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OpenUpSA / agari-folio Public

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Staging#249

Merged

desafinadude merged 105 commits into

masterOpenUpSA/agari-folio:masterfrom

stagingOpenUpSA/agari-folio:stagingCopy head branch name to clipboard

Dec 15, 2025

Conversation Commits105 (105)Checks Files changed

Merged

Staging#249
desafinadude merged 105 commits into
masterfrom
staging

Commits

Commits on Dec 6, 2025

handling fasta files with biopython
desafinadude
committed
pandas
desafinadude
committed

Commits on Dec 8, 2025

Merge pull request #201 from OpenUpSA/pandas
desafinadude
authored
Merge branch 'staging' into biopython
desafinadude
authored
Update worker.py

desafinadude
and
Copilot
authored
Update helpers.py

desafinadude
and
Copilot
authored
Merge pull request #202 from OpenUpSA/biopython
desafinadude
authored
Show project membership inheriting from org roles
michaelglenister
committed

Commits on Dec 9, 2025

Merge pull request #205 from OpenUpSA/michael-dev-5
michaelglenister
authored
wip
desafinadude
committed
Return user info
michaelglenister
committed
bulk indexing.
desafinadude
committed
Merge pull request #206 from OpenUpSA/michael-dev-5
michaelglenister
authored
Merge pull request #207 from OpenUpSA/elastic-bottleneck
desafinadude
authored
flatten isolate data
desafinadude
committed
update ci to use buld_send_to_elastic
desafinadude
committed
Merge pull request #208 from OpenUpSA/elastic-bottleneck
desafinadude
authored
UI tweaks to email templates
michaelglenister
committed
save parent_file_id
desafinadude
committed
Merge pull request #209 from OpenUpSA/michael-dev-5
michaelglenister
authored
Merge pull request #210 from OpenUpSA/overwrite
desafinadude
authored
Event log - submission overwrite
michaelglenister
committed
Refrsh access toke
michaelglenister
committed

Commits on Dec 10, 2025

avoid orphaned sequence files
desafinadude
committed
Merge pull request #212 from OpenUpSA/clean-up-before-validate
desafinadude
authored
tests for search & reindex api
cyber237
committed
Log project_overwrite
michaelglenister
committed
Merge pull request #211 from OpenUpSA/michael-dev-5
michaelglenister
authored
Document log types
michaelglenister
committed
Merge pull request #214 from OpenUpSA/michael-dev-5
michaelglenister
authored
Enhance SQL queries to include project visibility and names for isolates in publish/unpublish endpoints
desafinadude
committed
Merge pull request #213 from OpenUpSA/tests/search
desafinadude
authored
Fix SQL joins in project submission endpoints to correctly reference pathogen IDs
desafinadude
committed
Merge pull request #216 from OpenUpSA/isoalte-rbac-fix
desafinadude
authored
Refactor bulk_send_to_elastic function and enhance SQL query to include project visibility
desafinadude
committed
Merge branch 'staging' into isoalte-rbac-fix
cyber237
committed
unskip search rbac external user test
cyber237
committed
Refactor TSV to JSON conversion to replace NaN with None for valid Postgres JSON
desafinadude
committed
Merge pull request #218 from OpenUpSA/pandas-fix
desafinadude
authored
Merge pull request #217 from OpenUpSA/isoalte-rbac-fix
desafinadude
authored
Refactor TSV to JSON conversion for improved readability and error handling
desafinadude
committed
Merge pull request #219 from OpenUpSA/cleaning-debugs
desafinadude
authored
Endpoint to get user id from email
michaelglenister
committed
elastic debugging
desafinadude
committed
Merge pull request #221 from OpenUpSA/log-in-fix
michaelglenister
authored
Merge pull request #222 from OpenUpSA/elastic-debugging
desafinadude
authored
tsv_to_json update
desafinadude
committed
Merge pull request #223 from OpenUpSA/elastic-debugging
desafinadude
authored
Dealing with Nones
desafinadude
committed
Merge pull request #224 from OpenUpSA/elastic-debugging
desafinadude
authored
string Nans
desafinadude
committed
Merge pull request #225 from OpenUpSA/elastic-debugging
desafinadude
authored
NaN error
desafinadude
committed
Merge pull request #226 from OpenUpSA/elastic-debugging
desafinadude
authored
nones
desafinadude
committed
Merge pull request #227 from OpenUpSA/elastic-debugging
desafinadude
authored

