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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

Commits on Nov 9, 2023

  1. Add Seed file with metadata for ena

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  2. Add "ENA collection date" to template attribute validation schema

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  3. Add custom metadata functionality to Isa Assays

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  4. Add custom metadata functionality to Isa Studies

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  5. Only make custom metadatafields appear on the first assay

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  6. Fix failing tests

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  7. Make metadata show in edit form as well

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  8. Transfer custom metadata to the assay comments section of the ISA JSON

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  9. Split assays into streams of assays

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  10. Change assay position logic

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  11. Showing custom metadata if assay position is 0

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  12. Correction show_custom_metadata logic

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  13. fix failing tests

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  14. Prevent position to increment when editing

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  15. Add Assay stream name as custom metadata

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  16. Filter stream name out of the comments and set as filename

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  17. fix merge errors

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  18. Change Custom Metadata to Extended Metadata

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  19. Fix failing tests

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  20. Add Study title

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  21. Updated ISA exporter: 

    - Add assay publications
- Add linked assays as comment
    @kdp-cloud
    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  22. Fix failing test

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  23. Implement ENA custom metadata for ISA Study

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  24. Export Study extended metadata

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  25. Fixed the stream name in the isa_exporter

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  26. Fix isa_exporter. output is othermaterial if corresponding isatag is … 

    …found.
    @kdp-cloud
    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  27. fix error after rebase

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    Kevin De Pelseneer authored and kdp-cloud committed Nov 9, 2023
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  28. Remove seed file

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    kdp-cloud committed Nov 9, 2023
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  29. Add ENA specific sample attribute type to the sample attributes seed … 

    …file
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    kdp-cloud committed Nov 9, 2023
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Commits on Nov 14, 2023

  1. Fix failing tests.

    @kdp-cloud
    kdp-cloud committed Nov 14, 2023
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  2. Add test for adding custom metadata to an isa study

    @kdp-cloud
    kdp-cloud committed Nov 14, 2023
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  3. Add test for creating an isa assay with custom metadata

    @kdp-cloud
    kdp-cloud committed Nov 14, 2023
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  4. Merge branch 'main' of github.com:seek4science/seek into seek_ena_upload

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    kdp-cloud committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. Add seed task to seek upgrade_version

    @kdp-cloud
    kdp-cloud committed Nov 15, 2023
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  2. Change data type title to something more generic. 

    Also changed placeholder text to something more informative.
    @kdp-cloud
    kdp-cloud committed Nov 15, 2023
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