node, BNode): return False - if node in self._instance_cache: + if any(type(i) is not Resource for i in self._instance_cache.get(node, ())): return False has_out = False for _ in self.graph.predicate_objects(node): @@ -663,9 +664,8 @@ def _create_nested_statement(self, node): statement = Statement() statement.set_has_identifier(str(node)) - if node not in self._instance_cache: - self._instance_cache[node] = set() - self._instance_cache[node].add(statement) + # drop the placeholder Resource: the node is represented by the Statement + self._instance_cache[node] = {statement} for p, o in self.graph.predicate_objects(node): self._track(statement, (node, p, o)) @@ -691,7 +691,7 @@ def _create_nested_statement(self, node): elif self._is_unmapped_structured_bnode(o): o_inst = self._create_nested_statement(o) else: - o_inst = self.get_or_create(o, Individual) + o_inst = self.get_or_create(o, Resource) # The first (predicate, object) pair fills the Statement slots; # additional pairs are stored as side annotations on the Statement diff --git a/lode/templates/_entity_card.html b/lode/templates/_entity_card.html index 0e59b9c..55fd06b 100644 --- a/lode/templates/_entity_card.html +++ b/lode/templates/_entity_card.html @@ -1,58 +1,4 @@ -{% macro render_value(v, depth=0) %} -{% if v.link and 'erlangen' in v.link %} - -{% endif %} - {% if v.type == 'Statement' and v.nested %} -

- {% set main = v.nested.main %} - {% if main and main.value and main.value.text %} -
{{ main.predicate }}: {{ render_value(main.value, depth + 1) }}
- {% endif %} - {% if v.nested.siblings %} - {% for s in v.nested.siblings %} -
{{ s.predicate }}: {{ render_value(s.value, depth + 1) }}
- {% endfor %} - {% endif %} -
- {% else %} - {% set v_type = v.type.lower() if v.type else '' %} - {% set is_md = ('str' in v_type) or ('literal' in v_type) %} - {% set dep_class = 'text-decoration-line-through text-muted' if v.is_deprecated else '' %} - {% set dep_title = ' -- Deprecated ' if v.is_deprecated else '' %} - - {% if v.link %} - {% set precise_key = v.link ~ '|' ~ v_type %} - {% if v.is_external %} - {{ v.text }} - {% elif precise_key in anchor_map %} - {{ v.text }} - {% elif v.link in anchor_map %} - {{ v.text }} - {% elif is_static %} - {{ v.text }} - {% else %} - {{ v.text }} - {% endif %} - - {% if v_type in type_map %} - {{ type_map[v_type].abb }} - {% endif %} - - {% else %} -
-
- {{ v.text }} -
- {% if is_md and v.lan %} - {{ v.lan }} - {% endif %} -
- {% endif %} - {% endif %} -{% endmacro %} +{% from '_value.html' import render_value with context %}
diff --git a/lode/templates/_value.html b/lode/templates/_value.html new file mode 100644 index 0000000..1c10ed9 --- /dev/null +++ b/lode/templates/_value.html @@ -0,0 +1,55 @@ +{# Shared renderer for a resolved value: literals, links, restrictions and nested statements. #} +{% macro render_value(v, depth=0, full_link=false) %} + {% if v.type == 'Statement' and v.nested %} +
+ {% set main = v.nested.main %} + {% if main and main.value and main.value.text %} +
{{ main.predicate }}:{{ render_value(main.value, depth + 1, full_link) }}
+ {% endif %} + {% if v.nested.siblings %} + {% for s in v.nested.siblings %} +
{{ s.predicate }}:{{ render_value(s.value, depth + 1, full_link) }}
+ {% endfor %} + {% endif %} +
+ {% else %} + {% set v_type = v.type.lower() if v.type else '' %} + {% set is_md = ('str' in v_type) or ('literal' in v_type) %} + {% set dep_class = 'text-decoration-line-through text-muted' if v.is_deprecated else '' %} + {% set dep_title = ' -- Deprecated ' if v.is_deprecated else '' %} + + {% if v.link %} + {% set precise_key = v.link ~ '|' ~ v_type %} + {% if v.is_external %} + {{ v.link if full_link and v_type == 'resource' else v.text }} + {% elif precise_key in anchor_map %} + {{ v.text }} + {% elif v.link in anchor_map %} + {{ v.text }} + {% elif is_static %} + {{ v.text }} + {% else %} + {{ v.text }} + {% endif %} + + {% if v_type in type_map %} + {{ type_map[v_type].abb }} + {% endif %} + + {% else %} + {# inline inside a nested statement so "name: value" stays on one line #} + {% set tag = 'span' if depth else 'div' %} + <{{ tag }}> + <{{ tag }} class="markdown-with-badge {{ dep_class }} {% if is_md %}render-markdown inline-markdown{% endif %}" + title="{{ v.link }}{{dep_title}}" + {% if is_md %}data-md="{{ v.text | e }}"{% endif %}> + {{ v.text }} + + {% if is_md and v.lan %} + {{ v.lan }} + {% endif %} + + {% endif %} + {% endif %} +{% endmacro %} diff --git a/lode/templates/viewer.html b/lode/templates/viewer.html index a7393b7..e6d4cb5 100644 --- a/lode/templates/viewer.html +++ b/lode/templates/viewer.html @@ -46,6 +46,9 @@ {% set md_types = ['Literal', 'Str', 'literal', 'str', 'string'] %} + {# after the sets above: "with context" only sees variables defined before the import #} + {% from '_value.html' import render_value with context %} + {% include '_toc_sidebar.html' %} {% if not single_resource %} @@ -157,6 +160,8 @@

{% endif %}

+ {% elif item.type == 'Statement' and item.nested %} + {{ render_value(item, 0, true) }} {% else %}
{{ item.text }}
{% endif %} @@ -284,7 +289,7 @@

