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Feature: extend barcode collection search #323

Merged
merged 42 commits into from
Jun 18, 2024
Merged

Feature: extend barcode collection search #323

merged 42 commits into from
Jun 18, 2024

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marcomoscasgr
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@marcomoscasgr marcomoscasgr commented Jun 10, 2024 •
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Metadata updates works on ONT paths uploaded from the instrument to iRODS. This PR will add:

  • recursive search of barcode collections on which apply metadata for rebasecalled data
  • new tests for old and new rebasecalled and plexed data
  • two new test dataset: old and new plexed and rebasecalled folder structures
  • test updates for mlwh queries and html meta-report file

@marcomoscasgr
Update barcode_collection with recursive search of barcode subfolders
0cd94f1
@marcomoscasgr
Fix to barcode_collection function when checking tag ids
447264e
@marcomoscasgr
check tag_id and barcode collection
cea4344
@marcomoscasgr
fix to dictionary items returned
fff9982
@marcomoscasgr
Fix to barcode_collections to output multiple barcode folders
23f3c02
@marcomoscasgr
Add tests for metadata update on rebasecalled runs
ef41cbd
@marcomoscasgr
Update html report tests
af0b721
@marcomoscasgr
update mlwh queries tests
408626b
@marcomoscasgr
Update metadata update tests
667204a
@marcomoscasgr
Test rebasecalled data with 1 exp name and 1 slot
5d9747c
@marcomoscasgr
comments in test html report
c999dde
@marcomoscasgr
fix to barcode path variable in metadata update test
b360a0f
@marcomoscasgr
fix for metadata update of each barcode folder
b3fd7b3
@marcomoscasgr
Update barcode_collection with recursive search of barcode subfolders
f3b227f
@marcomoscasgr
Fix to barcode_collection function when checking tag ids
74561d6
@marcomoscasgr
check tag_id and barcode collection
4bf3123
@marcomoscasgr
fix to dictionary items returned
b70af01
@marcomoscasgr
Fix to barcode_collections to output multiple barcode folders
fd465c8
@marcomoscasgr
Add tests for metadata update on rebasecalled runs
006ef30
@marcomoscasgr
Update html report tests
3472fe4
@marcomoscasgr
update mlwh queries tests
90adf9e
@marcomoscasgr
Update metadata update tests
ca1677e
@marcomoscasgr
Test rebasecalled data with 1 exp name and 1 slot
bd6665b
@marcomoscasgr
comments in test html report
3d3c862
@marcomoscasgr
fix to barcode path variable in metadata update test
9a59199
@marcomoscasgr
fix for metadata update of each barcode folder
0aa147c
@marcomoscasgr
Merge branch 'feature/extend-barcode-collection-search' of github.com…
de86163 
…:marcomoscasgr/npg-irods-python into feature/extend-barcode-collection-search
@marcomoscasgr
Add 2024 to copyright statement
6756334
@marcomoscasgr marcomoscasgr self-assigned this Jun 10, 2024
@marcomoscasgr marcomoscasgr added enhancement New feature or request python Pull requests that update Python code labels Jun 10, 2024
@marcomoscasgr marcomoscasgr marked this pull request as ready for review June 10, 2024 15:35
@marcomoscasgr marcomoscasgr marked this pull request as draft June 10, 2024 15:49
@marcomoscasgr marcomoscasgr marked this pull request as ready for review June 11, 2024 10:19
@marcomoscasgr marcomoscasgr marked this pull request as draft June 12, 2024 14:10
@marcomoscasgr marcomoscasgr marked this pull request as ready for review June 14, 2024 12:04
kjsanger
kjsanger requested changes Jun 17, 2024
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src/npg_irods/ont.py Outdated Show resolved Hide resolved
tests/ont/conftest.py Outdated Show resolved Hide resolved
tests/ont/conftest.py Outdated Show resolved Hide resolved
tests/ont/test_metadata_update.py Outdated Show resolved Hide resolved
kjsanger
kjsanger reviewed Jun 17, 2024
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src/npg_irods/ont.py Outdated Show resolved Hide resolved
@kjsanger kjsanger self-requested a review June 18, 2024 11:06
kjsanger
kjsanger approved these changes Jun 18, 2024
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There's a lot of commits here, so I'll squash them to make the change clearer

@kjsanger kjsanger merged commit cc0244e into wtsi-npg:devel Jun 18, 2024
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