Add QC workflow (#108)

* update robot version

* simplify dashboard-config

* add qc workflow

* add robot install to qc workflow

* fix run to install robot

* add robot to system path

---------

Co-authored-by: Anita Caron <[email protected]>

Author: Anita Caron

.github/workflows/qc.yml

@@ -0,0 +1,30 @@
+name: QC
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  qc:
+    name: QC
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run:
+            pip install -r requirements.txt
+      - name: Install ROBOT
+        run: |
+            make build/robot.jar
+            make build/robot
+            chmod +x build/robot
+            echo "$PWD/build" >> $GITHUB_PATH
+      - name: Run dashboard
+        run:
+            python ./util/dashboard_config.py rundashboard -C dashboard-config.yml

Makefile

@@ -1,7 +1,8 @@
 MAKEFLAGS += --warn-undefined-variables
 ROBOT_JAR := build/robot.jar
 REPORT_LENGTH_LIMIT := 200
-ROBOT_URL := "https://github.com/ontodev/robot/releases/download/v1.8.3/robot.jar"
+ROBOT_URL := "https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar"
+ROBOT_SCRIPT := "https://raw.githubusercontent.com/ontodev/robot/v1.9.5/bin/robot"
 DASHBOARD_RESULTS := "dashboard/dashboard-results.yml"
 
 # ----------------- #
@@ -42,6 +43,9 @@ ROBOT := java -Xmx10G -jar build/robot.jar
 build/robot.jar: | build
 	curl -o $@ -Lk $(ROBOT_URL)
 
+build/robot:
+	curl -o $@ -Lk $(ROBOT_SCRIPT)
+
 # ------------------------- #
 ### EXTERNAL DEPENDENCIES ###
 # ------------------------- #

dashboard-config.yml

@@ -34,7 +34,9 @@ obo_score_weights:
 ontologies:
   #registry: "https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml"
   custom:
-    - id: genepio
+    - id: agro
+    - id: omo
+    #- id: genepio
     # - id: covoc
     #   mirror_from: "https://raw.githubusercontent.com/EBISPOT/covoc/master/covoc.owl"
     #   license:
@@ -43,51 +45,50 @@ ontologies:
     #     url: http://creativecommons.org/licenses/by/4.0/
     # - id: testx
     # - id: wbphenotype
-    - id: gombo
-      mirror_from: "https://raw.githubusercontent.com/BridgetSquidget/gombo/main/gombo_v1.owx"
-      title: General Ontology for Marine Bioluminescent Organs
-      contact:
-        email: [email protected]
-        label: Bridget Vincent
-        description: An ontology describing the structures in the bioluminescent components of marine animals.
-      domain: anatomy
-      homepage: https://github.com/BridgetSquidget/gombo/blob/main/gombo_v1.owx
-      products:
-        - id: gombo.owl
-        - id: gombo.obo
-      dependencies:
-        - id: uberon
-        - id: afm
-        - id: cl
-        - id: ncit
-        - id: fma
-        - id: spd
-        - id: zfa
-        - id: plana
-        - id: go
-        - id: chebi
-        - id: ms
-        - id: bao
-        - id: ogi
-        - id: scdo
-        - id: so
-        - id: pr
-        - id: obi
-        - id: txpo
-        - id: xco
-        - id: mod
-        - id: nbitaxon
-        - id: ceph
-        - id: xao
-        - id: emapa
-        - id: aeo
-        - id: mc
-        - id: mpath
-      tracker: https://github.com/BridgetSquidget/gombo/issues
-      license:
-        url: https://creativecommons.org/licenses/by/4.0/
-        label: CC BY 4.0
-    - id: omo
+    # - id: gombo
+    #   mirror_from: "https://raw.githubusercontent.com/BridgetSquidget/gombo/main/gombo_v1.owx"
+    #   title: General Ontology for Marine Bioluminescent Organs
+    #   contact:
+    #     email: [email protected]
+    #     label: Bridget Vincent
+    #     description: An ontology describing the structures in the bioluminescent components of marine animals.
+    #   domain: anatomy
+    #   homepage: https://github.com/BridgetSquidget/gombo/blob/main/gombo_v1.owx
+    #   products:
+    #     - id: gombo.owl
+    #     - id: gombo.obo
+    #   dependencies:
+    #     - id: uberon
+    #     - id: afm
+    #     - id: cl
+    #     - id: ncit
+    #     - id: fma
+    #     - id: spd
+    #     - id: zfa
+    #     - id: plana
+    #     - id: go
+    #     - id: chebi
+    #     - id: ms
+    #     - id: bao
+    #     - id: ogi
+    #     - id: scdo
+    #     - id: so
+    #     - id: pr
+    #     - id: obi
+    #     - id: txpo
+    #     - id: xco
+    #     - id: mod
+    #     - id: nbitaxon
+    #     - id: ceph
+    #     - id: xao
+    #     - id: emapa
+    #     - id: aeo
+    #     - id: mc
+    #     - id: mpath
+    #   tracker: https://github.com/BridgetSquidget/gombo/issues
+    #   license:
+    #     url: https://creativecommons.org/licenses/by/4.0/
+    #     label: CC BY 4.0
 prefer_base: True
 profile:
   baseprofile: "https://raw.githubusercontent.com/ontodev/robot/master/robot-core/src/main/resources/report_profile.txt"