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Add ability to set base IRIs for report in ODK #609

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merged 4 commits into from
May 27, 2022
Merged

Add ability to set base IRIs for report in ODK #609

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03a7da9
Add ability to set base IRIs for report in ODK
matentzn May 27, 2022
d6d993a
Merge branch 'master' into issue608
matentzn May 27, 2022
6644715
Fix issues and add test
matentzn May 27, 2022
2dd8371
fix to not accidentally exclude the ontology itself.
matentzn May 27, 2022
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3 changes: 3 additions & 0 deletions odk/odk.py
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Expand Up @@ -306,6 +306,9 @@ class ReportConfig(JsonSchemaMixin):
use_labels : bool = True
"""see http://robot.obolibrary.org/report#labels for details. """

use_base_iris: bool = True
"""If true, only reports on problems with entities belonging to this ontology. Set the base_iris using the 'namespaces' at project level."""

custom_profile : bool = False
"""This will replace the call to the standard OBO report to a custom profile instead."""

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4 changes: 2 additions & 2 deletions template/src/ontology/Makefile.jinja2
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Expand Up @@ -190,10 +190,10 @@ endif
# ----------------------------------------

$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
$(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 $@

$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
$(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 $@

# ----------------------------------------
# Release assets
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22 changes: 22 additions & 0 deletions tests/test-robot-report-baseiri.yaml
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@@ -0,0 +1,22 @@
id: rrcb
title: "Test ROBOT report: Base IRIs"
github_org: INCATools
repo: ontology-development-kit
edit_format: owl
namespaces:
- http://purl.obolibrary.org/obo/RRCB_
import_group:
products:
- id: ro
- id: omo
robot_report:
use_base_iris: True
release_reports: True
fail_on : ERROR
use_labels : False
custom_profile : True
report_on :
- edit
custom_sparql_checks : []
custom_sparql_exports :
- basic-report