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issue openedkids-first/kf-api-study-creator

Remove obsolete file types

Now that we have the new file types which correspond to the KF templates, we should remove old file types that do not have templates and are too general to be meaningful. Those would be: SHM - Shipping Manifest, CLN - Clinical Data. We should keep the other two file types without templates: OTH - Other, DBG - dbGaP file because the OTH can be used for any file that doesn't match a template/expedited type and DBG may still be an important categorization.

The frontend should also update its file types so that the old types are not displayed to the user.

To do:

  • [ ] Data migration that will set File.file_type=OTH for any File that has a file type of SHM, CLN
  • [ ] Remove the old file types: SHM, CLN from creator.analyses.file_types
  • [ ] Database schema migration to remove the old file type choices from File.file_type

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pull request commentkids-first/kf-api-study-creator

✨ Sort studies by last active

Oh I'm sorry I forgot that studies don't have versions they have files..nvmind

gsantia

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pull request commentkids-first/kf-api-study-creator

✨ Sort studies by last active

@gsantia Curious to know if this works well, did you try #681 (comment)?

I'm a bit confused by this. Should I create a new Study.versions field and populate it?

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:arrow_up: Bump django from 2.2.20 to 2.2.21 Bumps [django](https://github.com/django/django) from 2.2.20 to 2.2.21. - [Release notes](https://github.com/django/django/releases) - [Commits](https://github.com/django/django/compare/2.2.20...2.2.21) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

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pull request commentkids-first/kf-api-study-creator

✨ Sort studies by last active

@gsantia Curious to know if this works well, did you try https://github.com/kids-first/kf-api-study-creator/pull/681#issuecomment-865098170?

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Handling multiple cases Updating to handle multiple "studies" with the same accession number

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Pull request review commentkids-first/kf-api-study-creator

✨ Sort studies by last active

     "creator",     "corsheaders",     'creator.ingest_runs.apps.IngestRunsConfig',+    "creator.studies.apps.StudiesConfig",

@gsantia if you add something like this https://github.com/kids-first/kf-api-study-creator/blob/89176bd16e9fe2ea2cefdd8eb049b41b8742264e/creator/data_templates/init.py into your apps/__init__.py you can just have creator.studies in your settings files

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:white_check_mark: Test data template events + signals

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pull request commentkids-first/kf-api-study-creator

✨ Sort studies by last active

There seems to be an issue with one of the migrations from the organizations update?

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pull request commentkids-first/kf-api-study-creator

✨ Sort studies by last active

So I've been reading into all the links provided and elsewhere, and I've been unable to come up with a query that I'd consider easy. Maybe I'm missing something. But I think we can go with the method that I have here

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Pull request review commentd3b-center/d3b-bixu-data-assembly

add cwltools and workflow for RNA and DNA merge

+cwlVersion: v1.0+class: Workflow+id: data_assembly_RNA_wf+requirements:+  - class: MultipleInputFeatureRequirement+  - class: SubworkflowFeatureRequirement+inputs:++  # format fusion+  FusionGenome: { type: File }+  arriba_output_file: { type: File }+  star_fusion_output_file: { type: File }+  old_arriba: { type: File }+  old_starfusion: { type: File }++  # rsem +  input_rsem: { type: File }+  old_rsem_count: { type: File }+  old_rsem_fpkm: { type: File }+  old_rsem_tpm: { type: File }+  library:  {type: ['null', {type: enum, name: library, symbols: ["polya", "stranded"]}]}++  biospecimen_id_RNA: string++outputs:+  new_merged_star_fusion: { type: File, outputSource: merge_fusion/output_merged_star_fusion }+  new_merged_merged_arriba:  { type: File, outputSource: merge_fusion/output_merged_arriba }+  +  new_merged_rsem_count: { type: File, outputSource: merge_rsem/output_merged_rsem_count }+  new_merged_fpkm: { type: File, outputSource: merge_rsem/output_merged_fpkm }+  new_merged_tpm: {type: File, outputSource: merge_rsem/output_merged_tpm}++steps:+  format_fusion:+    run: ../tools/format_fusion.cwl+    in:+      arriba_output_file: arriba_output_file+      star_fusion_output_file: star_fusion_output_file+      biospceimens_id: biospecimen_id_RNA+    out: [output_formatted_starfusion,output_formatted_arriba]++  anno_fusion:+    run: ../tools/anno_fusion.cwl+    in:+      FusionGenome: FusionGenome+      output_formatted_arriba: format_fusion/output_formatted_arriba+      biospceimens_id: biospecimen_id_RNA

sorry about that, I made the update, should be fixed now

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PR merged kids-first/kf-ui-data-tracker

🐛 Fix allEvents query input event type bug

Screen Shot 2021-06-17 at 2 33 14 AM Screen Shot 2021-06-17 at 2 33 26 AM

Error: Variable \"eventType\" of type \"String\" used in position expecting type \"EventEventType\".

