tests/testthat/test_120_unit_process_survey_v3.R

In brucehoff/mPowerProcessing: Processes mPower data

# Test for process_survey_v3
# 
# Author: bhoff
###############################################################################

library(testthat)
library(synapseClient)

context("test_unit_process_survey_v3")

testDataFolder<-system.file("testdata", package="mPowerProcessing")
v3DataExpectedFile<-file.path(testDataFolder, "v3SurveyInput.RData")

# This is run once, to create the data used in the test
createV3Expected<-function() {
	id<-"syn4961472"
	schema<-synGet(id)
	query<-synTableQuery(paste0("SELECT * FROM ", id, " WHERE appVersion NOT LIKE '%YML%'"))
	vals <- query@values
	vals <- permuteMe(vals)
	vals <- prependHealthCodes(vals, "test-")
	query@values <- vals[1:min(nrow(vals), 100), ]
	save(schema, query, file=v3DataExpectedFile, ascii=TRUE)
}

if (createTestData()) createV3Expected()

# Mock the schema and table content
expect_true(file.exists(v3DataExpectedFile))
load(v3DataExpectedFile)

with_mock(
		synGet=function(id) {schema},
		synTableQuery=function(sql) {query},
		{
			pDat<-process_survey_v3("syn101")
			pDatFilePath<-file.path(testDataFolder, "pDatExpected.RData")
			# Here's how we created the 'expected' data frame:
			if (createTestData()) {
				expected<-pDat
				save(expected, file=pDatFilePath, ascii=TRUE)
			}
			load(pDatFilePath) # creates 'expected'
			expect_equal(pDat, expected)
		}
)

load(v3DataExpectedFile)
# now add a duplicate row (repeat the last row)
dfRef<-query@values
query@values<-dfRef[c(1:nrow(dfRef),nrow(dfRef)),]
row.names(query@values)<-c(row.names(dfRef), sprintf("%s_0", nrow(dfRef)))

with_mock(
		synGet=function(id) {schema},
		synTableQuery=function(sql) {query},
		{
			pDat<-process_survey_v3("syn101")
			pDatFilePath<-file.path(testDataFolder, "pDatExpected.RData")
			load(pDatFilePath) # creates 'expected'
			expect_equal(pDat, expected)
		}
)


load(v3DataExpectedFile)
# test the case that there's no new data:
lastMaxRowVersion<-5

with_mock(
		synGet=function(id) {schema},
		synTableQuery=function(sql) {
			truncatedQuery<-query
			truncatedQuery@values<-truncatedQuery@values[NULL,]
			truncatedQuery
		},
		{
			pDat<-process_survey_v3("syn101", lastMaxRowVersion)
			expect_equal(nrow(pDat$pDat), 0)
			expect_equal(pDat$maxRowVersion, lastMaxRowVersion)
		}
)