Initial commit

.github/workflows/dashboard.yaml

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+name: Run Dashboard
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths:
+      - 'dashboard-config.yml'
+      - 'Makefile'
+  schedule:
+    # This will run at 05:48 on first day of the month in every month from January through December.
+    - cron: "48 5 1 1-12 *"
+jobs:
+  dashboard:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.3.1
+    strategy:
+      max-parallel: 1
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+      - name: work around permission issue
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+      - name: Clean directories
+        run: rm -rf dashboard ontologies && mkdir -p dashboard ontologies
+      - name: Prepare run
+        run:  cp dashboard-config.yml /tools/OBO-Dashboard/dashboard-config.yml && cp -r sparql/ /tools/OBO-Dashboard/sparql
+      - name: Run dashboard
+        run: obodash -C dashboard-config.yml
+      - name: Copy results
+        run: cp -r /tools/OBO-Dashboard/dashboard/* dashboard/ &&  cp -r /tools/OBO-Dashboard/build/ontologies/* ontologies/
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v4
+        with:
+          commit-message: Update dashboard run
+          title: 'Update dashboard run'
+          body: |
+            Updates the Custom OBO Dashboard

.gitignore

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+ontologies

Makefile

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+dashboard/ ontologies/:
+	mkdir -p $@
+
+.PRECIOUS: dependencies
+dependencies:
+	#pip install networkx==2.6.2
+	echo "No dependencies needed."
+
+.PRECIOUS: run_dashboard
+run_dashboard: | dependencies dashboard/ ontologies/
+	obodash -C dashboard-config.yml

README.md

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+# Template repository to create Custom OBO Foundry Dashboard
+
+Custom configuration at `dashboard-config.yml`
+
+```yaml
+...
+ontologies:
+  custom:
+    - id: Ontology id
+      mirror_from: Link to the OWL file in your repository.
+      title: Ontology's title
+      contact: 
+        email: 
+        label: 
+        orcid: 
+        github: 
+      description: Ontology's description
+      domain: Ontology's domain
+      homepage: Ontology's page
+      products:
+        - id: 
+      dependencies:
+        - id: 
+      tracker: Link to ontology's issue tracker
+      license:
+        url: License's url
+        label: License's label
+      preferredPrefix:
+      base_ns: Base namespaces
+```

_config.yml

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+theme: jekyll-theme-minimal

dashboard-config.yml

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+title: "OBO Dashboard"
+description: "Dashboard for checking ontology quality. Under construction."
+obo_score_weights:
+  no_base:
+    impact_factor: 5
+    max_impact: 5
+  overall_error:
+    impact_factor: 5
+    max_impact: 20
+  overall_warning:
+    impact_factor: 0.5
+    max_impact: 10
+  overall_info:
+    impact_factor: 0.1
+    max_impact: 5
+  report_errors:
+    impact_factor: 0.05
+    max_impact: 10
+  report_warning:
+    impact_factor: 0.01
+    max_impact: 5
+  report_info:
+    impact_factor: 0.005
+    max_impact: 3
+  impact:
+    impact_factor: 1
+    max_impact: 1 
+  dashboard:
+    impact_factor: 1
+    max_impact: 1
+ontologies:
+  custom:
+    - id: tmp
+      mirror_from: "https://raw.githubusercontent.com/monarch-ebi-dev/robot_tests/master/custom-dashboard.owl"
+prefer_base: True
+profile:
+  baseprofile: "https://raw.githubusercontent.com/ontodev/robot/master/robot-core/src/main/resources/report_profile.txt"
+  custom:
+    - "WARN\tfile:./sparql/missing_xrefs.sparql"
+report_truncation_limit: 600
+redownload_after_hours: 0
+environment:
+  ROBOT_JAR: /tools/robot.jar
+  ROBOT: robot

index.md

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+## Welcome to the Custom OBO Foundry Dashboard
+
+
+
+[Dashboard](dashboard/index.html)

odk.sh

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+#!/bin/sh
+# Wrapper script for docker.
+#
+# This is used primarily for wrapping the GNU Make workflow.
+# Instead of typing "make TARGET", type "./run.sh make TARGET".
+# This will run the make workflow within a docker container.
+#
+# The assumption is that you are working in the src/ontology folder;
+# we therefore map the whole repo (../..) to a docker volume.
+#
+# See README-editors.md for more details.
+#echo "WARNING USING ODK 1.2.30!"
+
+docker run -e ROBOT_JAVA_ARGS='-Xmx4G' -e JAVA_OPTS='-Xmx4G' \
+  -v $PWD/dashboard:/tools/OBO-Dashboard/dashboard \
+  -v $PWD/dashboard-config.yml:/tools/OBO-Dashboard/dashboard-config.yml \
+  -v $PWD/Makefile:/work/Makefile \
+  -v $PWD/ontologies:/tools/OBO-Dashboard/build/ontologies \
+  -v $PWD/sparql:/tools/OBO-Dashboard/sparql \
+  -w /work --rm -ti obolibrary/odkfull:v1.3.1 "$@"
+
+#echo "WARNING USING ODK 1.2.30!"

run-dash.sh

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+#!/usr/bin/env bash
+
+set -e
+
+OBODASH="sh odk.sh "
+
+rm -rf dashboard ontologies
+mkdir -p dashboard ontologies
+#$OBODASH refresh -B
+$OBODASH make run_dashboard

sparql/missing_xrefs.sparql

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+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+ VALUES ?property { oboInOwl:hasDbXref }
+ ?entity ?any ?o .
+ FILTER NOT EXISTS { ?entity ?property ?value }
+ FILTER NOT EXISTS { ?entity a owl:Ontology }
+ FILTER NOT EXISTS { ?entity owl:deprecated true }
+ FILTER NOT EXISTS {
+   ?entity rdfs:subPropertyOf oboInOwl:SubsetProperty .
+ }
+ FILTER EXISTS {
+   ?entity ?prop2 ?object .
+   FILTER (?prop2 != rdf:type)
+   FILTER (?prop2 != owl:equivalentClass)
+   FILTER (?prop2 != owl:disjointWith)
+   FILTER (?prop2 != owl:equivalentProperty)
+   FILTER (?prop2 != owl:sameAs)
+   FILTER (?prop2 != owl:differentFrom)
+   FILTER (?prop2 != owl:inverseOf)
+ }
+ FILTER (!isBlank(?entity))
+}
+ORDER BY ?entity