From f77b169c09be92014dcfea49d427268381fe12e5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 27 Feb 2024 05:07:41 +0300 Subject: Update issues, closing some that are complete. --- .../rework-resources-system.gmi | 12 +++++++++-- .../temp-trait-error.gmi | 4 ++-- issues/error-handling-external-errors.gmi | 6 ++++++ ...ework-tests-remove-redis-as-test-dependency.gmi | 19 ++++++++++++++++++ issues/gn-uploader/upload-strains.gmi | 23 ++++++++++++++++++++++ ...ework-tests-remove-redis-as-test-dependency.gmi | 15 -------------- issues/gnqc-py/upload-strains.gmi | 23 ---------------------- issues/quality-control/Fix-opaque-errors.gmi | 4 ++-- .../quality-control/qc-fix-integration-tests.gmi | 10 ++++++++-- .../read-samples-from-database-by-species.gmi | 6 ++---- 10 files changed, 72 insertions(+), 50 deletions(-) create mode 100644 issues/gn-uploader/rework-tests-remove-redis-as-test-dependency.gmi create mode 100644 issues/gn-uploader/upload-strains.gmi delete mode 100644 issues/gnqc-py/rework-tests-remove-redis-as-test-dependency.gmi delete mode 100644 issues/gnqc-py/upload-strains.gmi (limited to 'issues') diff --git a/issues/authentication_authorisation/rework-resources-system.gmi b/issues/authentication_authorisation/rework-resources-system.gmi index eeec47d..85d37a1 100644 --- a/issues/authentication_authorisation/rework-resources-system.gmi +++ b/issues/authentication_authorisation/rework-resources-system.gmi @@ -3,10 +3,10 @@ ## Tags * assigned: fredm -* status: open +* status: closed, completed * priority: medium * type: refactor, feature request, design change -* keywords: auth, authorisation, resources, design change +* keywords: auth, authorisation, resources, design change, gn-auth ## Description @@ -29,3 +29,11 @@ This means that there is a need to refactor the code to make the concept of a "r * [x] Make resource to represent the system itself * [x] Make resources, each representing one of the "user groups" * [ ] Make resources, each representing the users of the system -- maybe? + +### Update 2024-02-27 + +The resource system was updated a while ago. + +We still do not view users as resources for the time being, and handle them slightly different from the rest of the system, controlling access to the users via other resources like the 'System' and 'Group' resources. + +This is considered completed. diff --git a/issues/authentication_authorisation/temp-trait-error.gmi b/issues/authentication_authorisation/temp-trait-error.gmi index 04ab99d..cc5d6db 100644 --- a/issues/authentication_authorisation/temp-trait-error.gmi +++ b/issues/authentication_authorisation/temp-trait-error.gmi @@ -4,8 +4,8 @@ * assigned: fredm, zsloan * priority: high -* status: open -* keywords: authentication, authorisation, oauth2, temp-traits +* status: closed, completed +* keywords: authentication, authorisation, oauth2, temp-traits, gn-auth * type: bug ## Description diff --git a/issues/error-handling-external-errors.gmi b/issues/error-handling-external-errors.gmi index 9208a5d..d1707de 100644 --- a/issues/error-handling-external-errors.gmi +++ b/issues/error-handling-external-errors.gmi @@ -27,3 +27,9 @@ So far, the error-handling for such services has been inconsistent at best. In t > => https://github.com/genenetwork/genenetwork2/pull/830 We can then maybe incorporate the use of UUIDs in the errors, to help with tracking the errors in the logs where necessary. + +---- + +Some work has been done on this, but it is still a work in progress. + +**Maybe link the commits here…** diff --git a/issues/gn-uploader/rework-tests-remove-redis-as-test-dependency.gmi b/issues/gn-uploader/rework-tests-remove-redis-as-test-dependency.gmi new file mode 100644 index 0000000..a305416 --- /dev/null +++ b/issues/gn-uploader/rework-tests-remove-redis-as-test-dependency.gmi @@ -0,0 +1,19 @@ +# Rework Test: Remove redis as Test Dependency + +## Tags + +* assigned: fred, fredm +* status: closed, completed +* priority: medium +* keywords: gn-uploader, tests +* type: improvement + +## Description + +Some tests depend on a running redis instance to work. + +Either move these to an integration tests harness, to be run after the system has run the unit tests and has been deployed, or remove them completely from the system. + +### Update 2024-02-27 + +The system was updated to use prefixed keys, and the full tests now run correctly. Still need to add the tests to the guix CI/CD system perhaps... diff --git a/issues/gn-uploader/upload-strains.gmi b/issues/gn-uploader/upload-strains.gmi new file mode 100644 index 0000000..6dce6bf --- /dev/null +++ b/issues/gn-uploader/upload-strains.gmi @@ -0,0 +1,23 @@ +# Upload Strains + +## Tags + +* status: closed, completed +* assigned: fredm, zachs, zsloan, acenteno +* priority: high +* type: feature-request +* keywords: QC, quality