#library(FirebrowseR)
context("build.Query")
test_that("Query Builder works for regular queries", {
q1 = "http://firebrowse.org/api/v1/Samples/mRNASeq?format=csv&gene=PTEN&cohort=BRCA&sample_type=NT&protocol=RSEM&page=1&page_size=250&sort_by=gene"
sort_by = "gene"
page_size = 250
page = 1
protocol = "RSEM"
sample_type = "NT"
tcga_participant_barcode = ""
cohort = "BRCA"
format = "csv"
gene = "PTEN"
parameters = list(format = format,
gene = gene,
cohort = cohort,
tcga_participant_barcode = tcga_participant_barcode,
sample_type = sample_type,
protocol = protocol,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_identical(build.Query(parameters, invoker = "Samples", method = "mRNASeq"), q1)
q2 = "http://firebrowse.org/api/v1/Samples/mRNASeq?format=json&gene=PTEN%2CRUNX1&cohort=BLCA%2CBRCA&sample_type=NBC%2CNBM%2CNT&protocol=RPKM&page=1&page_size=2000&sort_by=gene"
format = "json"
gene = c("PTEN", "RUNX1")
cohort = c("BLCA", "BRCA")
sample_type = c("NBC","NBM","NT")
protocol = "RPKM"
tcga_participant_barcode = ""
page = 1
page_size = 2000
parameters = list(format = format,
gene = gene,
cohort = cohort,
tcga_participant_barcode = tcga_participant_barcode,
sample_type = sample_type,
protocol = protocol,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_identical(build.Query(parameters, invoker = "Samples", method = "mRNASeq"), q2)
q3 = "http://firebrowse.org/api/v1/Samples/mRNASeq?format=csv&gene=PTEN%2CRUNX1&cohort=BRCA&tcga_participant_barcode=TCGA-GF-A4EO&sample_type=NBC%2CNBM&protocol=RPKM&page=1&page_size=2000&sort_by=gene"
format = "csv"
gene = c("PTEN", "RUNX1")
cohort = "BRCA"
sample_type = c("NBC","NBM")
protocol = "RPKM"
tcga_participant_barcode = "TCGA-GF-A4EO"
page = 1
page_size = 2000
parameters = list(format = format,
gene = gene,
cohort = cohort,
tcga_participant_barcode = tcga_participant_barcode,
sample_type = sample_type,
protocol = protocol,
page = page,
page_size = page_size,
sort_by = sort_by)
expect_identical(build.Query(parameters, invoker = "Samples", method = "mRNASeq"), q3)
})
test_that("Query Builder works for mass queries", {
q1 = "http://firebrowse.org/api/v1/Metadata/Cohort/ACC%2CBLCA%2CBRCA%2CCESC?format=json"
cohort = c("ACC", "BLCA", "BRCA", "CESC")
format = "json"
parameters = list(format = format,
cohort = cohort)
expect_identical(build.Query(parameters, invoker = "Metadata", method = "Cohort", mass = T), q1)
})
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