Merge pull request #8 from MetabolicAtlas/feat/memote

feat: memote annotation and consistency scoring
MetabolicAtlas · May 10, 2023 · 70e4409 · 70e4409
2 parents 312867d + 135945b
commit 70e4409
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Showing 17 changed files with 697 additions and 473 deletions.
diff --git a/.github/workflows/validation.yml b/.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:
@@ -19,33 +24,39 @@ 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
-
-      - id: set-matrix
-        run: echo "::set-output name=matrix::$(python -c 'import runner; runner.matrix()')"
+      - 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()'
 
-      - 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 }}
     strategy:
       fail-fast: false
-      matrix: ${{fromJson(needs.setup.outputs.matrix)}}
+      matrix:
+        gem: ${{ fromJSON(needs.setup.outputs.matrix) }}
       max-parallel: 1
 
     steps:
@@ -54,29 +65,16 @@ 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
 
       - name: Auto-commit results
-        uses: stefanzweifel/git-auto-commit-action@v4.4.0
+        uses: stefanzweifel/git-auto-commit-action@v4
         with:
           commit_user_name: validation-bot
           commit_message: update validation results for ${{ matrix.gem }}

diff --git a/index.json b/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", "tibbdc/vna-GEM", "SysBioChalmers/Rat-GEM"]
diff --git a/requirements.txt b/requirements.txt
diff --git a/results/SysBioChalmers_Fruitfly-GEM.json b/results/SysBioChalmers_Fruitfly-GEM.json
diff --git a/results/SysBioChalmers_Human-GEM.json b/results/SysBioChalmers_Human-GEM.json
@@ -1,121 +1,206 @@
 {
   "SysBioChalmers/Human-GEM": [
     {
-      "v0.5.2": {
+      "v1.14.0": {
         "standard-GEM": [
           {
-            "0.4": false
+            "0.4": true
           },
           {
-            "test_results": {}
+            "test_results": {
+              "cobrapy-load-json": {
+                "0.26.2": false,
+                "errors": "\"[Errno 2] No such file or directory: 'Human-GEM.json'\""
+              },
+              "cobrapy-load-matlab": {
+                "0.26.2": false,
+                "errors": "\"Error -3 while decompressing data: incorrect header check\""
+              },
+              "cobrapy-load-sbml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-load-yaml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-validate-sbml": {
+                "0.26.2": false,
+                "errors": "\"{'SBML_FATAL': [], 'SBML_ERROR': [], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n', 'E1 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n'], 'COBRA_FATAL': [], 'COBRA_ERROR': [], 'COBRA_WARNING': [], 'COBRA_CHECK': []}\""
+              },
+              "memote-score": {
+                "0.13.0": 0.4740305818784403,
+                "errors": ""
+              },
+              "yamllint": {
+                "1.29.0": true,
+                "errors": []
+              }
+            }
           }
         ]
       }
     },
     {
-      "v0.5.1": {
+      "v1.13.0": {
         "standard-GEM": [
           {
-            "0.4": false
+            "0.4": true
           },
           {
-            "test_results": {}
+            "test_results": {
+              "cobrapy-load-json": {
+                "0.26.2": false,
+                "errors": "\"[Errno 2] No such file or directory: 'Human-GEM.json'\""
+              },
+              "cobrapy-load-matlab": {
+                "0.26.2": false,
+                "errors": "\"Error -3 while decompressing data: incorrect header check\""
+              },
+              "cobrapy-load-sbml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-load-yaml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-validate-sbml": {
+                "0.26.2": false,
+                "errors": "\"{'SBML_FATAL': [], 'SBML_ERROR': [], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n', 'E1 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n'], 'COBRA_FATAL': [], 'COBRA_ERROR': [], 'COBRA_WARNING': [], 'COBRA_CHECK': []}\""
+              },
+              "memote-score": {
+                "0.13.0": 0.47403057916252217,
+                "errors": ""
+              },
+              "yamllint": {
+                "1.29.0": true,
+                "errors": []
+              }
+            }
           }
         ]
       }
     },
     {
-      "v0.5.0": {
+      "v1.12.0": {
         "standard-GEM": [
           {
-            "0.4": false
+            "0.4": true
           },
           {
-            "test_results": {}
+            "test_results": {
+              "cobrapy-load-json": {
+                "0.26.2": false,
+                "errors": "\"[Errno 2] No such file or directory: 'Human-GEM.json'\""
+              },
+              "cobrapy-load-matlab": {
