Added test caseologue (#7)

* Reorganization of caseologue python: test data moved into a test folder. test_caseologue.py script added in test folder
* modification of caseologue (dirpath)
* added github actions workflow to run test_caseologue.py + updated readme
* added some test data



Co-authored-by: Lucie Lamothe <[email protected]>

Author: LucieLamothe

.github/workflows/README.md

@@ -1,6 +1,6 @@
 ### GitHub Actions workflows for caseologue
 
-`build_docs.yml` : will run when a modification occurs in the docs/ directpry of the caseologye.py script. It will trigger the update and deployment of the github page documentation of caseologue. 
+`build_docs.yml` : will run when a modification occurs in the docs/ folder of the caseologye.py script. It will trigger the update and deployment of the github page documentation of caseologue. 
 
 `caseologue_python.yml`: Is a callable workflow to run the caseologue.py script, running custom SPARQL queries. It cannot be run on it's own, it needs to be called by another workflow. It requires as input the ontology path and optionnaly severity level. 
 
@@ -10,4 +10,6 @@
 
 `caseologue_all_tests.yml`: Calls the 3 workflows above (caseologue_python.yml, caseologue_robot_reason.yml, caseologue_robot_report.yml) and run them on the current dev version of EDAM. It can only be run mannualy on the GitHub Actions interface. It runs all test including the one with a "curation" level in caseologue python. 
 
-`caseologue_error_essential.yml`: Calls the 3 workflows above (caseologue_python.yml, caseologue_robot_reason.yml, caseologue_robot_report.yml) and run them on the current dev version of EDAM. It is triggered by every push on the caseologue repository and can be run manually on the GitHub Actions interface. For caseologue python, it only runs the test with a "error" and "essential" level. 
+`caseologue_error_essential.yml`: Calls the 3 workflows above (caseologue_python.yml, caseologue_robot_reason.yml, caseologue_robot_report.yml) and run them on the current dev version of EDAM. It is triggered by every push on the caseologue repository and can be run manually on the GitHub Actions interface. For caseologue python, it only runs the test with a "error" and "essential" level. 
+
+`test_caseologue.yml`: runs the test_caseologue.py script in th caseologue_oyhton/test/ folder. It tests that caseologue tests do catch errors in the test data owl files. 

.github/workflows/caseologue_python.yml

@@ -35,6 +35,7 @@ jobs:
     - name: run 
       run: |
         cd caseologue_python/
+        printf "\n_____________________________________________________________________________________________\n\nFollowing debug table can be found as a tsv file at the bottom of the summary of this job\n_____________________________________________________________________________________________"
         EDAM_PATH=${{inputs.edam_path}} python3 caseologue.py ${{inputs.caseologue_options}}
      
     # - name: Print output

.github/workflows/test_caseologue.yml

@@ -0,0 +1,31 @@
+
+name: test caseologue
+
+on: 
+  workflow_dispatch:
+  push:
+    paths: 
+      - 'caseologue_python/**'
+
+jobs:
+  
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      
+    - uses: actions/checkout@v2
+
+    - name: Install requirements
+      run: |
+        pip install -r caseologue_python/requirements.txt
+    - name: run test_caseologue
+      if: always()
+      run: |
+        cd caseologue_python/test/
+        python3 test_caseologue.py
+
+
+
+# duplicate all not tested, too long to run

caseologue_python/README.md

@@ -43,6 +43,11 @@ _____________________________________
 
       3.3. Update the suite() function at the top of the script. According to the error level you chose you will add after the "if curation/error/essential == True" line, a "suite.addTest(EdamQueryTest("XXXXtest_function_nameXXX"))" line. Warning: the test function name should be the same as the one defined in the function you defined just before. 
 
-4) **Run the test**
+
+4) **Add test to test_caseologue**
+
+  In the main function of test_caseologue.py, add a call of the "test_caseologue" function with the name of your newly added test and the number of expected error from your test data.
+
+5) **Run the test**
 
     First run it with its test data, see README.md in the ./caseologue_python/queries folder. Then test it with the whole EDAM, see README in the ./caseologue_python folder.