← Back to full documentation + ← Back to full documentation {% else %} ← Back to full documentation {% endif %} diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 548898d..8170e05 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -581,7 +581,13 @@ def _resolve_resource_value(self, obj, language=None) -> dict: 'predicate': self._clean_name(self, attr), 'value': resolved, }) - handler_dic['nested'] = {'main': inner, 'siblings': siblings} + # Reader order depends on the source file: sort by label, then by value + pairs = sorted( + [inner] + siblings, + key=lambda p: ((p['predicate'] or '').lower(), + ((p['value'] or {}).get('text') or '').lower()), + ) + handler_dic['nested'] = {'main': pairs[0], 'siblings': pairs[1:]} # Pick a primary text for collapsed display: the inner value's text handler_dic['text'] = (inner.get('value') or {}).get('text') or '[Statement]' return handler_dic @@ -645,7 +651,7 @@ def _format_statement(self, instances, target_instance, language=None) -> Dict: if obj_data['text'] and obj_data not in values: values.append(obj_data) if values: - statements[pred_label] = values + statements[pred_label] = sorted(values, key=lambda v: (str(v.get('nested')), v['text'].lower())) return statements diff --git a/tests/test_owl_viewer.py b/tests/test_owl_viewer.py index b82aefd..1580cce 100644 --- a/tests/test_owl_viewer.py +++ b/tests/test_owl_viewer.py @@ -347,6 +347,63 @@ def test_metadata_has_only_requested_language_and_no_none(self): assert texts == ["Title"] +# --------------------------------------------------------------------------- +# Structured blank nodes in the ontology header (e.g. bibo:editor [ a foaf:Person ... ]) +# --------------------------------------------------------------------------- + +_HEADER_TTL = """ +@prefix owl: . +@prefix bibo: . +@prefix foaf: . +@prefix org: . +@prefix rdfs: . + + a owl:Ontology ; + bibo:editor %s . +""" + +_PERSON_A = ('[ a foaf:Person ; foaf:name "Alice Example" ; ' + 'org:memberOf [ foaf:name "Example Org" ] ]') +_PERSON_B = '[ a foaf:Person ; foaf:name "Bob Example" ; rdfs:seeAlso ]' + + +def _render_index(tmp_path, ttl): + """Load `ttl` through the Reader and return the HTML of the static index page.""" + from lode.builder import build_html + from lode.reader import Reader + + src = tmp_path / "onto.ttl" + src.write_text(ttl, encoding="utf-8") + reader = Reader() + reader.load_instances(str(src), read_as="owl") + out = tmp_path / "site" + build_html(reader.get_viewer(), out, reader=reader) + return (out / "index.html").read_text(encoding="utf-8") + + +class TestHeaderStructuredBnodes: + """Header values that are blank nodes must show their content, not their id.""" + + def test_header_shows_bnode_content_not_ids(self, tmp_path): + html = _render_index(tmp_path, _HEADER_TTL % f"{_PERSON_A}, {_PERSON_B}") + for expected in ("Alice Example", "Bob Example", "Example Org"): + assert expected in html + assert not re.search(r"\b(?:N[0-9a-f]{32}|n[0-9a-f]{20,})\b", html), "raw BNode id in header" + + def test_header_order_is_independent_of_source_order(self, tmp_path): + """Same graph, triples written in a different order: same rendered header.""" + a = tmp_path / "a" + b = tmp_path / "b" + a.mkdir() + b.mkdir() + html_a = _render_index(a, _HEADER_TTL % f"{_PERSON_A}, {_PERSON_B}") + html_b = _render_index(b, _HEADER_TTL % f"{_PERSON_B}, {_PERSON_A}") + def alice_first(h): + """True when Alice is rendered before Bob.""" + return h.index("Alice Example") < h.index("Bob Example") + assert alice_first(html_a) == alice_first(html_b) + + # =========================================================================== # Integration: real corpus, same loader pattern as test_owl_integrity. # =========================================================================== From b202ac867b2af3cbc41be39073bf0052959b83c2 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 12:33:52 +0200 Subject: [PATCH 04/21] feat(builder): configurable artefact name for root page and serializations --- README.md | 2 +- docs/usage/cli.md | 8 ++++++++ lode/builder.py | 38 ++++++++++++++++++++++++++++-------- lode/cli.py | 9 ++++++--- tests/test_static_builder.py | 24 ++++++++++++++++++++--- 5 files changed, 66 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 4915a17..5d47bfb 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ pip install "oc-lode[server]" ```bash # Build static documentation from an ontology URL or a local file -lode build --url --read-as [--out ./docs] [--lang en] [--imported] [--closure] +lode build --url --read-as [--out ./docs] [--lang en] [--artefact-name index] [--imported] [--closure] lode build --file --read-as [--out ./docs] # Run the web service (requires the [server] extra) diff --git a/docs/usage/cli.md b/docs/usage/cli.md index 2f154a6..7efddd6 100644 --- a/docs/usage/cli.md +++ b/docs/usage/cli.md @@ -29,6 +29,7 @@ lode build (--url URL | --file FILE) --read-as FORMAT [OPTIONS] | `--read-as` | yes | Artefact type: `owl`, `rdf`, `skos` | | `--out` | no | Output directory (default `./lode_output`) | | `--lang` | no | Language tag for labels (default `en`) | +| `--artefact-name` | no | File name (without extension) of the root page and its serializations (if omitted, falls back to `index`, so the site starts at `index.html`). Only letters, digits, `.`, `_` and `-` are allowed | | `--imported` | no | Load `owl:imports` at depth 1 | | `--closure` | no | Load the full `owl:imports` closure | | `--partial-import` | no | Load only the imported entities that are actually used | @@ -44,8 +45,15 @@ lode build --file ontology.ttl --read-as owl --out ./site # with Italian labels and imports lode build --url http://purl.org/spar/fabio --read-as owl --lang it --imported --out ./fabio + +# rename the root page: writes fabio.html, fabio.ttl, fabio.rdf, ... +lode build --url http://purl.org/spar/fabio --read-as owl --artefact-name fabio --out ./site ``` +The artefact name applies only to the root files. Resource pages keep the name +derived from their IRI, and their "Back to full documentation" button points to +`.html`. + ## Environment variables | Variable | Default | Description | diff --git a/lode/builder.py b/lode/builder.py index eaf76fc..58d0969 100644 --- a/lode/builder.py +++ b/lode/builder.py @@ -16,6 +16,7 @@ from lode.viewer.base_viewer import SERIALIZATION_FORMATS from lode.helpers.html_utils import minify as _minify from lode.models.model import Model +from lode.exceptions import ArtefactValidationError _SER = [(f["fmt"], f["ext"]) for f in SERIALIZATION_FORMATS] @@ -79,6 +80,21 @@ def _local_name(uri: str) -> str: """Return the part of an IRI after '#', or its last path segment.""" return uri.split('#', 1)[1] if '#' in uri else uri.rstrip('/').rsplit('/', 1)[-1] +def _check_artefact_name(name: str) -> str: + """Return `name` if it is a plain file stem, else raise. + + The name is user-chosen (CLI) and becomes file names in the output folder + and links in every page: path separators or '..' would let the root files + escape the output directory. + """ + if not re.fullmatch(r"[A-Za-z0-9._-]+", name) or set(name) == {"."}: + raise ArtefactValidationError( + "Invalid artefact name: use only letters, digits, '.', '_' and '-' (no extension)", + context={"artefact_name": name}, + ) + return name + + def _copy_static(out_dir: Path) -> None: """Copy the package's static assets into the output folder, once. @@ -89,16 +105,21 @@ def _copy_static(out_dir: Path) -> None: if static_src.exists() and not static_dst.exists(): shutil.copytree(static_src, static_dst) -def build_html(viewer, out_dir: Path, lang: str = "en", reader=None) -> None: +def build_html(viewer, out_dir: Path, lang: str = "en", reader=None, + artefact_name: str = "index") -> None: """Write the whole static site for a viewer into `out_dir`. - Writes index.html, the serializations of the artefact and, under resources/, + Writes the index page, the serializations of the artefact and, under resources/, one page plus serializations for each resource that belongs to the ontology namespace or has local triples. Blocking and disk-heavy; existing files are overwritten. A page is never written outside resources/, whatever the IRI. + `artefact_name` is the file stem of the root files (.html, .ttl, ...): + links back to the index use it, so a renamed index stays reachable. Resource + files are not affected, they are named after their IRI. """ from collections import defaultdict + artefact_name = _check_artefact_name(artefact_name) out_dir.mkdir(parents=True, exist_ok=True) _copy_static(out_dir) @@ -134,7 +155,7 @@ def resource_url_resource(uri, section=None): return uri rel = _rel_slug(uri, graph) if rel.rsplit("/", 1)[-1] == "": # namespace IRI - return "../../index.html" + return f"../../{artefact_name}.html" return f"../{rel}.html" def resource_url_index(uri, section=None): @@ -143,7 +164,7 @@ def resource_url_index(uri, section=None): return uri rel = _rel_slug(uri, graph) if rel.rsplit("/", 1)[-1] == "": - return "index.html" + return f"{artefact_name}.html" return f"resources/{rel}.html" env_index = _get_template_env(static_path="static") @@ -154,7 +175,7 @@ def resource_url_index(uri, section=None): out = reader._graph.serialize(format=fmt) if isinstance(out, bytes): out = out.decode("utf-8") - (out_dir / f"ontology.{ext}").write_text(out, encoding="utf-8") + (out_dir / f"{artefact_name}.{ext}").write_text(out, encoding="utf-8") template_index = env_index.get_template("viewer.html") template_resource = env_resource.get_template("viewer.html") @@ -166,9 +187,9 @@ def resource_url_index(uri, section=None): data["request"] = _FakeRequest("/") data["is_static"] = True data["resource_url"] = resource_url_index - data["export_base"] = "ontology" - (out_dir / "index.html").write_text(_minify(template_index.render(**data)), encoding="utf-8") - print(" [build] index.html") + data["export_base"] = artefact_name + (out_dir / f"{artefact_name}.html").write_text(_minify(template_index.render(**data)), encoding="utf-8") + print(f" [build] {artefact_name}.html") if not toc_config: return @@ -207,6 +228,7 @@ def resource_url_index(uri, section=None): data_r["is_static"] = True data_r["resource_url"] = resource_url_resource data_r["export_base"] = _local_name(uri) + data_r["artefact_name"] = artefact_name page.write_text(_minify(template_resource.render(**data_r)), encoding="utf-8") class _FakeRequest: diff --git a/lode/cli.py b/lode/cli.py index c061a72..c8ad198 100644 --- a/lode/cli.py +++ b/lode/cli.py @@ -1,8 +1,8 @@ # lode/cli.py """ lode serve [--port 8000] -lode build --url --read-as [--out ./docs] [--lang en] [--imported] [--closure] -lode build --file --read-as [--out ./docs] [--lang en] [--imported] [--closure] +lode build --url --read-as [--out ./docs] [--lang en] [--artefact-name index] [--imported] [--closure] +lode build --file --read-as [--out ./docs] [--lang en] [--artefact-name index] [--imported] [--closure] """ import argparse @@ -47,7 +47,8 @@ def cmd_build(args): closure=args.closure or None, partial_import=args.partial_import or None, ) - build_html(reader.get_viewer(), out_dir, lang=args.lang, reader=reader) + build_html(reader.get_viewer(), out_dir, lang=args.lang, reader=reader, + artefact_name=args.artefact_name) print(f"Done -> {out_dir}") @@ -72,6 +73,8 @@ def main(): p_build.add_argument("--read-as", required=True, choices=["owl", "rdf", "skos"]) p_build.add_argument("--out", default="./lode_output") p_build.add_argument("--lang", default="en") + p_build.add_argument("--artefact-name", default="index", + help="File stem of the root page and its serializations (default: index)") p_build.add_argument("--imported", action="store_true") p_build.add_argument("--closure", action="store_true") p_build.add_argument("--partial-import", action="store_true") diff --git a/tests/test_static_builder.py b/tests/test_static_builder.py index da900b6..d14e74f 100644 --- a/tests/test_static_builder.py +++ b/tests/test_static_builder.py @@ -15,6 +15,7 @@ from rdflib import Graph from lode.reader import Reader +from lode.exceptions import ArtefactValidationError from lode.builder import build_html, _rel_slug, _prefix_map from rdflib import URIRef @@ -51,7 +52,7 @@ def test_index_and_ontology_serializations(built): out = built["out"] assert (out / "index.html").exists() for ext in _EXTS: - assert (out / f"ontology.{ext}").exists(), f"missing ontology.{ext}" + assert (out / f"index.{ext}").exists(), f"missing index.{ext}" def test_resources_folder_created(built): @@ -59,9 +60,26 @@ def test_resources_folder_created(built): def test_index_export_base(built): - """Index header must export the whole graph (ontology.*), not a single resource.""" + """Index header must export the whole graph (index.*), not a single resource.""" html = (built["out"] / "index.html").read_text(encoding="utf-8") - assert "ontology.ttl" in html + assert "index.ttl" in html + + +def test_renamed_artefact(built, tmp_path): + """A renamed artefact renames root page and RDF; resource pages link back to it.""" + out = tmp_path / "site" + build_html(built["viewer"], out, reader=built["reader"], artefact_name="home") + assert (out / "home.html").exists() and (out / "home.ttl").exists() + assert not (out / "index.html").exists() + page = next((out / "resources").rglob("*.html")) + assert "../../home.html" in page.read_text(encoding="utf-8") + + +@pytest.mark.parametrize("bad", ["../x", "a/b", "..", "x.html "]) +def test_artefact_name_rejected(bad, tmp_path): + """Names with path parts or odd characters are rejected before any file is written.""" + with pytest.raises(ArtefactValidationError): + build_html(None, tmp_path / "s", artefact_name=bad) # --- INVARIANT: every HTML resource has all three serializations --- From 8dc084409aa9b33fd677d3f0cba8847570908f63 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 13:07:07 +0200 Subject: [PATCH 05/21] feat(export): export loaded artefact as triples, provenance always as quads --- lode/api.py | 10 +- lode/builder.py | 15 +- lode/reader/loader.py | 16 +- lode/reader/reader.py | 24 ++- lode/viewer/base_viewer.py | 51 ++++--- tests/test_modules.py | 304 ++++++++++++++----------------------- 6 files changed, 194 insertions(+), 226 deletions(-) diff --git a/lode/api.py b/lode/api.py index 0bbff78..abf38ea 100644 --- a/lode/api.py +++ b/lode/api.py @@ -46,7 +46,7 @@ from lode.reader import Reader from lode.reader import security from lode.exceptions import LODEError, ArtefactValidationError -from lode.viewer.base_viewer import formats_for +from lode.viewer.base_viewer import SERIALIZATION_FORMATS from lode.reader.provenance_graph import ProvenanceGraph from lode.helpers.rdf import iri_local_name @@ -210,7 +210,7 @@ def _load_url(url, read_as, imported, closure, partial_import, warnings, use_cac # cache hit: rebuild from the saved Turtle reader = Reader() reader.load_instances(path, read_as, imported=imported, closure=closure, partial_import=partial_import, - warnings=warnings) + warnings=warnings, source_name=url) return reader if not use_cache: # cache=false: drop the stale copy so the fresh fetch replaces it @@ -434,9 +434,9 @@ def extract_get( reader = _resolve_reader(read_as.value, url, upload_id, imported, closure, partial_import, warnings, use_cache=cache) - # Content negotiation: the available formats depend on the graph (quads only with modules) + # Content negotiation: triples of the loaded artefact only, quads are never negotiable accept = request.headers.get("accept", "text/html") - available = formats_for(reader._graph) + available = SERIALIZATION_FORMATS serial = None if format: @@ -456,7 +456,7 @@ def extract_get( serialized = reader.get_viewer().export_resource(resource, serial["fmt"]) filename = iri_local_name(resource) or "resource" else: - serialized = reader._graph.serialize(format=serial["fmt"]) + serialized = reader.get_main_graph().serialize(format=serial["fmt"]) filename = (iri_local_name(url) if url else "") or "graph" return Response(content=serialized, media_type=serial["mime"], headers={"Content-Disposition": f'inline; filename="{filename}.{serial["ext"]}"'}) diff --git a/lode/builder.py b/lode/builder.py index 58d0969..2975fdb 100644 --- a/lode/builder.py +++ b/lode/builder.py @@ -125,6 +125,15 @@ def build_html(viewer, out_dir: Path, lang: str = "en", reader=None, ontology_ns = viewer._get_ontology_ns() graph = reader._graph if reader else viewer.reader._graph + main_graph = viewer.reader.get_main_graph() + + def _in_main_graph(uri) -> bool: + """Tell whether the loaded artefact itself says something about this IRI. + + Resources described only by imported modules get no page: their export + would be empty, as exports carry the triples of the loaded artefact only. + """ + return (URIRef(str(uri)), None, None) in main_graph grouped = defaultdict(list) for inst in viewer.get_all_instances(): @@ -139,7 +148,7 @@ def build_html(viewer, out_dir: Path, lang: str = "en", reader=None, u = inst.get_has_identifier() if not u: continue - if not (u.startswith(ontology_ns) or viewer._has_local_triples(u)): + if not (u.startswith(ontology_ns) or _in_main_graph(u)): continue if _rel_slug(u, graph).rsplit("/", 1)[-1] == "": # namespace IRI, no local continue @@ -172,7 +181,7 @@ def resource_url_index(uri, section=None): if reader is not None: for fmt, ext in _SER: - out = reader._graph.serialize(format=fmt) + out = reader.get_main_graph().serialize(format=fmt) if isinstance(out, bytes): out = out.decode("utf-8") (out_dir / f"{artefact_name}.