Merge pull request #512 from AndersenLab/fix/genome-browser-not-logge…

…d-in Fix Genome Browser login redirect bug (make endpoints public)
AndersenLab · Oct 31, 2024 · c29bb32 · c29bb32
2 parents 69d4b24 + 2efe2e0
commit c29bb32
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Showing 3 changed files with 28 additions and 21 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -7,7 +7,7 @@
 
         {
             "name": "Run Site-v2 (requires a local Postgres instance or cloud-sql-proxy)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}/src/modules/site-v2",
             "console": "integratedTerminal",
@@ -44,7 +44,7 @@
         },
         {
             "name": "Run Site  (requires a local Postgres instance or cloud-sql-proxy)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}/src/modules/site",
             "console": "integratedTerminal",
@@ -79,7 +79,7 @@
         },
         {
             "name": "Script: Create NemaScan Task",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/site/scripts/create-nemascan-mapping-task.py",
             "cwd": "${workspaceFolder}/src/modules/site",
@@ -91,7 +91,7 @@
         },
         {
             "name": "Run API pipeline server",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}/src/modules/api/pipeline-task",
             "console": "integratedTerminal",
@@ -121,7 +121,7 @@
         },
         {
             "name": "TEST img_thumb_gen",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/img_thumb_gen/test.py",
             "console": "integratedTerminal",
@@ -135,7 +135,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_STRAINS",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -158,7 +158,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_WORMBASE_GENES (WS283)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -181,7 +181,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_STRAIN_ANNOTATED_VARIANTS",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -204,7 +204,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_PHENOTYPE_METADATA",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -227,7 +227,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_PHENOTYPE_DB",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -250,7 +250,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_PHENOTYPES",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -273,7 +273,7 @@
         },
         {
             "name": "Run DROP_AND_POPULATE_ALL_TABLES",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -298,7 +298,7 @@
         },
         {
             "name": "DROP_AND_POPULATE_ALL_TABLES (USE MOCK DATA)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -324,7 +324,7 @@
         },
         {
             "name": "Run POPULATE_PHENOTYPES_DATASTORE",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -346,7 +346,7 @@
         },
         {
             "name": "DB_OP TEST_ECHO",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -372,7 +372,7 @@
         },
         {
             "name": "DbOp: Recompute Phenotype Report Cached Names",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/db_operations/main.py",
             "console": "integratedTerminal",
@@ -390,7 +390,7 @@
         },
         {
             "name": "Test Indel Finder",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/modules/indel_primer/main.py",
             "console": "integratedTerminal",
@@ -410,7 +410,7 @@
         },
         {
             "name": "Run Site-v2 (local API)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}/src/modules/site-v2",
             "console": "integratedTerminal",
@@ -440,7 +440,7 @@
         },
         {
             "name": "Run API pipeline server (local site)",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}/src/modules/api/pipeline-task",
             "console": "integratedTerminal",

diff --git a/README.md b/README.md
@@ -408,4 +408,13 @@ $ arch -x86_64 brew install openssl
 ```
 
 
+Q: I get an `ImportError` when running the API in VSCode:
+```
+    ImportError: cannot import name 'Literal' from 'typing' (/Users/ ... /.pyenv/versions/3.7.12/lib/python3.7/typing.py)
+```
+
+A: The VSCode extension `debugpy`, version `v2024.12.0`, appears to break on Python 3.7 -- it's not clear if this is a bug, or intentional dropping of support for older versions.
+You can get around this by pinning your extension to `v2024.10.0` -- see [the VSCode docs](https://code.visualstudio.com/updates/v1_30#_install-previous-versions) for instructions.
+
+(If this is a bug, further updates to `debugpy` might fix this issue.  Keep an eye on it, and try the newest version if necessary.)
 
diff --git a/src/modules/site-v2/base/views/api/tracks.py b/src/modules/site-v2/base/views/api/tracks.py
@@ -207,7 +207,6 @@ def edit_track(track: BrowserTrackDefault = None, form_data = None, no_cache: bo
 
 
 @api_tracks_bp.route('/tool/<string:tool_id>', methods=['GET'])
-@jwt_required()
 @jsonify_request
 def get_tool_tracks(tool_id: str):
   '''
@@ -227,7 +226,6 @@ def get_tool_tracks(tool_id: str):
 
 
 @api_tracks_bp.route('/templates', methods=['GET'])
-@jwt_required()
 @jsonify_request
 def get_track_templates():
   '''