NEVER merge: Tracking changes on DEV branch

docker/odklite/Dockerfile

@@ -15,7 +15,7 @@ ENV PATH="/tools:/tools/dosdptools/bin:$PATH"
 ARG ODK_VERSION=0.0.0
 ENV ODK_VERSION=$ODK_VERSION
 
-ARG ROBOT_JAR=https://github.com/ontodev/robot/releases/download/v$ROBOT_VERSION/robot.jar
+ARG ROBOT_JAR=https://incenp.org/files/softs/robot/1.9/robot-1.9.5-fix-owlapi1112.jar
 ENV ROBOT_JAR=$ROBOT_JAR
 
 # Install base tools from Ubuntu.

odk/odk.py

@@ -609,6 +609,10 @@ class OntologyProject(JsonSchemaMixin):
     """If set to True, the reasoner will be used during the release process. The reasoner is used for three operations:
     reason (the classification/subclassOf hierarchy computaton); materialize (the materialisation of simple existential/
     object property restrictions); reduce (the removal of redundant subclassOf axioms)."""
+
+    release_annotate_inferred_axioms : bool = False
+    """If set to True, axioms that are inferred during the reasoning process are annotated accordingly, 
+    see https://robot.obolibrary.org/reason."""
 
     release_materialize_object_properties : List[str] = None
     """Define which object properties to materialise at release time."""

template/_dynamic_files.jinja2

@@ -688,6 +688,8 @@ WARN	duplicate_label_synonym
 ERROR	duplicate_label
 WARN	duplicate_scoped_synonym
 WARN	equivalent_pair
+WARN	equivalent_class_axiom_no_genus
+ERROR	illegal_use_of_built_in_vocabulary
 WARN	invalid_xref
 ERROR	label_formatting
 ERROR	label_whitespace
@@ -698,11 +700,16 @@ WARN	missing_obsolete_label
 ERROR	missing_ontology_description
 ERROR	missing_ontology_license
 ERROR	missing_ontology_title
+WARN	missing_subset_declaration
 INFO	missing_superclass
+WARN	missing_synonymtype_declaration
 ERROR	misused_obsolete_label
+ERROR	misused_replaced_by
 ERROR	multiple_definitions
 ERROR	multiple_equivalent_classes
+ERROR	multiple_equivalent_class_definitions
 ERROR	multiple_labels
+WARN	invalid_entity_uri
 {%- endif %}
 {%- if 'basic' in project.release_artefacts or project.primary_release == 'basic' %}
 ^^^ src/ontology/keeprelations.txt
@@ -1845,4 +1852,92 @@ jobs:
           GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
           CONFIG_FILE: mkdocs.yaml
 {% endif -%}
-{% endif -%}
+{% endif -%}
+{% if (('github_actions' in project.ci) and ('github' in project.workflows)) %}
+^^^ .github/ISSUE_TEMPLATE/add-term.yml
+name: Add term- Request a New Ontology Term
+description: Request a new term to be added to the {{ project.title }}.
+title: Request for new term [ADD NAME HERE]
+labels: [ New term request ]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Use this form to request a new ontology term be added to {{ project.id | upper }}.
+  - type: input
+    id: Label
+    attributes:
+      label: Label
+      description: Preferred term label. Please add the label in lowercase, unless it is a proper name.
+      placeholder: ex. spindle cell rhabdomyosarcoma
+    validations:
+      required: true
+  - type: input
+    id: synonyms
+    attributes:
+      label: Synonyms
+      description: Alternative term(s) or acroynymm for the preferred label. Separate by a comma.
+      placeholder:  ex. SCRMS, SC rhabdomyosarcoma
+    validations:
+      required: false
+  - type: dropdown
+    id: synonym_type
+    attributes:
+      label: Synonym type
+      description: Please indicate if the synonym is exact, broad, narrow or related. See [here for more explanation of synonym scope](https://mondo.readthedocs.io/en/latest/editors-guide/f-entities/#synonym-scope).
+      options:
+        - exact
+        - broad
+        - narrow
+        - related
+    validations:
+      required: false
+  - type: textarea
+    id: description
+    attributes:
+      label: Definition
+      description: |
+        Please provide a definition of the term and a reference, such as a PubMed ID, if applicable, in format PMID:#######. 
+    validations:
+      required: true
+  - type: input
+    id: parent
+    attributes:
+      label: Parent term
+      description: Provide a parent term or superclass, i.e. the class this new term should be classified under. Provide the ID and label.
+      placeholder: BFO:0000001
+    validations:
+      required: true
+  - type: input
+    id: children
+    attributes:
+      label: Children term(s)
+      description: List any existing terms that should be classified underneath this new proposed term, if applicable. Provide the ID and label.
+      placeholder: ex. MONDO:0100067 childhood spindle cell rhabdomyosarcoma
+    validations:
+      required: false
+  - type: input
+    id: orcid
+    attributes:
+      label: ORCID Identifier
+      description: What is the ORCID identifier of the person requesting this term? ORCID identifiers can be made at https://orcid.org.
+      placeholder: e.g. https://orcid.org/0000-0001-5208-3432
+    validations:
+      required: false
+  - type: input
+    id: website
+    attributes:
+      label: Website URL
+      description: Provide a website URL that you'd like to be associated with this new term.
+      placeholder: e.g. https://clinicalgenome.org/affiliation/40005/
+    validations:
+      required: false
+  - type: textarea
+    id: comments
+    attributes:
+      label: Additional comments
+      description: |
+        Please provide any additional comments here. 
+    validations:
+      required: false
+{% endif -%}

