Repository navigation

Add derived dataset provenance to the ro-crate - #3

Merged

jswelling merged 59 commits into

mainfrom

welling/crate_builder_3

Sep 29, 2026

Merged

Add derived dataset provenance to the ro-crate#3
jswelling merged 59 commits into
mainfrom
welling/crate_builder_3

Commits on Aug 14, 2026
- introduce CroissantWrapper; add -d; logging; write zip
  jswelling
  committed
  9384684
Commits on Aug 18, 2026
- separate CroissantWrapper
  jswelling
  committed
  de508ac
- use a scratch directory; save only zip
  jswelling
  committed
  abb5621
Commits on Aug 20, 2026
- working on provenance. WIP.
  jswelling
  committed
  e68ccdf
Commits on Aug 21, 2026
- walk_ancestors is working. WIP.
  jswelling
  committed
  9c05578
Commits on Aug 25, 2026
- working walk_ancestors
  jswelling
  committed
  18197c5
- better docstring for walk_ancestors
  jswelling
  committed
  08620e9
Commits on Aug 26, 2026
- croissant provenance fully functional
  jswelling
  committed
  bc6b25f
- croissant now knows about files but not records
  jswelling
  committed
  9569375
Commits on Aug 27, 2026
- support version, cite_as, license, date_published for croissant
  jswelling
  committed
  eb6052f
- previous_version_uuid should be previous_revision_uuid
  jswelling
  committed
  6d18f77
- add some edam codes; fix edam logic
  jswelling
  committed
  35b2643
Commits on Aug 28, 2026
- first pass rocrate prov for derived dataset. WIP.
  jswelling
  committed
  e4612a3
- fix derived dataset workflow agent
  jswelling
  committed
  cda7854
Commits on Aug 31, 2026
- workflow crate passes validation
  jswelling
  committed
  932e00d
- cleanup
  jswelling
  committed
  ab54f5a
- more cleanup
  jswelling
  committed
  59397b5
Commits on Sep 1, 2026
- refactor out extractors
  jswelling
  committed
  5cd94bb
- move pipeline_steps to extractors
  jswelling
  committed
  950f722
- introduce WrappedEntity
  jswelling
  committed
  1b0a5c1
- use WrappedEntity throughout
  jswelling
  committed
  4e09468
- working on workflow steps. WIP.
  jswelling
  committed
  d7388ca
- checkpoint (WIP)
  jswelling
  committed
  a797e39
Commits on Sep 2, 2026
- fix cwl info for steps
  jswelling
  committed
  77766ac
- hardcode CWL version
  jswelling
  committed
  655794e
- add full workflow description
  jswelling
  committed
  119a6ec
Commits on Sep 3, 2026
- working but incomplete primary ds provenance
  jswelling
  committed
  16f23b5
- black/lint
  jswelling
  committed
  efa30a0
- spelling error
  jswelling
  committed
  0b3e27b
- black
  jswelling
  committed
  dd3f5f9
- croissant[dev] requires black 23.11.0
  jswelling
  committed
  e30381b
- lint
  jswelling
  committed
  fd9c3e1
- black
  jswelling
  committed
  743d9eb
- add pyproject.toml
  jswelling
  committed
  de7bb48
- trying to fix python 3.13 pandas build error
  jswelling
  committed
  8e84c2d
Commits on Sep 5, 2026
- clean up get() defaults
  jswelling
  committed
  9cdb341
Commits on Sep 8, 2026
- use parent doi_url if necessary
  jswelling
  committed
  6b9a69e
- fix croissant handling of snare-seq
  jswelling
  committed
  bf41e3e
- better info for failed entity fetches
  jswelling
  committed
  fdd99b9
- allow python steps to support IVT
  jswelling
  committed
  35683a6
- more flexible EDAM code handling
  jswelling
  committed
  4b482ef
Commits on Sep 9, 2026
- support datasets with missing workflow info
  jswelling
  committed
  261e3ef
- armor against earlier contributor format
  jswelling
  committed
  0d6b0e1
- make robust against missing file attributes
  jswelling
  committed
  f452a49
- support EDAM 2333
  jswelling
  committed
  b97f721
- armor against missing sample description
  jswelling
  committed
  c07b4a6
Commits on Sep 10, 2026
- fix walk_ancestors
  jswelling
  committed
  15dc521
- small lru cache for fetches
  jswelling
  committed
  4d83df3
- linting
  jswelling
  committed
  d72e390
Commits on Sep 11, 2026
- Add EDAM 3003
  jswelling
  committed
  7a82ec4
Commits on Sep 15, 2026
- croissant citeAs to BiBTeX
  jswelling
  committed
  0d09c5c
- linting
  jswelling
  committed
  1555ec6
- adding keywords. WIP.
  jswelling
  committed
  280b97c
- working keywords for rocrate and croissant
  jswelling
  committed
  e5a80f9
Commits on Sep 16, 2026
- lint
  jswelling
  committed
  b85d439
Commits on Sep 17, 2026
- missing import in inactive code?
  jswelling
  committed
  691431f
- flake8
  jswelling
  committed
  d8e9682
Commits on Sep 29, 2026
- added entity_iri(); black
  jswelling
  committed
  056b71c
- flake8
  jswelling
  committed
  db99ab7

Commits

Commits on Aug 14, 2026

Commits on Aug 18, 2026

Commits on Aug 20, 2026

Commits on Aug 21, 2026

Commits on Aug 25, 2026

Commits on Aug 26, 2026

Commits on Aug 27, 2026

Commits on Aug 28, 2026

Commits on Aug 31, 2026

Commits on Sep 1, 2026

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 5, 2026

Commits on Sep 8, 2026

Commits on Sep 9, 2026

Commits on Sep 10, 2026

Commits on Sep 11, 2026

Commits on Sep 15, 2026

Commits on Sep 16, 2026

Commits on Sep 17, 2026

Commits on Sep 29, 2026