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gouttegdgouttegd
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Update for ODK ROBOT plugin.
Replace my experimental ROBOT plugin by a proper ODK plugin. This involves modifying the calls to some commands, as the consolidated ODK plugin use slightly different options compared to the original experimental plugin.
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-21
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‎docker/odklite/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -60,7 +60,7 @@ RUN wget -nv https://github.com/INCATools/dosdp-tools/releases/download/v$DOSDP_
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# Install ODK plugin for ROBOT
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RUN mkdir -p /tools/robot-plugins && \
63-
wget -nv -O /tools/robot-plugins/odk.jar https://github.com/gouttegd/exp-robot-plugin/releases/download/exp-robot-plugin-$ODK_ROBOT_PLUGIN_VERSION/exp.jar
63+
wget -nv -O /tools/robot-plugins/odk.jar https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-$ODK_ROBOT_PLUGIN_VERSION/odk.jar
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# Install relation-graph
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RUN wget -nv https://github.com/balhoff/relation-graph/releases/download/v$RELATION_GRAPH/relation-graph-cli-$RELATION_GRAPH.tgz && \

‎template/src/ontology/Makefile.jinja2‎

Lines changed: 26 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -522,7 +522,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
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{% for pattern in project.import_group.exclude_iri_patterns %}remove --select "{{ pattern }}" {% endfor %} \{% endif %}
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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 }} \
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remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
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odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
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odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(ANNOTATE_CONVERT_FILE)
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{% else %}
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$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
@@ -532,30 +532,33 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
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{% if 'slme' == project.import_group.module_type %}
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$(IMPORTDIR)/%_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/%.owl{% endif %} $(IMPORTDIR)/%_terms_combined.txt | all_robot_plugins
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$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
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$(ROBOT) annotate -i $< --remove-annotations \
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odk:normalize --add-source true \
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extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations false --individuals {{ project.import_group.slme_individuals }} --method {{ project.import_group.module_type_slme }} \
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odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
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odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif 'minimal' == project.import_group.module_type %}
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$(IMPORTDIR)/%_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/%.owl{% endif %} $(IMPORTDIR)/%_terms_combined.txt | all_robot_plugins
541-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
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$(ROBOT) annotate -i $< --remove-annotations \
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odk:normalize --add-source true \
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extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --method BOT \
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remove --base-iri $(OBOBASE)"/$(shell echo $* | tr a-z A-Z)_" --axioms external --preserve-structure false --trim false \
544-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
546+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/$*_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
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$(ANNOTATE_CONVERT_FILE)
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{% elif 'mirror' == project.import_group.module_type %}
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$(IMPORTDIR)/%_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/%.owl{% endif %} $(IMPORTDIR)/%_terms_combined.txt | all_robot_plugins
549-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
550-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
551+
$(ROBOT) annotate -i $< --remove-annotations \
552+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true --add-source true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif 'filter' == project.import_group.module_type %}
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$(IMPORTDIR)/%_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/%.owl{% endif %} $(IMPORTDIR)/%_terms_combined.txt | all_robot_plugins
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$(ROBOT) merge -i $< \
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odk:annotate --remove-all true --add-source true \
557+
annotate --remove-annotations \
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odk:normalize --add-source true \
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remove --base-iri $(OBOBASE)"/$(shell echo $* | tr a-z A-Z)_" --axioms external --preserve-structure false --trim false \
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remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/$*_terms_combined.txt --select complement \
558-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
561+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif 'custom' == project.import_group.module_type %}
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$(IMPORTDIR)/%_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/%.owl{% endif %}
@@ -579,33 +582,36 @@ ifeq ($(IMP_LARGE),true)
579582
{% if (ont.is_large and ('slme' == ont.module_type or (ont.module_type is none and 'slme' == project.import_group.module_type))) or ('fast_slme' == ont.module_type) or (ont.module_type is none and 'fast_slme' == project.import_group.module_type) %}
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$(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %} $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt | all_robot_plugins
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$(ROBOT) extract -i $< -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --force true --copy-ontology-annotations false --individuals {% if ont.module_type is none %}{{ project.import_group.slme_individuals }} --method {{ project.import_group.module_type_slme }}{% else %}{{ ont.slme_individuals }} --method {{ ont.module_type_slme }}{% endif %} \
582-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
585+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif ('slme' == ont.module_type) or (ont.module_type is none and 'slme' == project.import_group.module_type) %}
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$(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %} $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt | all_robot_plugins
586-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
589+
$(ROBOT) annotate -i $< --remove-annotations \
590+
odk:normalize --add-source true \
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extract -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --individuals {% if ont.module_type is none %}{{ project.import_group.slme_individuals }} --method {{ project.import_group.module_type_slme }}{% else %}{{ ont.slme_individuals }} --method {{ ont.module_type_slme }}{% endif %} \
588-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
592+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif ('filter' == ont.module_type) or (ont.module_type is none and 'filter' == project.import_group.module_type) %}
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$(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %} $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt | all_robot_plugins
592-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
596+
$(ROBOT) annotate -i $< --remove-annotations \
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odk:normalize --add-source true \
593598
extract -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
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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 \
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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 \
596-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
601+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
597602
$(ANNOTATE_CONVERT_FILE)
598603
{% elif ('mirror' == ont.module_type) or (ont.module_type is none and 'mirror' == project.import_group.module_type) %}
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$(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %} $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt | all_robot_plugins
600-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
601-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
605+
$(ROBOT) annotate -i $< --remove-annotations \
606+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true --add-source true \
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$(ANNOTATE_CONVERT_FILE)
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{% elif ('minimal' == ont.module_type) or (ont.module_type is none and 'minimal' == project.import_group.module_type) %}
604609
$(IMPORTDIR)/{{ ont.id }}_import.owl: {% if project.import_group.use_base_merging %}$(MIRRORDIR)/merged.owl{% else %}$(MIRRORDIR)/{{ ont.id }}.owl{% endif %} $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt | all_robot_plugins
605-
$(ROBOT) odk:annotate -i $< --remove-all true --add-source true \
610+
$(ROBOT) annotate -i $< --remove-annotations \
611+
odk:normalize --add-source true \
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extract -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \
607613
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 \
608-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
614+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
609615
remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) {% if ont.annotation_properties is defined %}{% for p in ont.annotation_properties %}--term {{ p }} {% endfor %}{% endif %} -T $(IMPORTDIR)/{{ ont.id }}_terms_combined.txt --select complement --select "classes individuals annotation-properties" \
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$(ANNOTATE_CONVERT_FILE)
611617
{% elif ('custom' == ont.module_type) or (ont.module_type is none and 'custom' == project.import_group.module_type) %}
@@ -787,7 +793,7 @@ $(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl
787793
.PRECIOUS: $(SUBSETDIR)/%.tsv
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789795
$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) all_robot_plugins
790-
$(ROBOT) odk:subset -i $< --subset $* --fill-gaps true --replace true \
796+
$(ROBOT) odk:subset -i $< --subset $* --fill-gaps true \
791797
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@
792798
.PRECIOUS: $(SUBSETDIR)/%.owl
793799

@@ -1232,7 +1238,7 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE
12321238
remove --axioms equivalent \
12331239
filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \{% if project.release_use_reasoner %}
12341240
reduce -r $(REASONER) \{% endif %}
1235-
odk:normalize --base-iri {{ project.uribase }} --inject-subset-declarations true --inject-synonym-declarations true --merge-axioms true \
1241+
odk:normalize --base-iri {{ project.uribase }} --subset-decls true --synonym-decls true --merge-axioms true \
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$(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 $@
12371243
{% endif -%}
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