Commit Graph

36 Commits

Author SHA1 Message Date
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
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
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
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
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
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
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
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
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
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
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
026189ccd9 First Issues / Improvements detected in Beta (#36)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#36
2025-07-24 09:57:50 +12:00
2c4c9d95d9 Add Edge Template (#33)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#33
2025-07-23 07:50:39 +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
49e02ed97d feature/additional_information (#30)
Fixes #12

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#30
2025-07-19 08:10:40 +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
9950112311 Implemented Reaction Page (#5)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#5
2025-06-28 06:40:58 +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