Flask-side refactors

.github/workflows/testing.yml → .github/workflows/app_and_flask_coverage.yml

@@ -1,8 +1,9 @@
-name: Dev Tests
+name: App and Flask Coverage
 on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
   pull_request:
+  workflow_dispatch:
 
 concurrency:  # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -13,7 +14,7 @@ env:
 
 jobs:
   testing:
-    name: ${{ matrix.os }}  # Will read on the dashboard as 'Dev Tests / {os}'
+    name: ${{ matrix.os }}  # Will read on the dashboard as 'App and Flask Coverage / {os}'
     runs-on: ${{ matrix.os }}
     defaults:
       run:

.github/workflows/flask_dev_tests.yml

@@ -0,0 +1,92 @@
+name: Flask Dev Tests
+on:
+  schedule:
+    - cron: "0 17 * * *"  # Daily at 1pm EST
+  pull_request:
+  workflow_dispatch:
+
+# Cancel previous workflows on the same pull request
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CACHE_NUMBER: 1  # increase to reset cache manually
+
+jobs:
+  testing:
+    name: ${{ matrix.os }}  # Will read on the dashboard as 'Flask Dev Tests / {os}'
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # current linux installation instructions use dev mode instead of distributable
+          # - python-version: "3.9"
+          #   os: ubuntu-latest
+          #   label: environments/environment-Linux.yml
+          #   prefix: /usr/share/miniconda3/envs/nwb-guide
+
+          - python-version: "3.9"
+            os: macos-latest  # Mac arm64 runner
+            label: environments/environment-MAC-apple-silicon.yml
+            prefix: /Users/runner/miniconda3/envs/nwb-guide
+
+          - python-version: "3.9"
+            os: macos-13  # Mac x64 runner
+            label: environments/environment-MAC-intel.yml
+            prefix: /Users/runner/miniconda3/envs/nwb-guide
+
+          - python-version: "3.9"
+            os: windows-latest
+            label: environments/environment-Windows.yml
+            prefix: C:\Miniconda3\envs\nwb-guide
+
+    steps:
+      - uses: actions/checkout@v4
+      - run: git fetch --prune --unshallow --tags
+
+      - name: Printout architecture
+        run: uname -m
+
+      # see https://github.com/conda-incubator/setup-miniconda#caching-environments
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: nwb-guide
+          use-mamba: true
+
+      - name: Set cache date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Mamba env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key:
+            conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
+        env:
+          CACHE_NUMBER: ${{ env.CACHE_NUMBER }}
+        id: cache
+
+      - if: steps.cache.outputs.cache-hit != 'true'
+        name: Update environment
+        run: mamba env update -f ${{ matrix.label }}
+
+      - name: Setup Node.js 20
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - run: npm ci --verbose
+
+      - name: Run Python tests on local dev mode
+        run: npm run test:server

pyflask/apis/data.py

@@ -2,9 +2,9 @@
 
 import traceback
 
-from errorHandlers import notBadRequestException
 from flask_restx import Namespace, Resource, reqparse
 from manageNeuroconv import generate_dataset, generate_test_data
+from utils import catch_exception_and_abort, server_error_responses
 
 data_api = Namespace("data", description="API route for dataset generation in the NWB GUIDE.")
 
@@ -22,15 +22,14 @@ def exception_handler(error):
 @data_api.route("/generate")
 @data_api.expect(generate_test_data_parser)
 class GeneratetestData(Resource):
-    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    @data_api.doc(
+        description="Generate example ecephys data using SpikeInterface.",
+        responses=server_error_responses(codes=[200, 500]),
+    )
+    @catch_exception_and_abort(api=data_api, code=500)
     def post(self):
-        try:
-            arguments = generate_test_data_parser.parse_args()
-            generate_test_data(output_path=arguments["output_path"])
-        except Exception as exception:
-            if notBadRequestException(exception):
-                data_api.abort(500, str(exception))
-            raise exception
+        arguments = generate_test_data_parser.parse_args()
+        generate_test_data(output_path=arguments["output_path"])
 
 
 generate_test_dataset_parser = reqparse.RequestParser()
@@ -48,5 +47,4 @@ def post(self):
             return generate_dataset(input_path=arguments["input_path"], output_path=arguments["output_path"])
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                data_api.abort(500, str(exception))
+            data_api.abort(500, str(exception))

pyflask/apis/neuroconv.py

@@ -1,8 +1,8 @@
 """API endpoint definitions for interacting with NeuroConv."""
 
