Skip to content

mass repo cleanup + lots of documentation + added id_autocomplete and gene_density endpoints to replace legacy CGI scripts#313

Open
rmobmina wants to merge 54 commits intoBioAnalyticResource:devfrom
rmobmina:master
Open

mass repo cleanup + lots of documentation + added id_autocomplete and gene_density endpoints to replace legacy CGI scripts#313
rmobmina wants to merge 54 commits intoBioAnalyticResource:devfrom
rmobmina:master

Conversation

@rmobmina
Copy link
Copy Markdown
Contributor

@rmobmina rmobmina commented Apr 13, 2026 •
edited
Loading

  • Standardized docstrings and added attribution headers across all EFP files
  • Added comprehensive inline comments and notes throughout the codebase
  • Removed stale archive/sample data files and cleaned up repo structure
  • Fixed failing tests across EFP data, schemas, and resource endpoints
  • Converted idautocomplete.cgi to GET /gene_information/id_autocomplete
  • Converted genedensity.cgi to GET /gene_density
  • Added AgiNames SQLAlchemy model and agi_names table seed data to the eplant2 test mirror
  • Removed the limit query parameter from id_autocomplete, result size is now fixed at 15
  • Added 8 tests for gene_density and updated test_gene_information.py with 9 tests for id_autocomplete