+                "0.26.2": false,
+                "errors": "\"Error -3 while decompressing data: incorrect header check\""
+              },
+              "cobrapy-load-sbml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-load-yaml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-validate-sbml": {
+                "0.26.2": false,
+                "errors": "\"{'SBML_FATAL': [], 'SBML_ERROR': [], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n', 'E1 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n'], 'COBRA_FATAL': [], 'COBRA_ERROR': [], 'COBRA_WARNING': [], 'COBRA_CHECK': []}\""
+              },
+              "memote-score": {
+                "0.13.0": 0.47564756532249464,
+                "errors": ""
+              },
+              "yamllint": {
+                "1.29.0": true,
+                "errors": []
+              }
+            }
           }
         ]
       }
     },
     {
-      "v0.4.2": {
+      "v1.11.0": {
         "standard-GEM": [
           {
-            "0.4": false
+            "0.4": true
           },
           {
-            "test_results": {}
+            "test_results": {
+              "cobrapy-load-json": {
+                "0.26.2": false,
+                "errors": "\"[Errno 2] No such file or directory: 'Human-GEM.json'\""
+              },
+              "cobrapy-load-matlab": {
+                "0.26.2": false,
+                "errors": "\"Error -3 while decompressing data: incorrect header check\""
+              },
+              "cobrapy-load-sbml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-load-yaml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-validate-sbml": {
+                "0.26.2": false,
+                "errors": "\"{'SBML_FATAL': [], 'SBML_ERROR': [], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n', 'E1 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n'], 'COBRA_FATAL': [], 'COBRA_ERROR': [], 'COBRA_WARNING': [], 'COBRA_CHECK': []}\""
+              },
+              "memote-score": {
+                "0.13.0": 0.4813329434104094,
+                "errors": ""
+              },
+              "yamllint": {
+                "1.29.0": true,
+                "errors": []
+              }
+            }
           }
         ]
       }
     },
     {
-      "v0.4.1": {
+      "v1.10.0": {
         "standard-GEM": [
           {
-            "0.4": false
+            "0.4": true
           },
           {
-            "test_results": {}
-          }
-        ]
-      }
-    },
-    {
-      "v0.4.0": {
-        "standard-GEM": [
-          {
-            "0.4": false
-          },
-          {
-            "test_results": {}
-          }
-        ]
-      }
-    },
-    {
-      "v0.3.1": {
-        "standard-GEM": [
-          {
-            "0.4": false
-          },
-          {
-            "test_results": {}
-          }
-        ]
-      }
-    },
-    {
-      "v0.3.0": {
-        "standard-GEM": [
-          {
-            "0.4": false
-          },
-          {
-            "test_results": {}
-          }
-        ]
-      }
-    },
-    {
-      "v0.2.0": {
-        "standard-GEM": [
-          {
-            "0.4": false
-          },
-          {
-            "test_results": {}
-          }
-        ]
-      }
-    },
-    {
-      "v0.1.0": {
-        "standard-GEM": [
-          {
-            "0.4": false
-          },
-          {
-            "test_results": {}
+            "test_results": {
+              "cobrapy-load-json": {
+                "0.26.2": false,
+                "errors": "\"[Errno 2] No such file or directory: 'Human-GEM.json'\""
+              },
+              "cobrapy-load-matlab": {
+                "0.26.2": false,
+                "errors": "\"Error -3 while decompressing data: incorrect header check\""
+              },
+              "cobrapy-load-sbml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-load-yaml": {
+                "0.26.2": true,
+                "errors": ""
+              },
+              "cobrapy-validate-sbml": {
+                "0.26.2": false,
+                "errors": "\"{'SBML_FATAL': [], 'SBML_ERROR': [], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n', 'E1 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \\\\nReference: L3V1 Section 6.3\\\\n An invalid ModelHistory element has been stored.\\\\n'], 'COBRA_FATAL': [], 'COBRA_ERROR': [], 'COBRA_WARNING': [], 'COBRA_CHECK': []}\""
+              },
+              "memote-score": {
+                "0.13.0": 0.48129904134791174,
+                "errors": ""
+              },
+              "yamllint": {
+                "1.29.0": true,
+                "errors": []
+              }
+            }
           }
         ]
       }
Original file line number	Diff line number	Diff line change
		@@ -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", "tibbdc/vna-GEM", "SysBioChalmers/Rat-GEM"]