Adding draft for base-plus pipeline

CHANGELOG.md

@@ -4,6 +4,9 @@
 
 - Adding new `make reason_test` command ([pull](https://github.com/INCATools/ontology-development-kit/pull/639), [issue](https://github.com/INCATools/ontology-development-kit/issues/645))
 - Adding intermediate artefact `$(TMPDIR)/$(ONT)-preprocess.owl` to the release workflow which enable the centralisation of preprocessing in a single make step. Basically, rather than creating release artefacts directly from the editors file (e.g. bfo-edit.owl), we add intermediate step from which all releases are derived. This intermediate can then be customised by the user ([pull](https://github.com/INCATools/ontology-development-kit/pull/639), [issue](https://github.com/INCATools/ontology-development-kit/issues/544))
+- Re-defines the base from being "all axioms as edited by the ontology editors" to "all axioms and inferences as specified by the ontology editors". The new goal is much more rigorous in removing axioms from other ontologies as well. The old base file can now be exported as an  "editors release" instead ([pull](https://github.com/INCATools/ontology-development-kit/pull/643), [issue](https://github.com/INCATools/ontology-development-kit/issues/646)).
+- Introduces the option of skipping the use of reasoner during the release process (important for application ontologies), ([pull](https://github.com/INCATools/ontology-development-kit/pull/643), [issue](https://github.com/INCATools/ontology-development-kit/issues/644))
+- Introduces a new mode that enable the use of ODK entirely without owl:imports in the edit file (this is great in case we want to use the ODK workflows but not check in any files, imports or components, into version control, like huge application ontologies), ([pull](https://github.com/INCATools/ontology-development-kit/pull/643), [issue](https://github.com/INCATools/ontology-development-kit/issues/629)).
 
 # v1.3.1
 

odk/odk.py

@@ -531,12 +531,19 @@ class OntologyProject(JsonSchemaMixin):
     release_artefacts : List[str] = field(default_factory=lambda: ['full', 'base'])
     """A list of release artefacts you wish to be exported."""
 
+    release_use_reasoner : bool = True
+    """If set to True, the reasoner will be used during the release process."""
+
     export_formats : List[str] = field(default_factory=lambda: ['owl', 'obo'])
     """A list of export formats you wish your release artefacts to be exported to, such as owl, obo, gz, ttl."""
 
     namespaces : Optional[List[str]] = None
     """A list of namespaces that are considered at home in this ontology. Used for certain filter commands."""
-
+
+    use_edit_file_imports : bool = True
+    """If True, ODK will release the ontology with imports explicitly specified by owl:imports in the edit file.
+    If False, ODK will build and release the ontology with _all_ imports and _all_ components specified in the ODK config file."""
+
     dosdp_tools_options: str = "--obo-prefixes=true"
     """default parameters for dosdp-tools"""
 
@@ -583,7 +590,7 @@ class OntologyProject(JsonSchemaMixin):
     pattern_pipelines_group : Optional[PatternPipelineGroup] = None
     """Block that includes information on all ontology imports to be generated"""
 
-    robotemplate_group : Optional[RobotTemplateGroup] = None
+    robot_template_group : Optional[RobotTemplateGroup] = None
     """Block that includes information on all ROBOT templates used"""
 
     def fill_missing(self):

template/src/ontology/Makefile.jinja2

@@ -814,26 +814,49 @@ $(ONT).owl: $(ONT)-{{ project.primary_release }}.owl
 	cp $< $@
 {% endif -%}
 
+ROBOT_RELEASE_IMPORT_MODE={% if project.use_edit_file_imports -%}$(ROBOT) merge --input $< {% else -%}
+$(ROBOT) remove --input $< --select imports --trim false {% if project.use_dosdps or project.components is defined -%}
+merge $(patsubst %, -i %, $(OTHER_SRC)) {% endif %}{% if project.import_group is defined -%}
+merge $(patsubst %, -i %, $(IMPORT_FILES)){% endif %}{% endif %}
+
+{% if 'base' in project.release_artefacts or project.primary_release == 'base' -%}
 # base: OTHER sources of interest, such as definitions owl
-$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
+$(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 }} \{% endif %}
+	relax \{% if project.release_use_reasoner %}
+	reduce -r {{ project.reasoner }} \{% endif %}
+	remove {% if project.namespaces is not none %}{% for iri in project.namespaces %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(URIBASE)/{{ project.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false \
+	$(SHARED_ROBOT_COMMANDS) \
+	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		{% if project.release_date -%} --annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+{% endif -%}
+
+{% if 'editors' in project.release_artefacts or project.primary_release == 'editors' -%}
+# base: OTHER sources of interest, such as definitions owl
+$(ONT)-editors.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
 	$(ROBOT) remove --input $< --select imports --trim false \
-		{% if project.use_dosdps or project.components is defined %}merge $(patsubst %, -i %, $(OTHER_SRC)) \
-		{% endif %} $(SHARED_ROBOT_COMMANDS) annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		$(ROBOT_RELEASE_IMPORT_MODE) \
+		$(SHARED_ROBOT_COMMANDS) annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
 		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		{% if project.release_date -%} --annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+{% endif -%}
 
+{% if 'full' in project.release_artefacts or project.primary_release == 'full' -%}
 # Full: The full artefacts with imports merged, reasoned
 $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
-	$(ROBOT) merge --input $< \
-		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \
-		relax \
-		reduce -r {{ project.reasoner }} \
+	$(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 %}
+		relax \{% if project.release_use_reasoner %}
+		reduce -r {{ project.reasoner }} \{% endif %}
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+{% endif -%}
 
 {% if 'non-classified' in project.release_artefacts or project.primary_release == 'non-classified' -%}
 # foo-non-classified: (edit->imports-merged)
 $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
-	$(ROBOT) merge --input $< \
+	$(ROBOT_RELEASE_IMPORT_MODE) \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
 
@@ -842,13 +865,13 @@ $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 # drop every axiom: filter --term-file keep_terms.txt --trim true
 #	remove --select imports --trim false
 $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
-	$(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \
-		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \
+	$(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 %}
 		relax \
 		remove --axioms equivalent \
 		relax \
-		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
-		reduce -r {{ project.reasoner }} \
+		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \{% if project.release_use_reasoner %}
+		reduce -r {{ project.reasoner }} \{% endif %}
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
@@ -858,10 +881,9 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE
 # Should this be the non-classified ontology with the drop foreign axiom filter?
 # Consider adding remove --term "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
 $(ONT)-simple-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
-	$(ROBOT) remove --input $< --select imports --trim true \
-		merge  $(patsubst %, -i %, $(OTHER_SRC))  \
-		remove --axioms equivalent \
-		reduce -r {{ project.reasoner }} \
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+		remove --axioms equivalent \{% if project.release_use_reasoner %}
+		reduce -r {{ project.reasoner }} \{% endif %}
 		filter --select ontology --term-file $(SIMPLESEED) --trim false \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
 {% endif -%}
@@ -871,8 +893,8 @@ $(ONT)-simple-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED
 # See above (David comment) for explanation.
 # 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) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \
-		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \
+	$(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 %}
 		relax \
 		remove --axioms equivalent \
 		remove --axioms disjoint \

tests/test-non-import-release.yaml

@@ -9,6 +9,7 @@ release_artefacts:
   - editors
   - base
 primary_release: base
+release_use_reasoner: FALSE
 import_group:
   release_imports: TRUE
   products: