Merge branch 'master' of https://github.com/biolink/ontobio into go-s…

…ite-2246-gorule-0000001-rnac-rna-types-are-getting-mangled

.github/workflows/make-tests.yaml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ "3.7", "3.8", "3.9", "3.10", "3.11" ]
+        python: [ "3.9", "3.10", "3.11" ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.gitignore

@@ -49,6 +49,8 @@ coverage.xml
 *,cover
 .hypothesis/
 .pytest_cache/
+tests/resources/mgi.gpi
+tests/resources/mgi.gpi.gz
 
 # Translations
 *.mo

Makefile

@@ -24,13 +24,24 @@ foo:
 
 # only run local tests
 travis_test:
-	pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
-	       tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
-		   tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \
-		   tests/test_goassociation_model.py tests/test_relations.py \
-		   tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
-		   tests/unit/test_clinical_mod.py tests/test_collections.py \
-		   tests/test_gocamgen.py
+	@if [ -d ".venv" ] && [ -f "pyproject.toml" ]; then \
+		echo "Running tests in Poetry environment..."; \
+		poetry run pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
+		tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
+		tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \
+		tests/test_goassociation_model.py tests/test_relations.py \
+		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
+		tests/test_collections.py \
+		tests/test_gocamgen.py; \
+	else \
+		pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
+		tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
+		tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \
+		tests/test_goassociation_model.py tests/test_relations.py \
+		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
+		tests/test_collections.py \
+		tests/test_gocamgen.py; \
+	fi
 
 cleandist:
 	rm dist/* || true

bin/README.md

@@ -1 +1,17 @@
 See [command line docs](http://ontobio.readthedocs.io/en/latest/commandline.html#commandline) on ReadTheDocs
+
+To test validate.py "validate" command, the command that produces the final GPADs in the pipeline via the "mega make" 
+(aka: "produces GAFs, GPADs, ttl" stage), on a particular source:
+
+```bash
+poetry install
+poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/[PIPELINE_BRANCH_NAME]/" --only-dataset mgi MGI
+poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/[PIPELINE_BRANCH_NAME]/" --only-dataset goa_chicken goa
+```
+
+
+To test whether a GAF file is valid (passes all the GORules):
+```bash
+poetry install
+poetry run python3 ontobio-parse-assocs.py --file [path_to_file.gaf] --format GAF -o mgi_valid.gaf --report-md mgi.report.md -r [path_to_go.json] -l all validate
+```

bin/ontobio-parse-assocs.py

@@ -34,6 +34,7 @@
 import sys
 import json
 import logging
+from typing import Dict, List
 
 def main():
     """
@@ -80,7 +81,9 @@ def main():
     parser.add_argument("-g", "--gpi", type=str, required=False, default=None,
                         help="GPI file")
     parser.add_argument("-m", "--metadata_dir", type=dir_path, required=False,
-                        help="Path to metadata directory")
+                        help="Path to metadata directory") 
+    parser.add_argument("--retracted_pub_set", type=argparse.FileType('r'), required=False,
+                        help="Path to retracted publications file") 
     parser.add_argument("-l", "--rule", action="append", required=None, default=[], dest="rule_set",
                         help="Set of rules to be run. Default is no rules to be run, with the exception \
                             of gorule-0000027 and gorule-0000020. See command line documentation in the \
@@ -143,9 +146,17 @@ def main():
         rule_set = assocparser.RuleSet.ALL
 
     goref_metadata = None
+    ref_species_metadata = None  
     if args.metadata_dir:
         absolute_metadata = os.path.abspath(args.metadata_dir)
-        goref_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "gorefs"))    
+        goref_metadata = metadata.yamldown_lookup(os.path.join(absolute_metadata, "gorefs"))
+        ref_species_metadata = metadata.yaml_set(absolute_metadata, "go-reference-species.yaml", "taxon_id")
+
+    retracted_pub_set = None
+    if args.retracted_pub_set:
+        retracted_pub_set = metadata.retracted_pub_set(args.retracted_pub_set.name)
+    elif args.metadata_dir:
+       retracted_pub_set = metadata.retracted_pub_set_from_meta(absolute_metadata)     
 
     # set configuration
     filtered_evidence_file = open(args.filtered_file, "w") if args.filtered_file else None
@@ -161,6 +172,8 @@ def main():
         allow_unmapped_eco=args.allow_unmapped_eco,
         gpi_authority_path=args.gpi,
         goref_metadata=goref_metadata,
+        ref_species_metadata=ref_species_metadata,
+        retracted_pub_set=retracted_pub_set,
         rule_set=rule_set
     )
     p = None