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78f32a8
added schema and version to pathogen table
desafinadude Nov 7, 2025
42ff9c9
added pathogenId to index
desafinadude Nov 10, 2025
8ad5f6d
wip
desafinadude Nov 10, 2025
0ad417c
Get project and org invites list
michaelglenister Nov 11, 2025
bd141fe
Cleanup
michaelglenister Nov 11, 2025
b1aa257
Changing usernames
michaelglenister Nov 11, 2025
76ec272
Running migrations
michaelglenister Nov 11, 2025
83ae288
Running migrations
michaelglenister Nov 11, 2025
767cb19
Change db port
michaelglenister Nov 11, 2025
044c03d
Change db port
michaelglenister Nov 11, 2025
430209e
wip
desafinadude Nov 11, 2025
3c1e91d
wip
desafinadude Nov 12, 2025
6775083
Add org-partial role to project members without org membership
michaelglenister Nov 12, 2025
0df9bf5
work before file validation
desafinadude Nov 13, 2025
f123223
Changing usernames
michaelglenister Nov 11, 2025
c309c6f
Add org-partial role to project members without org membership
michaelglenister Nov 12, 2025
1ae1459
Merge pull request #68 from OpenUpSA/elastic
michaelglenister Nov 13, 2025
a516188
Merge pull request #75 from OpenUpSA/pathogens_schemas
michaelglenister Nov 13, 2025
d8642fb
Merge pull request #77 from OpenUpSA/invite-status
michaelglenister Nov 13, 2025
4daec3a
Merge pull request #76 from OpenUpSA/michael-dev
michaelglenister Nov 13, 2025
f310577
Merge branch 'staging' into working-uploads1
michaelglenister Nov 13, 2025
3d847e2
Merge pull request #78 from OpenUpSA/working-uploads1
michaelglenister Nov 13, 2025
9cf8de7
Test migration
michaelglenister Nov 13, 2025
78b650c
Refactor PublishSubmission to retrieve pathogen_id from project and i…
desafinadude Nov 13, 2025
35d8c16
Merge pull request #80 from OpenUpSA/elastic-indexing-fix
desafinadude Nov 13, 2025
cb9202f
Merge pull request #79 from OpenUpSA/michael-dev
michaelglenister Nov 13, 2025
a946c25
Updated schemas
desafinadude Nov 13, 2025
3f2a38b
Merge pull request #82 from OpenUpSA/advanced-uploads2
desafinadude Nov 13, 2025
aeb9c6f
Refactor validation logic and update schema handling in helpers.py; a…
desafinadude Nov 14, 2025
69cbd99
Update app
michaelglenister Nov 14, 2025
c7ea718
Update app
michaelglenister Nov 14, 2025
f931b94
Merge pull request #84 from OpenUpSA/michael-dev
michaelglenister Nov 14, 2025
d671dc0
Enhance validation logic and schema handling in ProjectSubmissionVali…
desafinadude Nov 14, 2025
484dbb4
added elastic indexing
desafinadude Nov 14, 2025
90dad3d
Refactor isolates table schema: drop isolate_id column, add tsv_row, …
desafinadude Nov 14, 2025
e27f771
fix migration script
desafinadude Nov 14, 2025
71a96e8
Fix migration script: add missing .sql extension for isolates table m…
desafinadude Nov 14, 2025
3834bcd
Merge pull request #85 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
ac7a48b
added async squence check
desafinadude Nov 14, 2025
27cc533
Merge branch 'staging' into uploads-work
desafinadude Nov 14, 2025
0eafa0a
Merge pull request #87 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
4f10974
Added PUT and DELETE endpoints for submission
desafinadude Nov 14, 2025
3c51477
Merge pull request #88 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
ef82a2e
added user_id to submissions
desafinadude Nov 14, 2025
3ec7b6a
Merge pull request #89 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
d5c109e
added description to error
desafinadude Nov 14, 2025
5557e88
updated submission status check to include 'validating' and 'validate…
desafinadude Nov 14, 2025
1195697
Merge pull request #90 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
dfa55a2
upload fix
desafinadude Nov 14, 2025
d044101
Merge pull request #91 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
378c8a3
removed unused import for get_isolate_from_elastic
desafinadude Nov 14, 2025
cbfd518
Merge pull request #92 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
8d508b5
removed unused imports for elastic functions
desafinadude Nov 14, 2025
f65fd61
Merge pull request #93 from OpenUpSA/uploads-work
desafinadude Nov 14, 2025
ec06e4d
Refactor sequence data handling and update submission status logic
desafinadude Nov 14, 2025
6d51570
cleanup and split and validation work
desafinadude Nov 14, 2025
ee34207
splitting works
desafinadude Nov 14, 2025
7dfb9a0
fixed seq error
desafinadude Nov 14, 2025
117fe71
working
desafinadude Nov 14, 2025
7c8c80e
indexing work
desafinadude Nov 15, 2025
855782a
Refactor submission handling and permissions; add object_id checks an…
desafinadude Nov 15, 2025
01146a1
added schemas endpoints
desafinadude Nov 16, 2025
acb6a7f
linked pathogen to shema via pathogen PUT