template/src/ontology/Makefile.jinja2

@@ -304,6 +304,21 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) {% if project.robot_report.use_base_iris %}{% if project.namespaces is not none %}{% for iri in project.namespaces %}--base-iri {{ iri }} {% endfor %}{% else %}--base-iri $(URIBASE)/{{ project.id.upper() }}_ --base-iri $(URIBASE)/{{ project.id }} {% endif %}{% endif -%} --print 5 -o $@
 
+ROBOT_DEFAULT_REPORT=https://raw.githubusercontent.com/ontodev/robot/master/robot-core/src/main/resources/report_profile.txt
+
+check_for_robot_updates:
+{%- if project.robot_report.custom_profile %}	
+	@wget "$(ROBOT_DEFAULT_REPORT)" -O $(TMPDIR)/report_profile_robot.txt
+	@cut -f2 "$(TMPDIR)/report_profile_robot.txt" | sort > $(TMPDIR)/sorted_tsv2.txt
+	@cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt
+	@comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt
+	@echo "Missing tests:"
+	@cat $(TMPDIR)/missing.txt
+	@rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt
+{%- else %}
+	echo "You are not using a custom profile, so you are getting the joy of the latest ROBOT report!"
+{% endif %}
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -448,6 +463,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \{% if project.import_group.exclude_iri_patterns is not none %}
 		{% for pattern in project.import_group.exclude_iri_patterns %}remove  --select "{{ pattern }}" {% endfor %} \{% endif %}
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals {{ project.import_group.slme_individuals }} --method {{ project.import_group.module_type_slme }} \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 {% else %}
@@ -514,7 +530,7 @@ $(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_mergin
 	if [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then $(ROBOT) {% if ont.is_large %}extract -i $< -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \{% else %}query -i $< --update ../sparql/preprocess-module.ru \
     extract -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \{% endif %}
     remove {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{ iri }} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false \
-		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --select complement \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) {% if ont.annotation_properties is defined %}{% for p in ont.annotation_properties %}--term {{ p }} {% endfor %}{% endif %} -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --select complement \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 {% elif ('mirror' == ont.module_type) or (ont.module_type is none and 'mirror' == project.import_group.module_type) %}
@@ -527,7 +543,7 @@ $(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_mergin
     extract -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \{% endif %}
 		remove {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
-		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) {% if ont.annotation_properties is defined %}{% for p in ont.annotation_properties %}--term {{ p }} {% endfor %}{% endif %} -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
 		$(ANNOTATE_CONVERT_FILE); fi
 {% elif ('custom' == ont.module_type) or (ont.module_type is none and 'custom' == project.import_group.module_type) %}
 $(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% elif 'no_mirror' != ont.mirror_type %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %}
@@ -987,7 +1003,7 @@ merge $(patsubst %, -i %, $(OTHER_SRC)) {% endif %}
 # base: A version of the ontology that does not include any externally imported axioms.
 $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %}
-	reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %}
+	reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %}
 	materialize {% for iri in project.release_materialize_object_properties %}--term {{iri}} {% endfor %} \{% endif %}{% endif %}
 	relax \{% if project.release_use_reasoner %}
 	reduce -r {{ project.reasoner }} \{% endif %}
@@ -1030,7 +1046,7 @@ $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 #	remove --select imports --trim false
 $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %}
-		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% endif %}
+		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms }} \{% endif %}
 		relax \
 		remove --axioms equivalent \
 		relax \
@@ -1058,7 +1074,7 @@ $(ONT)-simple-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED
 # removes any axioms that contains one of the ops that not in the whitelist file
 $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATIONS) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %}
-		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% endif %}
+		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms }} \{% endif %}
 		relax \
 		remove --axioms equivalent \
 		remove --axioms disjoint \

tests/test-release-reason.yaml

@@ -0,0 +1,19 @@
+id: rtrai
+title: "Release Test with reasoning and annotating inferred axioms."
+github_org: obophenotype
+repo: rtrai
+report_fail_on: ERROR
+namespaces: 
+  - http://purl.obolibrary.org/obo/RTRAI_
+  - http://purl.obolibrary.org/obo/PATO_
+release_artefacts: 
+  - full
+  - base
+primary_release: full
+release_annotate_inferred_axioms: true
+import_group:
+  products:
+    - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
+    - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl