Merge pull request #91 from EbiEga/mcb-update-actions

mcb-update-actions - Update matplotlib to latest version

.github/scripts/request_validation.py

@@ -2,29 +2,29 @@
 import os
 import sys
 
-from utils.json_validation import request_validation, \
-    get_errors_response
+from utils.json_validation import request_validation, get_errors_response
 
-# --------- #
 # Handling arguments
-# --------- #
 dirname = sys.argv[1]
 curl_URL = sys.argv[2]
 
-# - #
 # Hardcoded values
-# - #
 extension = ".json"
 
-# --------- #
 # Running validations
-# --------- #
 error_dict = {}
-# We iterate over the JSON documents to validate
+validated_files = []
+total_files = 0
+files_with_errors = 0
+
+# Iterate over the JSON documents to validate
 for file in os.scandir(dirname):
     if not file.path.endswith(extension):
         continue
 
+    total_files += 1
+    validated_files.append(file.name)
+
     request = request_validation(
         data_filepath=file,
         validator_url=curl_URL
@@ -36,7 +36,17 @@
     )
     if val_error:
         error_dict[file.name] = val_error
+        files_with_errors += 1
 
 # If the dictionary is not empty, fail the script returning it
+summary = {
+    "n_total_files": total_files,
+    "n_files_with_errors": files_with_errors,
+    "error_files": error_dict,
+    "all_files": validated_files
+}
+
 if error_dict:
-    sys.exit(json.dumps(error_dict, sort_keys=True, indent=4))
+    sys.exit(json.dumps(summary, sort_keys=True, indent=4))
+else:
+    print(json.dumps(summary, sort_keys=True, indent=4))

.github/scripts/requirements.txt

@@ -2,7 +2,7 @@ argparse
 typing
 requests==2.26.0
 pandas==1.5.3
-matplotlib==3.4.3
+matplotlib==3.9.0
 jsonpath_ng
 jsonref
 jsonschema==3.2.0

.github/scripts/update_version_manifest.py

@@ -14,7 +14,7 @@
 from utils.json_validation import validate_json
 
 # Script used to update the version manifest (./docs/releases) with the versions of the JSON schemas. For further details, please check:
-#   https://github.com/EbiEga/ega-metadata-schema/tree/main/docs/biovalidator_benchmarks
+#   https://github.com/EbiEga/ega-metadata-schema/tree/main/docs/releases
 
 # --------- #
 # Handling arguments

.github/scripts/utils/json_validation.py

@@ -49,11 +49,15 @@ def get_errors_response(
     if not response.status_code == requests.codes.ok:
         error_message = (
             f"The POST response was not successful: instead of {requests.codes.ok},"
-            f" the status code was '{response.status_code}' when validating file '{filename}'"
+            f" the status code was '{response.status_code}' when validating file '{filename}'."
+            f" Response content: {response.content.decode('utf-8')}"
         )
         return error_message
 
-    val_response_list = response.json()
+    try:
+        val_response_list = response.json()
+    except ValueError:
+        return f"Invalid JSON response when validating file '{filename}'. Response content: {response.content.decode('utf-8')}"
 
     # If the list is empty "[]", the validation found no errors
     if not len(val_response_list) == 0:

.github/workflows/check_project_version_change.yml

@@ -43,11 +43,24 @@ jobs:
           # This bit is needed for running the following python script
           python-version: '3.x'
 
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          # On subsequent runs, if the cache key matches (i.e., operating system and the hash of the requirements.txt file),
+          #   the dependencies are restored from the cache instead of being downloaded and installed again.
+          path: ~/.cache/pip
+          # combines the OS type and a hash of the requirements.txt file: the cache is specific to the dependencies listed
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+          # If there is no cache for this key, we create it at the end of the run, even if there was an error mid-way
+          save-always: true
+
       - name: Install dependencies
         run: |
           pip install --upgrade pip
           requirements_f="./.github/scripts/requirements.txt"
-          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f"; fi
+          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f" --prefer-binary --verbose; fi
 
       - name: Run version modification check
         id: run-version-modification-check

.github/workflows/json_validation_against_EGA_API.yml

@@ -39,11 +39,24 @@ jobs:
           # This bit is needed for running the following python script
           python-version: '3.x'
 
