Initial bayer app
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Adjusted docker compose to bayer specifics
Adjusted Dockerfile for Bayer
Adding secret flags to group, add secret pools to packages
Adjusted View for Package creation
Prep configs, added Package Create Modal
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More on PES
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**Warning depends on Timeseries feature to be merged**
Implements a way to display OECD 301F data on the pathway view.
This is mostly a PoC and needs to be improved once the pathway rendering is updated.
Co-authored-by: jebus <lorsbach@envipath.com>
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#319
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This implements a version of #274, relying on Pydantics built in JSON schema and JSON rendering.
Requires additional UI tagging in the ai model repo but will remove HTML tags.
Example scenario with filled information: 5882df9c-dae1-4d80-a40e-db4724271456/scenario/3a4d395a-6a6d-4154-8ce3-ced667fceec0
Reviewed-on: enviPath/enviPy#282
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
## Major Changes
- Implement a REST style API app in epapi
- Currently implements a GET method for all entity types in the browse menu (both package level and global)
- Provides paginated results per default with query style filtering for reviewed vs unreviewed.
- Provides new paginated templates with thin wrappers per entity types for easier maintainability
- Implements e2e tests for the API
## Minor changes
- Added more comprehensive gitignore to cover coverage reports and other test/node.js etc. data.
- Add additional CI file for API tests that only gets triggered on API relevant changes.
## ⚠️ Currently only works with session-based authentication. Token based will be added in new PR.
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Co-authored-by: jebus <lorsbach@envipath.com>
Reviewed-on: enviPath/enviPy#243
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
**This pull request will need a separate migration pull-request**
I have added an alert box in two places when the user tries to predict with stereo chemistry.
When a user predicts a pathway with stereo chemistry an alert box is shown in that node's hover.
To do this I added two new fields. Pathway now has a "predicted" BooleanField indicating whether it was predicted or not. It is set to True if the pathway mode for prediction is "predict" or "incremental" and False if it is "build". I think it is a flag that could be useful in the future, perhaps for analysing how many predicted pathways are in enviPath?
Node now has a `stereo_removed` BooleanField which is set to True if the Node's parent Pathways has "predicted" as true and the node SMILES has stereochemistry.
<img width="500" alt="{927AC9FF-DBC9-4A19-9E6E-0EDD3B08C7AC}.png" src="attachments/69ea29bc-c2d2-4cd2-8e98-aae5c5737f69">
When a user does a prediction on a model's page it shows at the top of the list. This did not require any new fields as the entered SMILES does not get saved anywhere.
<img width="500" alt="{BED66F12-5F07-419E-AAA6-FE1FE5B4F266}.png" src="attachments/5fcc3a9b-4d1a-4e48-acac-76b7571f6507">
I think the alert box is an alright solution but if you have a great idea for something that looks/fits better please change it or let me know.
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#250
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
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>
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>
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>
Tim Lorsbach
jebusandTim Lorsbach
liambrydonandt03i