Uncommented existing test_cli for "oaei-ordo-hp"

docs/conf.py

@@ -13,32 +13,32 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, os.path.abspath("../"))
 
 # -- Project information -----------------------------------------------------
 
-project = 'sssom-py'
-copyright = '2021, Chris Mungall; Nicolas Matentzoglu; Harshad Hegde'
-author = 'Chris Mungall; Nicolas Matentzoglu; Harshad Hegde'
+project = "sssom-py"
+copyright = "2021, Chris Mungall; Nicolas Matentzoglu; Harshad Hegde"
+author = "Chris Mungall; Nicolas Matentzoglu; Harshad Hegde"
 
 # The full version, including alpha/beta/rc tags
-release = '0.3.6-dev'
+release = "0.3.6-dev"
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.githubpages',
-    'sphinx_rtd_theme',
-    'sphinx_click',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.githubpages",
+    "sphinx_rtd_theme",
+    "sphinx_click",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "recommonmark",
 ]
 
 # Napoleon settings
@@ -55,24 +55,24 @@
 napoleon_use_rtype = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'setup.cfg']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "setup.cfg"]
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 html_theme_options = {
     "use_edit_page_button": True,
@@ -84,5 +84,5 @@
     "github_repo": "sssom-py",
     "github_version": "master/docs/",
     "display_github": True,  # Add 'Edit on Github' link instead of 'View page source'
-    "conf_py_path": "/master/docs/", # Path in the checkout to the docs root
+    "conf_py_path": "/master/docs/",  # Path in the checkout to the docs root
 }

sssom/constants.py

@@ -19,17 +19,25 @@
 
 # SCHEMA_VIEW = package_schemaview("sssom_schema")
 
-OWL_EQUIV_CLASS = "http://www.w3.org/2002/07/owl#equivalentClass"
+OWL_EQUIV_CLASS_URI = "http://www.w3.org/2002/07/owl#equivalentClass"
 RDFS_SUBCLASS_OF_URI = "http://www.w3.org/2000/01/rdf-schema#subClassOf"
+RDF_TYPE_URI = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
+SSSOM_SUPERCLASS_OF_URI = "http://w3id.org/sssom/superClassOf"
+SKOS_EXACT_MATCH_URI = "http://www.w3.org/2004/02/skos/core#exactMatch"
+SKOS_CLOSE_MATCH_URI = "http://www.w3.org/2004/02/skos/core#closeMatch"
+SKOS_BROAD_MATCH_URI = "http://www.w3.org/2004/02/skos/core#broadMatch"
+SKOS_NARROW_MATCH_URI = "http://www.w3.org/2004/02/skos/core#narrowMatch"
+OBO_HAS_DB_XREF_URI = "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
+SKOS_RELATED_MATCH_URI = "http://www.w3.org/2004/02/skos/core#relatedMatch"
 
 DEFAULT_MAPPING_PROPERTIES = [
-    "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
-    "http://www.w3.org/2004/02/skos/core#exactMatch",
-    "http://www.w3.org/2004/02/skos/core#broadMatch",
-    "http://www.w3.org/2004/02/skos/core#closeMatch",
-    "http://www.w3.org/2004/02/skos/core#narrowMatch",
-    "http://www.w3.org/2004/02/skos/core#relatedMatch",
-    OWL_EQUIV_CLASS,
+    SKOS_EXACT_MATCH_URI,
+    SKOS_CLOSE_MATCH_URI,
+    SKOS_BROAD_MATCH_URI,
+    SKOS_NARROW_MATCH_URI,
+    OBO_HAS_DB_XREF_URI,
+    SKOS_RELATED_MATCH_URI,
+    OWL_EQUIV_CLASS_URI,
 ]
 
 UNKNOWN_IRI = "http://w3id.org/sssom/unknown_prefix/"
@@ -125,6 +133,7 @@
 CROSS_SPECIES_NARROW_MATCH = "semapv:crossSpeciesNarrowMatch"
 CROSS_SPECIES_BROAD_MATCH = "semapv:crossSpeciesBroadMatch"
 RDF_SEE_ALSO = "rdfs:seeAlso"
+RDF_TYPE = "rdf:type"
 SSSOM_SUPERCLASS_OF = "sssom:superClassOf"
 
