Commit Graph

28 Commits

Author SHA1 Message Date
1a2c9bb543 [Feature] Modern UI roll out (#236)
This PR moves all the collection pages into the new UI in a rough push.
I did not put the same amount of care into these as into search, index, and predict.

## Major changes

- All modals are now migrated to a state based alpine.js implementation.
- jQuery is no longer present in the base layout; ajax is replace by native fetch api
- most of the pps.js is now obsolte (as I understand it; the code is not referenced any more @jebus  please double check)
- in-memory pagination for large result lists (set to 50; we can make that configurable later; performance degrades at around 1k) stukk a bit rough tracked in #235

## Minor things

- Sarch and index also use alpine now
- The loading spinner is now CSS animated (not sure if it currently gets correctly called)

## Not done

- Ihave not even cheked the admin pages. Not sure If these need migrations
- The temporary migration pages still use the old template. Not sure what is supposed to happen with those? @jebus

## What I did to test

- opend all pages in browse, and user ; plus all pages reachable from there.
- Interacted and tested the functionality of each modal superfically with exception of the API key modal (no functional test).

---
This PR is massive sorry for that; just did not want to push half-brokenn state.
@jebus @liambrydon I would be glad if you could click around and try to break it :)

Finally closes #133

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#236
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-26 23:16:44 +13:00
21d30a923f [Refactor] Large scale formatting/linting (#193)
All html files now prettier formatted and fixes for incompatible blocks applied

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#193
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 22:47:10 +13:00
9deca8867e [Feature] Possibility to Retrain Models (#190)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#190
2025-11-12 10:28:35 +13:00
df6056fb86 [Enhancement] Refactor of license django model (#187)
Fixes #119

Licenses are now created in the bootstrap management command. To only create the licenses use the command line argument `-ol` or `--only-licenses`.
These licenses are then fetched by there `cc_string` when adding a license to a package.

Co-authored-by: Liam Brydon <62733830+MyCreativityOutlet@users.noreply.github.com>
Co-authored-by: jebus <lorsbach@envipath.com>
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#187
Co-authored-by: liambrydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: liambrydon <lbry121@aucklanduni.ac.nz>
2025-11-12 08:20:43 +13:00
34589efbde [Fix] Mitigate XSS attack vector by cleaning input before it hits our Database (#171)
## Changes

- All text input fields are now cleaned with nh3 to remove html tags. We allow certain html tags under `settings.py/ALLOWED_HTML_TAGS` so we can easily update the tags we allow in the future.
- All names and descriptions now use the template tag `nh_safe` in all html files.
- Usernames and emails are a small exception and are not allowed any html tags

Co-authored-by: Liam Brydon <62733830+MyCreativityOutlet@users.noreply.github.com>
Co-authored-by: jebus <lorsbach@envipath.com>
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#171
Reviewed-by: jebus <lorsbach@envipath.com>
Co-authored-by: liambrydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: liambrydon <lbry121@aucklanduni.ac.nz>
2025-11-11 22:49:55 +13:00
13ed86a780 [Feature] Identify Missing Rules (#177)
Fixes #97
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#177
2025-10-30 00:47:45 +13:00
a952c08469 [Feature] Basic logging of Jobs, Model Evaluation (#169)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#169
2025-10-27 22:34:05 +13:00
1f863fdcd6 [Fix] Remove Scenarios from Objects (#159)
Fixes #155

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#159
2025-10-15 20:23:52 +13:00
68a3f3b982 [Feature] Alias Support (#151)
Fixes #149

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#151
2025-10-09 23:14:34 +13:00
7ad4112343 [Feature] External Identifier/References
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#139
2025-10-02 00:40:00 +13:00
3f5bb76633 [Fix] Remove all Scenarios, catch empty SMILES, prevent default Package delete (#134)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#134
2025-09-30 19:10:57 +13:00
50db2fb372 [Feature] MultiGen Eval (Backend) (#117)
Fixes #16

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#117
2025-09-18 18:40:45 +12:00
762a6b7baf [Feature] Package Export/Import (#116)
Fixes #90
Fixes #91
Fixes #115
Fixes #104

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#116
2025-09-16 02:41:10 +12:00
31783306e2 [Feature] Pathway SVG Export (#102)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#102
2025-09-10 18:44:18 +12:00
5477b5b3d4 [Feature] Rule Based Model (#92)
Fixes #89

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#92
2025-09-09 19:32:12 +12:00
2babe7f7e2 [Feature] Scenario Creation (#78)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#78
2025-09-02 08:06:18 +12:00
02d84a9b29 Fix wrong Button Label in "Compound -> Edit" (#64)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#64
2025-08-28 06:32:42 +12:00
00d9188c0c Copy Objects between Packages (#59)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#59
2025-08-28 06:27:11 +12:00
b95ec98a2f Added Shortcut to make Packages Public (#54)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#54
2025-08-22 07:31:08 +12:00
6e6b394289 Cleanup (#52)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#52
2025-08-22 06:36:22 +12:00
ec387cc12e Added UI elements to add/remove Scenarios to various objects (#51)
Fixes #23

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#51
2025-08-21 07:56:44 +12:00
79b4b1586c Download Pathway Functionality (#38)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#38
2025-07-31 01:30:16 +12:00
df896878f1 Basic System (#31)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#31
2025-07-23 06:47:07 +12:00
9323a9f7d7 Implement Compound CRUD (#22)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#22
2025-07-03 07:17:04 +12:00
4e58a1fad7 Implement functionality to assigne Licenses to Packages and show existing Licenses (#17)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#17
2025-07-03 06:28:49 +12:00
bcd9451450 Implement basic Group handling (#3)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#3
2025-06-26 00:18:40 +12:00
844d0708c9 Granting/Updating Permission for Packages (#2)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#2
2025-06-25 08:49:58 +12:00
ded50edaa2 Current Dev State 2025-06-23 20:13:54 +02:00