Commit Graph

63 Commits

Author SHA1 Message Date
12a20756d6 [Fix] Add/Update missing nav links (#196)
Adds packages to the footer (instead of Browse link) and removes search from footer (search page not directly linked anymore).
Packages are also available in Browse now.

This is temporary until there is a proper data browsing page.

Co-authored-by: jebus <lorsbach@envipath.com>
Reviewed-on: enviPath/enviPy#196
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 22:24:33 +13:00
d20a705011 [Feature] Add per-package pathway prediction (#195)
## Major Changes

- Introduces a new view for per-package predictions

Co-authored-by: jebus <lorsbach@envipath.com>
Reviewed-on: enviPath/enviPy#195
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 22:01:34 +13:00
debbef8158 [Enhancement] Cleanup Landing Page Form (#194)
I changed the toggle style to be more self evident.
Do you think this is enough, or should I add an (ugly) label?

![image.png](/attachments/0e4ce043-7544-4852-9db9-460517b36d64)

Co-authored-by: jebus <lorsbach@envipath.com>
Reviewed-on: enviPath/enviPy#194
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 21:42:02 +13:00
2799718951 fix: open and close search modal (#192)
Modal now opens on badge click.
Modal now closes on random click around

Reviewed-on: enviPath/enviPy#192
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 20:53:52 +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
c1553d9cd4 [Feature] Add Predict Pathway Page in Modern UI (#188)
## Major Changes
- Predict Pathway is now a separate view as it is meant as adavanced prediction interface

## Current status
![image.png](/attachments/c5bc3f5c-cf30-4b5f-acb3-a70117a96dae)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#188
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 02:38:57 +13:00
2b79adc2f7 [Feature] Implement Search modal in Modern UI (#185)
Implementing a search modal (stretching the level of dynamic that is possible without going to frameworks).

## Major Change
- Search needs packages and is available everywhere now; so had to add reviewed and user packages to global context.

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#185
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 01:52:41 +13:00
ddf1fd3515 Frontpage update (#179)
This PR introduces an overhaul for the front page and login features while keeping the rest of the application intact.

## Major Changes

- TailwindCSS + DaisyUI Integration: Add  modern CSS framework for component-based utility styling
- Build System: Added pnpm for CSS building; can be extended for updated frontend builds in the future
- Navbar + Footer: Redesigned and includable; old version retained for unstyled elements
- Optimized Assets: Added minified and CSS-stylable logos

## New Features

- Static Pages: Added comprehensive mockups of static pages (legal, privacy policy, terms of use, contact, etc.). **Note:** These have to be fixed before a public release, as their content is largely unreviewed and incorrect. Probably best to do in a separate PR that only contains updates to these.
- Discourse API: Implement minimal features based on RestAPI for controllable results.

## Current bugs
- [x] The static pages include the default navbar and footer on the login page. This will likely not work, as users need to access it before logging in; no good workaround so far (problem with Django templating system).
- [ ] The front page predict link is currently non-functional; the redesigned page is almost ready but better done in a separate PR as it also touches Django code.
- [x] Visual bug with the news cards. Still intend to fix for this PR

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#179
Reviewed-by: jebus <lorsbach@envipath.com>
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
2025-11-12 01:09:39 +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
98d62e1d1f [Feature] Make Matomo Site ID configurable via .env (#183)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#183
2025-11-05 10:19:07 +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
819a94aced [Fix] Catch Exception for Adding Structures / Show PubChem Substances (#168)
Fixes #163
Fixes #165

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#168
2025-10-22 01:13:06 +13:00
93dd811e39 [Fix] Pathway SVG Export (#157)
Fixes #103

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#157
2025-10-16 02:25:30 +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
386098b8a6 [Feature] EnzymeLink Annotations (#152)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#152
2025-10-15 19:35:26 +13:00
ef697ac5f5 [Fix] Added UZH Affiliation, Update UoA Images (#153)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#153
2025-10-15 19:25:23 +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
b757a07f91 [Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes (#132)
Bump Python Version to 3.12
Make use of "epauth" optional
Cache `srs` property of rules to speed up apply
Adjust view names for use of `reverse()`
Fix Views for Scenario Attachments
Added Simply Compare View/Template to identify differences between rdkit and ambit
Make migrations consistent with tests + compare
Fixes #76
Set default year for Scenario Modal
Fix html tags for package description
Added Tests for Pathway / Rule
Added remove stereo for apply

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#132
2025-09-26 19:33:03 +12:00
b3079834c1 [Fix] Registering Issue (#125)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#125
2025-09-19 01:17:03 +12:00
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
7905a8c2c1 [Bug] Fixes for Group handling, Load all objects only if necessary (#113)
Fixes #109
Fixes #110
Fixes #111
Fixes #112

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#113
2025-09-11 18:19:27 +12:00
62e6448448 [Feature] Legacy Package Import (#106)
Fixes #105

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#106
2025-09-11 01:18:04 +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
3453a169e1 [Feature] Async Prediction Status Poll (#93)
Fixed #81

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#93
2025-09-09 20:39:26 +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
1a6608287d [Feature] Password Reset Flow (#88)
Fixes #83

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#88
2025-09-06 19:53:36 +12:00
a16035677c [Bugfix] Added Missing Paper in Cite Modal (#87)
Fixes #77

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#87
2025-09-05 08:21:46 +12:00
3c8f0e80cb [Feature] OAuth2 Provider (#84)
Fixes #74

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#84
2025-09-05 06:50:16 +12:00
4e02910c62 Add Link to Community in Navbar (#79)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#79
2025-09-02 08:28:37 +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
dd7b28046c CSS Fix for Index Page (#69)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#69
2025-08-29 08:19:43 +12:00
8592cfae50 Change how List Pages are populated (#68)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#68
2025-08-29 08:09:57 +12:00
ec2b941a85 Fixes #60 (#66)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#66
2025-08-28 06:56:38 +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
6a4c8d96c3 Adjust Matomo Site ID (#57)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#57
2025-08-26 06:17:09 +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
a7637d046a External References (#50)
Fix for #24

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#50
2025-08-21 06:11:05 +12:00
c3c1d4f5cf App Domain Pathway Prediction (#47)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#47
2025-08-19 02:53:56 +12:00
1267ca8ace Enable App Domain Assessment on Model Page (#45)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#45
2025-08-12 09:02:11 +12:00
579cd519d0 Experimental App Domain (#43)
Backend App Domain done, Frontend missing

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#43
2025-08-08 20:52:21 +12:00
a1aebfa54d Model Building UI Flag (#39)
Fixes #8
Flag only disables UI Elements

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#39
2025-07-31 07:00:54 +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