{ext}").write_text(out, encoding="utf-8") @@ -203,7 +212,7 @@ def resource_url_index(uri, section=None): if not uri: continue native = uri.startswith(ontology_ns) - if not (native or viewer._has_local_triples(uri)): + if not (native or _in_main_graph(uri)): continue rel = _rel_slug(uri, graph) diff --git a/lode/reader/loader.py b/lode/reader/loader.py index 8d25027..25c02e5 100644 --- a/lode/reader/loader.py +++ b/lode/reader/loader.py @@ -20,18 +20,23 @@ class Loader: """Load an RDF artefact into a graph, optionally together with its imports. The loaded graph is a plain Graph, or a ProvenanceGraph (one named graph per - ontology) when imported, closure or partial_import is requested. + ontology) when imported, closure or partial_import is requested. In both cases + `ontology_iri` names the loaded artefact. """ - def __init__(self, file_path: Optional[str] = None, imported=None, closure=None, partial_import=None): + def __init__(self, file_path: Optional[str] = None, imported=None, closure=None, partial_import=None, + source_name: Optional[str] = None): """Prepare the loader and, when `file_path` is given, load it immediately. `imported`, `closure` and `partial_import` select the module applied after loading (see lode.reader.modules); at most one of them is used. + `source_name` is the name of the artefact when it differs from `file_path` + (e.g. a cached copy of a URL): it names the graph if the ontology declares no IRI. """ self.graph = Graph() self.ontology_iri = None + self._source_name = source_name self._imported = imported self._closure = closure self.imported_uris = set() # needed to keep track of original model to document @@ -69,10 +74,15 @@ def load(self, source: str) -> None: context={"source": source} ) + name = self._source_name or source if self._imported or self._closure or self._partial_import: raw, self.graph = self.graph, ProvenanceGraph() - self.ontology_iri = self.graph.add_document(raw, source) + self.ontology_iri = self.graph.add_document(raw, name) self._apply_modules() + else: + # no modules: the graph stays plain, only its name is needed so that + # the provenance of an entity can still be written as a quad + self.ontology_iri = ProvenanceGraph.ontology_iri(self.graph, name) # ---------------------------------------------------------- # MODULES MAIN HANDLER diff --git a/lode/reader/reader.py b/lode/reader/reader.py index 8465f23..4d5a7e4 100644 --- a/lode/reader/reader.py +++ b/lode/reader/reader.py @@ -7,7 +7,8 @@ from lode.reader.loader import Loader from lode.reader.config_manager import get_configuration from lode.models import * -from rdflib import URIRef +from typing import Optional +from rdflib import Graph, URIRef from lode.reader.provenance_graph import ProvenanceGraph import logging @@ -70,17 +71,20 @@ def _prioritize_documented_values(self) -> None: value.sort(key=lambda v: _value_key(v) not in local) - def load_instances(self, graph_path: str, read_as: str, imported=None, closure=None, partial_import=None, warnings=False): + def load_instances(self, graph_path: str, read_as: str, imported=None, closure=None, partial_import=None, + warnings=False, source_name: Optional[str] = None): """Load an artefact and extract its model instances. `read_as` selects the configuration (owl, rdf, skos). Imports, closure and partial_import are forwarded to the Loader; `warnings` turns on the reader - warnings. Blocking: it may fetch remote documents. + warnings. `source_name` names the artefact when `graph_path` is only a local + copy of it. Blocking: it may fetch remote documents. """ self._warnings_enabled = warnings # 1. Generic parsing - loader = Loader(graph_path, imported=imported, closure=closure, partial_import=partial_import) + loader = Loader(graph_path, imported=imported, closure=closure, partial_import=partial_import, + source_name=source_name) self._graph = loader.get_graph() self._ontology_iri = loader.ontology_iri @@ -158,11 +162,21 @@ def get_all_triples_map(self) -> dict: return self._logic._triples_map return {} + def get_main_graph(self) -> Graph: + """Return the triples of the loaded artefact only, as a plain Graph view. + + Imported and partially imported ontologies are left out: this is what + exports and content negotiation must return. Without modules it is the + loaded graph itself. + """ + if isinstance(self._graph, ProvenanceGraph): + return self._graph.graph(self._ontology_iri) + return self._graph + def get_provenance_subgraph(self, instance): """Return the rdflib.Graph subgraph that provenanced `instance`.""" if self._logic and hasattr(self._logic, 'build_provenance_subgraph'): return self._logic.build_provenance_subgraph(instance) - from rdflib import Graph return Graph() diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 8170e05..457e786 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -14,27 +14,21 @@ from lode.reader.provenance_graph import ProvenanceGraph from lode.helpers.rdf import iri_local_name +# Export formats: triples of the loaded artefact only. SERIALIZATION_FORMATS = [ - {"label": "Turtle", "fmt": "turtle", "mime": "text/turtle", "ext": "ttl", "icon": "bi-filetype-raw"}, + {"label": "Turtle", "fmt": "turtle", "mime": "text/turtle", "ext": "ttl", "icon": "bi-filetype-raw"}, {"label": "RDF/XML", "fmt": "xml", "mime": "application/rdf+xml", "ext": "rdf", "icon": "bi-file-code"}, {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, {"label": "N-Triples", "fmt": "nt", "mime": "application/n-triples", "ext": "nt", "icon": "bi-file-text"}, ] +# Provenance formats: quads, the named graph of each triple is always shown. QUAD_SERIALIZATION_FORMATS = [ {"label": "TriG", "fmt": "trig", "mime": "application/trig", "ext": "trig", "icon": "bi-filetype-raw"}, {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, {"label": "N-Quads", "fmt": "nquads", "mime": "application/n-quads", "ext": "nq", "icon": "bi-file-text"}, ] -def formats_for(graph): - """Return the serialization formats available for a graph. - - Quad formats are offered only for a ProvenanceGraph, because only it keeps - the named graph of each triple. - """ - return QUAD_SERIALIZATION_FORMATS if isinstance(graph, ProvenanceGraph) else SERIALIZATION_FORMATS - class BaseViewer: """Base viewer to display the instances extracted by the Reader.""" @@ -67,20 +61,27 @@ def _has_local_triples(self, uri) -> bool: return (URIRef(str(uri)), None, None) in self.reader._graph def _formats(self): - """Return the serialization formats available for the loaded graph.""" - return formats_for(self.reader._graph) + """Return the export formats (triples): the same whatever modules are active.""" + return SERIALIZATION_FORMATS def _with_provenance(self, sub): - """With modules active, put the triples of `sub` back into their original named graphs.""" + """Return `sub` as quads, each triple in the named graph(s) it comes from. + + With modules active the graphs are the ones of the source ontologies; + without, every triple goes in the graph of the loaded artefact. + """ ds = self.reader._graph - if not isinstance(ds, ProvenanceGraph): - return sub out = ProvenanceGraph() for prefix, ns in ds.namespaces(): out.bind(prefix, ns) - for s, p, o in sub: - for *_, c in ds.quads((s, p, o, None)): - out.graph(c).add((s, p, o)) + if isinstance(ds, ProvenanceGraph): + for s, p, o in sub: + for *_, c in ds.quads((s, p, o, None)): + out.graph(c).add((s, p, o)) + else: + main = out.graph(self.reader._ontology_iri) + for t in sub: + main.add(t) return out def _is_internal(self, uri) -> bool: @@ -955,7 +956,7 @@ def _build_provenance_subgraph(self, instance) -> List[Dict[str, str]]: sub = self._with_provenance(sub) return [ {"label": f["label"], "code": self._safe_serialize(sub, f["fmt"])} - for f in self._formats() + for f in QUAD_SERIALIZATION_FORMATS ] @staticmethod @@ -970,14 +971,20 @@ def _safe_serialize(g, fmt: str) -> str: return f"# serialization error ({fmt}): {e}" def export_resource(self, resource_uri: str, fmt: str = "turtle") -> str: - """Serialize the subgraph of a single resource (the union of its punned instances).""" + """Serialize the subgraph of a single resource (the union of its punned instances). + + Only triples of the loaded artefact are exported; the ones that come from + imported modules belong to the provenance, not to the export. + """ g = Graph() for prefix, ns in self.reader._graph.namespaces(): g.bind(prefix, ns) + main = self.reader.get_main_graph() instances = self.get_instances_from_single_resource(resource_uri) if instances: inst_iter = instances if isinstance(instances, set) else [instances] for inst in inst_iter: - for t in self.reader.get_provenance_subgraph(inst): # already exists - g.add(t) - return self._safe_serialize(self._with_provenance(g), fmt) \ No newline at end of file + for t in self.reader.get_provenance_subgraph(inst): + if t in main: + g.add(t) + return self._safe_serialize(g, fmt) \ No newline at end of file diff --git a/tests/test_modules.py b/tests/test_modules.py index 8031110..99faac6 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -5,8 +5,9 @@ Each module (imported, closure, partial_import) loads external documents into the graph of the documented ontology. With any module active the graph is a ProvenanceGraph: every triple sits in the named graph of the document that asserts -it, and keeps that context through the URL cache, per-entity export and the -quad serializations (TriG, N-Quads, JSON-LD). +it, and keeps that context through the URL cache and the per-entity provenance +(quads: TriG, N-Quads, JSON-LD). Exports and content negotiation, instead, return +only the triples of the loaded artefact, with or without modules. Sections -------- @@ -16,7 +17,7 @@ 4. partial_import only the home definition of each mentioned external term 5. URL cache only the main document is cached; modules re-applied on a hit 6. Per-entity provenance (viewer) -7. HTTP API the same guarantees end-to-end, through serialization +7. HTTP API exports are triples of the loaded artefact only, end-to-end Fixtures -------- @@ -45,9 +46,8 @@ from lode.exceptions import ArtefactNotFoundError from lode.reader.loader import Loader from lode.reader.provenance_graph import ProvenanceGraph -from lode.viewer.base_viewer import ( - QUAD_SERIALIZATION_FORMATS, SERIALIZATION_FORMATS, BaseViewer, formats_for, -) +from lode.reader.reader import Reader +from lode.viewer.base_viewer import QUAD_SERIALIZATION_FORMATS, BaseViewer # ========================================================================== # FIXTURES @@ -374,13 +374,14 @@ def test_caching_the_union_breaks_provenance(self, main_path, tmp_path): class FakeReader: """Minimal reader for BaseViewer: only the graph and an empty instance cache.""" - def __init__(self, graph): + def __init__(self, graph, ontology_iri=None): self._graph = graph self._instance_cache = {} + self._ontology_iri = ontology_iri def entity_provenance(ds, subject): - """What an entity card exports: its triples, placed back in their origin graphs.""" + """What an entity card shows as provenance: its triples, placed in their origin graphs.""" sub = Graph() for t in ds.triples((subject, None, None)): sub.add(t) @@ -390,19 +391,25 @@ def entity_provenance(ds, subject): class TestEntityProvenance: """Formats offered, and each triple of an entity in the graph(s) it comes from.""" - def test_formats_without_modules_are_triple_formats(self): - assert formats_for(Graph()) is SERIALIZATION_FORMATS - - def test_formats_with_modules_are_quad_formats(self): - assert formats_for(ProvenanceGraph()) is QUAD_SERIALIZATION_FORMATS + def test_quad_formats_have_no_rdfxml(self): assert "xml" not in {f["fmt"] for f in QUAD_SERIALIZATION_FORMATS} - def test_without_modules_provenance_is_unchanged(self): + def test_without_modules_provenance_is_a_quad_in_the_artefact_graph(self): g = Graph() g.add((M.A, RDF.type, OWL.Class)) sub = Graph() sub.add((M.A, RDF.type, OWL.Class)) - assert BaseViewer(FakeReader(g))._with_provenance(sub) is sub + out = BaseViewer(FakeReader(g, MAIN))._with_provenance(sub) + assert isinstance(out, ProvenanceGraph) + assert graphs(out) == {MAIN} + + def test_card_provenance_names_the_graph_without_modules(self, main_path): + reader = Reader() + reader.load_instances(main_path, "owl") + viewer = reader.get_viewer() + codes = [f["code"] for inst in reader._instance_cache[H.T] + for f in viewer._build_provenance_subgraph(inst) if f["label"] == "TriG"] + assert codes and all(f"<{MAIN}>" in c for c in codes) def test_partial_import_term_spans_main_and_home(self, main_path): """home#T: label from main, definition from home, nothing from imp.""" @@ -440,12 +447,14 @@ def test_no_blank_graph_names(self, main_path, flag): # 7. HTTP API (end-to-end) # ========================================================================== # +# Exports and content negotiation return the triples of the loaded artefact, with or +# without modules: imported documents show up only in the provenance of each card. # Uploads go through the spool (spool.save) and are requested with -# GET /extract?upload_id=..., the same path as _resolve_reader. Quad serializations -# are parsed back into a Dataset (default_union=True, so objects()/subjects()/`in` -# see the named graphs) to check that contexts survive serialization. +# GET /extract?upload_id=..., the same path as _resolve_reader. -RDFLIB_FMT = {"trig": "trig", "nq": "nquads", "jsonld": "json-ld"} +TRIPLE_FORMATS = {"ttl": "turtle", "nt": "nt", "rdf": "xml", "jsonld": "json-ld"} +QUAD_EXTS = ["trig", "nq"] +ALL_FLAGS = [None, *MODULES] @pytest.fixture(scope="module") @@ -468,6 +477,11 @@ def _flags(flags) -> dict: return {k: "true" for k, v in flags.items() if v} +def flags_of(flag) -> dict: + """Request flags for one module, or none.""" + return {flag: True} if flag else {} + + def get(client, token, fmt, resource=None, **flags): """GET /extract on an upload, with an explicit ?format=.""" params = {"read_as": "owl", "upload_id": token, "format": fmt, **_flags(flags)} @@ -494,16 +508,11 @@ def get_url(client, url, fmt=None, resource=None, cache=False, **flags): return client.get("/extract", params=params) -def as_dataset(resp, fmt) -> Dataset: +def as_graph(resp, fmt) -> Graph: + """Parse an export response back into a plain Graph (a quad format would not parse here).""" assert resp.status_code == 200, resp.text[:500] assert "text/html" not in resp.headers.get("content-type", ""), f"{fmt}: got HTML instead of RDF" - ds = Dataset(default_union=True) - ds.parse(data=resp.text, format=RDFLIB_FMT[fmt]) - return ds - - -def default_graph_is_empty(ds) -> bool: - return len(ds.graph(DATASET_DEFAULT_GRAPH_ID)) == 0 + return Graph().parse(data=resp.text, format=TRIPLE_FORMATS[fmt]) def filename(resp) -> str: @@ -512,73 +521,29 @@ def filename(resp) -> str: return cd.split('filename="', 1)[1].rstrip('"') -class TestUploadWithoutModules: - """No modules: plain graph, no quad formats.""" - - @pytest.mark.parametrize("fmt", ["trig", "nq"]) - def test_quad_formats_rejected(self, client, fmt): - assert get(client, upload(MAIN_TTL), fmt).status_code == 406 - - @pytest.mark.parametrize("fmt", ["ttl", "nt", "rdf", "jsonld"]) - def test_triple_formats_available(self, client, fmt): - assert get(client, upload(MAIN_TTL), fmt).status_code == 200 - - def test_html_offers_triple_formats_only(self, client): - html = client.post("/extract", data={"read_as": "owl"}, - files={"file": ("main.ttl", MAIN_TTL, "text/turtle")}).text - assert "N-Triples" in html - assert "TriG" not in html and "N-Quads" not in html - - -class TestUploadImportedClosure: - """Formal imports through the API: graphs survive serialization.""" - - def test_html_offers_quad_formats(self, client): - html = client.post("/extract", data={"read_as": "owl", "imported": "true"}, - files={"file": ("main.ttl", MAIN_TTL, "text/turtle")}).text - assert "TriG" in html and "N-Quads" in html - assert "N-Triples" not in html and "RDF/XML" not in html - - @pytest.mark.parametrize("fmt", ["trig", "nq", "jsonld"]) - def test_imported_graphs_survive_serialization(self, client, fmt): - ds = as_dataset(get(client, upload(MAIN_TTL), fmt, imported=True), fmt) - assert graphs(ds) == {MAIN, IMP} - assert default_graph_is_empty(ds) - assert contexts(ds, (I.I, RDF.type, OWL.Class)) == {IMP} - assert (D.D, None, None) not in ds - - def test_upload_context_is_declared_ontology_not_spool_path(self, client): - ds = as_dataset(get(client, upload(MAIN_TTL), "trig", imported=True), "trig") - assert not any(str(g).startswith("file:") for g in graphs(ds)) - - def test_closure_fallback_context_is_url(self, client): - ds = as_dataset(get(client, upload(MAIN_TTL), "nq", closure=True), "nq") - assert graphs(ds) == {MAIN, IMP, DEEP} - assert contexts(ds, (D.D, RDF.type, OWL.Class)) == {DEEP} - - def test_imported_redefinition_stays_in_imported_graph(self, client): - ds = as_dataset(get(client, upload(MAIN_TTL), "trig", imported=True), "trig") - assert contexts(ds, (H.T, RDFS.comment, Literal("T redefined by imp"))) == {IMP} - - -class TestUploadPartialImport: - """partial_import through the API: same boundary as TestPartialImport.""" +class TestExportIsLoadedArtefactOnly: + """Whatever the modules, an export holds the triples of the loaded document and nothing else.""" - @pytest.fixture - def ds(self, client): - return as_dataset(get(client, upload(MAIN_TTL), "trig", partial_import=True), "trig") + @pytest.mark.parametrize("flag", ALL_FLAGS) + @pytest.mark.parametrize("fmt", list(TRIPLE_FORMATS)) + def test_whole_export_is_the_main_document(self, client, fmt, flag): + g = as_graph(get(client, upload(MAIN_TTL), fmt, **flags_of(flag)), fmt) + assert isomorphic(g, doc("main")) - def test_graphs_are_main_and_homes_only(self, ds): - assert graphs(ds) == {MAIN, HOME, VER} + @pytest.mark.parametrize("flag", ALL_FLAGS) + @pytest.mark.parametrize("fmt", QUAD_EXTS) + def test_quad_formats_rejected(self, client, fmt, flag): + assert get(client, upload(MAIN_TTL), fmt, **flags_of(flag)).status_code == 406 - def test_both_definitions_kept_with_provenance(self, ds): - """main restates the label of home#T: both labels kept, each in its own graph.""" - assert contexts(ds, (H.T, RDFS.label, Literal("T from main", lang="en"))) == {MAIN} - assert contexts(ds, (H.T, RDFS.label, Literal("T from home", lang="en"))) == {HOME} + def test_resource_export_has_main_triples_only(self, client): + """home#T: the label restated by main is exported, the definition of home is not.""" + g = as_graph(get(client, upload(MAIN_TTL), "ttl", resource=H.T, partial_import=True), "ttl") + assert ground(g) <= ground(doc("main")) + assert (H.T, RDFS.label, Literal("T from main", lang="en")) in g + assert (H.T, RDFS.comment, Literal("T defined by home")) not in g def test_documented_values_come_first(self, main_path): """The Reader puts main's label of home#T before home's.""" - from lode.reader.reader import Reader reader = Reader() reader.load_instances(graph_path=main_path, read_as="owl", partial_import=True) for inst in reader._instance_cache[H.T]: @@ -586,71 +551,43 @@ def test_documented_values_come_first(self, main_path): if labels: assert labels[0] == "T from main", labels - def test_home_definition_in_home_graph(self, ds): - assert contexts(ds, (H.T, RDFS.comment, Literal("T defined by home"))) == {HOME} - - def test_third_party_redefinition_absent(self, ds): - assert (H.T, RDFS.comment, Literal("T redefined by imp")) not in ds - assert (H.T, OWL.equivalentClass, I.I) not in ds - - def test_restriction_blank_nodes_in_home_graph(self, ds): - (restr,) = [o for o in