Merge pull request #17 from MetabolicAtlas/chore/refactor-output

chore: refactor output

.github/workflows/validation.yml

@@ -30,7 +30,7 @@ jobs:
           python -c 'import runner; runner.matrix()'
 
       - name: Commit index of standard-GEMs
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_user_name: validation-bot
           commit_message: update index of standard-GEMs
@@ -61,7 +61,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
@@ -74,7 +74,7 @@ jobs:
         run: git pull --ff
 
       - name: Auto-commit results
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_user_name: validation-bot
           commit_message: update validation results for ${{ matrix.gem }}

index.json

@@ -1 +1 @@
-["SysBioChalmers/yeast-GEM", "SysBioChalmers/Human-GEM", "SysBioChalmers/Mouse-GEM", "SysBioChalmers/Fruitfly-GEM", "SysBioChalmers/Zebrafish-GEM", "SysBioChalmers/Sco-GEM", "iAMB-RWTH-Aachen/Opol-GSMM", "SysBioChalmers/Worm-GEM", "tibbdc/vna-GEM", "SysBioChalmers/Rat-GEM", "AlmaasLab/T66-GEM"]
+["SysBioChalmers/yeast-GEM", "SysBioChalmers/Human-GEM", "SysBioChalmers/Mouse-GEM", "SysBioChalmers/Fruitfly-GEM", "SysBioChalmers/Zebrafish-GEM", "SysBioChalmers/Sco-GEM", "iAMB-RWTH-Aachen/Opol-GSMM", "SysBioChalmers/Worm-GEM", "SysBioChalmers/Rat-GEM", "tibbdc/vna-GEM", "AlmaasLab/T66-GEM"]

results/AlmaasLab_T66-GEM.json

@@ -1,5 +1,60 @@
 {
   "AlmaasLab/T66-GEM": [
+    {
+      "main": {
+        "standard-GEM": [
+          {
+            "0.4": true
+          },
+          {
+            "test_results": {
+              "cobrapy-load-json": {
+                "description": "Check if the model in JSON format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
+              },
+              "cobrapy-load-matlab": {
+                "description": "Check if the model in Matlab format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
+              },
+              "cobrapy-load-sbml": {
+                "description": "Check if the model in SBML format can be loaded with cobrapy.",
+                "errors": "",
+                "status": true,
+                "version": "0.26.2"
+              },
+              "cobrapy-load-yaml": {
+                "description": "Check if the model in YAML can be loaded with cobrapy.",
+                "errors": "\"while parsing a block mapping\\n  in \\\"T66-GEM.yml\\\", line 51085, column 9\\nexpected <block end>, but found '<scalar>'\\n  in \\\"T66-GEM.yml\\\", line 51085, column 18\"",
+                "status": false,
+                "version": "0.26.2"
+              },
+              "cobrapy-validate-sbml": {
+                "description": "Check with cobrapy if the model in SBML format is valid.",
+                "errors": "",
+                "status": true,
+                "version": "0.26.2"
+              },
+              "memote-score": {
+                "description": "Check the score of the model in SBML format with Memote.",
+                "errors": "",
+                "status": 0.48120642579796324,
+                "version": "0.13.0"
+              },
+              "yamllint": {
+                "description": "Check if the model in YAML format is formatted correctly.",
+                "errors": "[\"51085:18: syntax error: expected <block end>, but found '<scalar>' (syntax)\"]",
+                "status": false,
+                "version": "1.29.0"
+              }
+            }
+          }
+        ]
+      }
+    },
     {
       "v0.1.0-alpha": {
         "standard-GEM": [
@@ -9,32 +64,46 @@
           {
             "test_results": {
               "cobrapy-load-json": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'T66-GEM.json'\""
+                "description": "Check if the model in JSON format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-load-matlab": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'T66-GEM.mat'\""
+                "description": "Check if the model in Matlab format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-load-sbml": {
-                "0.26.2": false,
-                "errors": "\"The file with 'T66-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check if the model in SBML format can be loaded with cobrapy.",
+                "errors": "",
+                "status": true,
+                "version": "0.26.2"
               },
               "cobrapy-load-yaml": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'T66-GEM.yml'\""
+                "description": "Check if the model in YAML can be loaded with cobrapy.",
+                "errors": "\"while parsing a block mapping\\n  in \\\"T66-GEM.yml\\\", line 51085, column 9\\nexpected <block end>, but found '<scalar>'\\n  in \\\"T66-GEM.yml\\\", line 51085, column 18\"",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-validate-sbml": {
-                "0.26.2": false,
-                "errors": "\"The file with 'T66-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check with cobrapy if the model in SBML format is valid.",
+                "errors": "",
+                "status": true,
+                "version": "0.26.2"
               },
               "memote-score": {
-                "0.13.0": false,
-                "errors": "\"The file with 'T66-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check the score of the model in SBML format with Memote.",
+                "errors": "",
+                "status": 0.48120642579796324,
+                "version": "0.13.0"
               },
               "yamllint": {
-                "1.29.0": false,
-                "errors": "\"[Errno 2] No such file or directory: 'T66-GEM.yml'\""
+                "description": "Check if the model in YAML format is formatted correctly.",
+                "errors": "[\"51085:18: syntax error: expected <block end>, but found '<scalar>' (syntax)\"]",
+                "status": false,
+                "version": "1.29.0"
               }
             }
           }

