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Seek ena upload #1650

Merged
merged 35 commits into from
Nov 15, 2023
Merged

Seek ena upload #1650

merged 35 commits into from
Nov 15, 2023

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kdp-cloud
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@kdp-cloud kdp-cloud commented Nov 9, 2023 •
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This PR contains changes specific for submitting to ENA, using the ENA upload tool:

  • Implementation for Extended Metadata in Studies and Assays from Single Page
  • Modify the ISA exporter to also export the Extended metadata
  • Organisation of assays in assay streams, based on the assay position.

Kevin De Pelseneer and others added 28 commits November 9, 2023 17:29
@kdp-cloud
Add Seed file with metadata for ena
f2c472b
@kdp-cloud
Add "ENA collection date" to template attribute validation schema
a297f6e
@kdp-cloud
Add custom metadata functionality to Isa Assays
f4070a0
@kdp-cloud
Add custom metadata functionality to Isa Studies
db3713f
@kdp-cloud
Only make custom metadatafields appear on the first assay
a629118
@kdp-cloud
Fix failing tests
93ace07
@kdp-cloud
Make metadata show in edit form as well
c94e172
@kdp-cloud
Transfer custom metadata to the assay comments section of the ISA JSON
a4bf9fd
@kdp-cloud
Split assays into streams of assays
edf9ad5
@kdp-cloud
Change assay position logic
0fc1ab3
@kdp-cloud
Showing custom metadata if assay position is 0
4edf9e3
@kdp-cloud
Correction show_custom_metadata logic
641eb81
@kdp-cloud
fix failing tests
55fbc50
@kdp-cloud
Prevent position to increment when editing
3a2300b
@kdp-cloud
Add Assay stream name as custom metadata
079c12c
@kdp-cloud
Filter stream name out of the comments and set as filename
28a0180
@kdp-cloud
fix merge errors
a0aaf24
@kdp-cloud
Change Custom Metadata to Extended Metadata
619ac5b
@kdp-cloud
Fix failing tests
ab0cebe
@kdp-cloud
Add Study title
b033f08
@kdp-cloud
Updated ISA exporter:
bbbb26d 
- Add assay publications
- Add linked assays as comment
@kdp-cloud
Fix failing test
03965b8
@kdp-cloud
Implement ENA custom metadata for ISA Study
a58e231
@kdp-cloud
Export Study extended metadata
ef9b67c
@kdp-cloud
Fixed the stream name in the isa_exporter
14f8581
@kdp-cloud
Fix isa_exporter. output is othermaterial if corresponding isatag is …
e16e802 
…found.
@kdp-cloud
fix error after rebase
5da37c3
@kdp-cloud
Remove seed file
95ab48e
@kdp-cloud kdp-cloud linked an issue Nov 9, 2023 that may be closed by this pull request
export for ENA upload tool #1589
Closed
@kdp-cloud kdp-cloud added this to the v1.15.0 milestone Nov 9, 2023
@kdp-cloud kdp-cloud marked this pull request as ready for review November 14, 2023 12:40
@kdp-cloud kdp-cloud added the datahub belgiumHub project label Nov 15, 2023
stuzart
stuzart requested changes Nov 15, 2023
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just a minor suggested change

db/seeds/007_sample_attribute_types.seeds.rb Outdated Show resolved Hide resolved
db/seeds/007_sample_attribute_types.seeds.rb Outdated Show resolved Hide resolved
@kdp-cloud kdp-cloud merged commit 9b55b7a into seek4science:main Nov 15, 2023
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@kdp-cloud kdp-cloud deleted the seek_ena_upload branch November 15, 2023 18:39
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@stuzart stuzart stuzart approved these changes

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datahub belgiumHub project
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DataHub
Status: Merged
SEEK 1.15.x
Status: Done
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v1.15.0
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export for ENA upload tool
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