Merge pull request #9 from MetabolicAtlas/feat/memote-docker

feat: use dockerized memote setup

.github/workflows/validation.yml

@@ -8,6 +8,11 @@ on:
 jobs:
   setup:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/metabolicatlas/memote-docker:0.13
+      volumes:
+        - ${{ github.workspace }}:/project:rw
+      options: --user root --workdir /project
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     env:
@@ -19,27 +24,32 @@ jobs:
         with:
           fetch-depth: 1
 
-      - name: Set up Python 3
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - name: Install dependencies
-        run: pip install -r requirements.txt
+      - name: Fetch list of repositories
+        run: |
+          git config --global --add safe.directory /__w/standard-GEM-validation/standard-GEM-validation
+          python -c 'import runner; runner.matrix()'
 
-      - id: set-matrix
-        run: echo "matrix=$(python -c 'import runner; runner.matrix()')" >> $GITHUB_OUTPUT
-
-      - name: Cache pip directory
-        uses: actions/cache@v3
-        id: cache
+      - name: Commit index of standard-GEMs
+        uses: stefanzweifel/git-auto-commit-action@v4
         with:
-          path: ~/.cache/pip
-          key: ${{ github.sha }}
+          commit_user_name: validation-bot
+          commit_message: update index of standard-GEMs
+          file_pattern: index.json
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Define job matrix from index
+        id: set-matrix
+        run: echo "matrix=$(cat index.json)" >> $GITHUB_OUTPUT
 
   validate:
     needs: setup
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/metabolicatlas/memote-docker:0.13
+      volumes:
+        - ${{ github.workspace }}:/project:rw
+      options: --user root --workdir /project
     continue-on-error: true
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -55,23 +65,10 @@ jobs:
         with:
           fetch-depth: 1
 
-      - name: Set up Python 3
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - name: Restore pip cache directory
-        uses: actions/cache@v3
-        id: cache
-        with:
-          path: ~/.cache/pip
-          key: ${{ github.sha }}
-
-      - name: Install dependencies
-        run: pip install -r requirements.txt
-
       - name: Validate repository
-        run: python -c 'import runner; runner.validate("${{ matrix.gem }}")'
+        run: |
+          git config --global --add safe.directory /__w/standard-GEM-validation/standard-GEM-validation
+          python -c 'import runner; runner.validate("${{ matrix.gem }}")'
 
       - name: Update branch
         run: git pull --ff

index.json

@@ -0,0 +1 @@
+["SysBioChalmers/yeast-GEM", "SysBioChalmers/Human-GEM", "SysBioChalmers/Fruitfly-GEM", "SysBioChalmers/Mouse-GEM", "SysBioChalmers/Sco-GEM", "SysBioChalmers/Zebrafish-GEM", "iAMB-RWTH-Aachen/Opol-GSMM", "SysBioChalmers/Worm-GEM", "haowang-bioinfo/Ecoli-GEM", "SysBioChalmers/Rat-GEM", "tibbdc/vna-GEM"]

runner.py

@@ -9,7 +9,7 @@
 API_TOKEN = environ['GH_TOKEN']
 MODEL_FILENAME = 'model'
 MODEL_FORMATS = ['.yml', '.xml', '.mat', '.json']
-RELEASES = 10
+RELEASES = 1
 
 header_auth = {'Authorization': 'token %s' % API_TOKEN}
 additional_branch_tags = []
@@ -59,7 +59,8 @@ def releases(nameWithOwner):
 
 def matrix():
     m = json.dumps(list(gem_repositories()))
-    print(m)
+    with open("index.json", "w") as file:
+        file.write(m)
 
 def gem_follows_standard(nameWithOwner, release, version):
     repo_standard = requests.get('https://raw.githubusercontent.com/{}/{}/.standard-GEM.md'.format(nameWithOwner, release))
@@ -86,12 +87,16 @@ def validate(nameWithOwner):
             if gem_is_standard:
                 for model_format in MODEL_FORMATS:
                     my_model = model + model_format
-                    response = requests.get('https://raw.githubusercontent.com/{}/{}/model/{}'.format(nameWithOwner, model_release, my_model))
-                    with open(my_model, 'w') as file:
-                        file.write(response.text)
+                    response = requests.get('https://raw.githubusercontent.com/{}/{}/model/{}'.format(nameWithOwner, model_release, my_model), timeout=10)
+                    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.load(model))
-                test_results.update(tests.cobra.validateSBML(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))
             else:
                 print('is not following standard')

tests/cobra.py

@@ -1,29 +1,60 @@
 import cobra
 import json
-from os.path import exists
 
-def load(model_filename):
-    print('  load model with cobrapy')
-    is_valid_cobrapy = False
+def loadYaml(model_name):
+    print('load yaml')
+    is_valid = False
     errors = ''
     try:
-        cobra.io.load_yaml_model(model_filename + '.yml')
-        cobra.io.read_sbml_model(model_filename + '.xml')
-        if exists(model_filename + '.mat'):
-            cobra.io.load_matlab_model(model_filename + '.mat')
-        if exists(model_filename + '.json'):
-            cobra.io.load_json_model(model_filename + '.json')
-        is_valid_cobrapy = True
+        cobra.io.load_yaml_model(model_name + '.yml')
+        is_valid = True
     except Exception as e:
         errors = json.dumps(str(e))
         print(e)
-    return {'cobrapy-load': { cobra.__version__ : is_valid_cobrapy, 'errors': errors } }
+    return {'cobrapy-load-yaml': { cobra.__version__ : is_valid, 'errors': errors } }
 