ds.objects(H.T, RDFS.subClassOf) if isinstance(o, BNode)] - for t in ds.triples((restr, None, None)): - assert contexts(ds, t) == {HOME} - def test_versioned_home_found_via_dereferenced_document(self, ds): - assert contexts(ds, (V.V, RDF.type, OWL.Class)) == {VER} - - def test_unreachable_home_gives_no_external_definition(self, ds): - assert set(ds.predicate_objects(X.X)) == {(RDFS.comment, Literal("X described by main"))} - - def test_external_ontology_headers_absent(self, ds): - assert set(ds.subjects(RDF.type, OWL.Ontology)) == {MAIN} +class TestHtmlOffers: + """The page offers triples to export and quads as provenance, with or without modules.""" - @pytest.mark.parametrize("fmt", ["trig", "nq", "jsonld"]) - def test_resource_export_has_origin_graphs(self, client, fmt): - ds = as_dataset(get(client, upload(MAIN_TTL), fmt, resource=H.T, partial_import=True), fmt) - assert graphs(ds) == {MAIN, HOME} - assert default_graph_is_empty(ds) - assert contexts(ds, (H.T, RDF.type, OWL.Class)) == {HOME} + @pytest.mark.parametrize("flag", ALL_FLAGS) + def test_export_in_triples_provenance_in_quads(self, client, flag): + html = client.post("/extract", data={"read_as": "owl", **_flags(flags_of(flag))}, + files={"file": ("main.ttl", MAIN_TTL, "text/turtle")}).text + assert "N-Triples" in html and "RDF/XML" in html + assert "TriG" in html and "N-Quads" in html class TestDownloadAccept: """Accept is a preference: an unavailable format falls back to HTML (406 only for an explicit ?format=).""" - @pytest.mark.parametrize("mime,fmt", [("application/trig", "trig"), - ("application/n-quads", "nq"), - ("application/ld+json", "jsonld")]) - def test_quad_mime_with_modules(self, client, mime, fmt): - resp = get_accept(client, upload(MAIN_TTL), mime, imported=True) - assert resp.headers["content-type"].startswith(mime) - assert graphs(as_dataset(resp, fmt)) == {MAIN, IMP} - - def test_first_available_mime_wins(self, client): - resp = get_accept(client, upload(MAIN_TTL), "application/n-quads;q=0.9, text/html;q=0.8", - imported=True) - assert resp.headers["content-type"].startswith("application/n-quads") - - def test_resource_export_via_accept(self, client): - resp = get_accept(client, upload(MAIN_TTL), "application/trig", resource=H.T, partial_import=True) - assert graphs(as_dataset(resp, "trig")) == {MAIN, HOME} - - def test_quad_mime_without_modules_falls_back_to_html(self, client): - resp = get_accept(client, upload(MAIN_TTL), "application/trig") + @pytest.mark.parametrize("flag", ALL_FLAGS) + @pytest.mark.parametrize("mime", ["application/trig", "application/n-quads"]) + def test_quad_mime_falls_back_to_html(self, client, mime, flag): + resp = get_accept(client, upload(MAIN_TTL), mime, **flags_of(flag)) assert resp.status_code == 200 assert resp.headers["content-type"].startswith("text/html") - def test_triple_mime_without_modules(self, client): - resp = get_accept(client, upload(MAIN_TTL), "text/turtle") + @pytest.mark.parametrize("flag", ALL_FLAGS) + def test_triple_mime(self, client, flag): + resp = get_accept(client, upload(MAIN_TTL), "text/turtle", **flags_of(flag)) assert resp.headers["content-type"].startswith("text/turtle") - assert len(Graph().parse(data=resp.text, format="turtle")) > 0 + assert isomorphic(as_graph(resp, "ttl"), doc("main")) - def test_triple_mime_with_modules_falls_back_to_html(self, client): - """Current behaviour: with modules, Turtle is not offered. Update this test if the - union is ever served as Turtle alongside the quad formats.""" - resp = get_accept(client, upload(MAIN_TTL), "text/turtle", imported=True) - assert resp.headers["content-type"].startswith("text/html") + def test_first_available_mime_wins(self, client): + resp = get_accept(client, upload(MAIN_TTL), "application/n-quads;q=0.9, text/turtle;q=0.8", + imported=True) + assert resp.headers["content-type"].startswith("text/turtle") + + def test_resource_export_via_accept(self, client): + resp = get_accept(client, upload(MAIN_TTL), "text/turtle", resource=H.T, partial_import=True) + assert (H.T, RDFS.comment, Literal("T defined by home")) not in as_graph(resp, "ttl") def test_browser_accept_gets_html(self, client): resp = get_accept(client, upload(MAIN_TTL), "text/html,application/xhtml+xml,*/*;q=0.8", @@ -662,73 +599,64 @@ class TestDownloadFilename: """Content-Disposition file name: resource -> local name; graph -> last URL segment, or 'graph' for uploads.""" - @pytest.mark.parametrize("fmt", ["trig", "nq", "jsonld"]) + @pytest.mark.parametrize("fmt", ["ttl", "jsonld"]) def test_upload_whole_graph(self, client, fmt): assert filename(get(client, upload(MAIN_TTL), fmt, imported=True)) == f"graph.{fmt}" - @pytest.mark.parametrize("fmt", ["trig", "nq"]) - def test_resource_uses_local_name(self, client, fmt): - resp = get(client, upload(MAIN_TTL), fmt, resource=H.T, partial_import=True) - assert filename(resp) == f"T.{fmt}" + def test_resource_uses_local_name(self, client): + resp = get(client, upload(MAIN_TTL), "ttl", resource=H.T, partial_import=True) + assert filename(resp) == "T.ttl" def test_url_whole_graph_uses_last_segment(self, client, served_main): - assert filename(get_url(client, served_main, "trig", imported=True)) == "main.trig" + assert filename(get_url(client, served_main, "ttl", imported=True)) == "main.ttl" def test_url_trailing_slash(self, client, served_main): - assert filename(get_url(client, served_main + "/", "trig", imported=True)) == "main.trig" - - def test_triple_format_without_modules(self, client): - assert filename(get(client, upload(MAIN_TTL), "ttl")) == "graph.ttl" + assert filename(get_url(client, served_main + "/", "ttl", imported=True)) == "main.ttl" class TestDownloadUrl: """?url= path: fetch of the main document plus the spool cache.""" - def test_imported_graphs(self, client, served_main): - ds = as_dataset(get_url(client, served_main, "trig", imported=True), "trig") - assert graphs(ds) == {MAIN, IMP} - assert contexts(ds, (I.I, RDF.type, OWL.Class)) == {IMP} + @pytest.mark.parametrize("flag", ALL_FLAGS) + def test_export_is_the_main_document(self, client, served_main, flag): + g = as_graph(get_url(client, served_main, "ttl", **flags_of(flag)), "ttl") + assert isomorphic(g, doc("main")) - def test_partial_import_homes(self, client, served_main): - ds = as_dataset(get_url(client, served_main, "nq", partial_import=True), "nq") - assert graphs(ds) == {MAIN, HOME, VER} - assert (H.T, RDFS.comment, Literal("T redefined by imp")) not in ds - - def test_quad_format_without_modules_is_406(self, client, served_main): - assert get_url(client, served_main, "trig").status_code == 406 + @pytest.mark.parametrize("flag", ALL_FLAGS) + def test_quad_format_is_406(self, client, served_main, flag): + assert get_url(client, served_main, "trig", **flags_of(flag)).status_code == 406 @pytest.mark.parametrize("flag", MODULES) def test_cache_stores_main_document_only(self, client, served_main, flag): """Regression: the cache held the enriched union, and on a hit the imported triples ended up in the main graph.""" - get_url(client, served_main, "trig", cache=False, **{flag: True}) + get_url(client, served_main, "ttl", cache=False, **{flag: True}) token = api._url_token(served_main, "owl", *(True if f == flag else None for f in MODULES)) cached = Graph().parse(spool.get_path(token), format="turtle") - assert isomorphic(cached, Graph().parse(data=MAIN_TTL, format="turtle")) - - @pytest.mark.parametrize("flag", MODULES) - def test_cache_hit_preserves_provenance(self, client, served_main, flag): - fresh = as_dataset(get_url(client, served_main, "trig", cache=False, **{flag: True}), "trig") - hit = as_dataset(get_url(client, served_main, "trig", cache=True, **{flag: True}), "trig") - assert graphs(hit) == graphs(fresh) - for g in graphs(fresh): - assert isomorphic(hit.graph(g), fresh.graph(g)), g - - -class TestUploadEdgeCases: - def test_upload_without_ontology_uses_spool_path(self, client): - """Known and accepted: without owl:Ontology the context is the spool path.""" - ds = as_dataset(get(client, upload(DOCS["http://ex.org/anon"]), "trig", imported=True), "trig") - local = {g for g in graphs(ds) if str(g).startswith("file:")} - assert len(local) == 1 - assert contexts(ds, (URIRef("http://ex.org/anon#A"), RDF.type, OWL.Class)) == local + assert isomorphic(cached, doc("main")) @pytest.mark.parametrize("flag", MODULES) - def test_same_upload_reloaded_gives_same_quads(self, client, flag): - token = upload(MAIN_TTL) - a = as_dataset(get(client, token, "trig", **{flag: True}), "trig") - b = as_dataset(get(client, token, "trig", **{flag: True}), "trig") - assert graphs(a) == graphs(b) - for g in graphs(a): - assert isomorphic(a.graph(g), b.graph(g)), g - \ No newline at end of file + def test_cache_hit_gives_the_same_export(self, client, served_main, flag): + fresh = as_graph(get_url(client, served_main, "ttl", cache=False, **{flag: True}), "ttl") + hit = as_graph(get_url(client, served_main, "ttl", cache=True, **{flag: True}), "ttl") + assert isomorphic(hit, fresh) + + def test_cache_hit_keeps_the_url_as_graph_name(self, monkeypatch): + """Without a declared owl:Ontology the graph is named after the URL, not the spool copy.""" + monkeypatch.setattr(security, "check_url_safe", lambda url: None) + url = "http://ex.org/anon" + for use_cache in (False, True): + reader = api._load_url(url, "owl", None, None, None, False, use_cache=use_cache) + assert reader._ontology_iri == URIRef(url) + + +class TestSourceName: + """`source_name` names the graph when the ontology declares no IRI.""" + + def test_names_the_graph_without_declared_ontology(self, tmp_path): + p = tmp_path / "x.ttl" + p.write_text(" a .", encoding="utf-8") + assert Loader(str(p), source_name="http://ex.org/x.ttl").ontology_iri == URIRef("http://ex.org/x.ttl") + + def test_declared_ontology_wins(self, main_path): + assert Loader(main_path, source_name="http://ex.org/other").ontology_iri == MAIN \ No newline at end of file From df7f805a105c22a24aa8ae781a403fe2fb7fc0b1 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 15:43:21 +0200 Subject: [PATCH 06/21] fix(viewer): deterministic order for ontology header metadata --- lode/viewer/base_viewer.py | 42 ++++++++++++++++++- ...del_annotations_deterministic_sorting.yaml | 42 +++++++++++++++++++ 2 files changed, 82 insertions(+), 2 deletions(-) create mode 100644 lode/viewer/config/model_annotations_deterministic_sorting.yaml diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 457e786..86c9c34 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -5,7 +5,10 @@ """ import hashlib import re +from pathlib import Path from typing import Dict, List, Optional, Tuple + +import yaml from lode.models import Literal, Model, Resource, Statement import urllib.parse @@ -29,6 +32,41 @@ {"label": "N-Quads", "fmt": "nquads", "mime": "application/n-quads", "ext": "nq", "icon": "bi-file-text"}, ] +_ANNOTATION_ORDER_FILE = Path(__file__).parent / "config" / "model_annotations_deterministic_sorting.yaml" + + +def _normalize_annotation_key(key: str) -> str: + """Reduce a displayed metadata key to a comparable form. + + Case, spaces, underscores and hyphens are dropped so that 'version info', + 'versionInfo' and 'version_info' land in the same slot of the order list. + """ + return re.sub(r"[\s_\-]+", "", key.lower()) + + +def _load_annotation_order() -> Dict[str, int]: + """Read the YAML order list and map each normalized key to its rank. + + Loaded once at import time. A missing or malformed file raises: a silent + fallback would make the page order depend on the environment again. + """ + with open(_ANNOTATION_ORDER_FILE, encoding="utf-8") as f: + order = yaml.safe_load(f)["order"] + return {_normalize_annotation_key(k): i for i, k in enumerate(order)} + + +_ANNOTATION_RANK = _load_annotation_order() + + +def _annotation_sort_key(key: str) -> Tuple[int, str]: + """Sort key for a header metadata entry: configured rank, then alphabetical. + + Unlisted keys get a rank past the last listed one, so they follow the known + ones and stay in alphabetical order among themselves. + """ + return (_ANNOTATION_RANK.get(_normalize_annotation_key(key), len(_ANNOTATION_RANK)), key.lower()) + + class BaseViewer: """Base viewer to display the instances extracted by the Reader.""" @@ -457,9 +495,9 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None # 9. Statements data.update(self._format_statement(all_instances, ontology_model, language)) - # Alphabetical order on all the metadata (uri/label first) + # uri/label first, then the order from the YAML, then alphabetical pinned = ['uri', 'label'] - rest = sorted(k for k in data if k not in pinned) + rest = sorted((k for k in data if k not in pinned), key=_annotation_sort_key) data = {k: data[k] for k in pinned if k in data} | {k: data[k] for k in rest} return data diff --git a/lode/viewer/config/model_annotations_deterministic_sorting.yaml b/lode/viewer/config/model_annotations_deterministic_sorting.yaml new file mode 100644 index 0000000..6edb35c --- /dev/null +++ b/lode/viewer/config/model_annotations_deterministic_sorting.yaml @@ -0,0 +1,42 @@ +# Deterministic display order of the ontology header metadata. +# Each entry is matched against the displayed key, ignoring case, spaces, +# underscores and hyphens, so dc:creator and dcterms:creator share one slot. +# Keys not listed here come after these, in alphabetical order. +order: + # versioning + - version info + - version + - prior version + - replaces + - is version of + - imports + - backward compatible with + - incompatible with + - top concept + - changes + # title and description + - title + - alternative + - description + - abstract + - comment + - keywords + # responsibility + - author + - creator + - contributor + - publisher + - rights holder + - funder + # dates + - created + - issued + - modified + - date + # rights + - license + - rights + # references + - source + - see also + - is defined by \ No newline at end of file From dab07df932eedd696f2d1f6a2aeac9911fe56869 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 15:45:39 +0200 Subject: [PATCH 07/21] fix(viewer): deterministic sorting for statements in cards - alphabetical order --- lode/viewer/base_viewer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 86c9c34..e612cea 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -692,7 +692,7 @@ def _format_statement(self, instances, target_instance, language=None) -> Dict: if values: statements[pred_label] = sorted(values, key=lambda v: (str(v.get('nested')), v['text'].lower())) - return statements + return dict(sorted(statements.items(), key=lambda kv: kv[0].lower())) @staticmethod def _clean_name(self, name: str) -> str: From 8471d4fbd6ba03da76cf5cfa654d4b64bf7e8299 Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 16:27:27 +0200 Subject: [PATCH 08/21] refactor(viewer): per-format YAML config, shared helpers and per-format card + configurable vocabulary --- lode/static/style.css | 118 ++++++++- .../{_entity_card.html => _card_owl.html} | 0 lode/templates/_card_skos.html | 50 ++++ lode/templates/owl_viewer.html | 133 ---------- lode/templates/skos_viewer.html | 245 ------------------ lode/templates/viewer.html | 2 +- lode/viewer/base_viewer.py | 232 +++++------------ lode/viewer/config/owl_viewer.yaml | 49 ++++ lode/viewer/config/rdf_viewer.yaml | 39 +++ lode/viewer/config/skos_viewer.yaml | 17 ++ lode/viewer/helpers.py | 190 ++++++++++++++ lode/viewer/owl_viewer.py | 43 +-- lode/viewer/rdf_viewer.py | 41 +-- lode/viewer/skos_viewer.py | 45 +--- 14 files changed, 533 insertions(+), 671 deletions(-) rename lode/templates/{_entity_card.html => _card_owl.html} (100%) create mode 100644 lode/templates/_card_skos.html delete mode 100644 lode/templates/owl_viewer.html delete mode 100644 lode/templates/skos_viewer.html create mode 100644 lode/viewer/config/owl_viewer.yaml create mode 100644 lode/viewer/config/rdf_viewer.yaml create mode 100644 lode/viewer/config/skos_viewer.yaml create mode 100644 lode/viewer/helpers.py diff --git a/lode/static/style.css b/lode/static/style.css index ac30622..55996f3 100644 --- a/lode/static/style.css +++ b/lode/static/style.css @@ -914,4 +914,120 @@ body.toc-sidebar-closed { margin-left: 5rem; } } .toggle-slider.url-mode { left: 0; width: 50%; } -.toggle-slider.file-mode { left: 50%; width: 50%; } \ No newline at end of file +.toggle-slider.file-mode { left: 50%; width: 50%; } + +/* ===== SKOS entity card (templates/_card_skos.html) ===== */ +/* LODE-style entity card */ +.entity-card { + border: 1px solid #dee2e6; + border-radius: 0.5rem; + margin-bottom: 1.5rem; + background: #fff; +} + +.entity-header { + background: #f8f9fa; + padding: 1rem 1.25rem; + border-bottom: 1px solid #dee2e6; + border-radius: 0.5rem 0.5rem 0 0; +} + +.entity-label { + font-size: 1.25rem; + font-weight: 600; + color: #0d6efd; + margin: 0; +} + +.entity-label a { + color: inherit; + text-decoration: none; +} + +.entity-label a:hover { + text-decoration: underline; +} + +.back-to-toc { + font-size: 0.8rem; + color: #6c757d; +} + +.back-to-toc a { + color: #6c757d; + text-decoration: none; +} + +.back-to-toc a:hover { + color: #0d6efd; +} + +.entity-uri { + font-family: monospace; + font-size: 0.85rem; + color: #495057; + word-break: break-all; +} + +.entity-body { + padding: 1.25rem; +} + +.entity-definition { + font-size: 1rem; + color: #212529; + margin-bottom: 1.25rem; + line-height: 1.6; +} + +/* Semantic sections */ +.semantic-section { + margin-bottom: 0.75rem; +} + +.semantic-title { + font-weight: 600; + color: #495057; + margin-right: 0.5rem; +} + +.semantic-items { + display: inline; +} + +.semantic-item { + color: #0d6efd; + text-decoration: none; +} + +.semantic-item:hover { + text-decoration: underline; +} + +.semantic-item.external { + color: #6f42c1; +} + +.semantic-item.external::after { + content: ' β†—'; + font-size: 0.75em; +} + +.semantic-separator { + color: #6c757d; + margin: 0 0.25rem; +} + +/* Subscript style for type indicators */ +.type-indicator { + font-size: 0.7rem; + vertical-align: sub; + color: #6c757d; + margin-left: 0.1rem; +} + +/* Anchor offset */ +.anchor-offset { + scroll-margin-top: 1rem; +} + diff --git a/lode/templates/_entity_card.html b/lode/templates/_card_owl.html similarity index 100% rename from lode/templates/_entity_card.html rename to lode/templates/_card_owl.html diff --git a/lode/templates/_card_skos.html b/lode/templates/_card_skos.html new file mode 100644 index 0000000..d43effd --- /dev/null +++ b/lode/templates/_card_skos.html @@ -0,0 +1,50 @@ +
+
+
+
+

