tests/testthat/test_100_unit_process_survey_v1.R

In brucehoff/mPowerProcessing: Processes mPower data

# Test for process_survey_v1
# 
# Author: bhoff
###############################################################################

require(testthat)
require(synapseClient)

context("test_unit_process_survey_v1")

testDataFolder<-system.file("testdata", package="mPowerProcessing")
v1SurveyInputFile<-file.path(testDataFolder, "v1SurveyInput.RData")

# This is run once, to create the data used in the test
createV1Expected<-function() {
	id<-"syn4961453"
	schema<-synGet(id)
	query<-synTableQuery(paste0("SELECT * FROM ", id, " WHERE appVersion NOT LIKE '%YML%'"))
	vals <- query@values
	## CLEAN AS PER GOVERNANCE REQUIREMENTS
	vals$Enter_State <- "blah"
	vals$age[ which(vals$age>90 & vals$age<101) ] <- 90
	vals <- vals[-which(vals$age < 18  | vals$age > 100), ]
	## PERMUTE
	vals <- permuteMe(vals)
	vals <- prependHealthCodes(vals, "test-")
	query@values <- vals[1:min(nrow(vals), 100), ]
	
	mockFiles<-mockFileAttachments(system.file("testdata/health-history", package="mPowerProcessing"))
	eComFiles<-mockFiles$mockFiles
	eComContent<-mockFiles$fileContent
	# Now update the file Handle IDs in the data frame to match these fake ones
	query@values$`health-history`[which(!is.na(query@values$`health-history`))]<-
			sample(names(eComFiles), size=length(which(!is.na(query@values$`health-history`))), replace=T)
	save(schema, query, eComFiles, eComContent, file=v1SurveyInputFile, ascii=TRUE)
}

if (createTestData()) createV1Expected()

# Mock the schema and table content
load(v1SurveyInputFile)

with_mock(
		synGet=function(id) {schema},
		synTableQuery=function(sql) {query},
		synDownloadTableColumns=function(synTable, tableColumns) {eComFiles},
		readLines=function(x) { # x is a file path with fileHandleId as name
			result<-eComContent[x] # this gets the file content.  The name is the file path
			names(result)<-names(x) # result must map fileHandleId to file content
			result
		}, 
		{
			eDat<-process_survey_v1("syn101", NULL)
			eDatFilePath<-file.path(testDataFolder, "eDatExpected.RData")
			# Here's how we created the 'expected' data frame:
			if (createTestData()) {
				expected<-eDat
				save(expected, file=eDatFilePath, ascii=TRUE)
			}
			load(eDatFilePath) # creates 'expected'
			expect_equal(eDat, expected)
		}
)

lastMaxRowVersion<-5

# test the case that there's no new data:
with_mock(
		synGet=function(id) {schema},
		synTableQuery=function(sql) {
			truncatedQuery<-query
			truncatedQuery@values<-truncatedQuery@values[NULL,]
			truncatedQuery
		},
		synDownloadTableColumns=function(synTable, tableColumns) {eComFiles},
		readLines=function(x) { # x is a file path with fileHandleId as name
			result<-eComContent[x] # this gets the file content.  The name is the file path
			names(result)<-names(x) # result must map fileHandleId to file content
			result
		}, 
		{
			eDat<-process_survey_v1("syn101", lastMaxRowVersion)
			expect_equal(nrow(eDat$eDat), 0)
			expect_equal(eDat$maxRowVersion, lastMaxRowVersion)
		}
)