@asherpasha
Merge pull request BioAnalyticResource#91 from BioAnalyticResource/dev
7fccc10 
Update master
@asherpasha
Merge pull request BioAnalyticResource#93 from BioAnalyticResource/dev
5b9265e 
Update Master branch
@asherpasha
Merge pull request BioAnalyticResource#97 from BioAnalyticResource/dev
7bcdbdf 
Update master branch before updating everything else.
@asherpasha
Merge pull request BioAnalyticResource#101 from BioAnalyticResource/dev
a05f196 
Update master branch
@asherpasha
Merge pull request BioAnalyticResource#119 from BioAnalyticResource/dev
29e97ab 
Update master branch
@asherpasha
Merge pull request BioAnalyticResource#123 from BioAnalyticResource/dev
b1fa5fe 
Sync master branch
@asherpasha
Merge pull request BioAnalyticResource#132 from BioAnalyticResource/dev
21b07f5 
Update master branch
@asherpasha
Merge pull request BioAnalyticResource#140 from BioAnalyticResource/dev
cf5fe5d 
Update Master Branch
@asherpasha
Merge pull request BioAnalyticResource#145 from BioAnalyticResource/dev
a184ca5 
Sync branches ...
@asherpasha
Merge pull request BioAnalyticResource#150 from BioAnalyticResource/dev
87259b8 
Sync master
@asherpasha
Merge pull request BioAnalyticResource#154 from BioAnalyticResource/dev
952e648 
Update Requirements
@asherpasha
Merge pull request BioAnalyticResource#156 from BioAnalyticResource/dev
5c98688 
Sync
@asherpasha
Merge pull request BioAnalyticResource#161 from BioAnalyticResource/dev
b0f3a50 
Updates.
@asherpasha
Merge pull request BioAnalyticResource#169 from BioAnalyticResource/dev
5cd3240 
Update master branch
@asherpasha
Merge pull request BioAnalyticResource#179 from BioAnalyticResource/dev
43fbe2a 
Update main branch
@asherpasha
Merge pull request BioAnalyticResource#185 from BioAnalyticResource/dev
8b2fdc5 
Sync
@asherpasha
Merge pull request BioAnalyticResource#187 from BioAnalyticResource/dev
804f4aa 
Redis is now working
@asherpasha
Merge pull request BioAnalyticResource#197 from BioAnalyticResource/dev
bf73dcc 
Update main branch
@asherpasha
Merge pull request BioAnalyticResource#202 from BioAnalyticResource/dev
6cd621b 
Update Main branch
@asherpasha
Merge pull request BioAnalyticResource#204 from BioAnalyticResource/dev
9e7d9b0 
Updates
@asherpasha
Merge pull request BioAnalyticResource#206 from BioAnalyticResource/dev
24a2290 
Sync
@asherpasha
Merge pull request BioAnalyticResource#208 from BioAnalyticResource/dev
20c1679 
Updates
@asherpasha
Merge pull request BioAnalyticResource#215 from BioAnalyticResource/dev
a995369 
Update main branch
@asherpasha
Merge pull request BioAnalyticResource#227 from BioAnalyticResource/dev
16ce80c 
Update from dev branch
@asherpasha
Merge pull request BioAnalyticResource#231 from BioAnalyticResource/dev
3131d5d 
Sync
@asherpasha
Merge pull request BioAnalyticResource#237 from BioAnalyticResource/dev
acf7770 
Update main ...
@asherpasha
Merge pull request BioAnalyticResource#241 from BioAnalyticResource/dev
a195141 
Update main branch
@asherpasha
Merge pull request BioAnalyticResource#243 from BioAnalyticResource/dev
9d6a957 
Sync
@asherpasha
Merge pull request BioAnalyticResource#246 from BioAnalyticResource/dev
2885de8 
Sync
@asherpasha
Merge pull request BioAnalyticResource#248 from BioAnalyticResource/dev
9c33aa2 
ThaleMine Updated
asherpasha and others added 24 commits December 23, 2024 14:27
@asherpasha
Merge pull request BioAnalyticResource#250 from BioAnalyticResource/dev
a4da029 
Update dep.
@asherpasha
Merge pull request BioAnalyticResource#253 from BioAnalyticResource/dev
36c52f6 
Update requirements.txt
@asherpasha
Merge pull request BioAnalyticResource#256 from BioAnalyticResource/dev
0168dae 
Sync
@asherpasha
Merge pull request BioAnalyticResource#258 from BioAnalyticResource/dev
9c31979 
Sync
@asherpasha
Merge pull request BioAnalyticResource#264 from BioAnalyticResource/dev
79ef834 
Update main branch
@asherpasha
Merge pull request BioAnalyticResource#274 from BioAnalyticResource/dev
2f612af 
Updates!
@asherpasha
Merge pull request BioAnalyticResource#277 from BioAnalyticResource/dev
30c03f2 
Added eFP Grape
@asherpasha
Merge pull request BioAnalyticResource#279 from BioAnalyticResource/dev
e719beb 
Updates
@asherpasha
Merge pull request BioAnalyticResource#281 from BioAnalyticResource/dev
78071ca 
Updates
@asherpasha
Merge pull request BioAnalyticResource#283 from BioAnalyticResource/dev
5aac55a 
Updates
@asherpasha
Merge pull request BioAnalyticResource#298 from BioAnalyticResource/dev
f039563 
Updated main branch
@asherpasha
Merge pull request BioAnalyticResource#311 from BioAnalyticResource/dev
a320300 
Updates
@rmobmina
resolve merge conflicts and add remaining EFP pipeline files
2f87b46 
- fix agi_to_probset typo (was agi_to_probst) in gene_id_utils.py
- add data_type field to microarray /samples endpoint response
- switch endpoint to efp_species_view_info_typed.json
- add typed eFP view info JSON and data type annotation script
- ignore large SQL dump files from git tracking
@rmobmina
standardise docstrings and add attribution headers across all EFP files
a51755c
@rmobmina
fix flake8 E226 whitespace around arithmetic operator
086115c
@rmobmina
lots of docs added and enhanced comments and notes
013d2c9
@rmobmina
cleaned entire repo one last time and ran flake8
708bcf5
@rmobmina
tests should now all pass
4549a93
@rmobmina
tests should pass now
e94514d
@rmobmina
converted gene_query endpoint from POST to GET
ae0ad34
@rmobmina
added auto complete endpoint
da3530f
@rmobmina
Added autocomplete and genedensity endpoints + tests
5a6430c
@rmobmina
add namespaces to init
4afa6b7
@rmobmina
Merge remote-tracking branch 'upstream/master'
999bdbf
@rmobmina rmobmina changed the title mass repo cleanup + lots of documentation mass repo cleanup + lots of documentation + added id_autocomplete and gene_density endpoints to replace legacy CGI scripts Apr 30, 2026
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@rmobmina @asherpasha