results/SysBioChalmers_Sco-GEM.json

@@ -1,5 +1,17 @@
 {
   "SysBioChalmers/Sco-GEM": [
+    {
+      "main": {
+        "standard-GEM": [
+          {
+            "0.4": false
+          },
+          {
+            "test_results": {}
+          }
+        ]
+      }
+    },
     {
       "v1.3.1": {
         "standard-GEM": [

results/tibbdc_vna-GEM.json

@@ -1,5 +1,17 @@
 {
   "tibbdc/vna-GEM": [
+    {
+      "main": {
+        "standard-GEM": [
+          {
+            "0.4": false
+          },
+          {
+            "test_results": {}
+          }
+        ]
+      }
+    },
     {
       "0.1": {
         "standard-GEM": [
@@ -9,32 +21,46 @@
           {
             "test_results": {
               "cobrapy-load-json": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'vna-GEM.json'\""
+                "description": "Check if the model in JSON format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-load-matlab": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'vna-GEM.mat'\""
+                "description": "Check if the model in Matlab format can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-load-sbml": {
-                "0.26.2": false,
-                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check if the model in SBML format can be loaded with cobrapy.",
+                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\"",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-load-yaml": {
-                "0.26.2": false,
-                "errors": "\"[Errno 2] No such file or directory: 'vna-GEM.yml'\""
+                "description": "Check if the model in YAML can be loaded with cobrapy.",
+                "errors": "File missing",
+                "status": false,
+                "version": "0.26.2"
               },
               "cobrapy-validate-sbml": {
-                "0.26.2": false,
-                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check with cobrapy if the model in SBML format is valid.",
+                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\"",
+                "status": false,
+                "version": "0.26.2"
               },
               "memote-score": {
-                "0.13.0": false,
-                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\""
+                "description": "Check the score of the model in SBML format with Memote.",
+                "errors": "\"The file with 'vna-GEM.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:\\n\"",
+                "status": false,
+                "version": "0.13.0"
               },
               "yamllint": {
-                "1.29.0": false,
-                "errors": "\"[Errno 2] No such file or directory: 'vna-GEM.yml'\""
+                "description": "Check if the model in YAML format is formatted correctly.",
+                "errors": "\"[Errno 2] No such file or directory: 'vna-GEM.yml'\"",
+                "status": false,
+                "version": "1.29.0"
               }
             }
           }

runner.py

@@ -12,8 +12,8 @@
 RELEASES = 5
 
 header_auth = {'Authorization': 'token %s' % API_TOKEN}
-additional_branch_tags = []
-# additional_branch_tags = ['develop']
+# additional_branch_tags = []
+additional_branch_tags = ['main']
 
 def gem_repositories():
     json_request = {"query" : """
@@ -55,7 +55,7 @@ def releases(nameWithOwner):
     release_tags = list(map(lambda x: x['node']['tagName'], json_data))
     if not release_tags:
         return []
-    return release_tags + additional_branch_tags
+    return additional_branch_tags + release_tags 
 
 def matrix():
     m = json.dumps(list(gem_repositories()))
@@ -81,7 +81,7 @@ def validate(nameWithOwner):
         standard_gem_releases = releases('MetabolicAtlas/standard-GEM')
         last_standard = standard_gem_releases[len(standard_gem_releases)-1:]
         for standard_version in last_standard:
-            print("{}: {} | Standard-GEM: {}".format(nameWithOwner, model_release, standard_version))
+            print("{}: {} | standard-GEM version: {}".format(nameWithOwner, model_release, standard_version))
             gem_is_standard = gem_follows_standard(nameWithOwner, model_release, standard_version)
             test_results = {}
             if gem_is_standard:
@@ -91,16 +91,20 @@ def validate(nameWithOwner):
                     if response.ok:
                         with open(my_model, 'w') as file:
                             file.write(response.text)
-                test_results.update(tests.yaml.validate(model))
-                test_results.update(tests.cobra.loadYaml(model))
-                test_results.update(tests.cobra.loadSbml(model))
-                test_results.update(tests.cobra.loadMatlab(model))
-                test_results.update(tests.cobra.loadJson(model))
-                test_results.update(tests.cobra.validateSbml(model))
-                test_results.update(tests.memote.scoreAnnotationAndConsistency(model))
+                test_results.update(resultJSONString(tests.cobra.loadYaml, model))
+                test_results.update(resultJSONString(tests.cobra.loadSbml, model))
+                test_results.update(resultJSONString(tests.cobra.loadMatlab, model))
+                test_results.update(resultJSONString(tests.cobra.loadJson, model))
+                test_results.update(resultJSONString(tests.cobra.validateSbml, model))
+                test_results.update(resultJSONString(tests.yaml.validate, model))
+                test_results.update(resultJSONString(tests.memote.scoreAnnotationAndConsistency, model))
             else:
                 print('is not following standard')
             release_data = { 'standard-GEM' : [ { standard_version : gem_is_standard }, { 'test_results' : test_results} ] }
         data[nameWithOwner].append({ model_release: release_data })
     with open('results/{}_{}.json'.format(owner, model), 'w') as output:
-        output.write(json.dumps(data, indent=2, sort_keys=True))
+        output.write(json.dumps(data, indent=2, sort_keys=True))
+
+def resultJSONString(testToRun, model):
+    testModule, description, moduleVersion, status, errors = testToRun(model)
+    return {testModule: { 'description': description, 'version': moduleVersion, 'status': status, 'errors': errors[:300] } }