Code

Next release#368

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YaphetKG merged 92 commits intomasterhelxplatform/dug:masterfrom develophelxplatform/dug:developCopy head branch name to clipboardAug 14, 2024

+1,007-674

Commits

Commits on Feb 5, 2024

• fixes for local dev

  YaphetKG

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  2a1aa93

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Commits on Feb 12, 2024

• end-point for study-id

  yskale

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• end-point for study-id and study-name

  yskale

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• end-point for study-id and study-name

  yskale

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Commits on Feb 21, 2024

• Moved code to get_query method

  vladimir2217

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Commits on Feb 22, 2024

• Moved code to _make_result method

  vladimir2217

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Commits on Feb 27, 2024

• radx parser

  YaphetKG

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• treat null desc

  YaphetKG

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Commits on Mar 14, 2024

• Updated BDC dbGaP IDs to the latest from BDC Gen3.

  gaurav

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• Delete variable directory if download fails.

  gaurav

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  07aab94

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• Added FTP timeout and reopen FTP connection after delay.

  gaurav

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• Ignore errors when deleting directories.

  gaurav

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  dd65693

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• Moved quit() further up.

  gaurav

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• Tweaked FTP reconnection code.

  gaurav

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• Clarified final count.

  gaurav

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Commits on Apr 4, 2024

• Added simple_search_query for concepts

  vladimir2217

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  107cc91

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• removed unnecessary key

  vladimir2217

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Commits on Apr 5, 2024

• added query to dict

  vladimir2217

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Commits on Apr 10, 2024

• Added program name search funtionality

  yskale

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• Merge branch 'develop' into end-point-program-name-id

  yskale

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Commits on Apr 15, 2024

• Merge pull request #346 from yskale/end-point-program-name-id

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  YaphetKG

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Commits on Apr 16, 2024

• Update Dockerfile

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  yskale

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Commits on Apr 17, 2024

• response to comments in CR

  vladimir2217

  committed
  4d29a42

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• Merge pull request #345 from helxplatform/VG1

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  vladimir2217

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  f1da5f8

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• patching security

  YaphetKG

  committed
  dcac227

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• Updated bdc_dbgap_ids.csv.

  gaurav

  committed
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Commits on Apr 18, 2024

• Merge branch 'develop' into program-id-search

  YaphetKG

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  ca57787

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• remove cruft comments

  YaphetKG

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  e05c49d

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• uncomment root path

  YaphetKG

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  11df9a4

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• patch another lib

  YaphetKG

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  d0b51f3

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• Merge pull request #347 from helxplatform/program-id-search

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  YaphetKG

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• Fix to var search

  vladimir2217

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Commits on Apr 19, 2024

• added handler if no concepts found

  vladimir2217

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  086a6d8

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• Merge pull request #349 from helxplatform/VG2

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  vladimir2217

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Commits on Apr 22, 2024

• Merge pull request #343 from helxplatform/update-bdc-studies

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  YaphetKG

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Commits on Apr 23, 2024

• Fix for missing score

  vladimir2217

  committed
  80f481a

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• Fix for failing studies fetch in UI

  vladimir2217

  committed
  d7c4f8b

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Commits on Apr 24, 2024

• Merge pull request #353 from helxplatform/VG2

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  YaphetKG

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Commits on Apr 25, 2024

• Added ProgramList and fixed the studies that are filtered by program name

  yskale

  committed
  cba7130

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Commits on Apr 26, 2024

• fixed study list

  yskale

  committed
  4254567

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• cleaned the code

  yskale

  committed
  c0d6098

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• Merge pull request #354 from helxplatform/Fixed_program_search

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  YaphetKG

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Commits on May 9, 2024

• Added a "Program" to the BDC output.

  gaurav

  committed
  acc8d40

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• Raised error if we find pipe characters in the group-by field.

  gaurav

  committed
  579e300

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• Fixed support for missing group-by values.

  gaurav

  committed
  c463155

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• Improved final log message.