control, strains, gn-uploader + +## Description + +Currently, the uploader simply fails when it encounters unknown strains in the files being uploaded. + +This issue will track the implementation of a system to allow the upload of strains, and the grouping of said strains into populations/tissue etc. + +## TODO + +* [x] UI to select species +* [x] UI to select or create a grouping for the strains (think InbredSet) +* [x] UI to select the CSV file with the strains data +* [x] UI to select the way to interprete the CSV file +* [x] Code to insert the new strains, into the database diff --git a/issues/gnqc-py/rework-tests-remove-redis-as-test-dependency.gmi b/issues/gnqc-py/rework-tests-remove-redis-as-test-dependency.gmi deleted file mode 100644 index c4ee5e8..0000000 --- a/issues/gnqc-py/rework-tests-remove-redis-as-test-dependency.gmi +++ /dev/null @@ -1,15 +0,0 @@ -# Rework Test: Remove redis as Test Dependency - -## Tags - -* assigned: fred, fredm -* status: open -* priority: medium -* keywords: gnqc-py, tests -* type: improvement - -## Description - -Some tests depend on a running redis instance to work. - -Either move these to an integration tests harness, to be run after the system has run the unit tests and has been deployed, or remove them completely from the system. diff --git a/issues/gnqc-py/upload-strains.gmi b/issues/gnqc-py/upload-strains.gmi deleted file mode 100644 index 4815a06..0000000 --- a/issues/gnqc-py/upload-strains.gmi +++ /dev/null @@ -1,23 +0,0 @@ -# Upload Strains - -## Tags - -* status: closed, completed -* assigned: fredm, zachs, zsloan, acenteno -* priority: high -* type: feature-request -* keywords: QC, quality control, strains - -## Description - -Currently, the uploader simply fails when it encounters unknown strains in the files being uploaded. - -This issue will track the implementation of a system to allow the upload of strains, and the grouping of said strains into populations/tissue etc. - -## TODO - -* [x] UI to select species -* [x] UI to select or create a grouping for the strains (think InbredSet) -* [x] UI to select the CSV file with the strains data -* [x] UI to select the way to interprete the CSV file -* [x] Code to insert the new strains, into the database diff --git a/issues/quality-control/Fix-opaque-errors.gmi b/issues/quality-control/Fix-opaque-errors.gmi index 0f81233..3864c81 100644 --- a/issues/quality-control/Fix-opaque-errors.gmi +++ b/issues/quality-control/Fix-opaque-errors.gmi @@ -2,11 +2,11 @@ ## Tags -* status: open +* status: closed, completed * assigned: fredm * type: bug * priority: high -* keywords: opaque errors, errors, UX, user experience +* keywords: opaque errors, errors, UX, user experience, gn-uploader ## Description diff --git a/issues/quality-control/qc-fix-integration-tests.gmi b/issues/quality-control/qc-fix-integration-tests.gmi index cf0b833..c233c20 100644 --- a/issues/quality-control/qc-fix-integration-tests.gmi +++ b/issues/quality-control/qc-fix-integration-tests.gmi @@ -4,8 +4,8 @@ * assigned: fredm * priority: medium -* status: open -* keywords: quality control, qc, tests +* status: closed, completed +* keywords: quality control, qc, tests, gn-uploader * type: bug ## Description @@ -19,3 +19,9 @@ command = [shutil.which("redis-server"), "--port", str(port)] This is because the `shutil.which("redis-server")` call returns `None` in the newer code, due to removal of redis (the server) from the list of dependencies. To work around the issue, I suggest the use of an explicit, albeit temporary, redis database for testing, by modifying the `REDIS_URL` value in the tests sessions. The modification will simply change the URL to point to a new database for the test session, enabling the tests to run unhindered, but also without tainting the production redis databases. + +### Update 2024-02-27 + +The system was updated to use prefixed keys, and the full tests now run correctly. + +=> /issues/gn-uploader/rework-tests-remove-redis-as-test-dependency related issue diff --git a/issues/quality-control/read-samples-from-database-by-species.gmi b/issues/quality-control/read-samples-from-database-by-species.gmi index fae1a18..fa66c17 100644 --- a/issues/quality-control/read-samples-from-database-by-species.gmi +++ b/issues/quality-control/read-samples-from-database-by-species.gmi @@ -5,8 +5,8 @@ * type: bug * priority: critical * assigned: fredm, acenteno -* keywords: QC, quality control, samples, strains, cases -* status: open +* keywords: QC, quality control, samples, strains, cases, gn-uploader +* status: closed, completed ## Description @@ -30,5 +30,3 @@ This was a myopic view of the data uploader, and needs to be expanded significan Fixed with this commit: => https://gitlab.com/fredmanglis/gnqc_py/-/commit/cdd4dc456e56bb4eb055e1cb7f2518d45fb3bfb9 - -Awaiting deployment -- cgit v1.2.3