+ {{ item.label }}c +

+ {% if section.id %} + + back to ToC or {{ section.title }} ToC + + {% endif %} +
+ + {{ item.type }} + +
+
+ IRI: {{ item.uri }} +
+
+ +
+ {% if item.definition %} +

{{ item.definition }}

+ {% endif %} + + {% if item.semantic_sections %} + {% for sem_section in item.semantic_sections %} +
+ {{ sem_section.title }} + + {% for concept in sem_section.concepts %} + {% if concept.external %} + {{ concept.label }} + {% else %} + {{ concept.label }}c + {% endif %} + {% if not loop.last %},{% endif %} + {% endfor %} + +
+ {% endfor %} + {% endif %} + + {% if not item.definition and not item.semantic_sections %} +

No definition or semantic relations defined.

+ {% endif %} +
+
diff --git a/lode/templates/owl_viewer.html b/lode/templates/owl_viewer.html deleted file mode 100644 index 42d0ef0..0000000 --- a/lode/templates/owl_viewer.html +++ /dev/null @@ -1,133 +0,0 @@ - - - - - - LODE 2.0 - Semantic Artefact Viewer - - - - -
-
-

LODE 2.0

-

Semantic Artefact Documentation

-
- - {% if error %} - - - {% else %} - - {% if grouped_view and sections %} -
- -
-
-
Table of Contents
-
- {% for section in sections %} - - {{ section.title }} - {{ section.entities|length }} - - {% endfor %} -
-
-
-
- - {% for section in sections %} -
-

- {{ section.title }} - {{ section.entities|length }} -

- -
-
-

Jump to:

-
- {% for item in section.entities %} - - {{ item.label }} - - {% endfor %} -
-
-
- - {% for item in section.entities %} -
-
-

{{ item.label }}

- - {{ item.type }} - -
- -
-
- URI -
- {{ item.uri }} - β†— -
-
- -
- {% if item.relations %} - {% for rel_name, rel_value in item.relations.items() %} -
-
-
- {{ rel_name }} -
-
- {% if rel_value is iterable and rel_value is not string %} -
    - {% for val in rel_value %} -
  • {{ val }}
    • - {% endfor %} -
- {% else %} - {{ rel_value }} - {% endif %} -
-
-
- {% endfor %} - {% else %} -
-

No attributes or relations defined.

-
- {% endif %} -
-
-
- {% if item.statements != [] %} - {% for statement in item.statements %} -
{{ statement.predicate }}: {{ statement.object }}
- {% endfor %} - {% endif %} -
-
- {% endfor %} -
- {% endfor %} - - {% if single_resource %} -
- ← Back to Index -
- {% endif %} - - {% endif %} {% endif %} - -
- - \ No newline at end of file diff --git a/lode/templates/skos_viewer.html b/lode/templates/skos_viewer.html deleted file mode 100644 index a512bf1..0000000 --- a/lode/templates/skos_viewer.html +++ /dev/null @@ -1,245 +0,0 @@ - - - - - - LODE 2.0 - SKOS Viewer - - - - - -
-
-

LODE 2.0

-

SKOS Vocabulary Documentation

-
- - {% if error %} - - - {% else %} - - {% if grouped_view and sections %} - -
-
-
Table of Contents
-
- {% for section in sections %} - - {{ section.title }} - {{ section.entities|length }} - - {% endfor %} -
-
-
- - - {% for section in sections %} -
-

- {{ section.title }} - {{ section.entities|length }} -

- - -
-
-

Jump to:

-
- {% for item in section.entities %} - - {{ item.label }} - - {% endfor %} -
-
-
- - - {% for item in section.entities %} -
-
-
- - - {{ item.type }} - -
-
- IRI: {{ item.uri }} -
-
- -
- {% if item.definition %} -

{{ item.definition }}

- {% endif %} - - {% if item.semantic_sections %} - {% for sem_section in item.semantic_sections %} -
- {{ sem_section.title }} - - {% for concept in sem_section.concepts %} - {% if concept.external %} - {{ concept.label }} - {% else %} - {{ concept.label }}c - {% endif %} - {% if not loop.last %},{% endif %} - {% endfor %} - -
- {% endfor %} - {% endif %} - - {% if not item.definition and not item.semantic_sections %} -

No definition or semantic relations defined.