  gaurav

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  6dd3e59

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• Replaced tag program names with authz program names.

  gaurav

  committed
  e2a19f3

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• Updated BDC dbGaP IDs with new Program code.

  gaurav

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Commits on May 10, 2024

• Merge pull request #355 from helxplatform/add-bdc-programs

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  YaphetKG

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Commits on May 13, 2024

• new parsers and fun things annotation change, config additions for threshold & direction

  YaphetKG

  committed
  2334650

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Commits on May 27, 2024

• retry

  YaphetKG

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  e2b215c

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• retry

  YaphetKG

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  3a21ecd

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Commits on May 31, 2024

• order_program_list

  yskale

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  6109c58

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• Merge pull request #358 from helxplatform/order_program_list

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  YaphetKG

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Commits on Jun 5, 2024

• adding cure sc parser

  YaphetKG

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  f621f17

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Commits on Jun 6, 2024

• fix tranqlizer

  YaphetKG

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  807aafa

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Commits on Jun 28, 2024

• remove cruft comment

  YaphetKG

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  f4521fc

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• Merge pull request #348 from helxplatform/radx-parser

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  YaphetKG

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• Merge branch 'develop' into dug-program-names-and-ner

  YaphetKG

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  0bac2c0

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• Merge pull request #356 from helxplatform/dug-program-names-and-ner

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  YaphetKG

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Commits on Jul 2, 2024

• initial bagel integration

  YaphetKG

  committed
  2ca28f1

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Commits on Jul 4, 2024

• add retry for bagel

  YaphetKG

  committed
  f81a359

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Commits on Jul 17, 2024

• added program description and sorted the program names alphabetically

  yskale

  committed
  9a85295

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• fix pr errors

  YaphetKG

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  b750a61

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• remove old lib install

  YaphetKG

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  a2e69af

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• fix test

  YaphetKG

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  c7cb2a1

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• parent program and description

  yskale

  committed
  e4b4f10

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Commits on Jul 18, 2024

• test fix

  YaphetKG

  authored
  fad5059

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• Merge pull request #360 from helxplatform/ProgramName_mappings

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  YaphetKG

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Commits on Jul 26, 2024

• disable default bagel

  YaphetKG

  committed
  011804e

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• increase bucket size

  YaphetKG

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  c040df4

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• Merge pull request #361 from helxplatform/fix-program-list-endpoint

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  YaphetKG

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Commits on Jul 29, 2024

• fixed consent id

  yskale

  committed
  377cb28

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• fix consent id

  yskale

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  6c355a8

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• fix consent id path

  yskale

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  f42fa85

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• Merge pull request #362 from helxplatform/fix-consent-id

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  YaphetKG

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Commits on Aug 7, 2024

• revert crawler logger

  YaphetKG

  committed
  6a60e1c

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• remove testing code

  YaphetKG

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  b1097c6

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• fix when bagel is not specified in config

  YaphetKG

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  7d5f1aa

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• fix up tests

  YaphetKG

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  9bc078f

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• Merge branch 'develop' into bagel

  YaphetKG

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  e6e6d41

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• Merge pull request #363 from helxplatform/bagel

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  YaphetKG

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• remove type from sapbert call to make things faster

  YaphetKG

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  1e3a847

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• Merge pull request #364 from helxplatform/bagel

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  YaphetKG

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Commits on Aug 8, 2024

• removed parent, sorted, added missing program and studies

  yskale

  committed
  8d96581

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• added missing program and studies

  yskale

  committed
  5693c0a

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• replaced sort

  yskale

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Commits on Aug 9, 2024

• Merge pull request #365 from helxplatform/fix-missing-program-and-studies

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  YaphetKG

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  f6a3d23

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• fix bug;

  YaphetKG

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  da5040b

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• Merge pull request #366 from helxplatform/patch-bug-program-name-lookup

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  YaphetKG

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Commits on Aug 12, 2024

• fix program query

  YaphetKG

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  29d155d

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• Merge pull request #367 from helxplatform/fix-program-match

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  yskale

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