desafinadude Nov 16, 2025
2d806c1
Refactor pathogen handling: replace schema and version with schema_id…
desafinadude Nov 16, 2025
da74371
Merge pull request #94 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
33e4769
Merge pull request #95 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
cc1bb00
validate fix
desafinadude Nov 17, 2025
30c50c8
Merge pull request #96 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
24074f8
fix schema check
desafinadude Nov 17, 2025
d3d4692
Merge pull request #97 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
f0a6460
added schemas.http
desafinadude Nov 17, 2025
87c0996
Toggle enabled users
michaelglenister Nov 17, 2025
c769931
Merge pull request #98 from OpenUpSA/toggle-enbabled-users
michaelglenister Nov 17, 2025
e9fc804
Send access enabled email
michaelglenister Nov 17, 2025
6a686e3
Merge pull request #99 from OpenUpSA/toggle-enbabled-users
michaelglenister Nov 17, 2025
f75c4f8
Enhance TSV to JSON conversion: include project ID for schema retriev…
desafinadude Nov 17, 2025
8bc5e41
Merge pull request #100 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
58e7d4c
Add activity logs and endpoint
michaelglenister Nov 17, 2025
65a8a61
download work
desafinadude Nov 17, 2025
ce6606e
Merge branch 'staging' into uploads-work
desafinadude Nov 17, 2025
2fcd35d
Merge pull request #102 from OpenUpSA/uploads-work
desafinadude Nov 17, 2025
4b11664
Merge branch 'staging' into activity-log
michaelglenister Nov 17, 2025
b589ae6
Merge pull request #101 from OpenUpSA/activity-log
michaelglenister Nov 17, 2025
6fbf2de
Add endpoint to download isolates by query in TSV format
desafinadude Nov 17, 2025
b10b8fd
Merge pull request #103 from OpenUpSA/downloads
desafinadude Nov 17, 2025
8c915d4
Store JSON correctly
michaelglenister Nov 17, 2025
7f56c3f
Merge pull request #104 from OpenUpSA/activity-log
michaelglenister Nov 17, 2025
49b10c1
Refactor submission validation logic to improve error handling and st…
desafinadude Nov 17, 2025
500b3e1
Merge pull request #105 from OpenUpSA/uploads-fixes
michaelglenister Nov 17, 2025
6f9fdb0
Adding activity logs
michaelglenister Nov 17, 2025
bbd540c
Merge pull request #107 from OpenUpSA/activity-log-2
michaelglenister Nov 17, 2025
594a39d
f string fix
michaelglenister Nov 17, 2025
fbfb687
Merge pull request #108 from OpenUpSA/activity-log-2
michaelglenister Nov 17, 2025
6bc72b4
pathogens insert fix
desafinadude Nov 17, 2025
dfcdfde
add migrations
desafinadude Nov 17, 2025
0e9493b
Merge pull request #109 from OpenUpSA/uploads-fixes
desafinadude Nov 17, 2025
4868788
Add logging for submission events in ProjectSubmissions2 and related …
desafinadude Nov 17, 2025
35ffff9
Merge pull request #110 from OpenUpSA/submission-logging
desafinadude Nov 17, 2025
734b4a0
date serialisation fix in logging
desafinadude Nov 17, 2025
602cf6f
Merge pull request #111 from OpenUpSA/submission-logging
desafinadude Nov 17, 2025
5888f2d
log fix
desafinadude Nov 17, 2025
cd25111
Merge pull request #112 from OpenUpSA/submission-logging
desafinadude Nov 17, 2025
19b52a0
Update log_event to include file_record details on file upload
desafinadude Nov 17, 2025
3fe8725
Merge pull request #113 from OpenUpSA/submission-logging
desafinadude Nov 17, 2025
c7a9394
Add actioner metadata to activity logs
michaelglenister Nov 17, 2025
abde393
Merge branch 'staging' into activity-log-2
michaelglenister Nov 17, 2025
16f5fa5
validation fix
desafinadude Nov 17, 2025
4e8e8a5
Add actioner metadata to activity logs
michaelglenister Nov 17, 2025
7c8cbc5
Merge pull request #115 from OpenUpSA/uploads-more-and-more
desafinadude Nov 17, 2025
5fba690
Merge branch 'staging' into activity-log-2
michaelglenister Nov 17, 2025
3b4cf52
validation flow fix
desafinadude Nov 17, 2025
49f4010
Merge pull request #114 from OpenUpSA/activity-log-2
michaelglenister Nov 17, 2025
16129d9
Merge pull request #116 from OpenUpSA/uploads-more-and-more
desafinadude Nov 17, 2025
d03e39d
Fix f string
michaelglenister Nov 17, 2025
7460e8e
Merge pull request #117 from OpenUpSA/activity-log-2
michaelglenister Nov 17, 2025
b481f71
worker
desafinadude Nov 18, 2025
3e4fc27
Tested working worker
desafinadude Nov 19, 2025
a9a41b1
error handling
desafinadude Nov 19, 2025
e4a614a
klebsiella
desafinadude Nov 20, 2025
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4 changes: 4 additions & 0 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,10 @@ jobs:
- name: Install MJML
run: npm install -g mjml

- name: Run migrations
run: |
./migrations/migrate.sh

- name: Run tests
run: |
pytest -v
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