- {% endif %} -
-
- {% endfor %} -
- {% endfor %} - - {% endif %} - - {% if single_resource %} -
- ← Back to Index -
- {% endif %} - - {% endif %} -
- - - - \ No newline at end of file diff --git a/lode/templates/viewer.html b/lode/templates/viewer.html index e6d4cb5..9acd7aa 100644 --- a/lode/templates/viewer.html +++ b/lode/templates/viewer.html @@ -264,7 +264,7 @@

{% for item in section.entities %} - {% include '_entity_card.html' %} + {% include card_template %} {% endfor %}

diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index e612cea..6ea2112 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -4,78 +4,57 @@ and display names. It also serializes the provenance of each entity. """ import hashlib -import re -from pathlib import Path from typing import Dict, List, Optional, Tuple -import yaml from lode.models import Literal, Model, Resource, Statement -import urllib.parse from rdflib import Graph, URIRef, BNode, Literal as RDFlibLiteral from lode.reader.provenance_graph import ProvenanceGraph from lode.helpers.rdf import iri_local_name -# Export formats: triples of the loaded artefact only. -SERIALIZATION_FORMATS = [ - {"label": "Turtle", "fmt": "turtle", "mime": "text/turtle", "ext": "ttl", "icon": "bi-filetype-raw"}, - {"label": "RDF/XML", "fmt": "xml", "mime": "application/rdf+xml", "ext": "rdf", "icon": "bi-file-code"}, - {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, - {"label": "N-Triples", "fmt": "nt", "mime": "application/n-triples", "ext": "nt", "icon": "bi-file-text"}, -] +from lode.viewer.helpers import ( + QUAD_SERIALIZATION_FORMATS, + SERIALIZATION_FORMATS, + annotation_sort_key, + clean_name, + is_likely_ontology, + load_viewer_config, + safe_serialize, +) -# Provenance formats: quads, the named graph of each triple is always shown. -QUAD_SERIALIZATION_FORMATS = [ - {"label": "TriG", "fmt": "trig", "mime": "application/trig", "ext": "trig", "icon": "bi-filetype-raw"}, - {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, - {"label": "N-Quads", "fmt": "nquads", "mime": "application/n-quads", "ext": "nq", "icon": "bi-file-text"}, -] -_ANNOTATION_ORDER_FILE = Path(__file__).parent / "config" / "model_annotations_deterministic_sorting.yaml" - - -def _normalize_annotation_key(key: str) -> str: - """Reduce a displayed metadata key to a comparable form. - - Case, spaces, underscores and hyphens are dropped so that 'version info', - 'versionInfo' and 'version_info' land in the same slot of the order list. - """ - return re.sub(r"[\s_\-]+", "", key.lower()) - - -def _load_annotation_order() -> Dict[str, int]: - """Read the YAML order list and map each normalized key to its rank. - - Loaded once at import time. A missing or malformed file raises: a silent - fallback would make the page order depend on the environment again. - """ - with open(_ANNOTATION_ORDER_FILE, encoding="utf-8") as f: - order = yaml.safe_load(f)["order"] - return {_normalize_annotation_key(k): i for i, k in enumerate(order)} - - -_ANNOTATION_RANK = _load_annotation_order() - - -def _annotation_sort_key(key: str) -> Tuple[int, str]: - """Sort key for a header metadata entry: configured rank, then alphabetical. +class BaseViewer: + """Base viewer to display the instances extracted by the Reader. - Unlisted keys get a rank past the last listed one, so they follow the known - ones and stay in alphabetical order among themselves. + It orchestrates the view: everything that differs between formats (display + names, table of contents, hierarchy, card template, vocabulary) is read from + the YAML file named by CONFIG_NAME. Subclasses set that name and override + only the steps that really need code. """ - return (_ANNOTATION_RANK.get(_normalize_annotation_key(key), len(_ANNOTATION_RANK)), key.lower()) - -class BaseViewer: - """Base viewer to display the instances extracted by the Reader.""" + # Name of config/_viewer.yaml; None gives the generic flat list view. + CONFIG_NAME: Optional[str] = None def __init__(self, reader): - """Bind the viewer to a Reader and share its instance cache.""" + """Bind the viewer to a Reader, share its instance cache and load its config.""" self.reader = reader - self._cache = reader._instance_cache # it uses + self._cache = reader._instance_cache # it uses self._internal_iris = None - self._ontology_ns = None + self._ontology_ns = None + self._config = ( + load_viewer_config(self.CONFIG_NAME) if self.CONFIG_NAME + else {"type_map": {}, "toc": [], "card": "_card_owl.html", + "vocabulary": {}, "hierarchy": {}, "characteristics": []} + ) + + def get_toc_config(self) -> List[Tuple[str, str, str]]: + """Return the table of contents: (class name, section id, type_map key) in display order.""" + return [tuple(entry) for entry in self._config["toc"]] + + def _clean_name(self, name: str) -> str: + """Turn an attribute or getter name into a display label, using this viewer's vocabulary.""" + return clean_name(name, self._config["vocabulary"]) def _get_ontology_ns(self) -> str: """Return the namespace of the documented ontology (its IRI ending in '/' or '#'), or ''. @@ -198,33 +177,36 @@ def _get_best_label(self, resource, language: Optional[str] = None) -> Optional[ if resource_id: clean_resource_id = iri_local_name(resource_id) # ONLY clean the identifier! - return self._clean_name(self, clean_resource_id) + return self._clean_name(clean_resource_id) return None def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: - """ - Main entry point called by the API - Subclasses should override this to define their specific view strategy + """Build the template data for one resource, or for the whole artefact grouped by entity type. + + Main entry point called by the API and by the static builder. Both views also + carry the header metadata, the export formats, the display names of the types + and the card template. Without a table of contents (generic viewer) the + artefact is shown as a flat list. """ # If no language is provided, the default would be English language = language.strip() if language else "en" - # Fallback: generic flat list all_instances = self.get_all_instances() metadata_dict = self._find_and_format_metadata(all_instances, language) if resource_uri: data = self._handle_single_resource(resource_uri, language) - data['metadata'] = metadata_dict - data['export_formats'] = self._formats() - return data + elif self._config["toc"]: + data = self._build_grouped_view(self.get_toc_config(), language) + else: + data = {'entities': self._format_entities(all_instances, language)} - return { - 'metadata': metadata_dict, - 'entities': self._format_entities(all_instances, language), - 'export_formats': self._formats(), - } + data['metadata'] = metadata_dict + data['export_formats'] = self._formats() + data['type_map'] = self._config["type_map"] + data['card_template'] = self._config["card"] + return data def _is_toc_entity(self, instance) -> bool: """Browsable (own card + clickable link) iff its type is in get_toc_config. @@ -282,7 +264,7 @@ def _build_grouped_view(self, group_definitions: List[Tuple[str, str, str]], lan 'entities': self._format_entities(instances, language), } - parent_getter = self._HIERARCHY_PARENT_GETTERS.get(class_key) + parent_getter = self._config["hierarchy"].get(class_key) if parent_getter: section['tree'] = self._build_hierarchy(instances, parent_getter, language) @@ -318,7 +300,7 @@ def _format_entities(self, instances: List, language: Optional[str] = None) -> L if not attr.startswith('_') and value: # Skip attributes that are handled elsewhere or are empty # Clean up name: - clean_name = self._clean_name(self,attr) + clean_name = self._clean_name(attr) # Process value (could be a list of objects)clean # We use the helper to get clean text for each item @@ -372,12 +354,7 @@ def _format_entities(self, instances: List, language: Optional[str] = None) -> L ordered_relations[key] = relations[key] characteristics = {} - char_attributes = [ - 'is_functional', 'is_inverse_functional', 'is_transitive', - 'is_symmetric', 'is_asymmetric', 'is_reflexive', 'is_irreflexive' - ] - - for attr in char_attributes: + for attr in self._config["characteristics"]: getter = f"get_{attr}" # Safely get the boolean value is_true = getattr(instance, getter)() if hasattr(instance, getter) else getattr(instance, attr, False) @@ -461,7 +438,7 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None if values: # 4. Auto-format the key name - clean_key = self._clean_name(self, attr_name) + clean_key = self._clean_name(attr_name) # 5. Ensure values are in a list if not isinstance(values, list): @@ -474,7 +451,7 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None if entry['text']: # 7. Check if the link if an visualizable ontology or not if entry.get('link'): - entry['is_visualizable'] = self._is_likely_ontology(entry['link']) + entry['is_visualizable'] = is_likely_ontology(entry['link']) else: entry['is_visualizable'] = False @@ -497,7 +474,7 @@ def _find_and_format_metadata(self, all_instances: List[Resource], language=None # uri/label first, then the order from the YAML, then alphabetical pinned = ['uri', 'label'] - rest = sorted((k for k in data if k not in pinned), key=_annotation_sort_key) + rest = sorted((k for k in data if k not in pinned), key=annotation_sort_key) data = {k: data[k] for k in pinned if k in data} | {k: data[k] for k in rest} return data @@ -617,7 +594,7 @@ def _resolve_resource_value(self, obj, language=None) -> dict: resolved = self._resolve_resource_value(v, language) if resolved.get('text') or resolved.get('nested'): siblings.append({ - 'predicate': self._clean_name(self, attr), + 'predicate': self._clean_name(attr), 'value': resolved, }) # Reader order depends on the source file: sort by label, then by value @@ -694,29 +671,6 @@ def _format_statement(self, instances, target_instance, language=None) -> Dict: return dict(sorted(statements.items(), key=lambda kv: kv[0].lower())) - @staticmethod - def _clean_name(self, name: str) -> str: - """Turn an attribute or getter name into a display label. - - Drops the has_/get_ prefix, splits camelCase, replaces underscores with - spaces and lowercases. It is a staticmethod that still takes `self` as its - first argument, so callers pass it explicitly. - """ - if not name: return "" - - name = re.sub(r'^(get_has_|get_|has_)', '', name) - # Put space between camelCase letters - name = re.sub(r'([a-z0-9])([A-Z])', r'\1 \2', name) - name = name.replace('_', ' ') - - # Strip extra spaces - name = ' '.join(name.split()) - - # lowercase everything - name = name.lower() - - return name - def _parse_restriction(self, obj, language=None, _seen=None) -> list: """ Recursively unpacks nested restrictions into a list of display parts @@ -864,65 +818,6 @@ def _get(instance, prop_name, default=None): return [] - def _is_likely_ontology(self, url: str) -> bool: - """Determines if a URL likely points to an ontology based on naming patterns.""" - if not url or not isinstance(url, str) or not url.startswith('http'): - return False - - # 1. Clean the string - clean_url = url.strip().lower() - - # 2. Safely parse the URL to ignore fragments (#) and queries (?) for extension checking - parsed = urllib.parse.urlparse(clean_url) - path = parsed.path.rstrip('/') - - # 3. Standard Ontology File Extensions - ontology_exts = ['.owl', '.rdf', '.ttl', '.nt', '.n3', '.jsonld'] - if any(path.endswith(ext) for ext in ontology_exts): - return True - - # Match registries against the parsed hostname, not the raw string: - # a substring check would also match e.g. https://evil.com/w3id.org/x - host = parsed.hostname or '' - - def _host_is(domain: str) -> bool: - """True if the URL host is the domain or one of its subdomains.""" - return host == domain or host.endswith('.' + domain) - - # 4. Common Ontology Registries & Permanent URLs - ontology_domains = [ - 'w3id.org', - 'purl.org', - 'xmlns.com' # Often used for FOAF - ] - if any(_host_is(domain) for domain in ontology_domains): - return True - - # 5. Core W3C Namespaces - w3c_core = ['/1999/02/22-rdf-syntax-ns', '/2000/01/rdf-schema', '/2002/07/owl'] - if _host_is('w3.org') and any(ns in path for ns in w3c_core): - return True - - # 6. Broad Keywords & Famous Standard Acronyms - # Looking for these anywhere in the URL string - path_keywords = [ - 'ontology', 'vocab', 'schema', # General terms - 'skos', 'foaf', 'crm', 'cidoc' # Famous standards - ] - if any(keyword in clean_url for keyword in path_keywords): - return True - - return False - - # Map class_key -> name of the parent getter (missing = no hierarchy) - _HIERARCHY_PARENT_GETTERS = { - 'Concept': 'get_is_sub_concept_of', - 'Relation': 'get_is_sub_property_of', - 'Attribute': 'get_is_sub_property_of', - 'Property': 'get_is_sub_property_of', - # Annotation, Individual: no hierarchy -> not in the map - } - _FULL_IRI_ATTRS = {'is_defined_by'} def _build_hierarchy(self, instances, parent_getter_name, language=None): @@ -993,21 +888,10 @@ def _build_provenance_subgraph(self, instance) -> List[Dict[str, str]]: return [] sub = self._with_provenance(sub) return [ - {"label": f["label"], "code": self._safe_serialize(sub, f["fmt"])} + {"label": f["label"], "code": safe_serialize(sub, f["fmt"])} for f in QUAD_SERIALIZATION_FORMATS ] - @staticmethod - def _safe_serialize(g, fmt: str) -> str: - """Serialize a graph, returning a comment with the error instead of raising. - - One format that fails must not break the page that shows all of them. - """ - try: - return g.serialize(format=fmt) - except Exception as e: - return f"# serialization error ({fmt}): {e}" - def export_resource(self, resource_uri: str, fmt: str = "turtle") -> str: """Serialize the subgraph of a single resource (the union of its punned instances). @@ -1025,4 +909,4 @@ def export_resource(self, resource_uri: str, fmt: str = "turtle") -> str: for t in self.reader.get_provenance_subgraph(inst): if t in main: g.add(t) - return self._safe_serialize(g, fmt) \ No newline at end of file + return safe_serialize(g, fmt) \ No newline at end of file diff --git a/lode/viewer/config/owl_viewer.yaml b/lode/viewer/config/owl_viewer.yaml new file mode 100644 index 0000000..d826d78 --- /dev/null +++ b/lode/viewer/config/owl_viewer.yaml @@ -0,0 +1,49 @@ +# Settings of the OWL viewer. Read by lode.viewer.helpers.load_viewer_config. + +# Partial included once per entity by viewer.html. +card: _card_owl.html + +# Display vocabulary: internal word -> shown word. Applied to whole words of the +# property labels (e.g. "is sub concept of" -> "is sub class of"). +vocabulary: + concept: class + concepts: classes + relation: object property + relations: object properties + attribute: data property + attributes: data properties + +# Display names of the entity types, keyed by the lowercase model class name. +# abb is the badge shown next to a label. +type_map: + concept: {singular: Class, plural: Classes, abb: c} + relation: {singular: Object Property, plural: Object Properties, abb: op} + attribute: {singular: Data Property, plural: Data Properties, abb: dp} + annotation: {singular: Annotation Property, plural: Annotation Properties, abb: ap} + individual: {singular: Named Individual, plural: Named Individuals, abb: ni} + +# Table of contents in display order: model class name, section id, type_map key. +# Only these classes are browsable (own card and link). +toc: + - [Concept, concepts, Concept] + - [Relation, relations, Relation] + - [Attribute, attributes, Attribute] + - [Individual, individuals, Individual] + - [Annotation, annotations, Annotation] + +# Model class -> getter of its parents, for the hierarchy tree of a section. +# A class that is missing has no hierarchy. +hierarchy: + Concept: get_is_sub_concept_of + Relation: get_is_sub_property_of + Attribute: get_is_sub_property_of + +# Boolean flags shown as characteristics of a property. +characteristics: + - is_functional + - is_inverse_functional + - is_transitive + - is_symmetric + - is_asymmetric + - is_reflexive + - is_irreflexive diff --git a/lode/viewer/config/rdf_viewer.yaml b/lode/viewer/config/rdf_viewer.yaml new file mode 100644 index 0000000..02a1f9d --- /dev/null +++ b/lode/viewer/config/rdf_viewer.yaml @@ -0,0 +1,39 @@ +# Settings of the RDF/RDFS viewer. Read by lode.viewer.helpers.load_viewer_config. + +# Same card as OWL for now; point to a dedicated partial when the two diverge. +card: _card_owl.html + +# Display vocabulary: internal word -> shown word. Applied to whole words of the +# property labels (e.g. "is sub concept of" -> "is sub class of"). +vocabulary: + concept: class + concepts: classes + +# Display names of the entity types, keyed by the lowercase model class name. +type_map: + concept: {singular: Class, plural: Classes, abb: c} + property: {singular: Property, plural: Properties, abb: p} + container: {singular: Container, plural: Containers, abb: cont} + resource: {singular: Resource, plural: Resources, abb: r} + model: {singular: Vocabulary, plural: Vocabularies, abb: v} + +# Table of contents in display order: model class name, section id, type_map key. +toc: + - [Concept, concepts, Concept] + - [Property, properties, Property] + - [Container, containers, Container] + +# Model class -> getter of its parents, for the hierarchy tree of a section. +hierarchy: + Concept: get_is_sub_concept_of + Property: get_is_sub_property_of + +# Boolean flags shown as characteristics of a property. +characteristics: + - is_functional + - is_inverse_functional + - is_transitive + - is_symmetric + - is_asymmetric + - is_reflexive + - is_irreflexive diff --git a/lode/viewer/config/skos_viewer.yaml b/lode/viewer/config/skos_viewer.yaml new file mode 100644 index 0000000..7ce90ec --- /dev/null +++ b/lode/viewer/config/skos_viewer.yaml @@ -0,0 +1,17 @@ +# Settings of the SKOS viewer. Read by lode.viewer.helpers.load_viewer_config. + +# Partial included once per entity by viewer.html. +card: _card_skos.html + +# SKOS keeps the model terms as they are. +vocabulary: {} + +# Display names of the entity types, keyed by the lowercase model class name. +type_map: + collection: {singular: Collection, plural: Collections, abb: col} + concept: {singular: Concept, plural: Concepts, abb: c} + +# Table of contents in display order: model class name, section id, type_map key. +toc: + - [Collection, collections, Collection] + - [Concept, concepts, Concept] diff --git a/lode/viewer/helpers.py b/lode/viewer/helpers.py new file mode 100644 index 0000000..21a81d7 --- /dev/null +++ b/lode/viewer/helpers.py @@ -0,0 +1,190 @@ +"""Stateless helpers shared by the viewers. + +Nothing here needs a Reader or a model instance: serialization formats, the +deterministic order of the header metadata, label cleaning, URL heuristics and +the loader of the per-format YAML configuration. +""" +import re +import urllib.parse +from pathlib import Path +from typing import Dict, Optional, Tuple + +import yaml + +_CONFIG_DIR = Path(__file__).parent / "config" + +# ========================================================================== +# 1. SERIALIZATION FORMATS +# ========================================================================== + +# Export formats: triples of the loaded artefact only. +SERIALIZATION_FORMATS = [ + {"label": "Turtle", "fmt": "turtle", "mime": "text/turtle", "ext": "ttl", "icon": "bi-filetype-raw"}, + {"label": "RDF/XML", "fmt": "xml", "mime": "application/rdf+xml", "ext": "rdf", "icon": "bi-file-code"}, + {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, + {"label": "N-Triples", "fmt": "nt", "mime": "application/n-triples", "ext": "nt", "icon": "bi-file-text"}, +] + +# Provenance formats: quads, the named graph of each triple is always shown. +QUAD_SERIALIZATION_FORMATS = [ + {"label": "TriG", "fmt": "trig", "mime": "application/trig", "ext": "trig", "icon": "bi-filetype-raw"}, + {"label": "JSON-LD", "fmt": "json-ld", "mime": "application/ld+json", "ext": "jsonld", "icon": "bi-filetype-json"}, + {"label": "N-Quads", "fmt": "nquads", "mime": "application/n-quads", "ext": "nq", "icon": "bi-file-text"}, +] + + +def safe_serialize(g, fmt: str) -> str: + """Serialize a graph, returning a comment with the error instead of raising. + + One format that fails must not break the page that shows all of them. + """ + try: + return g.serialize(format=fmt) + except Exception as e: + return f"# serialization error ({fmt}): {e}" + + +# ========================================================================== +# 2. HEADER METADATA ORDER +# ========================================================================== + +_ANNOTATION_ORDER_FILE = _CONFIG_DIR / "model_annotations_deterministic_sorting.yaml" + + +def _normalize_annotation_key(key: str) -> str: + """Reduce a displayed metadata key to a comparable form. + + Case, spaces, underscores and hyphens are dropped so that 'version info', + 'versionInfo' and 'version_info' land in the same slot of the order list. + """ + return re.sub(r"[\s_\-]+", "", key.lower()) + + +def _load_annotation_order() -> Dict[str, int]: + """Read the YAML order list and map each normalized key to its rank. + + Loaded once at import time. A missing or malformed file raises: a silent + fallback would make the page order depend on the environment again. + """ + with open(_ANNOTATION_ORDER_FILE, encoding="utf-8") as f: + order = yaml.safe_load(f)["order"] + return {_normalize_annotation_key(k): i for i, k in enumerate(order)} + + +_ANNOTATION_RANK = _load_annotation_order() + + +def annotation_sort_key(key: str) -> Tuple[int, str]: + """Sort key for a header metadata entry: configured rank, then alphabetical. + + Unlisted keys get a rank past the last listed one, so they follow the known + ones and stay in alphabetical order among themselves. + """ + return (_ANNOTATION_RANK.get(_normalize_annotation_key(key), len(_ANNOTATION_RANK)), key.lower()) + + +# ========================================================================== +# 3. LABELS AND URLS +# ========================================================================== + +def clean_name(name: str, vocabulary: Optional[Dict[str, str]] = None) -> str: + """Turn an attribute or getter name into a display label. + + Drops the has_/get_ prefix, splits camelCase, replaces underscores with + spaces and lowercases. The vocabulary of the viewer (internal word -> shown + word) is applied last, on whole words only, so that e.g. "concept" does not + touch "conceptual". + """ + if not name: + return "" + + name = re.sub(r'^(get_has_|get_|has_)', '', name) + # Put space between camelCase letters + name = re.sub(r'([a-z0-9])([A-Z])', r'\1 \2', name) + name = name.replace('_', ' ') + + # Strip extra spaces and lowercase everything + name = ' '.join(name.split()).lower() + + for word, shown in (vocabulary or {}).items(): + name = re.sub(rf'\b{re.escape(word)}\b', shown, name) + + return name + + +def is_likely_ontology(url: str) -> bool: + """Determines if a URL likely points to an ontology based on naming patterns.""" + if not url or not isinstance(url, str) or not url.startswith('http'): + return False + + # 1. Clean the string + clean_url = url.strip().lower() + + # 2. Safely parse the URL to ignore fragments (#) and queries (?) for extension checking + parsed = urllib.parse.urlparse(clean_url) + path = parsed.path.rstrip('/') + + # 3. Standard Ontology File Extensions + ontology_exts = ['.owl', '.rdf', '.ttl', '.nt', '.n3', '.jsonld'] + if any(path.endswith(ext) for ext in ontology_exts): + return True + + # Match registries against the parsed hostname, not the raw string: + # a substring check would also match e.g. https://evil.com/w3id.org/x + host = parsed.hostname or '' + + def _host_is(domain: str) -> bool: + """True if the URL host is the domain or one of its subdomains.""" + return host == domain or host.endswith('.' + domain) + + # 4. Common Ontology Registries & Permanent URLs + ontology_domains = [ + 'w3id.org', + 'purl.org', + 'xmlns.com' # Often used for FOAF + ] + if any(_host_is(domain) for domain in ontology_domains): + return True + + # 5. Core W3C Namespaces + w3c_core = ['/1999/02/22-rdf-syntax-ns', '/2000/01/rdf-schema', '/2002/07/owl'] + if _host_is('w3.org') and any(ns in path for ns in w3c_core): + return True + + # 6. Broad Keywords & Famous Standard Acronyms + # Looking for these anywhere in the URL string + path_keywords = [ + 'ontology', 'vocab', 'schema', # General terms + 'skos', 'foaf', 'crm', 'cidoc' # Famous standards + ] + if any(keyword in clean_url for keyword in path_keywords): + return True + + return False + + +# ========================================================================== +# 4. PER-FORMAT VIEWER CONFIGURATION +# ========================================================================== + +_REQUIRED_CONFIG_KEYS = ("type_map", "toc", "card") + + +def load_viewer_config(name: str) -> dict: + """Read config/_viewer.yaml and fill in the optional keys. + + The file holds everything that differs between formats (display names, table + of contents, hierarchy getters, card template, display vocabulary), so the + viewer classes carry no per-format data. A missing file or required key + raises: a silent default would change the page without any trace. + """ + path = _CONFIG_DIR / f"{name}_viewer.yaml" + with open(path, encoding="utf-8") as f: + config = yaml.safe_load(f) + missing = [k for k in _REQUIRED_CONFIG_KEYS if k not in config] + if missing: + raise ValueError(f"{path.name}: missing required keys {missing}") + config.setdefault("vocabulary", {}) + config.setdefault("hierarchy", {}) + config.setdefault("characteristics", []) + return config diff --git a/lode/viewer/owl_viewer.py b/lode/viewer/owl_viewer.py index db01eed..135d543 100644 --- a/lode/viewer/owl_viewer.py +++ b/lode/viewer/owl_viewer.py @@ -1,45 +1,8 @@ """Viewer for OWL artefacts.""" -from typing import Dict, Optional from