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Stockholm transfer #169

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Stockholm transfer #169

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Commits on Feb 6, 2024

  1. Add results_dev to dockerfile

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Commits on Apr 5, 2024

  1. Removed caching of display_case route

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  2. Changed caching type from simple to FileSystem

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  3. Updated CHANGELOG

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    mhkc committed Apr 5, 2024
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  4. Fix error when searching for a gene

    @mhkc
    mhkc committed Apr 5, 2024
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  5. Updated CHANGELOG

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Commits on Apr 8, 2024

  1. Merge pull request #151 from Clinical-Genomics-Lund/149-api-throws-ma… 

    …x-arg-is-an-empty-sequence-error-when-searching-for-gpr101

Fixed max args error when searching for genes
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  2. Merge branch 'master' into 133-sometimes-the-wrong-variant-is-being-d… 

    …isplayed-in-gens-using-links-from-scout
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  3. use temp dir for flask caches

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  4. Merge branch '133-sometimes-the-wrong-variant-is-being-displayed-in-g… 

    …ens-using-links-from-scout' of github.com:Clinical-Genomics-Lund/gens into 133-sometimes-the-wrong-variant-is-being-displayed-in-gens-using-links-from-scout
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  5. Merge pull request #150 from Clinical-Genomics-Lund/133-sometimes-the… 

    …-wrong-variant-is-being-displayed-in-gens-using-links-from-scout

Fix caching to prevent displaying the wrong variant
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  6. Updated versions

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  7. Updated CHANGELOG

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  8. Merge pull request #152 from Clinical-Genomics-Lund/release-2.1.2 

    Release 2.1.2
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Commits on May 10, 2024

  1. Fixed bug that prevented updating annotation tracks

    @mhkc
    mhkc committed May 10, 2024
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Commits on May 23, 2024

  1. Merge pull request #157 from Clinical-Genomics-Lund/156-error-loading… 

    …-annotation-tracks

Fixed bug that prevented updating annotation tracks
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Commits on Nov 15, 2024

  1. Fixes parse_bed to use csv.DictReader correctly

    @raysloks @Jakob37
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  2. Create stage_docker_push.yml

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  3. Change main to master in docker workflow

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  4. db config tweak: host+port->URI & split gens/scout

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  5. Fixes io operation on closed file error

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  6. Fixes the list of expected database config vars

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  7. Gitignore

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  8. Resolve merge

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  9. Adds parsing support for common .bed column names

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  10. Adds gunicorn default command to dockerfile

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  11. Adds docker build and push for master branch

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  12. Adds --chdir to gunicorn command

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  13. Changes to accurately reflect Gens' WSGI setup

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  14. Adds case name as an additional database field

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  15. Adds case name to most, if not all, places needed

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  16. Merge

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  17. Replaces the last case name

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  18. merge

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  19. Adds msg to LOG.warning

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  20. Adds github action for prod docker image

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  21. Merge

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  22. Merge

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  23. Removes a now obsolete query

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  24. Fixes some descriptions

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  25. Fixes a typo

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  26. Fixes a few descriptions

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  27. Adds case id to where it's missing

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  28. Merge

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  29. Merge

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  30. Merge

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  31. fetch case_id..

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  32. make that conditional on if case_id is set

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  33. typo, and use latest github actions

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  34. A few more action versions plus slightly better compatibility with ol… 

    …d gens
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  35. also use latest changelog enforcer action

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  36. Jest config

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  37. yarn that identity module

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  38. Merge

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  39. Fixes titles, var names still mixed up in spots

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  40. Add some docs info for track loading

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  41. Always this changelog

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  42. Oauth merge

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  43. Merge remote-tracking branch 'stockholm/sample_id_for_variant' into s… 

    …tockholm-transfer-get-their-commits
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  44. Clear visual clutter by hiding balanced variants

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  45. Changelog merge

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  46. also hide text

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  47. Variant tooltip includes length

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  48. lint

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  49. lint

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  50. Merge remote-tracking branch 'stockholm/fast_pan' into stockholm-tran… 

    …sfer-get-their-commits
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  51. Fix #58 - dont shrink distance on pan over chr start

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  52. addition is hard :)

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  53. indeed

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  54. Version 2.2 merge

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Commits on Nov 19, 2024

  1. Remove markus from docker compose

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  2. Fix leftover diff

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  3. Fix #48 - produce prod docker image copy with branch tag, and update … 

    …actions.
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  4. Changelog

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  5. and switch

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  6. changelog action setting

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  7. Broken DNA backround static path

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  8. Merge

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  9. reading and spelling

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  10. Changelog

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  11. Sync package lock

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  12. linkout preparation

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  13. Merge

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  14. slight mod to scout endpoint uri

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  15. add interaction for pinning and variant link out

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  16. missing closing if

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  17. quote url

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  18. Changelog

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  19. a little less anonymous listener

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  20. move event handler to object

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  21. click and dblclick coord events, and en passant spello

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  22. await url

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  23. make that a bit more variant specific

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  24. moved most..

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  25. Merge

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  26. curlies

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  27. test for existence

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  28. debug..

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  29. re-pass scoutBaseURL

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  30. use document id..

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  31. correct log

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  32. package.json conflict

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  33. lets wait with pinning and classifying - this is a lot already

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  34. Bump version to 2.3

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  35. fix docker push

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  36. docker preproc push as well

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  37. Changelog

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  38. again...

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  39. Makes genomeBuild get passed on in drawTrack

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  40. adds to changelog

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  41. Reraises DuplicateKeyError when storing sample, and better error message

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  42. changelog

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  43. Adds nonfunctional --force flag

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  44. Adds --force flag functionality

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  45. Disables re-raising of DuplicateKeyError

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  46. Updates changelog

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  47. prints warning to stderr when overwriting old entry

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  48. updates changelog

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  49. Fixes update_one call

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  50. update changelog

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  51. Merge

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  52. Updates changelog

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  53. Fixes "# samples loaded into gens"

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  54. Updates changelog

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  55. Merge

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  56. Merge

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  57. Updates changelog

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  58. Changes start to position

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  59. Sorts filteredVariants to maybe fix faulty height stacking

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  60. Does proper calculation of max height order before rendering

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  61. Limits height stacking to supported variant categories

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  62. Fixes other typos and a docstring

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  63. Updates changelog

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  64. Merge

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  65. adds proper scaling to overlay

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  66. only draw labels for visible variants

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  67. adds hardcoded margin

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  68. adjusts hardcoded margin

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  69. updates changelog

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  70. fixes overlay not rendering right after expanding variant track

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  71. adds very basic expand button

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  72. Merge

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  73. oc to this - looks like a small bug

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  74. unused imports

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  75. replace a couple of map statements with forEach

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  76. note the global apiHost in request js

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  77. format

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  78. Sync remaining diff with Stockholm

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