Code

Production Deploy#3457

Code

Merged

davidsmejia merged 103 commits intomasterAlexsLemonade/refinebio:masterfrom devAlexsLemonade/refinebio:devCopy head branch name to clipboardNov 9, 2023

+235,688-75,813

Commits

Commits on Sep 12, 2023

• Update workers test data

  Show description for 026fb66
  arkid15r

  committed
  026fb66

  Copy full SHA for 026fb66

• Update post downloads summary job

  Show description for 10ab7d4
  arkid15r

  committed
  10ab7d4

  Copy full SHA for 10ab7d4

Commits on Sep 13, 2023

• Update build badge status

  Show description for 21f453d
  arkid15r

  committed
  21f453d

  Copy full SHA for 21f453d

• Merge pull request #3383 from AlexsLemonade/ark/3379-fix-smasher-tests

  Show description for f702947
  arkid15r

  authored
  f702947

  Copy full SHA for f702947

• Merge pull request #3384 from AlexsLemonade/ark/update-build-status-badge

  Show description for 48a7649
  arkid15r

  authored
  48a7649

  Copy full SHA for 48a7649

• Merge pull request #3385 from AlexsLemonade/ark/3382-weekly-stats-update

  Show description for dbc6464
  arkid15r

  authored
  dbc6464

  Copy full SHA for dbc6464

Commits on Sep 15, 2023

• Implement data request tracking

  Show description for 1085869
  arkid15r

  committed
  1085869

  Copy full SHA for 1085869

• Update common/foreman scripts

  Show description for 2ba36c0
  arkid15r

  committed
  2ba36c0

  Copy full SHA for 2ba36c0

• Extend using of staging images cache

  Show description for 928acef
  arkid15r

  committed
  928acef

  Copy full SHA for 928acef

Commits on Sep 21, 2023

• Merge pull request #3388 from AlexsLemonade/ark/update-sh-scripts

  Show description for ece29d6
  arkid15r

  authored
  ece29d6

  Copy full SHA for ece29d6

• Merge pull request #3389 from AlexsLemonade/ark/3380-use-docker-cache-for-prod-image-builds

