Feature 1419 competency question coverage report

.github/workflows/automated-testing.yml

@@ -12,6 +12,50 @@ jobs:
       - name: make
         run: |
           make
+      - name: validate-profile
+        run: |
+          echo "java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt"
+          java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt
+      - name: verify
+        run: |
+          java -jar build/robot.jar verify --input build/oeo/$(cat VERSION)/oeo-full.owl --queries tests/verify/*
+      - uses: actions/upload-artifact@master
+        with:
+          name: build-artifacts
+          path: build/oeo
+  test:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.7'
+          architecture: x64
+      - uses: actions/setup-java@v2
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+      - uses: actions/download-artifact@master
+        with:
+          name: build-artifacts
+          path: build/oeo
+      - name: install python dependencies
+        run: pip install -r src/scripts/requirements.txt
+      - name: setup robot 1.9.0
+        run: |
+          wget https://github.com/ontodev/robot/releases/download/v1.9.0/robot.jar -O build/robot19.jar
+      - name: Build ETD xlsx
+        run: |
+          java -jar build/robot19.jar merge --input build/oeo/$(cat VERSION)/oeo-full.omn \
+            --include-annotations true \
+          export  --header "ID|LABEL|definition" \
+                  --prefix "OEO: http://openenergy-platform.org/ontology/oeo/OEO_" \
+                  --sort "LABEL" \
+                  --export $(pwd)/build/oeo/$(cat VERSION)/etd.xlsx
+      - name: Build ETD csv
+        run: |
+          python $(pwd)/src/scripts/etd/etd.py $(pwd)/build/oeo/$(cat VERSION)
       - name: consistency
         run: |
           wget https://github.com/owlcs/releases/raw/master/HermiT/org.semanticweb.hermit-packaged-1.4.6.519-SNAPSHOT.jar -O build/hermit.jar
@@ -22,21 +66,39 @@ jobs:
           fi
           echo "Ontology is inconsistent: $OUT"
           exit 1
-      - name: validate-profile
-        run: | 
-          echo "java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt"
-          java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt
-      - name: verify
-        run: |
-          java -jar build/robot.jar verify --input build/oeo/$(cat VERSION)/oeo-full.owl --queries tests/verify/*
-      - name: competency
-        run: |
-          bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl true
-          bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl false
-      - name: Upload Artifacts
+      - name: Upload Ontology
+        if: always()
         uses: actions/upload-artifact@v3
         with:
           name: build-files
           path: |
             build/**/*
-            !build/**/*.jar
+            !build/**/*.jar
+      - name: competency
+        continue-on-error: true
+        run: |
+          pytest -s -v
+          # bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl true
+          # bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl false
+      - name: Upload Artifacts
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: test-report
+          path: build/report.json
+      - name: Get Coverage for badge
+        run : |
+          echo "COVERAGE=$(head build/report.json | grep -o '"coverage": "[^"]*"' | grep -o '[^"]*\%')" >> $GITHUB_ENV
+          REF=${{ github.ref }}
+          IFS='/' read -ra PATHS <<< "$REF"
+          BRANCH_NAME="${PATHS[1]}_${PATHS[2]}"
+          echo "BRANCH=$(echo ${BRANCH_NAME})" >> $GITHUB_ENV
+      - name: Coverage Badge
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: 6d00affa9fbc89c79684d62091d96551
+          filename: open_energy_ontology__${{ env.BRANCH }}.json
+          label: CQ Coverage
+          message: ${{ env.COVERAGE }}
+          color: green

.gitignore

@@ -1 +1,2 @@
 build/
+*/__pycache__/*

CHANGELOG.md

@@ -26,9 +26,12 @@ and the versioning aims to respect [Semantic Versioning](http://semver.org/spec/
 - secondary energy production (#1619)
 - hydro energy, solar energy, wind energy (#1620)
 - gross domestic product (#1623)
-
+- reimplemented competency question tests in pytest (#1420)
+- added commands to filter competency questions from the command line (#1420)
+- added descriptive names to competency questions. and organized them in directories (#1420)
 
 ### Removed
+- old compteency question bash script (#1420)
 
 ## [1.15.0] - 2023-05-31
 

README.md

@@ -2,6 +2,7 @@
 
 [![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
 ![GitHub release (latest by date)](https://img.shields.io/github/v/release/OpenEnergyPlatform/ontology)
+![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/areleu/6d00affa9fbc89c79684d62091d96551/raw/open_energy_ontology__heads_feature-1419-competency-question-coverage-report.json)
 
 # Open Energy Family - Open Energy Ontology (OEO)
 

src/scripts/etd/etd.py

@@ -25,9 +25,7 @@
     df = df.replace('\n', '<br>', regex=True)
     df = df.sort_values("LABEL", key=lambda col: col.str.strip().str.lower())
     # Create one table per letter:
-
-    pathlib.Path(cwd + "/src/scripts/etd/glossary/").mkdir(parents=True, exist_ok=True) 
-
+    pathlib.Path(target_path).joinpath("glossary").mkdir(parents=True, exist_ok=True) 
     # header = GLOSSARY_HEADER + " ".join([f"[{letter}]({BASE_LINK_WIKI}{letter})" for letter in string.ascii_uppercase]) + "\n"
 
