kids-first/kf-lib-data-ingest

Issues

• Add constants for visibility_reason

  #660 opened a year ago by znatty22
  0

• Capture source data that cannot be mapped

  #652 opened 2 years ago by znatty22
  0

• Authentication failure is masked by file get error

  #651 opened 2 years ago by znatty22
  0

• Report skipped entities with warning log level

  #650 opened 2 years ago by Christina-J-Diaz
  1

• Loader silently fails during unique key lookup

  #649 opened 2 years ago by znatty22
  0

• Sequencing prep and selection don't get used by the dataservice API plugin

  #640 opened 3 years ago by fiendish
  1

• Get S3 metadata for genomic files

  #628 opened 3 years ago by gsantia
  2

• flip_col doesn't flip False when it is a string

  #634 opened 3 years ago by chris-s-friedman
  0

• Optionally exclude tests in validation report

  #636 opened 3 years ago by znatty22
  0

• Automate transform

  #632 opened 3 years ago by fiendish
  1

• Unexpected list instead of dict during LoadStage

  #629 opened 3 years ago by gsantia
  5

• [Discussion] should the ingest library detect if a target api is using http instead of https

  #630 opened 3 years ago by chris-s-friedman
  3

• Allow extraction of data via passed in SQL query

  #627 opened 3 years ago by gsantia
  8

• Genomic Workflow Output manifest CLI incorporation

  #625 opened 3 years ago by gsantia
  3

• Should warehousing default to off?

  #612 opened 3 years ago by chris-s-friedman
  6

• Address backwards compatibility by tagging package configurations with library version

  #504 opened 3 years ago by fiendish
  1

• relationship entities are not being created during testing

  #613 opened 3 years ago by chris-s-friedman
  0

• It would be nice if non-debug logging could indicate post/patch/fallback during load

  #559 opened 3 years ago by fiendish
  1

• Standalone Extractor Utility

  #593 opened 3 years ago by znatty22
  0

• Does anyone use user defined tests in their ingest packages?

  #595 opened 3 years ago by znatty22
  7

• Documentation for required components in loading entities

  #584 opened 4 years ago by gsantia
  0

• Non-obvious local file loading paths

  #581 opened 4 years ago by gsantia
  5

• Outside suggestion: extract operations conditional on applicability (e.g. in_col existence)

  #579 opened 4 years ago by fiendish
  3

• Google's FHIR requires GUIDs for ID (and overwrites anything you provide for ID at create time)

  #577 opened 4 years ago by torstees
  6

• New BS and DG fields?

  #575 opened 4 years ago by fiendish
  0

• "Build and publish" github workflow never runs

  #573 opened 4 years ago by fiendish
  0

• Need more insight into skipped loads

  #545 opened 4 years ago by fiendish
  1

• More graceful handling of GF missing required attributes

  #569 opened 4 years ago by znatty22
  0

• Update ingest docs to incorporate new validation

  #512 opened 4 years ago by znatty22
  0

• target api config validator doesn't check version

  #560 opened 4 years ago by fiendish
  0

• Newbie: feedback on quickstart.

  #503 opened 4 years ago by bwalsh
  1

• Cryptic error message if do_after_read returns an empty DF

  #557 opened 4 years ago by fiendish
  0

• Possible issue with sqlite3worker on WSL2

  #540 opened 4 years ago by torstees
  10

• validation reports not written if they aren't all written

  #538 opened 4 years ago by chris-s-friedman
  2

• The new pip resolver in 20.3 errors on renamed editable sphinx theme egg

  #544 opened 4 years ago by fiendish
  0

• The new pip resolver in 20.3 generates infinite loop on slight URL git format variations

  #543 opened 4 years ago by fiendish
  1

• Validation markdown format needs imported strings to be escaped

  #535 opened 4 years ago by fiendish
  0

• Validation tabular output looks malformed

  #534 opened 4 years ago by fiendish
  0

• Dry run mode doesn't dry-load relationships

  #530 opened 4 years ago by fiendish
  0

• Bad call order in target service plugin blocks loading BS and SE with missing replaceable fields

  #528 opened 4 years ago by fiendish
  0

• Blank cells are treated as invalid values

  #526 opened 4 years ago by fiendish
  0

• New study creator subdomains break FileRetriever default configs because auth isn't set

  #525 opened 4 years ago by fiendish
  0

• loader fills STUDY.ID instead of STUDY.TARGET_SERVICE_ID

  #515 opened 4 years ago by fiendish
  0

• Display test result summary as a table

  #519 opened 4 years ago by znatty22
  0

• Imports in Extract Config example in the docs should import Split()

  #516 opened 4 years ago by chris-s-friedman
  0

• Treat all data as text always

  #505 opened 4 years ago by fiendish
  0

• Need new concepts for new templates

  #494 opened 4 years ago by fiendish
  0

• Auto-populate BIOSPECIMEN|ID, BIOSPECIMEN_GROUP|ID cols

  #510 opened 4 years ago by znatty22
  0

• read_df confused by (useless in utf8) byte order marks

  #508 opened 4 years ago by fiendish
  0

• Path to file path list method doesn't prepend dir

  #506 opened 4 years ago by znatty22
  0