  Show description for 40e8463
  arkid15r

  authored
  40e8463

  Copy full SHA for 40e8463

• Use 1Password as a secrets storage

  Show description for 6294e5f
  arkid15r

  committed
  6294e5f

  Copy full SHA for 6294e5f

Commits on Sep 25, 2023

• Merge branch 'dev' into ark/3361-tracking-data-requests

  arkid15r

  committed
  e54872e

  Copy full SHA for e54872e

• Address PR review comments

  arkid15r

  committed
  cac1ead

  Copy full SHA for cac1ead

Commits on Sep 26, 2023

• Merge pull request #3387 from AlexsLemonade/ark/3361-tracking-data-requests

  Show description for bc365b2
  arkid15r

  authored
  bc365b2

  Copy full SHA for bc365b2

• Merge branch 'dev' into ark/1password-integration

  arkid15r

  committed
  85b7774

  Copy full SHA for 85b7774

• Customize Sentry environment tag

  arkid15r

  committed
  439899b

  Copy full SHA for 439899b

Commits on Sep 27, 2023

• Merge pull request #3391 from AlexsLemonade/ark/1password-integration

  Show description for 3cd73b0
  arkid15r

  authored
  3cd73b0

  Copy full SHA for 3cd73b0

• show taxonomy id on exception

  davidsmejia

  committed
  3374b30

  Copy full SHA for 3374b30

• add species taxonomy id

  davidsmejia

  committed
  67efe9b

  Copy full SHA for 67efe9b

• add helpers for transcriptome index

  davidsmejia

  committed
  d3c19d0

  Copy full SHA for d3c19d0

• switch to http from ftp

  davidsmejia

  committed
  95a578b

  Copy full SHA for 95a578b

• use requests and helper

  davidsmejia

  committed
  cd44faa

  Copy full SHA for cd44faa

• add fallbacks for different filenames

  davidsmejia

  committed
  a41a069

  Copy full SHA for a41a069

• add missing session variable

  davidsmejia

  committed
  d476f8e

  Copy full SHA for d476f8e

• fetch bacteria fungi by assembly assign species_taxonomy_id

  davidsmejia

  committed
  4213147

  Copy full SHA for 4213147

• update tests for all orgaisms

  davidsmejia

  committed
  bada128

  Copy full SHA for bada128

• delimiter not delimeter

  davidsmejia

  committed
  f3d53e8

  Copy full SHA for f3d53e8

• delete and recreate survey transcriptome cassettes

  davidsmejia

  committed
  a743e17

  Copy full SHA for a743e17

Commits on Sep 28, 2023

• Update docker files: use heredocs syntax

  Show description for 7e98e1f
  arkid15r

  committed
  7e98e1f

  Copy full SHA for 7e98e1f

• Move smasher test jobs to larger runners

  Show description for 82324dc
  arkid15r

  committed
  82324dc

  Copy full SHA for 82324dc

• Update GH workflows: add test_base to test_api_base dependencies

  arkid15r

  committed
  c3c4a43

  Copy full SHA for c3c4a43

• fix typos

  davidsmejia

  committed
  da4847c

  Copy full SHA for da4847c

• only check if the last check failed

  davidsmejia

  committed
  51fd6d1

  Copy full SHA for 51fd6d1

• update return type

  davidsmejia

  committed
  2febe1a

  Copy full SHA for 2febe1a

• remove variable and switch comparison order

  davidsmejia

  committed
  09337d7

  Copy full SHA for 09337d7

• remove variable and switch comparison order

  davidsmejia

  committed
  5c0622a

  Copy full SHA for 5c0622a

• update util and add test

  davidsmejia

  committed
  1e61329

  Copy full SHA for 1e61329

• Merge pull request #3399 from AlexsLemonade/ark/move-smasher-jobs-to-larger-runners

  Show description for 78f1410
  arkid15r

  authored
  78f1410

  Copy full SHA for 78f1410

• Merge branch 'dev' into ark/make-test-api-depend-on-base

  arkid15r

  committed
  a18fd44

  Copy full SHA for a18fd44

• Merge pull request #3400 from AlexsLemonade/ark/make-test-api-depend-on-base

  Show description for b3e5f66
  arkid15r

  authored
  b3e5f66

  Copy full SHA for b3e5f66

Commits on Sep 29, 2023

• adds filter_dicts_on_key

  davidsmejia

  committed
  bb96ad9

  Copy full SHA for bb96ad9

• use filter_dicts_on_key

  davidsmejia

  committed
  b54ed9e

  Copy full SHA for b54ed9e

• add test for filter_dicts_on_key

  davidsmejia

  committed
  ccb5535

  Copy full SHA for ccb5535

• format comments

  davidsmejia

  committed
  f105c2f

  Copy full SHA for f105c2f

• use list comprehension

  davidsmejia

  committed
  baa1b99

  Copy full SHA for baa1b99

• update docstring

  davidsmejia

  committed
  4869107

  Copy full SHA for 4869107

• assertIsNone

  davidsmejia

  committed
  77741b2

  Copy full SHA for 77741b2

• Merge branch 'dev' of https://github.com/AlexsLemonade/refinebio into davidsmejia/3381-strain-mapping-on-assembly

  davidsmejia

  committed
  7ca18f6

  Copy full SHA for 7ca18f6

Commits on Oct 2, 2023

• Merge pull request #3397 from AlexsLemonade/davidsmejia/3381-strain-mapping-on-assembly