     # with open(cwd + "/src/scripts/etd/glossary/glossary.md", "w") as fil:
@@ -55,4 +53,4 @@
     df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-physical/", "")
     df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-model/", "")
     df_csv["ID"] = df_csv["ID"].str.replace(":", "_")
-    df_csv.to_csv(pathlib.Path(target_path).joinpath("glossary/glossary.csv").as_posix(), index=False)
+    df_csv.to_csv(pathlib.Path(target_path).joinpath("glossary/glossary.csv").as_posix(), index=False)

src/scripts/requirements.txt

@@ -1,3 +1,5 @@
 pandas
 tabulate
-openpyxl
+openpyxl
+pytest
+pytest_harvest

tests/competency_questions/q1.omn → tests/competency_questions/deprecated/001_biofuel_is_renewable_fuel.omn

@@ -3,11 +3,11 @@ Prefix: : <http://openenergy-platform.org/ontology/oeo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 # Competency Question: Is  biofuel renewable fuel?
- 
+
 Class: OEO_00000033
 Class: OEO_00000072
 
 Class: OEO_00000072
   SubClassOf: OEO_00000033
-    
+
 # This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409

tests/competency_questions/q29.omn → tests/competency_questions/deprecated/029_biofuel_is_classified_as_renewable_fuel.omn

@@ -12,4 +12,4 @@ Class: OEO_00000033
 Class: OEO_00000072
     SubClassOf: OEO_00000033
 
-# This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409
+# This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409

tests/competency_questions/q43.omn → tests/competency_questions/implementing/043_thermal_energy_bearers_carry_energy.omn

@@ -5,15 +5,14 @@ Prefix: obo: <http://purl.obolibrary.org/obo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 
-# Do all hot things carry energy? 
+# Do all hot things carry energy?
 
 Class: owl:Nothing
 
-ObjectProperty: obo:RO_0000053 #bearer_of 
+ObjectProperty: obo:RO_0000053 #bearer_of
 Class: OEO_00000207      #Thermal energy
 ObjectProperty: obo:RO_0000091 #has_disposition
 Class: OEO_00000151 #energy carrier disposition
 
 EquivalentClasses: ((obo:RO_0000053 some OEO_00000207) and not (obo:RO_0000091 some OEO_00000151)), owl:Nothing
 # All bearers of thermal energy have the disposition of being energy carriers
-

tests/competency_questions/q4.omn → tests/competency_questions/physical/completeness/004_equivalences_to_flourinated_greenhouse_gases.omn

@@ -9,7 +9,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 Class: OEO_00000026
 Class: OEO_00000038
 Class: OEO_00000219
-Class: OEO_00000321
+Class: OEO_00000322
 
 Class: OEO_00000013
     EquivalentTo: OEO_00000026 or OEO_00000038 or OEO_00000219 or OEO_00000322

tests/competency_questions/q5.omn → tests/competency_questions/physical/completeness/005_methane_has_normal_state_of_matter_gaseous.omn

@@ -8,7 +8,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 
 Class: OEO_00000025
 ObjectProperty: OEO_00000529
-Class: OEO_00000182
+Individual: OEO_00000182
 
 Class: OEO_00000025
     SubClassOf: OEO_00000529 value OEO_00000182

tests/competency_questions/q12.omn → tests/competency_questions/physical/completeness/012_gas_fired_power_unit_is_fueled_power_unit.omn

@@ -4,7 +4,7 @@ Prefix: : <http://openenergy-platform.org/ontology/oeo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 
-#Is a gas fired power unit a fuelled power unit?
+#Is a gas fired power unit a fueled power unit?
 
 Class: OEO_00000017
 Class: OEO_00000175

tests/competency_questions/q47.omn → tests/competency_questions/physical/completeness/047_portion_of_hydrogen_is_energy_carrier.omn

@@ -8,7 +8,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 # Every portion of hydrogen is an energy carrier
 
 ObjectProperty: obo:RO_0000091 # has disposion
-Class: OEO_00000028 # energy carrier disposition
+Class: OEO_00000151 # energy carrier disposition
 
 Class: OEO_00000220 # hydrogen
-    SubClassOf: obo:RO_0000091 some OEO_00000028
+    SubClassOf: obo:RO_0000091 some OEO_00000151

tests/conftest.py

@@ -0,0 +1,8 @@
+
+
+def pytest_addoption(parser):
+    parser.addoption("--selected", action="store", default="")
+    parser.addoption("--report", action="store", default="report.json")
+    parser.addoption("--implementation", action="store_true", default=False, help="Run in development tests")
+    parser.addoption("--deprecated", action="store_true", default=False, help="Run deprecated tests")
+