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Merge pull request #18 from INCATools/orcidio-support
Add basic support for ORCIDIO.
2 parents ac5c30a + c973b3d commit a8230e7

6 files changed

Lines changed: 76 additions & 3 deletions

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‎src/incatools/odk/model.py‎

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@@ -1143,6 +1143,16 @@ class OntologyProject(JsonSchemaMixin):
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release_diff: bool = False
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"""Generates a diff with the previous release."""
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orcidio_support: bool = False
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"""Enables the automatic production of an ORCIDIO import module.
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If enabled, this option will cause the build pipeline to (1) scan
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the ontology for references to ORCID identifiers in all IRI-valued
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annotations, and (2) create a orcidio_import.owl import module
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containing all ORCIDIO individuals corresponding to the referenced
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ORCID identifiers.
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"""
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robot: RobotOptionsGroup = field(default_factory=lambda: RobotOptionsGroup())
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"""ROBOT-related options."""
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‎src/incatools/odk/setup.py‎

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@@ -24,7 +24,7 @@
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SSSOM_SOURCE = "https://github.com/gouttegd/sssom-java/releases/download/sssom-java-1.11.2/sssom-cli-1.11.2.jar"
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DOSDP_SOURCE = "https://github.com/INCATools/dosdp-tools/releases/download/v0.20.0/dosdp-tools-0.20.0.tgz"
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RELGR_SOURCE = "https://github.com/INCATools/relation-graph/releases/download/v2.3.4/relation-graph-cli-2.3.4.tgz"
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ODK_PLUGIN_SOURCE = "https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.1/odk.jar"
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ODK_PLUGIN_SOURCE = "https://github.com/INCATools/odk-robot-plugin/releases/download/odk-robot-plugin-0.3.3/odk.jar"
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SSSOM_PLUGIN_SOURCE = "https://github.com/gouttegd/sssom-java/releases/download/sssom-java-1.11.2/sssom-robot-plugin-1.11.2.jar"
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OBO_EPM_SOURCE = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.epm.json"
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‎src/incatools/odk/template.py‎

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@@ -394,6 +394,8 @@ def update_import_declarations(self) -> None:
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cmd += f" --add {base}/patterns/definitions.owl"
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if self.project.import_pattern_ontology:
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cmd += f" --add {base}/patterns/pattern.owl"
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if self.project.orcidio_support:
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cmd += f" --add {base}/imports/orcidio_import.owl"
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if self.project.edit_format == "owl":
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cmd += f" convert -f ofn -o {self.project.id}-edit.owl"

‎src/incatools/odk/templates/_dynamic_files.jinja2‎

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@@ -32,6 +32,9 @@ import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ proj
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{% endfor -%}
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{% endif -%}
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{% endif -%}
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{% if project.orcidio_support -%}
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import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/orcidio_import.owl
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{% endif -%}
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{% if project.components is defined -%}
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{% for component in project.components.products -%}
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import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/components/{{ component.filename }}
@@ -89,7 +92,10 @@ Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ proj
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Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/{{ imp.id }}_import.owl>)
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{% endfor -%}
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{% endif -%}
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{% endif %}
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{% endif -%}
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{% if project.orcidio_support -%}
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Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/orcidio_import.owl>)
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{% endif -%}
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{% if project.components is defined -%}
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{% for component in project.components.products -%}
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Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/components/{{ component.filename }}>)
@@ -256,6 +262,21 @@ Ontology(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ pr
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^^^ src/ontology/imports/{{ imp.id }}_terms.txt
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{% endfor -%}
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{% endif %}{# ! project.import_group is defined -#}
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{% if project.orcidio_support -%}
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^^^ src/ontology/imports/orcidio_import.owl
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Prefix(:=<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/orcidio_import.owl>)
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Prefix(obo:=<http://purl.obolibrary.org/obo/>)
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Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
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Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
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Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
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Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
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Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
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Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
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Ontology(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/orcidio_import.owl>
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# This is a placeholder, it will be regenerated when makefile is first executed.
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)
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{% endif -%}
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{#
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Metadata files.

‎src/incatools/odk/templates/src/ontology/Makefile.jinja2‎

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@@ -249,7 +249,7 @@ IMPORTS = {% for imp in project.import_group.products %} {{ imp.id }}{% endfor %
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{% else %}
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IMPORTS =
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{% endif %}
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IMPORT_ROOTS = {% if project.import_group.use_base_merging %} $(IMPORTDIR)/merged_import{% else %}$(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)){% endif %}
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IMPORT_ROOTS = {% if project.import_group.use_base_merging %} $(IMPORTDIR)/merged_import{% else %}$(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)){% endif %}{% if project.orcidio_support %} $(IMPORTDIR)/orcidio_import{% endif %}
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IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
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{%- if project.import_group.export_obo %}
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IMPORT_OBO_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).obo)
@@ -786,6 +786,43 @@ no-mirror-refresh-%:
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{% endif %}{# !project.import_group is defined -#}
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{% if project.orcidio_support -%}
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# ----------------------------------------
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# ORCIDIO module
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# ----------------------------------------
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# By default, the ORCIDIO module is seeded from ORCID references in ALL
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# IRI-valued annotations in the ontology, regardless of the annotation
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# property. To seed only from annotations using specific properties,
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# override the following variable with the desired list of properties.
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ORCIDIO_PROPERTIES =
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ifeq ($(IMP),true)
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$(IMPORTDIR)/orcidio_import.owl: $(SRCMERGED) $(MIRRORDIR)/orcidio.owl | all_robot_plugins
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$(ROBOT) odk:extract-orcids --input $(SRCMERGED) \
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--orcid-file $(MIRRORDIR)/orcidio.owl \
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$(foreach p, $(ORCIDIO_PROPERTIES),--property $(p)) \
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$(ANNOTATE_CONVERT_FILE)
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endif
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ifeq ($(MIR),true)
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.PHONY: download-mirror-orcidio
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download-mirror-orcidio: | $(TMPDIR) $(MIRRORDIR)
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@odk-helper download --output $(TMPDIR)/$@.owl \
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--reference $(MIRRORDIR)/orcidio.owl{% if project.import_group is defined %} \
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--max-retry {{ project.import_group.mirror_retry_download }}{% endif %} \
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https://w3id.org/orcidio/orcidio.owl
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$(MIRRORDIR)/orcidio.owl: download-mirror-orcidio
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@if [ -f $(TMPDIR)/download-mirror-orcidio.owl ]; then \
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cp $(TMPDIR)/download-mirror-orcidio.owl $@ ; \
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fi
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endif
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{% endif -%}
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{% if project.components is not none -%}
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# ----------------------------------------
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# Components

‎src/incatools/odk/templates/src/ontology/catalog-v001.xml.jinja2‎

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@@ -11,6 +11,9 @@
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{%- endfor %}
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{%- endif %}
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{%- endif %}
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{%- if project.orcidio_support %}
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<uri name="{{project.uribase}}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/orcidio_import.owl" uri="imports/orcidio_import.owl"/>
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{%- endif %}
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{%- if project.components is defined %}
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{%- for component in project.components.products %}
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<uri name="{{project.uribase}}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/components/{{component.filename}}" uri="components/{{component.filename}}"/>

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