Code

Ah spike writeapi#7530

Code

Merged

ahaessly merged 57 commits intoah_var_storebroadinstitute/gatk:ah_var_storefrom ah_spike_writeapibroadinstitute/gatk:ah_spike_writeapiCopy head branch name to clipboardDec 8, 2021

+1,136-953

Commits

Commits on Dec 8, 2021

• first pass, oom exception

  ahaessly

  committed
  8262b62

  Copy full SHA for 8262b62

• use pending BQ writer

  ahaessly

  committed
  7562863

  Copy full SHA for 7562863

• fix bugs

  ahaessly

  committed
  314aff3

  Copy full SHA for 314aff3

• finalize stream before commit

  ahaessly

  committed
  ca14141

  Copy full SHA for ca14141

• cleanup

  ahaessly

  committed
  b05bca0

  Copy full SHA for b05bca0

• update messages

  ahaessly

  committed
  d1f99ee

  Copy full SHA for d1f99ee

• change back to committed mode for write api

  ahaessly

  committed
  9796635

  Copy full SHA for 9796635

• back to pending

  ahaessly

  committed
  bae4faa

  Copy full SHA for bae4faa

• cleanup

  ahaessly

  committed
  b7e6b98

  Copy full SHA for b7e6b98

• change class names

  ahaessly

  committed
  f05d966

  Copy full SHA for f05d966

• undo name change

  ahaessly

  committed
  0b89c89

  Copy full SHA for 0b89c89

• new wdl

  ahaessly

  committed
  191823f

  Copy full SHA for 191823f

• update create tables for ref ranges

  ahaessly

  committed
  4a04770

  Copy full SHA for 4a04770

• update dockstore

  ahaessly

  committed
  937485f

  Copy full SHA for 937485f

• fix flushing and closing

  ahaessly

  committed
  0ee4e26

  Copy full SHA for 0ee4e26

• use python to update data model

  Show description for d230036
  ahaessly

  committed
  d230036

  Copy full SHA for d230036

• add bq table creation to assign ids, cleanup

  ahaessly

  committed
  af528e3

  Copy full SHA for af528e3

• fix exit

  ahaessly

  committed
  9a6879c

  Copy full SHA for 9a6879c

• fix errors

  ahaessly

  committed
  2435823

  Copy full SHA for 2435823

• fix errors

  ahaessly

  committed
  7316cba

  Copy full SHA for 7316cba

• fix errors

  ahaessly

  committed
  ecb897c

  Copy full SHA for ecb897c

• fix errors

  ahaessly

  committed
  20ddce1

  Copy full SHA for 20ddce1

• fix output

  ahaessly

  committed
  91ed78c

  Copy full SHA for 91ed78c

• python3

  ahaessly

  committed
  4705aad

  Copy full SHA for 4705aad

• still trying to fix

  ahaessly

  committed
  cab81d5

  Copy full SHA for cab81d5

• still trying to fix

  ahaessly

  committed
  b4e6d23

  Copy full SHA for b4e6d23

• still trying to fix

  ahaessly

  committed
  d78e3a5

  Copy full SHA for d78e3a5

• change field to nullable

  ahaessly

  committed
  41982ea

  Copy full SHA for 41982ea

• update import with ref_ranges as default and 40 as drop state. update docs

  ahaessly

  committed
  59420a4

  Copy full SHA for 59420a4

• fix params

  ahaessly

  committed
  96ef89d

  Copy full SHA for 96ef89d

• remove mode

  ahaessly

  committed
  c3bfec5

  Copy full SHA for c3bfec5

• update docs

  ahaessly

  committed
  c307e93

  Copy full SHA for c307e93

• fix tables for duplicate check

  ahaessly

  committed
  710b48b

  Copy full SHA for 710b48b

• rename PetCreator

  ahaessly

  committed
  dae2026

  Copy full SHA for dae2026

• create separate readme for AoU Gvs workspace

  ahaessly

  committed
  cb75688

  Copy full SHA for cb75688

• change title of doc

  ahaessly

  committed
  f0971f2

  Copy full SHA for f0971f2

• change empty string to null

  ahaessly

  committed
  5c4ffae

  Copy full SHA for 5c4ffae

• pass load params

  ahaessly

  committed
  afe4a1f

  Copy full SHA for afe4a1f

• pass load params

  ahaessly

  committed
  71368f9

  Copy full SHA for 71368f9

• handle null vet and pet creator

  ahaessly

  committed
  a27ae74

  Copy full SHA for a27ae74

• remove old if stmt

  ahaessly

  committed
  d4c941b

  Copy full SHA for d4c941b

• modify sample_table to input var

  ahaessly

  committed
  d580a98

  Copy full SHA for d580a98

• add back is_loaded

  ahaessly

  committed
  62d3e3e

  Copy full SHA for 62d3e3e

• simplify calling create tables sub workflow

  ahaessly

  committed
  1e12090

  Copy full SHA for 1e12090

• close writer too

  ahaessly

  committed
  184405a

  Copy full SHA for 184405a

• add manual step to set is_loaded

  ahaessly

  committed
  f2a52cc

  Copy full SHA for f2a52cc

• Updated Quickstart (#7568)

  Show description for 9129670
  

  kcibul

  authored and

  ahaessly

  committed
  9129670

  Copy full SHA for 9129670

• close vet writer (#7571)

  

  kcibul

  authored and

  ahaessly

  committed
  7537a4d

  Copy full SHA for 7537a4d

• add initial test for write api

  ahaessly

  committed
  6600a82

  Copy full SHA for 6600a82

• Move to Sample Set based write-api (#7573)

  Show description for 6490a37
  

  kcibul

  authored and

  ahaessly

  committed
  6490a37

  Copy full SHA for 6490a37

• used _default stream instead (#7588)

  Show description for 972f315
  

  kcibul

  authored and

  ahaessly

  committed
  972f315

  Copy full SHA for 972f315

• safety checks for restarts via preemptibles (#7590)

  Show description for 51897ec
  

  kcibul

  authored and

  ahaessly

  committed
  51897ec

  Copy full SHA for 51897ec

• revert dockstore.yml

  ahaessly

  committed
  0dd6d4c

  Copy full SHA for 0dd6d4c

• remove GvsImportSample.wdl

  ahaessly

  committed
  fa30742

  Copy full SHA for fa30742

• add is_loaded check back to GvsCreateFilterSet

  ahaessly

  committed
  837b5ad

  Copy full SHA for 837b5ad

• 3 retries and bigger machine for writeAPI ingest (#7592)

  Show description for 76f78c6
  

  RoriCremer

  authored and

  ahaessly

  committed
  76f78c6

  Copy full SHA for 76f78c6

• remove branch

  ahaessly

  committed
  c16efde

  Copy full SHA for c16efde