Update MIME types to include application/gzip; Validate prints to stderr instead of stdout

.github/workflows/Docker-build-release.yaml

@@ -1,53 +1,33 @@
 ---
-name: Docker-build-release
+name: Update image in GHCR
+
+run-name: >
+  ${{
+    github.event_name == 'delete' && format(
+      'Delete `{0}{1}`',
+      github.event.ref_type == 'branch' && 'branch-' || '',
+      github.event.ref
+    )
+    || github.ref == 'refs/heads/main' && 'Update `dev`'
+      || format(
+        'Update `{0}{1}`',
+        !startsWith(github.ref, 'refs/tags') && 'branch-' || '',
+        github.ref_name
+      )
+  }} docker tag
 
 on:
   push:
-    branches: ['main']
+    branches-ignore: ['gh-pages']
     tags: ['v*']
-  release:
-    types: [published]
+  delete:
 
 jobs:
-  build-and-push-image:
+  push-or-delete-image:
     runs-on: ubuntu-latest
-    name: A job to build and push a docker image
+    name: Update GitHub Container Registry
     permissions:
       contents: read
       packages: write
-
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      - name: Read YAML
-        id: yaml-data
-        uses: jbutcher5/[email protected]
-        with:
-          file: metadata.yaml
-          key-path: '["image_name"]'
-
-      - name: Create tags
-        id: meta
-        uses: docker/metadata-action@v3
-        with:
-          flavor: |
-            latest=false
-          images: ghcr.io/uclahs-cds/${{ steps.yaml-data.outputs.data }}
-          tags: |
-            type=raw,enable=${{github.event_name == 'push'}},value=dev,event=branch
-            type=match,pattern=v(.*),group=1
-      - name: Log in to the Container registry
-        uses: docker/login-action@v1
-        with:
-          registry: ghcr.io/uclahs-cds
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v2
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          file: ./docker/Dockerfile
+      - uses: uclahs-cds/tool-Docker-action@v2

pipeval/validate/validate.py

@@ -63,11 +63,11 @@ def _validate_file(
 
 def _print_error(path:Path, err:BaseException):
     ''' Prints error message '''
-    print(f'PID:{os.getpid()} - Error: `{str(path)}` {str(err)}')
+    print(f'PID:{os.getpid()} - Error: `{str(path)}` {str(err)}', file=sys.stderr)
 
 def _print_success(path:Path, file_type:str):
     ''' Prints success message '''
-    print(f'PID:{os.getpid()} - Input: `{path}` is valid {file_type}')
+    print(f'PID:{os.getpid()} - Input: `{path}` is valid {file_type}', file=sys.stderr)
 
 def _detect_file_type_and_extension(path:Path):
     ''' File type and extension detection '''
@@ -98,7 +98,7 @@ def _validation_worker(path: Path, args:Union[ValidateArgs,Dict[str, Union[str,l
         file_type, file_extension = _detect_file_type_and_extension(path)
         _validate_file(path, file_type, file_extension, args)
     except FileNotFoundError as file_not_found_err:
-        print(f"Warning: {str(path)} {str(file_not_found_err)}")
+        print(f"Warning: {str(path)} {str(file_not_found_err)}", file=sys.stderr)
     except (TypeError, ValueError, IOError, OSError) as err:
         _print_error(path, err)
         return False

pipeval/validate/validators/fastq.py

@@ -86,6 +86,7 @@ def _get_file_handler(self):
         '''Detect file format and return approriate handler to read file'''
         _handler_map = {
             'application/x-gzip': gzip.open,
+            'application/gzip': gzip.open,
             'application/x-bzip2': bz2.open,
             'text/plain': open
         }

test/unit/test_validate.py

@@ -125,6 +125,7 @@ def test__check_compressed__raises_warning_for_uncompressed_path(mock_path, mock
     'compression_mime',
     [
         ('application/x-gzip'),
+        ('application/gzip'),
         ('application/x-bzip2')
     ]
 )
@@ -491,6 +492,7 @@ def test__validate_record__passes_valid_read():
     'test_file_type, test_handler',
     [
         ('application/x-gzip', gzip.open),
+        ('application/gzip', gzip.open),
         ('application/x-bzip2', bz2.open),
         ('text/plain', open)
     ]
@@ -580,6 +582,7 @@ def test__validate_fastq__passes_valid_fastq(
     'test_file_type, test_handler',
     [
         ('application/x-gzip', gzip.open),
+        ('application/gzip', gzip.open),
         ('application/x-bzip2', bz2.open),
         ('any/other', None)
     ]