Merge pull request #436 from INCATools/odk1229

Preparing ODK 1.2.29

Author: matentzn

Dockerfile

@@ -41,14 +41,12 @@ RUN apt-get update &&\
     libfreetype6-dev \
     libpng-dev \
     pkg-config \
-    xlsx2csv &&\
-    cd /usr/local/bin \
-    && ln -s /usr/bin/python3 python \
-    && pip3 install --upgrade pip setuptools \
-    && pip3 install -r /tools/requirements.txt \
-  	&& if [ ! -e /usr/bin/pip ]; then ln -s pip3 /usr/bin/pip ; fi \
-  	&& if [[ ! -e /usr/bin/python ]]; then ln -sf /usr/bin/python3 /usr/bin/python; fi \
-  	&& rm -r /root/.cache
+    xlsx2csv \
+    && python3 -m pip install --upgrade pip setuptools \
+    && python3 -m pip install -r /tools/requirements.txt \
+    && if [ ! -e /usr/bin/pip ]; then ln -sf /usr/bin/pip3 /usr/bin/pip ; fi \
+    && if [ ! -e /usr/bin/python ]; then ln -sf /usr/bin/python3 /usr/bin/python; fi \
+    && rm -r /root/.cache
 
 
 ### 3. Install SWI-Prolog

odk/odk.py

@@ -440,6 +440,9 @@ class OntologyProject(JsonSchemaMixin):
     use_external_date: bool = False
     """Flag to set if you want odk to use the host `date` rather than the docker internal `date`"""
 
+    remove_owl_nothing: bool = False
+    """Flag to set if you want odk to remove owl:Nothing from releases."""
+    
     export_project_yaml: bool = False
     """Flag to set if you want a full project.yaml to be exported, including all the default options."""
 

requirements.txt

@@ -18,9 +18,13 @@ rdflib >=0.0
 requests >=0.0
 ruamel.yaml >=0.0
 seaborn>=0.0
-upsetplot==0.4.1
+upsetplot>=0.0
 plotly>=0.0
 networkx==2.5
 ontodev-cogs>=0.0
 sssom==0.14.11.dev0
 mkdocs >= 0.0
+funowl >= 0.0
+kgx >= 0.0
+linkml >= 0.0
+

template/src/ontology/Makefile.jinja2

@@ -672,6 +672,7 @@ $(ONT).json: $(ONT)-{{ project.primary_release }}.owl
 # -----------------------------------------------------
 # Release artefacts: variants (base, full, simple, etc)
 # -----------------------------------------------------
+SHARED_ROBOT_COMMANDS = {% if project.remove_owl_nothing -%}remove --term owl:Nothing{% endif %}
 
 $(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
 	touch $(ONTOLOGYTERMS) && \
@@ -696,7 +697,7 @@ $(ONT).owl: $(ONT)-{{ project.primary_release }}.owl
 $(ONT)-base.owl: $(SRC) $(OTHER_SRC)
 	$(ROBOT) remove --input $< --select imports --trim false \
 		{% if project.use_dosdps or project.components is defined %}merge $(patsubst %, -i %, $(OTHER_SRC)) \
-		{% endif %}annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		{% endif %} $(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 $@
 
@@ -706,13 +707,13 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC)
 		reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \
 		relax \
 		reduce -r {{ project.reasoner }} \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+		$(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 $@
 
 {% if 'non-classified' in project.release_artefacts or project.primary_release == 'non-classified' -%}
 # foo-non-classified: (edit->imports-merged)
 $(ONT)-non-classified.owl: $(SRC) $(OTHER_SRC)
 	$(ROBOT) merge --input $< \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+		$(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 'simple' in project.release_artefacts or project.primary_release == 'simple' -%}
@@ -729,7 +730,7 @@ $(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED)
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
 		reduce -r {{ project.reasoner }} \
 		query --update ../sparql/inject-subset-declaration.ru \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+		$(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 'simple-non-classified' in project.release_artefacts or project.primary_release == 'simple-non-classified' -%}
@@ -743,7 +744,7 @@ $(ONT)-simple-non-classified.owl: $(SRC) $(OTHER_SRC) $(ONTOLOGYTERMS)
 		remove --axioms equivalent \
 		reduce -r {{ project.reasoner }} \
 		filter --select ontology --term-file $(ONTOLOGYTERMS) --trim false \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+		$(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 'basic' in project.release_artefacts or project.primary_release == 'basic' -%}
@@ -760,7 +761,7 @@ $(ONT)-basic.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATIONS)
 		relax \
 		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
 		reduce -r {{ project.reasoner }} \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@
+		$(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 -%}
 {% for r in project.release_artefacts %}
 {%- if r.startswith('custom-') %}