jebus/enviPy-bayer
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Author SHA1 Message Date
Tim Lorsbach 8839626255 PW interactions 2026-06-10 16:12:42 +02:00
Tim Lorsbach d0c52b51ee minor 2026-06-10 16:09:02 +02:00
Tim Lorsbach c045b0680c Wip 2026-06-10 16:09:01 +02:00
Tim Lorsbach 17ae593d95 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
 2026-06-10 16:09:01 +02:00
jebusandTim Lorsbach 6ab9180291 [Feature] Vizualize Reaction Circles (#410) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#410
 2026-06-11 02:07:49 +12:00
jebusandTim Lorsbach 3657d14659 [Fix] Cascade deletion of Reactions to Edges (#409) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#409
 2026-06-11 00:24:06 +12:00
jebusandTim Lorsbach ef6091d416 [Fix] Set depth to -1 when adding a Node via Pathway.add_node to be in sync with legacy_api (#408) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#408
 2026-06-09 23:55:16 +12:00
jebusandTim Lorsbach 14cfc1e4d7 [Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407
 2026-06-03 06:00:38 +12:00
jebusandTim Lorsbach 868bbf5c05 [Fix] False as multi_step default in legacy API (#406) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#406
 2026-05-29 08:12:52 +12:00
jebusandTim Lorsbach be5ee1d1d7 [Fix] Propagate multi_step in Edge.create to Reaction.create to ensure deduplication is working (#405) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#405
 2026-05-29 07:39:32 +12:00
jebusandTim Lorsbach 20fd949dfd [Fix] Implement legacy PFASConfidence object construction (#404) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#404
 2026-05-28 23:57:34 +12:00
jebusandTim Lorsbach c9b643fe6e [Feature] Make JobLog Page Paginated (#403) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#403
 2026-05-28 23:01:27 +12:00
jebusandTim Lorsbach 1a9f1cf9af [Fix] Legacy API Node Depth Parsing, description validation in Reaction.create (#402) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#402
 2026-05-28 09:53:39 +12:00
jebusandTim Lorsbach c7c7e17e43 [Feature] Implement legacy endpoints to enable copy via python client (#400) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#400
 2026-05-28 01:41:28 +12:00
jebusandTim Lorsbach 674e10c7fa [Fix] Legacy API Package Endpoint, Pepper Unit in Pathway View (#399) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#399
 2026-05-27 21:09:17 +12:00
jebusandTim Lorsbach 8079b80d57 [Fix] Fix Typo in multi_step assignment (#397) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#397
 2026-05-21 09:56:21 +12:00
jebusandTim Lorsbach 76e63fda2c [Fix] Fix BART Upload (#396) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#396
 2026-05-21 03:16:02 +12:00
jebusandTim Lorsbach 1e43c298d2 [Fix] Simplify Depth adjustment (#386) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#386
 2026-05-12 21:04:56 +12:00
jebusandTim Lorsbach b39fc7eaf8 [Fix] Update Node depth when adding new Edges to a Pathway (#384) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#384
 2026-05-12 09:40:35 +12:00
jebusandTim Lorsbach a2fc9f72cb [Feature] Make use of HalfLifeModel Enum (#383) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#383
 2026-05-12 09:23:56 +12:00
t03i 734b02767e [Fix] Update plotting imports and thread handling in Pepper class (#382) 
- plt.subplot does not work reliably with async/ threads.
- Bug in thread run that would fail with env set (string to number)

Reviewed-on: enviPath/enviPy#382
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
 2026-05-12 06:43:26 +12:00
jebusandTim Lorsbach 9d70db2ca2 [Fix] Wrong indentation in welcome mail (#373) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#373
 2026-04-22 08:47:05 +12:00
jebusandTim Lorsbach fec26d0233 [Feature] Admin Actions for Activation and Affiliation Request (#372) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#372
 2026-04-22 08:36:31 +12:00
jebusandTim Lorsbach 689f7998eb [Dep] Updated enviFormer, additional information lib, aiohttp, fsspec (#371) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#371
 2026-04-22 06:38:31 +12:00
jebusandTim Lorsbach 8498e59fa1 [Feature] Changes required for non public tenants (#370) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#370
 2026-04-22 06:08:39 +12:00
Tim Lorsbach b508511cd6 Implement basic group listing and re-enabled group creation 2026-04-14 20:58:12 +02:00
jebusandTim Lorsbach 877804c0ff [Feature] Path prefixes (#369) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#369
 2026-04-14 21:59:29 +12:00
jebusandTim Lorsbach 964574c700 [Feature] Biotransformer in enviPath (#364) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#364
 2026-04-10 00:00:13 +12:00
jebusandTim Lorsbach 5029a8cda5 [Feature] Dockerized Setup (#366) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#366
 2026-04-07 20:06:46 +12:00
t03i d06bd0d4fd [Feature] Minimal IUCLID export (#338) 
This is an initial implementation that creates a working minimal .i6z document.
It passes schema validation and can be imported into IUCLID.

Caveat:
IUCLID files target individual compounds.
Pathway is not actually covered by the format.

It can be added in either soil or water and soil OECD endpoints.
**I currently only implemented the soil endpoint for all data.**

This sort of works, and I can report all degradation products in a pathway (not a nice view, but we can report many transformation products and add a diagram attachment in the future).

Adding additional information is an absolute pain, as we need to explicitly map each type of information to the relevant OECD field.
I use the XSD scheme for validation, but unfortunately the IUCLID parser is not fully compliant and requires a specific order, etc.

