v0.0.23

What's Changed

• Add globus_token to get_assaytype_data by @gesinaphillips in #1343

Full Changelog: v0.0.22...v0.0.23

v0.0.22

What's Changed

• Upload.multi_parent logging fix by @gesinaphillips in #1340
• Juranic/visium dirschema updates by @j-uranic in #1341
• Juranic/visium dirschema updates by @jpuerto-psc in #1342

Full Changelog: v0.0.21...v0.0.22

v0.0.21

Development (#1337)

* Entity type constraints (#1330)

* work in progress on entity constraints querying

* basic logic sketched in

* fixing linting error

* very unfinished, need to review entity constraint endpoint documentation further

* architected, testing, definitely broken

* at least one existing test passing, need to run all + design new tests

* added testing

* still testing, lots of edge cases

* messy code, will tidy up

* removed unnecessary code

* fixing formatting errors

* putting enums where they belong

* forgot a file

* need to fix my linter

* made sample constraints work I hope

* working on tests

* fixed broken test

* removed testing from dataset file, hopefully fixed requirements-dev install

* testing fixing action

* second testing fixing actions

* changes to fixtures from assaytype endpoint; fixing globus_token mistake

* fixing malformed constraints endpoint query

* removing breakpoint

* fixing sample checking logic error

* removing breakpoint again

* fixing adding dataset sub_type to SchemaVersion.entity_type_info

* fixing the same query URL mistake in test file

* updating test output with line number changes

* General: Update changelog to reflect releases/versioning updates. (#1334)

Co-authored-by: Juan Puerto <=>

* Update to entity constraints error reporting (#1335)

* scaffolding for update to error reporting to use get_errors

* updated constraint checking to use _get_message

* fixing bugs

* missed some files

* row numbering changes from online testing

* fixing some enum referencing

* linting update

* updated validate_tsv.py for testing get_tsv_errors; fixed some issues with type enums

* sources do not need constraint checks

* Docs: Update CHANGELOG

* Revert "Update to entity constraints error reporting (#1335)"

This reverts commit f92146dfffb14269d23ef7e61f3a6e19b1909e19.

* Phillips/entity constraints errors (#1338)

* scaffolding for update to error reporting to use get_errors

* updated constraint checking to use _get_message

* fixing bugs

* missed some files

* row numbering changes from online testing

* fixing some enum referencing

* linting update

* updated validate_tsv.py for testing get_tsv_errors; fixed some issues with type enums

* sources do not need constraint checks

---------

Co-authored-by: Gesina Phillips <gesina@psc.edu>

* Plugin run reporting (#1336)

* Mods to handle signaling of whether work was done by plugins

* changed the way info is reported via get_info to allow plugin names to be returned

* fixing weird TODO

* changelog

* added test

* moved plugin test to manual testing

---------

Co-authored-by: Joel Welling <welling@psc.edu>

---------

Co-authored-by: gesinaphillips <117199180+gesinaphillips@users.noreply.github.com>
Co-authored-by: Juan Puerto <=>
Co-authored-by: Gesina Phillips <gesina@psc.edu>
Co-authored-by: Joel Welling <welling@psc.edu>

v0.0.20

What's Changed

• Entity type constraints (#1330) by @jpuerto-psc in #1333

Full Changelog: v0.0.19...v0.0.20

v0.0.19

What's Changed

• Stripping trailing slash on ingest url by @sunset666 in #1316
• URL checks error reformatting by @gesinaphillips in #1315
• Jpuerto/nihdev 454 ivt adjust dir schema validation for shared uploads by @jpuerto-psc in #1290
• Juranic/phenocycler dirschema updates by @j-uranic in #1317
• Juranic/lcms dirschema fix by @j-uranic in #1318
• Allow comma-separated parent_sample_id values in URL checking by @gesinaphillips in #1320
• Dir schema major/minor versions by @gesinaphillips in #1312
• ORCID bugfix by @gesinaphillips in #1322
• Juranic/music dir schema by @j-uranic in #1324
• Documentation update by @gesinaphillips in #1321
• Convert upload errors from dict to dataclass by @gesinaphillips in #1319
• Add CEDAR template for murine-source by @jpuerto-psc in #1326
• Reverting deprecation of -fields.yaml files by @gesinaphillips in #1327
• Juranic/music dirschema update by @j-uranic in #1328
• Add 'version' to plugin base class by @jswelling in #1323
• Jpuerto/donor yaml update by @jpuerto-psc in #1329
• Docs: Exclude docs from index by @jpuerto-psc in #1332
• Change to fix row numbering discrepancy by @gesinaphillips in #1331

Full Changelog: v0.0.18...v0.0.19

v0.0.18

What's Changed

• Update phenocycler-v2.yaml by @j-uranic in #1295
• Adding black, isort, flake8 by @gesinaphillips in #1296
• Prevent data_paths that are unique to a component dataset in multi-assay upload by @gesinaphillips in #1297
• Prevent multiple dataset types in a single non-multi-assay upload by @gesinaphillips in #1298
• Adding app_context from SenNet by @gesinaphillips in #1299
• Juranic/mibi dir schema update by @j-uranic in #1302
• Jpuerto/visium with probes bugfix by @jpuerto-psc in #1304
• Juranic/update sfm dir schemas by @j-uranic in #1305
• Testing fix by @gesinaphillips in #1303
• Small error messaging/testing updates by @gesinaphillips in #1306
• Juranic/lightsheet dir schema update by @j-uranic in #1307
• Jpuerto/histology description update by @jpuerto-psc in #1308
• Jpuerto/histology description update by @jpuerto-psc in #1309
• Juranic/geomxngs dirschema update by @j-uranic in #1313
• Maxsibilla/murine port by @maxsibilla in #1311
• Juranic/histology dirschema update by @j-uranic in #1314

Full Changelog: v0.0.17...v0.0.18

v0.0.17

What's Changed

• General: Regenerate docs for atacseq by @jpuerto-psc in #1279
• J uranic/phenocycler dir schema by @j-uranic in #1281
• Phenocycler and Histology bump to 2.2.0 by @gesinaphillips in #1283
• Phillips/phenocycler and histology by @jpuerto-psc in #1284
• Prevent repeated processing of files/contributors.tsv by @gesinaphillips in #1285
• Jpuerto/nihdev 472 ivt add new pages for derived datasets segmentation mask by @jpuerto-psc in #1287
• Directories: Fix the issue with the directory validation not handling… by @jpuerto-psc in #1286
• J uranic/publication nextgen dir schema by @j-uranic in #1288
• Jpuerto/nihdev 479 ivt update rna atac 10 x documentation by @jpuerto-psc in #1289
• Jpuerto/1291 metadata release release cell dive v220 by @jpuerto-psc in #1292
• Update to support change to ingest-validation-tests by @gesinaphillips in #1293
• Docs: Update CHANGELOG for release by @jpuerto-psc in #1294

Full Changelog: v0.0.16...v0.0.17

v0.0.16

This release includes changes to support multi-assay datasets and the rules classifier which lives on Ingest API.