Fixed by: In allEvents query input change $eventType: String to $eventType: EventEventType

+9 -2

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🐛 Fix study release version display

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🐛 Fix allEvents query input event type

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✨ Add mutation to add member to an organization

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✅ Add test for add and remove member of an organization

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commit sha 3d0504c04b8dbf1efa8da6f9c106a02ac78ac334

:x: Add error message for updating organization

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Dan Kolbman

commit sha bdefc5ea7c77e016bba63743792fa0a6db168f14

:recycle: Update current org in storage if it has changed

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Daniel Kolbman

commit sha 8b5b46774a1ec90088211d44f885bd320e299504

Merge pull request #1053 from kids-first/organizations/admin ✨ Organizations admin view

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Dan Kolbman

commit sha 613f37d479c9fb954129b8065e525ca72dc733ef

:recycle: Attach current organization to invites

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Daniel Kolbman

commit sha 39df82002b00ff34788b03a969eb382134af2900

Merge pull request #1059 from kids-first/organizations/update-invites ♻️ Attach organization to invites

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Dan Kolbman

commit sha 9e4e69b5584d5c1764634f891732a9d2d6298ce0

:white_check_mark: Update study tests

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Dan Kolbman

commit sha f1fc3164682d04043c46264444279674727a15e3

:recycle: Attach current org to new studies

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Daniel Kolbman

commit sha 7f498eb2eca704eb1cef7ae09faf83d80d6a833e

Merge pull request #1061 from kids-first/organizations/update-add-study ✨ Add org to new studies

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Dan Kolbman

commit sha 8687dbeffb6aaf5ccb8b26afc5ec455649e3bea3

:white_check_mark: Update cypress tests for new mock data

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Daniel Kolbman

commit sha 8e55c43259a9fe01254ab849c3e56354cc34c938

Merge pull request #1063 from kids-first/organizations/update-tests ✅ Update cypress tests for new mock data

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XuTheBunny

commit sha 467196cc1989386f9acf9e54bfd86632a1edca4c

🐛 Fix study release version display

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XuTheBunny

commit sha e705df337876c1eb20e982f4b4553ba052eed4c0

🐛 Fix allEvents query input event type

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pull request commentkids-first/kf-ui-data-tracker

✨ Add organizations features

:heavy_check_mark: Deploy Preview for kf-ui-data-tracker ready!

:hammer: Explore the source changes: 8e55c43259a9fe01254ab849c3e56354cc34c938

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dankolbman

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push eventkids-first/kf-api-study-creator

gsantia

commit sha 36bf6eff9e90232135a17222cb73d3121e6836aa

:recycle: Fix pandas indexing warnings

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gsantia

commit sha 6175d3582f9d55b838a62213c16cfbc677a1c807

:recycle: Add timezones to banner dates

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gsantia

commit sha a8713b9d42e2bc0f8573d49570b1f6897d1f5206

:art: Apply black to banner mutations and tests

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Dan Kolbman

commit sha 2910131595be7370b73fc6edf27cde4d2eb1ed73

:sparkles: Add new document types and extract configs

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Dan Kolbman

commit sha 75ba7c7db2444ffd700ad3d2269fe7b08668b2d8

:mute: Ignore extract config templates in pytest.ini

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Natasha Singh

commit sha 482eae65988e8d78ed4ffcb10038b49a0eb27a9d

:truck: Mv test extract cfg download into extract cfg tests

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Natasha Singh

commit sha e4d7eade5d526cceeca705b746fd649a28d63916

:recycle: Study generator makes data, uses extract cfgs that conform to templates

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Natasha Singh

commit sha 66b8ba731f3a09c32ba794180b905df19f44d025

:white_check_mark: Test doc types and extract configs

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Natasha Singh

commit sha 59d7368046f1dd247f6db53a450a7e1984f54601

:arrow_up: Bump ingest library to 1.8.0

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Daniel Kolbman

commit sha 1abe0031b42c9429a767f5069cb94141f3262d2a

Merge pull request #571 from kids-first/add-document-types ✨ Add new doc types and extract configs

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Dan Kolbman

commit sha 4a69de98040790af141616a03826a0046bfeac1c

:arrow_up: Bump Django version to fix regression

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Dan Kolbman

commit sha 52c312e9a67cbba5989b4be7b7135ef25d439a18

:recycle: Use relative upload paths

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Daniel Kolbman

commit sha 08b0e6716ff58669d6d0234fbb4e0e1da5c339d2

Merge pull request #665 from kids-first/bump-django ⬆️ Bump Django version to fix regression

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Giovanni Santia

commit sha 6877ef7ac0536e490aa70053d4af9ca4a380a45f

Merge pull request #664 from kids-first/pandas-index ♻️ Fix pandas indexing warnings

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Giovanni Santia

commit sha 79709668d66752f2ca91be8ad8b049849973f74c

Merge pull request #662 from kids-first/banner-dates ♻️ Add timezone to Banner mutation datetimes

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Dan Kolbman

commit sha 5ffe69241fa6fe079ee72995fcc8852d1b1a4896

:wrench: Overwrite files in s3

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Dan Kolbman

commit sha 5a01eb31a3ce9250febc58e722be61d70dd2fafc

:pencil2: Add uuid to file name in storage

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Daniel Kolbman

commit sha 88dc9f1639baa578710c6b32f67dbe61fc8d571c

Merge pull request #660 from kids-first/overwrite-s3 ♻️ Overwrite S3 files when appending

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gsantia

commit sha 41a1349f9c1d7a658b79d3c7f89087a36f8cc403

:arrow_up: Bump pytest and plugins

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gsantia

commit sha 9b97e60d5ddb8d761970bb68910b550e26fd3dca

:wrench: Update pytest config

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