Initial stable release

- Update: Upgraded oaklib (OAK). This was a necessary, requisite upgrade, and now owl-on-fhir should be functional. - Bugfix: Removed some Obographs JSON patching that I believe was necessary prior. I think what changed is that now OAK is handling something that was causing an error before, but now that it is handling it, the patching I'm doing is causing an OAK error. See: ontodev/robot#1082
timsbiomed · Apr 15, 2023 · 194a00c · 194a00c
1 parent fae696a
commit 194a00c
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diff --git a/owl_on_fhir/__main__.py b/owl_on_fhir/__main__.py
@@ -120,28 +120,6 @@ def owl_to_obograph(inpath: str, native_uri_stems: List[str] = None, use_cache=F
     # graph = parse_results.graph_document.graphs[0]
     _run_shell_command(command)
 
-    # Patch missing roots / etc issue (until resolved: https://github.com/ontodev/robot/issues/1082)
-    if native_uri_stems:
-        with open(outpath, 'r') as f:
-            data = json.load(f)
-        nodes = data['graphs'][0]['nodes']
-        node_ids = set([node['id'] for node in nodes])
-        edges = data['graphs'][0]['edges']
-        # edges = [x for x in edges if x['pred'] in missing_nodes_from_important_edge_preds]
-        edge_subs = set([edge['sub'] for edge in edges])
-        edge_objs = set([edge['obj'] for edge in edges])
-        edge_ids = edge_subs.union(edge_objs)
-        missing = set([x for x in edge_ids if x not in node_ids])  # all missing
-        missing = [x for x in missing if any([x.startswith(y) for y in native_uri_stems])]  # filter
-
-        if missing:
-            print(f'INFO: The following nodes were found in Obographs edges, but not nodes. Adding missing '
-                  f'declarations: {missing}')
-            for node_id in missing:
-                nodes.append({'id': node_id})
-            with open(outpath, 'w') as f:
-                json.dump(data, f)
-
     return outpath
 
 
@@ -151,7 +129,7 @@ def owl_to_obograph(inpath: str, native_uri_stems: List[str] = None, use_cache=F
 #  - https://github.com/geneontology/obographs/issues/89
 def obograph_to_fhir(
     inpath: str, out_dir: str, out_filename: str = None, code_system_id: str = None, code_system_url: str = None,
-    include_all_predicates=False, native_uri_stems: List[str] = None, dev_oak_path: str = None,
+    include_all_predicates=True, native_uri_stems: List[str] = None, dev_oak_path: str = None,
     dev_oak_interpreter_path: str = None
 ) -> str:
     """Convert Obograph to FHIR"""
@@ -176,9 +154,16 @@ def obograph_to_fhir(
     else:
         converter = OboGraphToFHIRConverter()
         converter.curie_converter = curies.Converter.from_prefix_map(get_default_prefix_map())
-        gd: GraphDocument = json_loader.load(inpath, target_class=GraphDocument)
-        converter.dump(gd, out_path, include_all_predicates=include_all_predicates)
-        # todo: update w/ these params when released
+        # TODO: it's erroring on `gd`
+        gd: GraphDocument = json_loader.load(str(inpath), target_class=GraphDocument)
+        converter.dump(
+            gd,
+            out_path,
+            code_system_id=code_system_id,
+            code_system_url=code_system_url,
+            include_all_predicates=include_all_predicates,
+            native_uri_stems=native_uri_stems)
+        # TODO: add these params once supported: use_curies_native_concepts, use_curies_foreign_concepts
         # converter.dump(
         #     gd, out_path, code_system_id='', code_system_url='', include_all_predicates=include_all_predicates,
         #     native_uri_stems=native_uri_stems, use_curies_native_concepts=False, use_curies_foreign_concepts=True)