 PREDICATE_LIST = [

sssom/parsers.py

@@ -34,9 +34,17 @@
     OBJECT_LABEL,
     OBJECT_SOURCE,
     OBJECT_SOURCE_ID,
-    OWL_EQUIV_CLASS,
+    OWL_EQUIV_CLASS_URI,
     PREDICATE_ID,
+    RDF_TYPE,
+    RDF_TYPE_URI,
     RDFS_SUBCLASS_OF,
+    SKOS_BROAD_MATCH,
+    SKOS_BROAD_MATCH_URI,
+    SKOS_EXACT_MATCH,
+    SKOS_EXACT_MATCH_URI,
+    SKOS_NARROW_MATCH,
+    SKOS_NARROW_MATCH_URI,
     SUBJECT_ID,
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
@@ -667,7 +675,7 @@ def from_obographs(
                         mdict[PREDICATE_ID] = curie_from_uri(predicate_id, prefix_map)
                         mdict[MAPPING_JUSTIFICATION] = MAPPING_JUSTIFICATION_UNSPECIFIED
                         mlist.append(Mapping(**mdict))
-            if "equivalentNodesSets" in g and OWL_EQUIV_CLASS in mapping_predicates:
+            if "equivalentNodesSets" in g and OWL_EQUIV_CLASS_URI in mapping_predicates:
                 for equivalents in g["equivalentNodesSets"]:
                     if "nodeIds" in equivalents:
                         for ec1 in equivalents["nodeIds"]:
@@ -677,7 +685,7 @@ def from_obographs(
                                     mdict[SUBJECT_ID] = curie_from_uri(ec1, prefix_map)
                                     mdict[OBJECT_ID] = curie_from_uri(ec2, prefix_map)
                                     mdict[PREDICATE_ID] = curie_from_uri(
-                                        OWL_EQUIV_CLASS, prefix_map
+                                        OWL_EQUIV_CLASS_URI, prefix_map
                                     )
                                     mdict[
                                         MAPPING_JUSTIFICATION
@@ -817,8 +825,27 @@ def _cell_element_values(
                     mdict[CONFIDENCE] = child.firstChild.nodeValue
                 elif child.nodeName == "relation":
                     relation = child.firstChild.nodeValue
-                    if (relation == "=") and (OWL_EQUIV_CLASS in mapping_predicates):
-                        mdict[PREDICATE_ID] = "owl:equivalentClass"
+                    if (relation == "=") and (
+                        SKOS_EXACT_MATCH_URI in mapping_predicates
+                    ):
+                        mdict[PREDICATE_ID] = SKOS_EXACT_MATCH
+                    elif (relation == "<") and (
+                        SKOS_BROAD_MATCH_URI in mapping_predicates
+                    ):
+                        mdict[PREDICATE_ID] = SKOS_BROAD_MATCH
+                    elif (relation == ">") and (
+                        SKOS_NARROW_MATCH_URI in mapping_predicates
+                    ):
+                        mdict[PREDICATE_ID] = SKOS_NARROW_MATCH
+                    # elif (relation == "%") and (SOMETHING in mapping_predicates)
+                    #     # Incompatible.
+                    #     pass
+                    # elif (relation == "HasInstance") and (SOMETHING in mapping_predicates):
+                    #     pass
+                    elif (relation == "InstanceOf") and (
+                        RDF_TYPE_URI in mapping_predicates
+                    ):
+                        mdict[PREDICATE_ID] = RDF_TYPE
                     else:
                         logging.warning(f"{relation} not a recognised relation type.")
                 else:

sssom/util.py

@@ -1440,7 +1440,7 @@ def get_all_prefixes(msdf: MappingSetDataFrame) -> list:
                         # print(
                         #     f"Slot '{slot}' has an incorrect value: {msdf.metadata[slot]}"
                         # )
-                        raise ValidationError(
+                        logging.warning(
                             f"Slot '{slot}' has an incorrect value: {msdf.metadata[slot]}"
                         )
                     prefix_list.append(get_prefix_from_curie(msdf.metadata[slot]))

sssom/validators.py

@@ -83,7 +83,7 @@ def check_all_prefixes_in_curie_map(msdf: MappingSetDataFrame) -> None:
 