  Show description for 5139f7e
  davidsmejia

  authored
  5139f7e

  Copy full SHA for 5139f7e

• Merge pull request #3398 from AlexsLemonade/ark/docker-heredocs-refactoring

  Show description for 6304213
  arkid15r

  authored
  6304213

  Copy full SHA for 6304213

• Update scripts: set platform and system version

  arkid15r

  committed
  e7acc18

  Copy full SHA for e7acc18

Commits on Oct 3, 2023

• Run agilent tests after affymetrix image is ready

  arkid15r

  committed
  a1f59e6

  Copy full SHA for a1f59e6

Commits on Oct 6, 2023

• Merge pull request #3402 from AlexsLemonade/ark/optimize-gh-tests

  Show description for 7ab86ce
  arkid15r

  authored
  7ab86ce

  Copy full SHA for 7ab86ce

• Untrack dev.tfvars

  arkid15r

  committed
  c2a9cee

  Copy full SHA for c2a9cee

• Merge pull request #3401 from AlexsLemonade/ark/update-scripts

  Show description for 1369e34
  arkid15r

  authored
  1369e34

  Copy full SHA for 1369e34

• Update SENTRY_DSN configuration

  Show description for dac43c9
  arkid15r

  committed
  dac43c9

  Copy full SHA for dac43c9

Commits on Oct 9, 2023

• Merge pull request #3407 from AlexsLemonade/ark/update-sentry-dsn-config

  Show description for ee0de0a
  davidsmejia

  authored
  ee0de0a

  Copy full SHA for ee0de0a

• Fix SENTRY_DSN env name mismatch

  arkid15r

  committed
  9c6afc8

  Copy full SHA for 9c6afc8

Commits on Oct 10, 2023

• Merge pull request #3409 from AlexsLemonade/ark/update-sentry-dsn

  Show description for d937e57
  davidsmejia

  authored
  d937e57

  Copy full SHA for d937e57

• Merge pull request #3403 from AlexsLemonade/ark/untrack-infrastructure-env-dev

  Show description for 06f1610
  arkid15r

  authored
  06f1610

  Copy full SHA for 06f1610

Commits on Oct 11, 2023

• Use STAGE variable for Sentry environment tag

  arkid15r

  committed
  15d7142

  Copy full SHA for 15d7142

Commits on Oct 12, 2023

• Merge pull request #3412 from AlexsLemonade/ark/3410-fix-stage-environment-variables

  Show description for 760fdc3
  davidsmejia

  authored
  760fdc3

  Copy full SHA for 760fdc3

• Update downloaders image: fix rvm.io keys issue

  arkid15r

  committed
  2b5a81d

  Copy full SHA for 2b5a81d

• Rename Sample::genotype to Sample::genetic_information

  arkid15r

  committed
  548dc82

  Copy full SHA for 548dc82

Commits on Oct 13, 2023

• Merge pull request #3414 from AlexsLemonade/ark/update-downloader-image

  Show description for 2da4ec9
  arkid15r

  authored
  2da4ec9

  Copy full SHA for 2da4ec9

Commits on Oct 16, 2023

• Update deprecated AWS elastic IP address configuration

  arkid15r

  committed
  c0e7ff1

  Copy full SHA for c0e7ff1

• Explicitly remove existing API containers

  arkid15r

  committed
  b3adda4

  Copy full SHA for b3adda4

• Merge pull request #3418 from AlexsLemonade/ark/update-terraform-config

  Show description for 3007d7d
  arkid15r

  authored
  3007d7d

  Copy full SHA for 3007d7d

• Merge pull request #3419 from AlexsLemonade/ark/update-api-instance-user-data

  Show description for 06511fa
  arkid15r

  authored
  06511fa

  Copy full SHA for 06511fa

Commits on Oct 17, 2023

• Merge pull request #3415 from AlexsLemonade/ark/3408-change-sample-genotype-field

  Show description for f5d4b39
  arkid15r

  authored
  f5d4b39

  Copy full SHA for f5d4b39

• Fix deploy issues

  Show description for 1b22efb
  arkid15r

  committed
  1b22efb

  Copy full SHA for 1b22efb

• Merge pull request #3422 from AlexsLemonade/ark/fix-deploy-issues

  Show description for 517b276
  arkid15r

  authored
  517b276

  Copy full SHA for 517b276

• Add STAGE to surveyor batch environment

  arkid15r

  committed
  3d79f3c

  Copy full SHA for 3d79f3c

Commits on Oct 18, 2023

• Add Sample::developmental_stage field support

  arkid15r

  committed
  40e34d6

  Copy full SHA for 40e34d6

Commits on Oct 19, 2023

• Merge pull request #3423 from AlexsLemonade/ark/add-stage-to-surveyor-batch-env

  Show description for 56333e6
  arkid15r

  authored
  56333e6

  Copy full SHA for 56333e6

Commits on Oct 20, 2023

• Fix downloaders/no-op tests

  arkid15r

  committed
  81b6e60

  Copy full SHA for 81b6e60

• Update pip requirements

  Show description for 0f114da
  arkid15r

  committed
  0f114da

  Copy full SHA for 0f114da

• Merge pull request #3429 from AlexsLemonade/ark/fix-downloaders-no-op-tests

  Show description for a5555cb
  arkid15r

  authored
  a5555cb

  Copy full SHA for a5555cb

• Merge pull request #3430 from AlexsLemonade/ark/update-python-dependencies

  Show description for c926647
  arkid15r

  authored
  c926647

  Copy full SHA for c926647

• Split downloaders/no_op test jobs

  arkid15r

  committed
  4692b48

  Copy full SHA for 4692b48

Commits on Oct 23, 2023

• Merge pull request #3431 from AlexsLemonade/ark/split-downloaders-no-op-test-jobs