diff --git a/requirements.txt b/requirements.txt
@@ -1,140 +1,178 @@
 aiohttp==3.8.3
 aiosignal==1.3.1
-alabaster==0.7.12
+airium==0.2.5
+alabaster==0.7.13
 antlr4-python3-runtime==4.9.3
 appdirs==1.4.4
 arrow==1.2.3
 async-timeout==4.0.2
-attrs==22.1.0
+attrs==22.2.0
 Babel==2.11.0
 bcp47==0.0.4
+beautifulsoup4==4.12.2
 bioontologies==0.2.1
-bioregistry==0.5.143
-certifi==2022.9.24
+bioregistry==0.6.99
+bleach==6.0.0
+certifi==2022.12.7
 CFGraph==0.2.1
-chardet==4.0.0
+chardet==5.1.0
 charset-normalizer==2.1.1
-class-resolver==0.3.10
+class-resolver==0.4.2
 click==8.1.3
-curies==0.4.0
+colorama==0.4.6
+contourpy==1.0.7
+curies==0.4.2
+cycler==0.11.0
 decorator==5.1.1
 Deprecated==1.2.13
 deprecation==2.1.0
 distlib==0.3.6
 docutils==0.17.1
+EditorConfig==0.12.3
 et-xmlfile==1.1.0
-exceptiongroup==1.0.4
+exceptiongroup==1.1.0
 fastobo==0.12.2
-filelock==3.8.2
+filelock==3.9.0
+fonttools==4.39.3
 fqdn==1.5.1
 frozenlist==1.3.3
-fsspec==2022.11.0
-funowl==0.1.12
+fsspec==2023.1.0
+funowl==0.1.13
+ghp-import==2.1.0
 graphviz==0.20.1
-greenlet==2.0.1
+greenlet==2.0.2
 hbreader==0.9.1
 idna==3.4
+ijson==3.2.0.post0
 imagesize==1.4.1
 importlib-metadata==4.13.0
-iniconfig==1.1.1
+iniconfig==2.0.0
 isodate==0.6.1
 isoduration==20.11.0
+jaraco.classes==3.2.3
 Jinja2==3.1.2
+jsbeautifier==1.14.7
 json-flattener==0.1.9
 jsonasobj==1.3.1
 jsonasobj2==1.0.4
 jsonpatch==1.32
 jsonpath-ng==1.5.3
 jsonpointer==2.3
 jsonschema==4.17.3
+keyring==23.13.1
 kgcl-rdflib==0.3.0
-kgcl-schema==0.3.1
+kgcl-schema==0.3.6
+kiwisolver==1.4.4
 lark==1.1.5
-linkml==1.3.15
+linkml==1.4.3
 linkml-dataops==0.1.0
-linkml-runtime==1.3.7
-markdown-it-py==2.1.0
-MarkupSafe==2.1.1
+linkml-renderer==0.1.2
+linkml-runtime==1.4.3
+Markdown==3.3.7
+markdown-it-py==2.2.0
+MarkupSafe==2.1.2
+matplotlib==3.7.1
 mdit-py-plugins==0.3.3
 mdurl==0.1.2
+mergedeep==1.3.4
+mkdocs==1.4.2
+mkdocs-material==9.1.6
+mkdocs-material-extensions==1.1.1
+mkdocs-mermaid2-plugin==0.6.0
 more-click==0.1.2
-multidict==6.0.3
+more-itertools==9.1.0
+multidict==6.0.4
 myst-parser==0.18.1
+ndex2==3.5.1
 networkx==2.8.8
-numpy==1.23.5
+numpy==1.24.1
 nxontology==0.4.1
-oaklib==0.1.67
+oaklib==0.5.1
 ols-client==0.1.2
 ontoportal-client==0.0.3
 openpyxl==3.0.10
-packaging==21.3
-pandas==1.5.2
+packaging==23.0
+pandas==1.5.3
 pandasql==0.7.3
+pansql==0.0.1
 parse==1.19.0
-pbr==5.11.0
-platformdirs==2.5.4
+pbr==5.11.1
+Pillow==9.5.0
+pkginfo==1.9.6
+platformdirs==2.6.2
 pluggy==1.0.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.1.4
-pronto==2.5.1
+pronto==2.5.3
 py==1.11.0
-pydantic==1.10.2
-Pygments==2.13.0
+pydantic==1.10.4
+Pygments==2.14.0
 PyJSG==0.11.10
+pymdown-extensions==9.11
 pyparsing==3.0.9
-pyrsistent==0.19.2
+pyrsistent==0.19.3
 PyShEx==0.8.1
 PyShExC==0.9.1
-pystow==0.4.7
-pytest==7.2.0
+pystow==0.5.0
+pytest==7.2.1
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 PyTrie==0.4.0
-pytz==2022.6
+pytz==2022.7.1
 PyYAML==6.0
+pyyaml_env_tag==0.1
 ratelimit==2.2.1
 rdflib==6.2.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
-requests==2.28.1
+readme-renderer==37.3
+regex==2023.3.23
+requests==2.28.2
+requests-toolbelt==0.10.1
 rfc3339-validator==0.1.4
+rfc3986==2.0.0
 rfc3987==1.3.8
+rich==13.3.2
 ruamel.yaml==0.17.21
 ruamel.yaml.clib==0.2.7
-scipy==1.9.3
-semsql==0.2.5
+scipy==1.10.0
+semsql==0.3.2
 ShExJSG==0.8.2
 six==1.16.0
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
+soupsieve==2.4
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
 Sphinx==5.3.0
 sphinx-click==4.4.0
 sphinx-rtd-theme==1.1.1
-sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-applehelp==1.0.4
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
-SQLAlchemy==1.4.44
+SQLAlchemy==1.4.46
 SQLAlchemy-Utils==0.38.3
-sssom==0.3.17
-sssom-schema==0.9.4
+sssom==0.3.28
+sssom-schema==0.11.0
 stevedore==4.1.1
 tomli==2.0.1
-tox==3.27.1
+tox==3.28.0
 tqdm==4.64.1
+twine==4.0.2
 typing_extensions==4.4.0
+UpSetPlot==0.8.0
 uri-template==1.2.0
-urllib3==1.26.13
+urllib3==1.26.14
 validators==0.20.0
 virtualenv==20.17.1
 virtualenv-clone==0.5.7
-watchdog==2.2.0
+watchdog==2.2.1
 webcolors==1.12
+webencodings==0.5.1
 wrapt==1.14.1
 yarl==1.8.2
-zipp==3.11.0
+zipp==3.12.0
diff --git a/setup.py b/setup.py
@@ -15,7 +15,7 @@
 EMAIL = '[email protected]'
 AUTHOR = 'Joe Flack'
 REQUIRES_PYTHON = '>=3.9.0'
-VERSION = '0.1.11'
+VERSION = '0.1.14'
 
 # Requirements
 REQUIRED = [