-def validateSBML(model_filename):
-    print('  validate sbml with cobrapy')
+def loadSbml(model_name):
+    print('load sbml')
+    is_valid = False
+    errors = ''
+    try:
+        cobra.io.read_sbml_model(model_name + '.xml')
+        is_valid = True
+    except Exception as e:
+        errors = json.dumps(str(e))
+        print(e)
+    return {'cobrapy-load-sbml': { cobra.__version__ : is_valid, 'errors': errors } }
+
+def loadMatlab(model_name):
+    print('load matlab')
+    is_valid = False
+    errors = ''
+    try:
+        cobra.io.load_matlab_model(model_name + '.mat')
+        is_valid = True
+    except Exception as e:
+        errors = json.dumps(str(e))
+        print(e)
+    return {'cobrapy-load-matlab': { cobra.__version__ : is_valid, 'errors': errors } }
+
+def loadJson(model_name):
+    print('load json')
+    is_valid = False
+    errors = ''
+    try:
+        cobra.io.load_json_model(model_name + '.json')
+        is_valid = True
+    except Exception as e:
+        errors = json.dumps(str(e))
+        print(e)
+    return {'cobrapy-load-json': { cobra.__version__ : is_valid, 'errors': errors } }
+
+
+def validateSbml(model_name):
+    print('validate sbml with cobrapy')
     is_valid_sbml = False
     try:
-        _, result = cobra.io.sbml.validate_sbml_model(model_filename + '.xml')
+        _, result = cobra.io.sbml.validate_sbml_model(model_name + '.xml')
         if result != {}:
             raise Exception(result)
     except Exception as e:

tests/memote.py

@@ -2,15 +2,16 @@
 import json
 import memote
 
-def scoreAnnotationAndConsistency(model_filename):
-    print('  memote scoring')
-    memote_score = 'Scoring failed'
+def scoreAnnotationAndConsistency(model_name):
+    print('memote scoring')
+    memote_score = False
     errors = ''
     try:
-        model = cobra.io.read_sbml_model(model_filename + '.xml')
-        _, results = memote.suite.api.test_model(model, None, True, None, {"basic", "annotation", "consistency"})
-        processed_results = memote.suite.api.snapshot_report(results, None, False)
+        model = cobra.io.read_sbml_model(model_name + '.xml')
+        _, results = memote.suite.api.test_model(model=model, results=True, exclusive=['test_stoichiometric_consistency', 'test_reaction_mass_balance', 'test_reaction_charge_balance', 'test_find_disconnected', 'test_find_reactions_unbounded_flux_default_condition', 'test_metabolite_annotation_presence', 'test_metabolite_annotation_overview', 'test_metabolite_annotation_wrong_ids', 'test_metabolite_id_namespace_consistency', 'test_reaction_annotation_presence', 'test_reaction_annotation_overview', 'test_reaction_annotation_wrong_ids', 'test_reaction_id_namespace_consistency', 'test_gene_product_annotation_presence', 'test_gene_product_annotation_overview', 'test_gene_product_annotation_wrong_ids', 'test_model_id_presence', 'test_metabolites_presence', 'test_reactions_presence', 'test_genes_presence', 'test_compartments_presence', 'test_metabolic_coverage', 'test_unconserved_metabolites', 'test_inconsistent_min_stoichiometry', 'test_find_unique_metabolites', 'test_find_duplicate_metabolites_in_compartments', 'test_metabolites_charge_presence', 'test_metabolites_formula_presence', 'test_find_medium_metabolites', 'test_find_pure_metabolic_reactions', 'test_find_constrained_pure_metabolic_reactions', 'test_find_transport_reactions', 'test_find_constrained_transport_reactions', 'test_find_candidate_irreversible_reactions', 'test_find_reactions_with_partially_identical_annotations', 'test_find_duplicate_reactions', 'test_find_reactions_with_identical_genes'])
+        processed_results = memote.suite.api.snapshot_report(results, config=None, html=False)
         results_json = json.loads(processed_results)
+        print(results_json['score'])
         memote_score = results_json['score']['total_score']
     except Exception as e:
         errors = json.dumps(str(e))

tests/yaml.py

@@ -2,18 +2,19 @@
 from yamllint.config import YamlLintConfig
 import json
 
-def validate(model_filename):
-    print('  validate YAML with yamllint')
-    is_valid_yaml = False
+def validate(model_name):
+    print('validate YAML with yamllint')
+    is_valid = False
     errors = ''
     try:
         conf = YamlLintConfig('{extends: default, rules: {line-length: disable}}')
-        with open(model_filename + '.yml', 'r') as file:
+        with open(model_name + '.yml', 'r') as file:
             errors = list(map(str, yamllint.linter.run(file, conf)))
         if len(errors) == 0:
-            is_valid_yaml = True
+            is_valid = True
         else:
             errors = json.dumps(errors)
     except Exception as e:
+        errors = json.dumps(str(e))
         print(e)
-    return {'yamllint': { yamllint.__version__ : str(is_valid_yaml), 'errors': errors } }
+    return {'yamllint': { yamllint.__version__ : is_valid, 'errors': errors } }