 import traceback
+from typing import Dict
 
-from errorHandlers import notBadRequestException
 from flask import Response, request
 from flask_restx import Namespace, Resource, reqparse
 from manageNeuroconv import (
@@ -25,16 +25,18 @@
 )
 from manageNeuroconv.info import announcer
 
-neuroconv_api = Namespace("neuroconv", description="Neuroconv neuroconv_api for the NWB GUIDE.")
+neuroconv_api = Namespace(name="neuroconv", description="Neuroconv neuroconv_api for the NWB GUIDE.")
 
 parser = reqparse.RequestParser()
-parser.add_argument("interfaces", type=str, action="split", help="Interfaces cannot be converted")
+parser.add_argument("interfaces", type=str, action="split", help="Interfaces cannot be converted.")
 
 
 @neuroconv_api.errorhandler(Exception)
-def exception_handler(error):
-    exceptiondata = traceback.format_exception(type(error), error, error.__traceback__)
-    return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}
+def exception_handler(error: Exception) -> Dict[str, str]:
+    full_traceback = traceback.format_exception(type(error), error, error.__traceback__)
+    message = full_traceback[-1]
+    remaining_traceback = "".join(full_traceback[:-1])
+    return {"message": message, "traceback": remaining_traceback}
 
 
 @neuroconv_api.route("/")
@@ -50,8 +52,7 @@ def get(self):
                 **get_all_converter_info(),
             }
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
             raise exception
 
 
@@ -62,8 +63,7 @@ def post(self):
         try:
             return get_source_schema(neuroconv_api.payload)
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/locate")
@@ -73,8 +73,7 @@ def post(self):
         try:
             return locate_data(neuroconv_api.payload)
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/locate/autocomplete")
@@ -84,8 +83,7 @@ def post(self):
         try:
             return autocomplete_format_string(neuroconv_api.payload)
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/metadata")
@@ -97,8 +95,7 @@ def post(self):
                 neuroconv_api.payload.get("source_data"), neuroconv_api.payload.get("interfaces")
             )
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/convert")
@@ -109,8 +106,7 @@ def post(self):
             return convert_to_nwb(neuroconv_api.payload)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/alignment")
@@ -121,8 +117,7 @@ def post(self):
             return get_interface_alignment(neuroconv_api.payload)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 validate_parser = neuroconv_api.parser()
@@ -143,8 +138,7 @@ def post(self):
             return validate_metadata(args.get("parent"), args.get("function_name"))
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/upload/project")
@@ -163,8 +157,7 @@ def post(self):
             return upload_project_to_dandi(**upload_options)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/upload/folder")
@@ -183,8 +176,7 @@ def post(self):
             return upload_folder_to_dandi(**upload_options)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/upload")
@@ -206,8 +198,7 @@ def post(self):
                 return upload_multiple_filesystem_objects_to_dandi(**neuroconv_api.payload)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/inspect_file")
@@ -217,8 +208,7 @@ def post(self):
         try:
             return inspect_nwb_file(neuroconv_api.payload)
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/inspect_folder")
@@ -230,8 +220,7 @@ def post(self):
             return inspect_nwb_folder(url, neuroconv_api.payload)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/announce")
@@ -243,8 +232,7 @@ def post(self):
             announcer.announce(data)
             return True
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/inspect")
@@ -271,8 +259,7 @@ def post(self):
                 return inspect_multiple_filesystem_objects(url, paths, **kwargs)
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 @neuroconv_api.route("/html")
@@ -287,8 +274,7 @@ def post(self):
             return html
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))
 
 
 # Create an events endpoint
@@ -301,5 +287,4 @@ def get(self):
             return Response(listen_to_neuroconv_events(), mimetype="text/event-stream")
 
         except Exception as exception:
-            if notBadRequestException(exception):
-                neuroconv_api.abort(500, str(exception))
+            neuroconv_api.abort(500, str(exception))

pyflask/apis/startup.py

@@ -1,6 +1,5 @@
 """API endpoint definitions for startup operations."""
 
-from errorHandlers import notBadRequestException
 from flask_restx import Namespace, Resource
 
 startup_api = Namespace("startup", description="API for startup commands related to the NWB GUIDE.")
@@ -40,6 +39,5 @@ def get(self):
 
             return True
         except Exception as exception:
-            if notBadRequestException(exception=exception):
-                startup_api.abort(500, str(exception))
+            startup_api.abort(500, str(exception))
             raise exception