lode.viewer.base_viewer import BaseViewer -class OwlViewer(BaseViewer): - """OWL viewer""" - - TYPE_MAP = { - 'concept': {'singular': 'Class', 'plural': 'Classes', 'abb': 'c'}, - 'relation': {'singular': 'Object Property', 'plural': 'Object Properties', 'abb': 'op'}, - 'attribute': {'singular': 'Data Property', 'plural': 'Data Properties', 'abb': 'dp'}, - 'annotation': {'singular': 'Annotation Property', 'plural': 'Annotation Properties', 'abb': 'ap'}, - 'individual': {'singular': 'Named Individual', 'plural': 'Named Individuals', 'abb': 'ni'}, - } - - def get_toc_config(self): - """Return the table of contents: (class name, section id, TYPE_MAP key) in display order.""" - return [ - ('Concept', 'concepts', 'Concept'), - ('Relation', 'relations', 'Relation'), - ('Attribute', 'attributes', 'Attribute'), - ('Individual', 'individuals', 'Individual'), - ('Annotation', 'annotations', 'Annotation'), - ] - - - def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: - """Build the template data for one resource, or for the whole ontology grouped by entity type. - Both views also carry the ontology metadata and the TYPE_MAP of display names. - """ - - anguage = language.strip() if language else "en" - - all_instances = self.get_all_instances() - metadata_dict = self._find_and_format_metadata(all_instances, language) - - if resource_uri: - data = super().get_view_data(resource_uri, language) - else: - data = self._build_grouped_view(self.get_toc_config(), language) +class OwlViewer(BaseViewer): + """OWL viewer: display names, table of contents and card come from config/owl_viewer.yaml.""" - data['metadata'] = metadata_dict - data['type_map'] = self.TYPE_MAP - return data \ No newline at end of file + CONFIG_NAME = "owl" diff --git a/lode/viewer/rdf_viewer.py b/lode/viewer/rdf_viewer.py index 34840a0..7b10986 100644 --- a/lode/viewer/rdf_viewer.py +++ b/lode/viewer/rdf_viewer.py @@ -1,45 +1,8 @@ """Viewer for RDF/RDFS artefacts.""" -from typing import Dict, Optional from lode.viewer.base_viewer import BaseViewer class RdfViewer(BaseViewer): - """Viewer RDF / RDFS""" + """RDF / RDFS viewer: display names, table of contents and card come from config/rdf_viewer.yaml.""" - TYPE_MAP = { - 'concept': {'singular': 'Class', 'plural': 'Classes', 'abb': 'c'}, - 'property': {'singular': 'Property', 'plural': 'Properties', 'abb': 'p'}, - 'container': {'singular': 'Container', 'plural': 'Containers', 'abb': 'cont'}, - 'resource': {'singular': 'Resource', 'plural': 'Resources', 'abb': 'r'}, - 'model': {'singular': 'Vocabulary','plural': 'Vocabularies','abb': 'v'}, - } - - def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: - """Build the template data for one resource, or for the vocabulary grouped by concepts, properties and containers. - - Both views also carry the vocabulary metadata and the TYPE_MAP of display names. - """ - - language = language.strip() if language else "en" - - all_instances = self.get_all_instances() - metadata_dict = self._find_and_format_metadata(all_instances, language) - - if resource_uri: - data = super().get_view_data(resource_uri, language) - data['metadata'] = metadata_dict - data['type_map'] = self.TYPE_MAP - return data - - # title in SINGULAR to match the TYPE_MAP keys - toc_config = [ - ('Concept', 'concepts', 'Concept'), - ('Property', 'properties', 'Property'), - ('Container', 'containers', 'Container'), - ] - - data = self._build_grouped_view(toc_config, language) - data['metadata'] = metadata_dict - data['type_map'] = self.TYPE_MAP - - return data \ No newline at end of file + CONFIG_NAME = "rdf" diff --git a/lode/viewer/skos_viewer.py b/lode/viewer/skos_viewer.py index f434aca..96ea462 100644 --- a/lode/viewer/skos_viewer.py +++ b/lode/viewer/skos_viewer.py @@ -5,47 +5,16 @@ from lode.helpers.rdf import iri_local_name class SkosViewer(BaseViewer): - """SKOS viewer with LODE-style rendering.""" + """SKOS viewer with LODE-style rendering. - def get_view_data(self, resource_uri: Optional[str] = None, language: Optional[str] = None) -> Dict: - """Build the template data for one resource, or for the scheme grouped by collections and concepts.""" - # 1. Single resource detail view - if resource_uri: - return super().get_view_data(resource_uri, language) + Display names, table of contents and card come from config/skos_viewer.yaml; + only the entity formatting differs from the base, because SKOS cards show + semantic relations between concepts instead of OWL-style statements. + """ - # 2. Define the Table of Contents structure for SKOS - toc_config = [ - ('Collection', 'collections', 'Collections'), - ('Concept', 'concepts', 'Concepts'), - ] + CONFIG_NAME = "skos" - # 3. Build grouped view with SKOS-specific formatting - return self._build_skos_grouped_view(toc_config, language) - - def _build_skos_grouped_view(self, group_definitions: List, language: Optional[str] = None) -> Dict: - """Build the grouped view with SKOS-style formatting.""" - all_instances = self.get_all_instances() - sections = [] - - for class_key, section_id, section_title in group_definitions: - instances = [ - inst for inst in all_instances - if type(inst).__name__ == class_key - ] - - if instances: - sections.append({ - 'id': section_id, - 'title': section_title, - 'entities': self._format_skos_entities(instances, language) - }) - - return { - 'grouped_view': True, - 'sections': sections - } - - def _format_skos_entities(self, instances: List, language: Optional[str] = None) -> List[Dict]: + def _format_entities(self, instances: List, language: Optional[str] = None) -> List[Dict]: """Format the SKOS entities in LODE style, sorted by label (or IRI when there is none).""" entities = [] From 8d20be5608831d4368de5c632c19bef9dca62e5b Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 16:33:47 +0200 Subject: [PATCH 09/21] fix(owlViewer): moved parse restrictions in specifically in owl viewer --- lode/viewer/base_viewer.py | 180 +++--------------------------------- lode/viewer/owl_viewer.py | 181 ++++++++++++++++++++++++++++++++++++- 2 files changed, 193 insertions(+), 168 deletions(-) diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 6ea2112..795fa70 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -505,6 +505,14 @@ def _resolve_chain_value(self, chain, language=None) -> dict: 'type': 'PropertyChain', } + def _resolve_special(self, obj, handler_dic: dict, language=None) -> Optional[dict]: + """Resolve a value only one format knows how to render, or return None. + + The base knows none: a format viewer overrides this to intercept its own + constructs (OWL class expressions) before the generic resolution runs. + """ + return None + def _resolve_resource_value(self, obj, language=None) -> dict: """Helper: Extracts text and link from any object.""" handler_dic = { @@ -520,27 +528,12 @@ def _resolve_resource_value(self, obj, language=None) -> dict: if not obj: return handler_dic - # --- 1. INTERCEPT RESTRICTIONS --- - restriction_types = ["Restriction", "PropertyConceptRestriction", "Quantifier", "Cardinality", "TruthFunction", - "OneOf", "Value", "DatatypeRestriction"] - obj_type = type(obj).__name__ + # --- 1. FORMAT-SPECIFIC VALUES (e.g. OWL restrictions) --- + special = self._resolve_special(obj, handler_dic, language) + if special is not None: + return special - if obj_type in restriction_types: - is_dep = getattr(obj, 'get_is_deprecated')() if hasattr(obj, 'get_is_deprecated') else getattr(obj, - 'is_deprecated', - False) - handler_dic['is_deprecated'] = bool(is_dep) - - # Recursively parse the restriction into clickable parts - parts = self._parse_restriction(obj, language) - - handler_dic['parts'] = parts - handler_dic['text'] = "".join([p['text'] for p in parts if p.get('text')]) - handler_dic['link'] = None # Forces Jinja to ignore the blank node URI - handler_dic['is_external'] = False - handler_dic['is_imported'] = False - handler_dic['type'] = obj_type - return handler_dic + obj_type = type(obj).__name__ # --- 2. String Handling --- if isinstance(obj, str): @@ -671,153 +664,6 @@ def _format_statement(self, instances, target_instance, language=None) -> Dict: return dict(sorted(statements.items(), key=lambda kv: kv[0].lower())) - def _parse_restriction(self, obj, language=None, _seen=None) -> list: - """ - Recursively unpacks nested restrictions into a list of display parts - (each part being a dict with 'text' and 'link'). - Guards against cyclic class expressions (possible once owl:imports - completes cross-ontology definitions) via a visited set. - """ - if not obj: return [] - - if _seen is None: - _seen = set() - - # 1. Handle lists of restrictions/concepts (e.g., in TruthFunctions or OneOf) - if isinstance(obj, list) or isinstance(obj, set): - parts = [] - for i, item in enumerate(obj): - if i > 0: - parts.append({'text': ', ', 'link': None}) - parts.extend(self._parse_restriction(item, language, _seen)) - return parts - - obj_type = type(obj).__name__ - restriction_types = ["Restriction", "PropertyConceptRestriction", "Quantifier", "Cardinality", "TruthFunction", - "OneOf", "Value", "DatatypeRestriction"] - - # 2. If it is a Restriction, recursively unpack its specific components - if obj_type in restriction_types: - # cycle guard: a class expression already being expanded upstream - if id(obj) in _seen: - return [{'text': '…', 'link': None}] - _seen.add(id(obj)) - - parts = [] - - # Helper to safely call getter methods (e.g., get_applies_on_property) - def _get(instance, prop_name, default=None): - """Read a property through its getter, or directly as an attribute, with a default for None.""" - getter = f"get_{prop_name}" - if hasattr(instance, getter): - res = getattr(instance, getter)() - return res if res is not None else default - return getattr(instance, prop_name, default) - - if obj_type == "Quantifier": - prop = _get(obj, 'applies_on_property') - quant = _get(obj, 'has_quantifier_type', "some") - concept = _get(obj, 'applies_on_concept') - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.extend(self._parse_restriction(prop, language, _seen)) - parts.append({'text': f' {quant} ', 'link': None}) - parts.extend(self._parse_restriction(concept, language, _seen)) - - elif obj_type == "Cardinality": - prop = _get(obj, 'applies_on_property') - card = _get(obj, 'has_cardinality_type', "exactly") - card_num = _get(obj, 'has_cardinality') - concept = _get(obj, 'applies_on_concept') - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.extend(self._parse_restriction(prop, language, _seen)) - parts.append({'text': f' {card} {card_num}', 'link': None}) - parts.extend(self._parse_restriction(concept, language, _seen)) - - elif obj_type == "TruthFunction": - operator = _get(obj, 'has_logical_operator', "and") - concepts = _get(obj, 'applies_on_concept', []) - if not isinstance(concepts, list): concepts = [concepts] - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.append({'text': '(', 'link': None}) - for i, c in enumerate(concepts): - if i > 0: - parts.append({'text': f' {operator} ', 'link': None}) - parts.extend(self._parse_restriction(c, language, _seen)) - parts.append({'text': ')', 'link': None}) - - elif obj_type == "OneOf": - resources = _get(obj, 'applies_on_resource', []) - if not isinstance(resources, list): resources = [resources] - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.append({'text': 'one of { ', 'link': None}) - for i, r in enumerate(resources): - if i > 0: - parts.append({'text': ', ', 'link': None}) - parts.extend(self._parse_restriction(r, language, _seen)) - parts.append({'text': ' }', 'link': None}) - - elif obj_type == "Value": - prop = _get(obj, 'applies_on_property') - resource = _get(obj, 'applies_on_resource') - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.extend(self._parse_restriction(prop, language, _seen)) - parts.append({'text': ' value ', 'link': None}) - parts.extend(self._parse_restriction(resource, language, _seen)) - - elif obj_type == "DatatypeRestriction": - concept = _get(obj, 'applies_on_concept') # Datatype(xsd:string) - constraint = _get(obj, 'has_constraint') # "pattern" - value = _get(obj, 'has_restriction_value') # Literal("[0-9]+") - - # Safely check if the is_inverse flag is True - is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) - if is_inv: - parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) - - parts.extend(self._parse_restriction(concept, language, _seen)) - if constraint: - parts.append({'text': f' with {constraint} ', 'link': None, 'type': 'Text'}) - else: - parts.append({'text': ' restricted by ', 'link': None, 'type': 'Text'}) - - parts.extend(self._parse_restriction(value, language, _seen)) - - return parts - - # 3. Base Case: We hit a non-blank node (Concept, Relation, String) - # Send it to the main resolver to extract its URI link and clean text. - resolved = self._resolve_resource_value(obj, language) - - if resolved.get('text'): - return [{'text': resolved['text'], 'link': resolved.get('link'), 'type': resolved.get('type'), 'is_external': resolved.get('is_external', False)}] - - return [] - _FULL_IRI_ATTRS = {'is_defined_by'} def _build_hierarchy(self, instances, parent_getter_name, language=None): diff --git a/lode/viewer/owl_viewer.py b/lode/viewer/owl_viewer.py index 135d543..91aa2a4 100644 --- a/lode/viewer/owl_viewer.py +++ b/lode/viewer/owl_viewer.py @@ -1,8 +1,187 @@ """Viewer for OWL artefacts.""" +from typing import Optional + from lode.viewer.base_viewer import BaseViewer class OwlViewer(BaseViewer): - """OWL viewer: display names, table of contents and card come from config/owl_viewer.yaml.""" + """OWL viewer: display names, table of contents and card come from config/owl_viewer.yaml. + + It adds the rendering of class expressions (restrictions, cardinalities, + boolean combinations), which only OWL has. + """ CONFIG_NAME = "owl" + + # Model classes that are anonymous class expressions, shown inline as clickable parts. + _RESTRICTION_TYPES = ["Restriction", "PropertyConceptRestriction", "Quantifier", "Cardinality", "TruthFunction", + "OneOf", "Value", "DatatypeRestriction"] + + def _resolve_special(self, obj, handler_dic: dict, language=None) -> Optional[dict]: + """Render a class expression as clickable parts; None for any other value. + + The blank node of the expression is never linked: its parts carry the links. + """ + obj_type = type(obj).__name__ + if obj_type not in self._RESTRICTION_TYPES: + return None + + is_dep = getattr(obj, 'get_is_deprecated')() if hasattr(obj, 'get_is_deprecated') else getattr( + obj, 'is_deprecated', False) + handler_dic['is_deprecated'] = bool(is_dep) + + # Recursively parse the restriction into clickable parts + parts = self._parse_restriction(obj, language) + + handler_dic['parts'] = parts + handler_dic['text'] = "".join([p['text'] for p in parts if p.get('text')]) + handler_dic['link'] = None # Forces Jinja to ignore the blank node URI + handler_dic['is_external'] = False + handler_dic['is_imported'] = False + handler_dic['type'] = obj_type + return handler_dic + + def _parse_restriction(self, obj, language=None, _seen=None) -> list: + """ + Recursively unpacks nested restrictions into a list of display parts + (each part being a dict with 'text' and 'link'). + Guards against cyclic class expressions (possible once owl:imports + completes cross-ontology definitions) via a visited set. + """ + if not obj: return [] + + if _seen is None: + _seen = set() + + # 1. Handle lists of restrictions/concepts (e.g., in TruthFunctions or OneOf) + if isinstance(obj, list) or isinstance(obj, set): + parts = [] + for i, item in enumerate(obj): + if i > 0: + parts.append({'text': ', ', 'link': None}) + parts.extend(self._parse_restriction(item, language, _seen)) + return parts + + obj_type = type(obj).__name__ + + # 2. If it is a Restriction, recursively unpack its specific components + if obj_type in self._RESTRICTION_TYPES: + # cycle guard: a class expression already being expanded upstream + if id(obj) in _seen: + return [{'text': '…', 'link': None}] + _seen.add(id(obj)) + + parts = [] + + # Helper to safely call getter methods (e.g., get_applies_on_property) + def _get(instance, prop_name, default=None): + """Read a property through its getter, or directly as an attribute, with a default for None.""" + getter = f"get_{prop_name}" + if hasattr(instance, getter): + res = getattr(instance, getter)() + return res if res is not None else default + return getattr(instance, prop_name, default) + + if obj_type == "Quantifier": + prop = _get(obj, 'applies_on_property') + quant = _get(obj, 'has_quantifier_type', "some") + concept = _get(obj, 'applies_on_concept') + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.extend(self._parse_restriction(prop, language, _seen)) + parts.append({'text': f' {quant} ', 'link': None}) + parts.extend(self._parse_restriction(concept, language, _seen)) + + elif obj_type == "Cardinality": + prop = _get(obj, 'applies_on_property') + card = _get(obj, 'has_cardinality_type', "exactly") + card_num = _get(obj, 'has_cardinality') + concept = _get(obj, 'applies_on_concept') + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.extend(self._parse_restriction(prop, language, _seen)) + parts.append({'text': f' {card} {card_num}', 'link': None}) + parts.extend(self._parse_restriction(concept, language, _seen)) + + elif obj_type == "TruthFunction": + operator = _get(obj, 'has_logical_operator', "and") + concepts = _get(obj, 'applies_on_concept', []) + if not isinstance(concepts, list): concepts = [concepts] + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.append({'text': '(', 'link': None}) + for i, c in enumerate(concepts): + if i > 0: + parts.append({'text': f' {operator} ', 'link': None}) + parts.extend(self._parse_restriction(c, language, _seen)) + parts.append({'text': ')', 'link': None}) + + elif obj_type == "OneOf": + resources = _get(obj, 'applies_on_resource', []) + if not isinstance(resources, list): resources = [resources] + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.append({'text': 'one of { ', 'link': None}) + for i, r in enumerate(resources): + if i > 0: + parts.append({'text': ', ', 'link': None}) + parts.extend(self._parse_restriction(r, language, _seen)) + parts.append({'text': ' }', 'link': None}) + + elif obj_type == "Value": + prop = _get(obj, 'applies_on_property') + resource = _get(obj, 'applies_on_resource') + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.extend(self._parse_restriction(prop, language, _seen)) + parts.append({'text': ' value ', 'link': None}) + parts.extend(self._parse_restriction(resource, language, _seen)) + + elif obj_type == "DatatypeRestriction": + concept = _get(obj, 'applies_on_concept') # Datatype(xsd:string) + constraint = _get(obj, 'has_constraint') # "pattern" + value = _get(obj, 'has_restriction_value') # Literal("[0-9]+") + + # Safely check if the is_inverse flag is True + is_inv = obj.get_is_inverse() if hasattr(obj, 'get_is_inverse') else getattr(obj, 'is_inverse', False) + if is_inv: + parts.append({'text': 'inverse of ', 'link': None, 'type': 'Text'}) + + parts.extend(self._parse_restriction(concept, language, _seen)) + if constraint: + parts.append({'text': f' with {constraint} ', 'link': None, 'type': 'Text'}) + else: + parts.append({'text': ' restricted by ', 'link': None, 'type': 'Text'}) + + parts.extend(self._parse_restriction(value, language, _seen)) + + return parts + + # 3. Base Case: We hit a non-blank node (Concept, Relation, String) + # Send it to the main resolver to extract its URI link and clean text. + resolved = self._resolve_resource_value(obj, language) + + if resolved.get('text'): + return [{'text': resolved['text'], 'link': resolved.get('link'), 'type': resolved.get('type'), 'is_external': resolved.get('is_external', False)}] + + return [] From a00a18aef88564d05bc548454751bc5f7d13ba6f Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 17:49:46 +0200 Subject: [PATCH 10/21] fix(warnings): show reader warnings as toasts in serve, report.txt and console output in build. --- lode/api.py | 2 +- lode/builder.py | 15 ++++++++- lode/cli.py | 14 ++++++++- lode/reader/logic/base_logic.py | 19 ------------ lode/reader/reader.py | 6 ++-- lode/templates/viewer.html | 43 +++++++++++++++++++------- lode/viewer/base_viewer.py | 17 +++++++++++ lode/warnings.json | 22 -------------- tests/test_packaging.py | 1 - tests/test_static_builder.py | 54 ++++++++++++++++++++++++++++++++- 10 files changed, 133 insertions(+), 60 deletions(-) delete mode 100644 lode/warnings.json diff --git a/lode/api.py b/lode/api.py index abf38ea..dbb58aa 100644 --- a/lode/api.py +++ b/lode/api.py @@ -168,7 +168,7 @@ def _render_view(request, reader, *, resource, lang, source_url, upload_id, read """ viewer = reader.get_viewer() data = viewer.get_view_data(resource_uri=resource, language=lang) - data["warnings"] = reader.get_warnings() + data["warnings"] = viewer.format_warnings(reader.get_warnings()) resp = templates.TemplateResponse(request, "viewer.html", { "source_url": source_url, "upload_id": upload_id, diff --git a/lode/builder.py b/lode/builder.py index 2975fdb..3e6f12a 100644 --- a/lode/builder.py +++ b/lode/builder.py @@ -105,6 +105,17 @@ def _copy_static(out_dir: Path) -> None: if static_src.exists() and not static_dst.exists(): shutil.copytree(static_src, static_dst) +def _write_warnings_report(warnings: list, out_dir: Path) -> None: + """Write the reader warnings to report.txt in the output folder. + + Written only when there is something to report, so a build without warnings + leaves no file. An older report.txt is not removed: it may be the user's own. + """ + if not warnings: + return + lines = [f"[{w['code']}] {w['message']}" for w in warnings] + (out_dir / "report.txt").write_text("\n".join(lines) + "\n", encoding="utf-8") + def build_html(viewer, out_dir: Path, lang: str = "en", reader=None, artefact_name: str = "index") -> None: """Write the whole static site for a viewer into `out_dir`. @@ -122,7 +133,9 @@ def build_html(viewer, out_dir: Path, lang: str = "en", reader=None, artefact_name = _check_artefact_name(artefact_name) out_dir.mkdir(parents=True, exist_ok=True) _copy_static(out_dir) - + if reader is not None: + _write_warnings_report(viewer.format_warnings(reader.get_warnings()), out_dir) + ontology_ns = viewer._get_ontology_ns() graph = reader._graph if reader else viewer.reader._graph main_graph = viewer.reader.get_main_graph() diff --git a/lode/cli.py b/lode/cli.py index c8ad198..c21e2fe 100644 --- a/lode/cli.py +++ b/lode/cli.py @@ -46,9 +46,19 @@ def cmd_build(args): imported=args.imported or None, closure=args.closure or None, partial_import=args.partial_import or None, + warnings=args.warnings, ) - build_html(reader.get_viewer(), out_dir, lang=args.lang, reader=reader, + viewer = reader.get_viewer() + build_html(viewer, out_dir, lang=args.lang, reader=reader, artefact_name=args.artefact_name) + if args.warnings: + warnings = viewer.format_warnings(reader.get_warnings()) + for w in warnings: + print(f"[{w['code']}] {w['message']}") + if warnings: + print(f"Warnings report -> {out_dir / 'report.txt'}") + else: + print("No reader warnings") print(f"Done -> {out_dir}") @@ -78,6 +88,8 @@ def main(): p_build.add_argument("--imported", action="store_true") p_build.add_argument("--closure", action="store_true") p_build.add_argument("--partial-import", action="store_true") + p_build.add_argument("--warnings", action="store_true", + help="Print reader warnings and write them to report.txt in the output folder") args = parser.parse_args() {"serve": cmd_serve, "build": cmd_build}[args.cmd](args) diff --git a/lode/reader/logic/base_logic.py b/lode/reader/logic/base_logic.py index a718670..1411e26 100644 --- a/lode/reader/logic/base_logic.py +++ b/lode/reader/logic/base_logic.py @@ -46,25 +46,6 @@ def add_warning(self, code, subject, message): """Record a reader warning with a machine-readable code, its subject and a message.""" self._warnings.append({'code': code, 'subject': str(subject), 'message': message}) - def get_warnings(self): - """Return the collected warnings, or [] when they were not requested.""" - if not getattr(self, '_warnings_enabled', False): # self is the logic here - return [] - - def save_warnings(self, filepath: str = None): - """Save warnings to JSON file.""" - import json - from pathlib import Path - - if not self._warnings: - return - - if filepath is None: - filepath = Path(__file__).parent.parent.parent / 'warnings.json' - - with open(filepath, 'w', encoding='utf-8') as f: - json.dump(self._warnings, f, indent=2, ensure_ascii=False) - def _get_allowed_classes(self) -> set: """Resolve the 'allowed_classes' names of the config into the model classes.""" class_names = self._strategy.config.get('allowed_classes', []) diff --git a/lode/reader/reader.py b/lode/reader/reader.py index 4d5a7e4..3679fad 100644 --- a/lode/reader/reader.py +++ b/lode/reader/reader.py @@ -270,10 +270,10 @@ def _extract_instances(self): if self._logic._warnings: logger.warning("%d reader warnings", len(self._logic._warnings)) + # details only at DEBUG: the viewer words them with display names + # for popups, report and CLI, so raw model names would be confusing for w in self._logic._warnings: - logger.warning("[%s] %s", w['code'], w['message']) - - self._logic.save_warnings() + logger.debug("[%s] %s", w['code'], w['message']) def _phase5_fallback(self): """Fallback per risorse non categorizzate (comune)""" diff --git a/lode/templates/viewer.html b/lode/templates/viewer.html index 9acd7aa..f3120b6 100644 --- a/lode/templates/viewer.html +++ b/lode/templates/viewer.html @@ -71,17 +71,6 @@ {% endif %}
- {% if warnings %} -
- {% for w in warnings %} - - {% endfor %} -
- {% endif %} - {% if metadata %} {% if single_resource %} {% set current = entities[0] if entities else None %} @@ -300,6 +289,37 @@

