2 files changed, 83 insertions, 0 deletions

diff --git a/issues/gn-uploader/AuthorisationError-gn-uploader.gmi b/issues/gn-uploader/AuthorisationError-gn-uploader.gmi
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+++ b/issues/gn-uploader/AuthorisationError-gn-uploader.gmi
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+# AuthorisationError in gn uploader 
+
+## Tags 
+* assigned: fredm 
+* status: open 
+* priority: critical 
+* type: error 
+* key words: authorisation, permission 
+
+## Description 
+
+Trying to create population for Kilifish dataset in the gn-uploader webpage, 
+then encountered the following error: 
+```sh 
+Traceback (most recent call last):
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/flask/app.py", line 917, in full_dispatch_request
+   rv = self.dispatch_request()
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/flask/app.py", line 902, in dispatch_request
+   return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/uploader/authorisation.py", line 23, in __is_session_valid__
+   return session.user_token().either(
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/pymonad/either.py", line 89, in either
+   return right_function(self.value)
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/uploader/authorisation.py", line 25, in <lambda>
+   lambda token: function(*args, **kwargs))
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/uploader/population/views.py", line 185, in create_population
+   ).either(
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/pymonad/either.py", line 91, in either
+   return left_function(self.monoid[0])
+ File "/gnu/store/wxb6rqf7125sb6xqd4kng44zf9yzsm5p-profile/lib/python3.10/site-packages/uploader/monadic_requests.py", line 99, in __fail__
+   raise Exception(_data)
+Exception: {'error': 'AuthorisationError', 'error-trace': 'Traceback (most recent call last):
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/flask/app.py", line 917, in full_dispatch_request
+      rv = self.dispatch_request()
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/flask/app.py", line 902, in dispatch_request
+    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/authlib/integrations/flask_oauth2/resource_protector.py", line 110, in decorated
+    return f(*args, **kwargs)
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/gn_auth/auth/authorisation/resources/inbredset/views.py", line 95, in create_population_resource
+    ).then(
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/pymonad/monad.py", line 152, in then
+    result = self.map(function)
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/pymonad/either.py", line 106, in map
+    return self.__class__(function(self.value), (None, True))
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/gn_auth/auth/authorisation/resources/inbredset/views.py", line 98, in <lambda>
+    "resource": create_resource(
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/gn_auth/auth/authorisation/resources/inbredset/models.py", line 25, in create_resource
+    return _create_resource(cursor,
+  File "/gnu/store/38iayxz7dgm86f2x76kfaa6gwicnnjg4-profile/lib/python3.10/site-packages/gn_auth/auth/authorisation/checks.py", line 56, in __authoriser__
+    raise AuthorisationError(error_description)
+gn_auth.auth.errors.AuthorisationError: Insufficient privileges to create a resource
+', 'error_description': 'Insufficient privileges to create a resource'}
+
+```
+The error above resulted from the attempt to upload the following information on the gn-uploader-`create population section` 
+Input details are as follows: 
+Full Name: Kilifish F2 Intercross Lines
+Name: KF2_Lines
+Population code: KF2
+Description: Kilifish second generation population 
+Family: Crosses, AIL, HS 
+Mapping Methods: GEMMA, QTLReaper, R/qtl 
+Genetic type: intercross 
+
+And when pressed the `Create Population` icon, it led to the error above.  
+
diff --git a/issues/gn-uploader/replace-redis-with-sqlite3.gmi b/issues/gn-uploader/replace-redis-with-sqlite3.gmi
new file mode 100644
index 0000000..3e5020a
--- /dev/null
+++ b/issues/gn-uploader/replace-redis-with-sqlite3.gmi
@@ -0,0 +1,17 @@
+# Replace Redis with SQL
+
+## Tags
+
+* status: open
+* priority: low
+* assigned: fredm
+* type: feature, feature-request, feature request
+* keywords: gn-uploader, uploader, redis, sqlite, sqlite3
+
+## Description
+
+We currently (as of 2024-06-27) use Redis for tracking any asynchronous jobs (e.g. QC on uploaded files).
+
+A lot of what we use redis for, we can do in one of the many SQL databases (we'll probably use SQLite3 anyway), which are more standardised, and easier to migrate data from and to. It has the added advantage that we can open multiple connections to the database, enabling the different processes to update the status and metadata of the same job consistently.
+
+Changes done here can then be migrated to the other systems, i.e. GN2, GN3, and gn-auth, as necessary.