Commits on Dec 11, 2025

Remove parent_file_id from print statement and database insert query in save_sequence_data function
desafinadude
committed
Merge pull request #228 from OpenUpSA/split-fix
desafinadude
authored
Enhance file upload functionality: add duplicate file check and improve error handling
desafinadude
committed
Merge pull request #229 from OpenUpSA/upload-duplicate-check
desafinadude
authored
Left align email buttons
michaelglenister
committed
Merge pull request #230 from OpenUpSA/michael-dev-6
michaelglenister
authored
Add debug print statements to log incoming JSON data in Search resource
desafinadude
committed
Merge pull request #231 from OpenUpSA/search-debug
desafinadude
authored
search filter
desafinadude
committed
Merge pull request #232 from OpenUpSA/search-debug
desafinadude
authored
delete from elastic fix
desafinadude
committed
Merge pull request #233 from OpenUpSA/search-debug
desafinadude
authored
delete isolate
desafinadude
committed
Merge pull request #234 from OpenUpSA/search-debug
desafinadude
authored

Commits on Dec 12, 2025

docs update
desafinadude
committed
updated diagram
desafinadude
committed
refactor: update project visibility handling in Project resource
desafinadude
committed
witht the helpers file
desafinadude
committed
Merge pull request #236 from OpenUpSA/reindex-on-project-policy-change
desafinadude
authored
Hard delete users
michaelglenister
committed
Hard delete users
michaelglenister
committed
Merge pull request #237 from OpenUpSA/michael-dev-6
michaelglenister
authored
feat: add debug print statements for user project IDs and access filter in search
desafinadude
committed
Merge pull request #238 from OpenUpSA/reindex-on-project-policy-change
desafinadude
authored
wip: fix search api tests
cyber237
committed
remove send_to_elastic2
desafinadude
committed
Merge pull request #239 from OpenUpSA/remove-send_to_elastic2
desafinadude
authored
api-docs
desafinadude
committed
feat: add response example for health check endpoint
desafinadude
committed
Merge branch 'staging' into fix/broken-tests
cyber237
committed
rm send_to_elastic2 from tests
cyber237
committed
all info endpoints documents
desafinadude
committed
feat: enhance API documentation with detailed descriptions for health and permissions endpoints
desafinadude
committed
Merge pull request #241 from OpenUpSA/api-docs
desafinadude
authored
add semi-private to project privacy check
cyber237
committed
wip: fix search api tests
cyber237
committed

Commits on Dec 14, 2025

Updated init.sql to final schema
desafinadude
committed
update init.sql
desafinadude
committed
Merge pull request #242 from OpenUpSA/fix/broken-tests
desafinadude
authored
removed .keyword from filters
desafinadude
committed
Merge pull request #243 from OpenUpSA/filter-fix
desafinadude
authored
turn on all skipped tests
cyber237
committed
refactor: streamline token retrieval for project contributors in semi-private draft tests
desafinadude
committed

Commits on Dec 15, 2025

Fix for test_public_project_external_user_has_implicit_viewer_role
desafinadude
committed
feat: enhance project submissions visibility based on user roles
desafinadude
committed
Fix for: test_submissions_rbac.py::test_viewer_cannot_see_drafts
desafinadude
committed
fix for: test_contributor_cannot_unpublish_other_submission and test_contributor_cannot_delete_other_draft
desafinadude
committed
Disabled search test
desafinadude
committed
Merge pull request #244 from OpenUpSA/fix/broken-tests
desafinadude
authored

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