+ {% if warnings %} +
+ + {% endif %} +

+
Powered by LODE
\ No newline at end of file diff --git a/lode/viewer/base_viewer.py b/lode/viewer/base_viewer.py index 795fa70..18f1fbb 100644 --- a/lode/viewer/base_viewer.py +++ b/lode/viewer/base_viewer.py @@ -4,6 +4,7 @@ and display names. It also serializes the provenance of each entity. """ import hashlib +import re from typing import Dict, List, Optional, Tuple from lode.models import Literal, Model, Resource, Statement @@ -52,6 +53,22 @@ def get_toc_config(self) -> List[Tuple[str, str, str]]: """Return the table of contents: (class name, section id, type_map key) in display order.""" return [tuple(entry) for entry in self._config["toc"]] + def format_warnings(self, warnings: List[Dict]) -> List[Dict]: + """Return the reader warnings with model class names replaced by this viewer's display names. + + The reader words its messages with internal class names (Attribute, Annotation) and + cannot know how a format shows them; the display names live in the type_map of this + viewer, so the swap happens here, before the warnings reach any output. Only standalone + words are replaced: a class name inside an IRI (.../Concept, ...#Concept) is left alone. + Returns copies, the reader's own list is never modified. + """ + names = {key.capitalize(): entry["singular"] for key, entry in self._config["type_map"].items()} + if not names: + return [dict(w) for w in warnings] + pattern = re.compile(r"(? str: """Turn an attribute or getter name into a display label, using this viewer's vocabulary.""" return clean_name(name, self._config["vocabulary"]) diff --git a/lode/warnings.json b/lode/warnings.json deleted file mode 100644 index e8a6926..0000000 --- a/lode/warnings.json +++ /dev/null @@ -1,22 +0,0 @@ -[ - { - "code": "property_type_conflict", - "subject": "http://purl.org/dc/terms/creator", - "message": "Β§5.8.1: http://purl.org/dc/terms/creator has multiple property types: ['Annotation', 'Relation']" - }, - { - "code": "property_type_conflict", - "subject": "http://purl.org/dc/terms/issued", - "message": "Β§5.8.1: http://purl.org/dc/terms/issued has multiple property types: ['Annotation', 'Attribute']" - }, - { - "code": "property_type_conflict", - "subject": "http://purl.org/dc/terms/modified", - "message": "Β§5.8.1: http://purl.org/dc/terms/modified has multiple property types: ['Annotation', 'Attribute']" - }, - { - "code": "property_type_conflict", - "subject": "http://purl.org/dc/terms/language", - "message": "Β§5.8.1: http://purl.org/dc/terms/language has multiple property types: ['Annotation', 'Relation']" - } -] \ No newline at end of file diff --git a/tests/test_packaging.py b/tests/test_packaging.py index a985522..bd3efb9 100644 --- a/tests/test_packaging.py +++ b/tests/test_packaging.py @@ -15,7 +15,6 @@ def test_package_data_present(): assert (files / "templates" / "viewer.html").is_file() assert (files / "static" / "style.css").is_file() assert (files / "reader" / "config" / "owl.yaml").is_file() - assert (files / "warnings.json").is_file() # --- 2. i template si risolvono a prescindere dalla cwd (prende il path cwd-relative) --- diff --git a/tests/test_static_builder.py b/tests/test_static_builder.py index d14e74f..b87509f 100644 --- a/tests/test_static_builder.py +++ b/tests/test_static_builder.py @@ -157,4 +157,56 @@ def test_internal_links_resolve(built): target = (html.parent / href).resolve() if not target.exists(): broken.append(f"{html.name} -> {href}") - assert not broken, "broken internal links:\n" + "\n".join(broken) \ No newline at end of file + assert not broken, "broken internal links:\n" + "\n".join(broken) + + +# --- warnings report --- + +_WARN_TTL = """ +@prefix owl: . +@prefix rdfs: . +@prefix : . + a owl:Ontology . +:A a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty :p ; + owl:someValuesFrom :B ; owl:allValuesFrom :B ] . +""" + + +def _build_warn_ttl(tmp_path, warnings): + """Load the malformed-restriction ontology and build it into tmp_path/out.""" + src = tmp_path / "w.ttl" + src.write_text(_WARN_TTL, encoding="utf-8") + reader = Reader() + reader.load_instances(str(src), "owl", warnings=warnings) + out = tmp_path / "out" + build_html(reader.get_viewer(), out, reader=reader) + return out + + +def test_report_written_with_warnings(tmp_path): + """The report lists the warning code.""" + out = _build_warn_ttl(tmp_path, warnings=True) + assert "malformed_restriction" in (out / "report.txt").read_text(encoding="utf-8") + + +def test_format_warnings_uses_display_names(tmp_path): + """Viewer swaps model class names for display names, but leaves IRIs alone.""" + src = tmp_path / "h.ttl" + src.write_text(""" +@prefix owl: . +@prefix rdfs: . +@prefix : . + a owl:Ontology . +:p a owl:ObjectProperty ; rdfs:subPropertyOf :q . +:q a owl:DatatypeProperty . +""", encoding="utf-8") + reader = Reader() + reader.load_instances(str(src), "owl", warnings=True) + msg = reader.get_viewer().format_warnings(reader.get_warnings())[0]["message"] + assert "Object Property http://ex.org/Attribute/p" in msg + assert "Data Property http://ex.org/Attribute/q" in msg + + +def test_no_report_without_warnings_flag(tmp_path): + """No report.txt when warnings were not requested.""" + assert not (_build_warn_ttl(tmp_path, warnings=False) / "report.txt").exists() \ No newline at end of file From 69757f676f5cca11f8f128d3113af6f3e8e5481e Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 18:04:29 +0200 Subject: [PATCH 11/21] fix(ui): responsive index form, wrap long IRIs, add shared footer --- lode/static/style.css | 54 ++++++++++++++++++++++++++++++++++++++ lode/templates/index.html | 21 ++++++++++----- lode/templates/viewer.html | 13 ++++++--- 3 files changed, 78 insertions(+), 10 deletions(-) diff --git a/lode/static/style.css b/lode/static/style.css index 55996f3..ff2bd10 100644 --- a/lode/static/style.css +++ b/lode/static/style.css @@ -1031,3 +1031,57 @@ body.toc-sidebar-closed { margin-left: 5rem; } scroll-margin-top: 1rem; } + +/* ========================================================================== + 14. RESPONSIVE + Long IRIs must wrap instead of widening the page; the index form must + stay usable on narrow phones. + ========================================================================== */ + +/* "anywhere" breaks only when a word would overflow, unlike break-all */ +.container-fluid a, +.container-fluid code, +.container-fluid dd, +.container-fluid .card-body { + overflow-wrap: anywhere; +} + +/* Header IRI: wrap on as many lines as needed instead of being cut */ +.resource-meta-uri { + min-width: 0; + overflow-wrap: anywhere; +} + +@media (max-width: 767.98px) { + .submission-form-container { padding: 1.5rem 1rem; } + .submission-form-container img { + display: block; + max-width: 10rem; + margin: 0 auto 1rem; + } + .resource-meta-uri { max-width: 100%; } +} + +@media (max-width: 575.98px) { + /* full-width toggle: the 50% slider keeps working */ + .toggle-switch { display: flex; width: 100%; } + .toggle-option { flex: 1 1 0; padding: 8px 12px; text-align: center; } +} + + +/* ========================================================================== + 15. FOOTER + Shared by the index page and the viewer (live and static site). + ========================================================================== */ + +.site-footer { + margin-top: 3rem; + padding: 1rem; + border-top: 1px solid var(--lode-blue-hairline); + text-align: center; + font-size: .85rem; + color: var(--lode-muted); +} + +.site-footer a { color: var(--lode-blue); } + diff --git a/lode/templates/index.html b/lode/templates/index.html index 3140436..2daf65e 100644 --- a/lode/templates/index.html +++ b/lode/templates/index.html @@ -25,9 +25,9 @@
-
+
-
+
@@ -57,7 +57,7 @@
-
+
@@ -155,7 +155,7 @@
-
+
@@ -169,7 +169,7 @@
-
+

LODE 2.0 is an open source service that automatically extracts entities from semantic artefacts (OWL, RDF/RDFS, SKOS) and renders them, together with their textual definitions, as a human-readable HTML page designed for browsing and @@ -203,6 +203,7 @@

Endpoints

Parameters

+
@@ -279,6 +280,7 @@

Parameters

+

Examples

@@ -340,7 +342,14 @@

Reporting bugs

LODE 2.0 is developed in the open. Open an issue at github.com/opencitations/lode/issues.

-
+
+ +
-
Powered by LODE
+ \ No newline at end of file From 6c4a679272e377919b074da841b6a0805d817a1d Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 18:11:14 +0200 Subject: [PATCH 12/21] chore(packaging): add keywords and Documentation/Issues URLs --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a706a01..94a6425 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = [{name = "Valentina Pasqual, Silvio Peroni", email = "valentina.pasqua readme = "README.md" license = {text = "ISC"} requires-python = ">=3.10" -keywords = [] +keywords = ["owl", "ontology", "rdf", "skos", "documentation", "semantic-web", "opencitations"] classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", @@ -39,6 +39,8 @@ lode = "lode.cli:main" [project.urls] Homepage = "https://github.com/opencitations/lode" Repository = "https://github.com/opencitations/lode" +Documentation = "https://opencitations.github.io/lode/" +Issues = "https://github.com/opencitations/lode/issues" [dependency-groups] dev = [ From 930b0290e410a4f3fc83364f9ef510b8c627af2e Mon Sep 17 00:00:00 2001 From: Valentina Date: Fri, 16 Oct 2026 18:27:18 +0200 Subject: [PATCH 13/21] docs: explain base install vs [server] extra --- docs/api/endpoints.md | 5 ++++- docs/getting_started.md | 19 +++++++++++++++++++ docs/usage/cli.md | 3 +-- docs/usage/web_form.md | 5 +++-- 4 files changed, 27 insertions(+), 5 deletions(-) diff --git a/docs/api/endpoints.md b/docs/api/endpoints.md index 44baec1..567acdc 100644 --- a/docs/api/endpoints.md +++ b/docs/api/endpoints.md @@ -1,5 +1,8 @@ # API endpoints +The API is part of the web service and needs the `[server]` extra +(`pip install "oc-lode[server]"`, see [Getting started](../getting_started.md#which-install-do-i-need)). + Interactive docs available at `/docs` (Swagger) and `/redoc` (ReDoc) when the server is running. ## GET / @@ -16,7 +19,7 @@ Render an artefact as HTML or RDF. | Parameter | Type | Required | Description | |-----------|------|----------|-------------| -| `read_as` | enum | yes | `owl` \| `rdf` \| `skos` | +| `read_as` | enum | yes | `owl` \| `rdf` \| `skos` - Currently only `owl` is available| | `url` | string | one of | Public http(s) URL | | `upload_id` | string | one of | Token from a previous upload | | `resource` | string | no | IRI of a single resource | diff --git a/docs/getting_started.md b/docs/getting_started.md index 8f38258..be76823 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -14,6 +14,25 @@ pip install oc-lode pip install "oc-lode[server]" ``` +### Which install do I need? + +The base install is enough for the CLI and for using LODE as a library: `lode build` +and the `lode.reader` / `lode.viewer` modules. It installs `rdflib`, `jinja2`, +`requests`, `minify-html` and `pyyaml`. + +The web service and the REST API (`lode serve`, `lode.api`) need the `[server]` extra, +which adds `fastapi`, `uvicorn`, `gunicorn` and `python-multipart`. + +| You want to... | Install | +|----------------|---------| +| Build static docs with `lode build` | `pip install oc-lode` | +| Run `lode serve` or import `lode.api` | `pip install "oc-lode[server]"` | + +!!! warning + Without the extra, `lode serve` exits with + `Server dependencies missing: pip install oc-lode[server]`, and + `import lode.api` fails with `ModuleNotFoundError: No module named 'fastapi'`. + ## First run Start the web server (requires the `[server]` extra): diff --git a/docs/usage/cli.md b/docs/usage/cli.md index 7efddd6..1d4c251 100644 --- a/docs/usage/cli.md +++ b/docs/usage/cli.md @@ -26,14 +26,13 @@ lode build (--url URL | --file FILE) --read-as FORMAT [OPTIONS] |--------|----------|-------------| | `--url` | one of | Public http(s) URL of the artefact | | `--file` | one of | Local file path | -| `--read-as` | yes | Artefact type: `owl`, `rdf`, `skos` | +| `--read-as` | yes | Artefact type: `owl`, `rdf`, `skos` - Currently only `owl` is available | | `--out` | no | Output directory (default `./lode_output`) | | `--lang` | no | Language tag for labels (default `en`) | | `--artefact-name` | no | File name (without extension) of the root page and its serializations (if omitted, falls back to `index`, so the site starts at `index.html`). Only letters, digits, `.`, `_` and `-` are allowed | | `--imported` | no | Load `owl:imports` at depth 1 | | `--closure` | no | Load the full `owl:imports` closure | | `--partial-import` | no | Load only the imported entities that are actually used | - ## Examples ```bash diff --git a/docs/usage/web_form.md b/docs/usage/web_form.md index 902270c..3f2666c 100644 --- a/docs/usage/web_form.md +++ b/docs/usage/web_form.md @@ -1,6 +1,7 @@ # Web form -Start the server and open `http://localhost:8000`. +Start the server and open `http://localhost:8000`. This needs the `[server]` extra: +`pip install "oc-lode[server]"` (see [Getting started](../getting_started.md#which-install-do-i-need)). ## Input @@ -8,7 +9,7 @@ Start the server and open `http://localhost:8000`. |-------|-------------| | **URL** | Public http(s) URL of the artefact | | **File** | Upload a local `.ttl`, `.rdf`, `.owl`, `.n3`, `.jsonld` file | -| **Format** | Artefact type (`owl`, `rdf`, `skos`) | +| **Format** | Artefact type (`owl`, `rdf`, `skos`) - Currently only `owl` is available | | **Language** | Preferred language for labels (e.g. `en`, `it`) | | **Load imports** | Also fetch `owl:imports` at depth 1 | | **Load closure** | Fetch the full `owl:imports` closure | From dce5eadf938a6c4cc75af73b133ecf2cf126da3e Mon Sep 17 00:00:00 2001 From: Valentina Date: Mon, 19 Oct 2026 12:08:03 +0200 Subject: [PATCH 14/21] chore: align package version with release tag --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 94a6425..1c4b169 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "oc-lode" -version = "0.3.15" +version = "2.1.0" description = "New reengineered version of LODE, maintained by OpenCitations" authors = [{name = "Valentina Pasqual, Silvio Peroni", email = "valentina.pasqual2@unibo.it"}] readme = "README.md" diff --git a/uv.lock b/uv.lock index 9a44003..2fa91d0 100644 --- a/uv.lock +++ b/uv.lock @@ -574,7 +574,7 @@ wheels = [ [[package]] name = "oc-lode" -version = "0.3.15" +version = "2.1.0" source = { editable = "." } dependencies = [ { name = "jinja2" }, From 871f97521ca4251ebc6b3453899fa4efcb639680 Mon Sep 17 00:00:00 2001 From: Valentina Date: Mon, 19 Oct 2026 13:34:40 +0200 Subject: [PATCH 15/21] chore: update documentation for pypi publication --- README.md | 48 ++++++++++++++++++++++++++++++++++++++++++------ pyproject.toml | 19 +++++++++++++------ 2 files changed, 55 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 5d47bfb..0b60680 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,9 @@ LODE 2.0 is an open source service that automatically extracts entities from semantic artefacts (OWL, RDF/RDFS, SKOS) and renders them, together with their textual definitions, as a human-readable HTML page designed for browsing and navigation through embedded links. This new reengineered version of LODE is maintained by OpenCitations. +**Try it online:** a hosted instance of the web service is available at https://lode.opencitations.net/, with no installation needed. + + ## Installation ```bash @@ -16,13 +19,13 @@ pip install "oc-lode[server]" ``` ## Usage - + ```bash # Build static documentation from an ontology URL or a local file lode build --url --read-as [--out ./docs] [--lang en] [--artefact-name index] [--imported] [--closure] lode build --file --read-as [--out ./docs] -# Run the web service (requires the [server] extra) +# Run the web service locally (requires the [server] extra) lode serve --port 8000 ``` @@ -77,14 +80,47 @@ Replace `latest` with the desired version tag. The app will be available at `localhost:8080`. - -