5 Commits

Include renames

Author	SHA1	Message	Date
Tim Lorsbach	e5e0dcee3b	adjusted migration ... Initial bayer app Show Pack Classification 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 wip More on PES wip wip Wip minor PW interactions API PES wip Make Select Widget reflect required make required generallay available Update UI if pathway mode is set to build Added ais circle adjustments Initial Zoom, fix AD Creation wip auth log, bb4g fix missing import Added viz hint if PES is part of reaction Add Edge check for pes flip boolean ... pes Added extra ... In / Out Edges Viz, Submitting Button Text ... Make PES Link clickable Return proper http response instead of error Fixed error return, removed unused options Fix PES Link HTML for other entities Fixed molfile assignment, adjusted Export Package Export/Import cycle highlight Description links implemented non persistent Harmonised proposed field in Json output Added pesLink field to PW Api output PES Fields in API Output removed debug Fix Classification import, Fix PES Deserialization underline pes link in templates Fix alter name/desc for node, make /node /edge funcitonal provide setting link and copy button Implemented Compound Names / Reaction Names View Option Unconnected Nodes Make links thicker, reduce timeout trigger time Show proposed info in popover Pathway Build no stereo removal Include probs in reaction name option viz Detect clicks outside nodes/edges	2026-07-16 22:26:23 +02:00
t03iandTim Lorsbach	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
t03iandTim Lorsbach	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
4 people	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
jebusandTim Lorsbach	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