  Show description for 087618e
  arkid15r

  authored
  087618e

  Copy full SHA for 087618e

• Merge pull request #3425 from AlexsLemonade/ark/3306-sample-developmental-stage

  Show description for e34095d
  arkid15r

  authored
  e34095d

  Copy full SHA for e34095d

Commits on Oct 25, 2023

• Add API server SSH connection check

  arkid15r

  committed
  adf0b40

  Copy full SHA for adf0b40

• Merge pull request #3441 from AlexsLemonade/ark/3437-api-server-wont-start

  Show description for d0b17b9
  arkid15r

  authored
  d0b17b9

  Copy full SHA for d0b17b9

Commits on Oct 26, 2023

• Add deploy box cleanup instructions

  Show description for c95a4eb
  arkid15r

  committed
  c95a4eb

  Copy full SHA for c95a4eb

• Merge pull request #3442 from AlexsLemonade/ark/post-deploy-cleanup

  Show description for 504b31f
  arkid15r

  authored
  504b31f

  Copy full SHA for 504b31f

Commits on Oct 27, 2023

• Fix no-op tests

  Show description for 273afb3
  arkid15r

  committed
  273afb3

  Copy full SHA for 273afb3

Commits on Oct 28, 2023

• Merge pull request #3446 from AlexsLemonade/ark/3436-fix-no-op-tests

  Show description for 14e1835
  arkid15r

  authored
  14e1835

  Copy full SHA for 14e1835

Commits on Oct 30, 2023

• Add restart flag to API docker container

  arkid15r

  committed
  e51c389

  Copy full SHA for e51c389

• Merge pull request #3447 from AlexsLemonade/ark/add-api-container-restart-flag

  Show description for 8fbf245
  arkid15r

  authored
  8fbf245

  Copy full SHA for 8fbf245

Commits on Oct 31, 2023

• bump up staging instance

  davidsmejia

  committed
  8d67102

  Copy full SHA for 8d67102

• Merge pull request #3448 from AlexsLemonade/davidsmejia/scale-up-staging

  Show description for d95a8e0
  davidsmejia

  authored
  d95a8e0

  Copy full SHA for d95a8e0

Commits on Nov 3, 2023

• update nginx log location

  davidsmejia

  committed
  6f928b6

  Copy full SHA for 6f928b6

• serve static files from var/www/static_volumes

  davidsmejia

  committed
  488d32b

  Copy full SHA for 488d32b

• Merge pull request #3453 from AlexsLemonade/davidsmejia/3452-tmp-to-var

  davidsmejia

  authored
  47ce019

  Copy full SHA for 47ce019

Commits on Nov 6, 2023

• map static to /var/www/volumes_static on deploy

  davidsmejia

  committed
  b111556

  Copy full SHA for b111556

• Merge pull request #3454 from AlexsLemonade/davidsmejia/3452-var-on-restart

  Show description for 1a78ca1
  davidsmejia

  authored
  1a78ca1

  Copy full SHA for 1a78ca1

Commits on Nov 7, 2023

• ensure /var/www/volumes_static exists on container restart

  davidsmejia

  committed
  7a7277c

  Copy full SHA for 7a7277c

• combine mkdir + chmod commands

  Show description for 111a821
  

  davidsmejia

  and

  arkid15r

  authored
  111a821

  Copy full SHA for 111a821

• Merge pull request #3455 from AlexsLemonade/davidsmejia/3452-ensure-api-static-dir

  Show description for 401c869
  davidsmejia

  authored
  401c869

  Copy full SHA for 401c869

Commits on Nov 9, 2023

• scale up worker volume

  davidsmejia

  committed
  a9efff4

  Copy full SHA for a9efff4

• Merge pull request #3456 from AlexsLemonade/davidsmejia/scale-workers-volume

  Show description for 07d3759
  davidsmejia

  authored
  07d3759

  Copy full SHA for 07d3759