The workflow is: finding the AI structure from the XSD scheme -> make the scheme validation pass -> upload to IUCLID to get obscure error messages -> guess what could be wrong -> repeat 💣

New specifications get released once per year, so we will have to update accordingly.
I believe that this should be a more expensive feature, as it requires significant effort to uphold.

Currently implemented for root compound only in SOIL:

- Soil Texture 2
- Soil Texture 1
- pH value
- Half-life per soil sample / scenario (mapped to disappearance; not sure about that).
- CEC
- Organic Matter (only Carbon)
- Moisture content
- Humidity

<img width="2123" alt="image.png" src="attachments/d29830e1-65ef-4136-8939-1825e0959c62">
<img width="2124" alt="image.png" src="attachments/ac9de2ac-bf68-4ba4-b40b-82f810a9de93">
<img width="2139" alt="image.png" src="attachments/5674c7e6-865e-420e-974a-6b825b331e6c">

Reviewed-on: enviPath/enviPy#338
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
 2026-04-07 19:46:12 +12:00
jebusandTim Lorsbach f7c45b8015 [Feature] Add legacy api endpoint to mimic ReferringScenarios (#362) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#362
 2026-03-17 19:44:47 +13:00
jebusandTim Lorsbach 68aea97013 [Feature] Simple template extension mechanism (#361) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#361
 2026-03-16 21:06:20 +13:00
jebusandTim Lorsbach 3cc7fa9e8b [Fix] Add Captcha vars to Template (#359) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#359
 2026-03-13 11:46:34 +13:00
jebusandTim Lorsbach 21f3390a43 [Feature] Add Captchas to avoid spam registrations (#358) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#358
 2026-03-13 11:36:48 +13:00
jebusandTim Lorsbach 8cdf91c8fb [Fix] Broken Model Creation (#356) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#356
 2026-03-12 11:34:14 +13:00
jebusandTim Lorsbach bafbf11322 [Fix] Broken Enzyme Links (#353) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#353
 2026-03-12 10:25:47 +13:00
jebusandTim Lorsbach f1a9456d1d [Fix] enviFormer prediction (#352) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#352
 2026-03-12 08:49:44 +13:00
jebusandTim Lorsbach e0764126e3 [Fix] Scenario Review Status + Depth issues (#351) 
https://envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1d537657-298c-496b-9e6f-2bec0cbe0678

-> Node.depth can be float for Dummynodes
-> Scenarios in Edge.d3_json were lacking a reviewed flag

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#351
 2026-03-12 08:28:20 +13:00
liambrydon ef0c45b203 [Fix] Pepper display probability calculation (#349) 
Probability of persistent is now calculated to include very persistent.

Reviewed-on: enviPath/enviPy#349
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
 2026-03-11 19:12:55 +13:00
jebusandTim Lorsbach b737fc93eb [Feature] Search for Permissions, Prep Compound / Structure to be extended, Prep Template overwrites (#347) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#347
 2026-03-11 11:27:15 +13:00
jebusandTim Lorsbach d4295c9349 [Fix] bootstrap command now reflects new Scenario/AdditionalInformation structure (#346) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#346
 2026-03-07 03:14:28 +13:00
jebusandTim Lorsbach c6ff97694d [Feature] PEPPER in enviPath (#332) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#332
 2026-03-06 22:11:22 +13:00
jebusandTim Lorsbach 6e00926371 [Feature] Scenario and Additional Information creation via enviPath-python, Add Half Lifes to API Output, Fix source/target ids in legacy API (#340) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#340
 2026-03-06 07:20:18 +13:00
jebusandTim Lorsbach 81cc612e69 [Feature] Populate Batch Predict Table by CSV (#339) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#339
 2026-03-06 03:15:44 +13:00
jebusandTim Lorsbach cc9598775c [Fix] Fix Perm for creating entities (#341) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#341
 2026-02-27 03:56:33 +13:00
jebusandTim Lorsbach d2c2e643cb [Fix] Compound Grouping, Identity prediction of enviFormer, Setting params (#337) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#337
 2026-02-20 10:14:28 +13:00
jebusandTim Lorsbach 0ff046363c [Fix] Fixed failing frontend tests due to renaming (#335) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#335
 2026-02-17 03:09:32 +13:00
Tim Lorsbach 5150027f0d [Fix] Login via email, prevent Usernames with certain chars 2026-02-16 13:58:06 +01:00
liambrydon 58ab5b33e3 [Fix] Filter Active Users (#314) (#329) 
Adding users to a group or setting permissions on a package now filter for active users. Also any inactive members of group/package get marked as such.

<img width="490" alt="{3B906C71-F3AE-41E4-A61C-B8377D79F685}.png" src="attachments/09cf149a-9d7a-4560-8ce7-9f3487527ee2">

Reviewed-on: enviPath/enviPy#329
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
 2026-02-12 20:20:16 +13:00
liambrydonandTim Lorsbach 73f0202267 [Fix] Filter Scenarios with Parent (#311) (#323) 
The scenarios lists both in /scenarios and /package/<id>/scenario no longer show related scenarios (children).
All related scenarios are shown on the scenario page under Related Scenarios if there are any.
<img width="500" alt="{C2D38DED-A402-4A27-A241-BC2302C62A50}.png" src="attachments/1371c177-220c-42d5-94ff-56f9fbab761f">

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#323
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
 2026-02-11 23:19:20 +13:00