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          # On subsequent runs, if the cache key matches (i.e., operating system and the hash of the requirements.txt file),
+          #   the dependencies are restored from the cache instead of being downloaded and installed again.
+          path: ~/.cache/pip
+          # combines the OS type and a hash of the requirements.txt file: the cache is specific to the dependencies listed
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+          # If there is no cache for this key, we create it at the end of the run, even if there was an error mid-way
+          save-always: true
+
       - name: Install dependencies
         run: |
           pip install --upgrade pip
           requirements_f="./.github/scripts/requirements.txt"
-          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f"; fi
+          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f" --prefer-binary --verbose; fi
 
       - name: Validate JSON examples
           # Validate all JSON documents against their corresponding schemas

.github/workflows/json_validation_deploying_biovalidator.yml

@@ -27,7 +27,6 @@ name: |
   (json_validation_deploying_biovalidator.yml)
 
 on:
-  # Executes on any commit to a PR to the "main" branch
   pull_request:
     branches: [main]
 
@@ -38,13 +37,32 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
         with:
-          # Full git history
           fetch-depth: 0
 
+      - uses: actions/setup-python@v4
+        with:
+          # We'll use the latest version of python from major 3 release
+          # This bit is needed for running the following python script
+          python-version: '3.x'
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          # On subsequent runs, if the cache key matches (i.e., operating system and the hash of the requirements.txt file),
+          #   the dependencies are restored from the cache instead of being downloaded and installed again.
+          path: ~/.cache/pip
+          # combines the OS type and a hash of the requirements.txt file: the cache is specific to the dependencies listed
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+          # If there is no cache for this key, we create it at the end of the run, even if there was an error mid-way
+          save-always: true
+
       - name: Clone Biovalidator
           # See https://github.com/elixir-europe/biovalidator#installation
           # We want to test the "main" branch of the project
         run: git clone https://github.com/elixir-europe/biovalidator.git
+
       - name: Install Biovalidator
           # We want to test with the latest Node.js version, but if not, we 
           # could make use of action: https://github.com/actions/setup-node
@@ -59,23 +77,28 @@ jobs:
           #   changes. Therefore we specify the schemas at deployment level (-r)
         run: |
           schemas_dir="./schemas"
+          node biovalidator/src/biovalidator -r "$schemas_dir/*.json" > biovalidator.log 2>&1 &
           
-          node biovalidator/src/biovalidator -r "$schemas_dir/*.json" &
-          
-          # We stop for a few seconds to give the server time
-          sleep 3
-
-      - uses: actions/setup-python@v4
-        with:
-          # We'll use the latest version of python from major 3 release
-          # This bit is needed for running the following python script
-          python-version: '3.x'
+          # Check if the server is up and running, and wait for a few seconds if not
+          for i in {1..10}; do
+            if curl --output /dev/null --silent --head --fail "http://localhost:3020/validate"; then
+              echo "Biovalidator server is up!"
+              break
+            fi
+            echo "Waiting ($i time(s)) for Biovalidator server to start..."
+            sleep 5
+          done
+          if ! curl --output /dev/null --silent --head --fail "http://localhost:3020/validate"; then
+            echo "Biovalidator server failed to start"
+            cat biovalidator.log
+            exit 1
+          fi
 
       - name: Install dependencies
         run: |
           pip install --upgrade pip
           requirements_f="./.github/scripts/requirements.txt"
-          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f"; fi
+          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f" --prefer-binary --verbose; fi
 
       - name: Validate JSON examples
           # Validate all JSON documents against their corresponding schemas
@@ -86,5 +109,4 @@ jobs:
           # The following URL points to the locally deployed server of
           #   Biovalidator
           url="http://localhost:3020/validate"
-
-          python3 ./.github/scripts/request_validation.py "$json_ex_dir" "$url"
+          python3 ./.github/scripts/request_validation.py "$json_ex_dir" "$url"

.github/workflows/update_version_manifest.yml

@@ -40,11 +40,24 @@ jobs:
           # This bit is needed for running the following python script
           python-version: '3.x'
 
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          # On subsequent runs, if the cache key matches (i.e., operating system and the hash of the requirements.txt file),
+          #   the dependencies are restored from the cache instead of being downloaded and installed again.
+          path: ~/.cache/pip
+          # combines the OS type and a hash of the requirements.txt file: the cache is specific to the dependencies listed
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+          # If there is no cache for this key, we create it at the end of the run, even if there was an error mid-way
+          save-always: true
+
       - name: Install dependencies
         run: |
           pip install --upgrade pip
           requirements_f="./.github/scripts/requirements.txt"
-          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f"; fi
+          if [ -f "$requirements_f" ]; then pip install -r "$requirements_f" --prefer-binary --verbose; fi
 
       - name: Update version manifest
         run: |