     missing_prefixes = []
     for pref in prefixes:
-        if pref not in list(msdf.prefix_map.keys()):
+        if pref != "" and pref not in list(msdf.prefix_map.keys()):
             missing_prefixes.append(pref)
     if missing_prefixes:
         raise ValidationError(

tests/data/oaei-ordo-hp.yaml

@@ -0,0 +1,2 @@
+license: "https://w3id.org/sssom/license/unspecified"
+mapping_set_id: "https://w3id.org/sssom/sssompy/tests/oeai-ordo-hp"

tests/test_cli.py

@@ -47,9 +47,11 @@ def test_cli_single_input(self):
         # Initially returned 2 tsv and 1 rdf. The RDF failed test
         test_cases = get_all_test_cases()
         for test in test_cases:
-            self.run_convert(runner, test)
-            if test.inputformat == "tsv":
+            if test.inputformat == "alignment-api-xml":
+                self.run_parse(runner, test)
+            elif test.inputformat == "tsv":
                 # These test only run on TSV inputs
+                self.run_convert(runner, test)
                 self.run_validate(runner, test)
                 self.run_parse(runner, test)
 
@@ -123,7 +125,7 @@ def run_parse(self, runner: CliRunner, test_case: SSSOMTestCase) -> Result:
         ]
         if test_case.metadata_file:
             params.append("--metadata")
-            params.append(test_case.metadata_file)
+            params.append(data_dir / test_case.metadata_file)
 
         result = runner.invoke(parse, params)
         self.run_successful(result, test_case)

tests/test_config.yaml

@@ -38,18 +38,20 @@ tests:
 #      HP: "http://purl.obolibrary.org/obo/HP_"
 #      ORDO: "http://www.orpha.net/ORDO/Orphanet_"
 #      oboInOwl: "http://www.geneontology.org/formats/oboInOwl#"
-  # - filename: "oaei-ordo-hp.rdf"
-  #   inputformat: "alignment-api-xml"
-  #   ct_json_elements: 1293
-  #   ct_data_frame_rows: 646
-  #   ct_graph_queries_owl:
-  #     query_count_equivalent_classes: 646
-  #   ct_graph_queries_rdf:
-  #     query_count_equivalent_classes: 646
-  #   curie_map:
-  #     HP: "http://purl.obolibrary.org/obo/HP_"
-  #     ORDO: "http://www.orpha.net/ORDO/Orphanet_"
-  #     oboInOwl: "http://www.geneontology.org/formats/oboInOwl#"
+  - filename: "oaei-ordo-hp.rdf"
+    inputformat: "alignment-api-xml"
+    multiple_input: False
+    ct_json_elements: 7
+    ct_data_frame_rows: 646
+    ct_graph_queries_owl:
+      query_count_equivalent_classes: 0
+    ct_graph_queries_rdf:
+      query_count_equivalent_classes: 0
+    curie_map:
+      HP: "http://purl.obolibrary.org/obo/HP_"
+      ORDO: "http://www.orpha.net/ORDO/Orphanet_"
+      oboInOwl: "http://www.geneontology.org/formats/oboInOwl#"
+    metadata_file: "oaei-ordo-hp.yaml"
 queries:
   query_count_equivalent_classes: >
     SELECT DISTINCT ?e1 ?e2 WHERE {

tests/test_conversion.py

@@ -6,6 +6,7 @@
 import unittest
 from typing import Dict
 
+import yaml
 from rdflib import Graph
 
 from sssom.parsers import get_parsing_function, to_mapping_set_document
@@ -23,6 +24,7 @@
     write_table,
 )
 
+from .constants import data_dir
 from .test_data import SSSOMTestCase, get_all_test_cases
 
 
@@ -36,7 +38,12 @@ def test_conversion(self):
         for test in test_cases:
             with self.subTest(test=test.id):
                 read_func = get_parsing_function(test.inputformat, test.filepath)
-                msdf = read_func(test.filepath, prefix_map=test.prefix_map)
+                if test.metadata_file:
+                    with open(data_dir / test.metadata_file, "r") as f:
+                        meta = yaml.safe_load(f)
+                else:
+                    meta = None
+                msdf = read_func(test.filepath, prefix_map=test.prefix_map, meta=meta)
                 mdoc = to_mapping_set_document(msdf)
                 logging.info(f"Testing {test.filepath}")
                 self.assertEqual(