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Author SHA1 Message Date
jebus
9bc9f86ff1 [Fix] Pathway SVG Export has Edges again, Fix In/Out Edge coloring (#422) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#422
 2026-07-03 07:24:02 +12:00
jebus
dba6514013 [Chore] Package Export, Blanks for fields, Styling (#421) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#421
 2026-07-02 20:12:26 +12:00
jebus
a092d4a558 [Chore] Updated Dockerfile (#418) 
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#418
 2026-06-17 08:33:02 +12:00
jebus
2502c020f7 [Fix] Collection of minor Bugfixes (#417) 
User feedback from on-prem installation

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#417
 2026-06-17 07:56:32 +12:00
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
Tobias O
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
Tobias O
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
Liam Brydon
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
jebus
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
Liam Brydon
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
Liam Brydon
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