tests/testthat/_snaps/Query.md

In hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds: Simplified R library to communicate with HPDS-hosted services on the BioData Catalyst network

buildQuery(): should not add harmonized or topmed consent filters if a field does not have a harmonized or genotype path

Code
  query$buildQuery()
Output
  $query
  $query$fields
  $query$fields[[1]]
  [1] "\\phs000001\\unit_test\\test_variable\\"


  $query$crossCountFields
  list()

  $query$requiredFields
  list()

  $query$anyRecordOf
  list()

  $query$numericFilters
  list()

  $query$categoryFilters
  $query$categoryFilters$`\\_consents\\`
  $query$categoryFilters$`\\_consents\\`[[1]]
  [1] "phs000001.c1"

  $query$categoryFilters$`\\_consents\\`[[2]]
  [1] "phs000002.c1"



  $query$variantInfoFilters
  $query$variantInfoFilters[[1]]
  $query$variantInfoFilters[[1]]$categoryVariantInfoFilters
  list()

  $query$variantInfoFilters[[1]]$numericVariantInfoFilters
  list()



  $query$expectedResultType
  [1] "COUNT"


  $resourceUUID
  [1] "36363664-6231-6134-2d38-6538652d3131"

buildQuery(): should add harmonized consent filters if a field has a harmonized path

Code
  query$buildQuery()
Output
  $query
  $query$fields
  $query$fields[[1]]
  [1] "\\DCC Harmonized data set\\unit_test\\test_variable\\"


  $query$crossCountFields
  list()

  $query$requiredFields
  list()

  $query$anyRecordOf
  list()

  $query$numericFilters
  list()

  $query$categoryFilters
  $query$categoryFilters$`\\_consents\\`
  $query$categoryFilters$`\\_consents\\`[[1]]
  [1] "phs000001.c1"

  $query$categoryFilters$`\\_consents\\`[[2]]
  [1] "phs000002.c1"


  $query$categoryFilters$`\\_harmonized_consent\\`
  [1] "phs000001.c1"


  $query$variantInfoFilters
  $query$variantInfoFilters[[1]]
  $query$variantInfoFilters[[1]]$categoryVariantInfoFilters
  list()

  $query$variantInfoFilters[[1]]$numericVariantInfoFilters
  list()



  $query$expectedResultType
  [1] "COUNT"


  $resourceUUID
  [1] "36363664-6231-6134-2d38-6538652d3131"

buildQuery(): should add topmed consent filters if a field has a genotpye path

Code
  query$buildQuery()
Output
  $query
  $query$fields
  list()

  $query$crossCountFields
  list()

  $query$requiredFields
  list()

  $query$anyRecordOf
  list()

  $query$numericFilters
  list()

  $query$categoryFilters
  $query$categoryFilters$`\\_consents\\`
  $query$categoryFilters$`\\_consents\\`[[1]]
  [1] "phs000001.c1"

  $query$categoryFilters$`\\_consents\\`[[2]]
  [1] "phs000002.c1"


  $query$categoryFilters$`\\_topmed_consents\\`
  [1] "phs000001.c1"


  $query$variantInfoFilters
  $query$variantInfoFilters[[1]]
  $query$variantInfoFilters[[1]]$categoryVariantInfoFilters
  $query$variantInfoFilters[[1]]$categoryVariantInfoFilters$Gene_with_variant
  $query$variantInfoFilters[[1]]$categoryVariantInfoFilters$Gene_with_variant[[1]]
  [1] "CHD8"



  $query$variantInfoFilters[[1]]$numericVariantInfoFilters
  list()



  $query$expectedResultType
  [1] "COUNT"


  $resourceUUID
  [1] "36363664-6231-6134-2d38-6538652d3131"

hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds documentation built on Sept. 24, 2022, 9:24 a.m.