inst/unitTests/test_AnnotationHubMethods.R

In dtenenba/AnnotationHub.new: A client for retrieving Bioconductor objects from AnnotationHub

## Unit tests for methods and helpers that are used to set and use
## filters on an AnnotationHub object.

## require(AnnotationHub)
## debug(AnnotationHub:::.metadata)

x <- AnnotationHub()

sampleFile <- paste("goldenpath/hg19/encodeDCC/wgEncodeUwTfbs",
                   "wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak_0.0.1.RData",
                  sep="/")
sampleFileDot <- paste("goldenpath.hg19.encodeDCC.wgEncodeUwTfbs",
                   "wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak_0.0.1.RData",
                  sep=".")

sampleSource <- paste("goldenpath/hg19/encodeDCC/wgEncodeUchicagoTfbs",
    "wgEncodeUchicagoTfbsK562Enr4a1ControlPk.narrowPeak.gz",
    sep="/")

## m <- metadata(x, cols="Title")

##  What is the shortest example to DL? A: stamH3K4me3ProfilePromoters.RData


## can we get and set filters() for an object?
test_filters <- function(){
    ## by default: no filters (this may change)
    checkTrue(length(filters(x))==0)
    ## then add a filter
    filters(x) <- list(TaxonomyId="9606",
        SourceFile=sampleSource)
    checkTrue(length(filters(x))==2)
    ## can we set them back to nothing?
    filters(x) <- NULL
    checkTrue(length(filters(x))==0)
}


## when the user hits enter, they should either get a DL OR a list of paths.
## Does that happen?
test_getResource <- function(){
    ## try a specific name
#    name <- "pub.databases.ensembl.encode.supplementary.integration_data_jan2011.byDataType.openchrom.jan2011.promoter_predictions.master_known.bed_0.0.1.RData"
    res <- AnnotationHub:::.getResource(x, sampleFileDot)
    checkTrue(class(res) == "GRanges")
    
    ## try a less specific name    
    name <- "goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage"
    suppressWarnings(res2 <- AnnotationHub:::.getResource(x, name))
    checkTrue(class(res2) == "character")

    ## check the two accessor methods
    foo <- x$goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak_0.0.1.RData
    bar <- x[[sampleFileDot]]
    checkTrue(identical(foo, bar))
}


## test our filter Validation
## Who watches the watchmen?
test_validFilterValues <- function(){
    badFilter <- list(Foo="9606") ## bad name
    checkException(AnnotationHub:::.validFilterValues(x,badFilter))
    badFilter2 <- list(Tags="9606") ## bad value
    checkException(AnnotationHub:::.validFilterValues(x,badFilter2))
}



## .getMetadata needs to get metadata that is filtered OR NOT, depending.
## Both methods of access should work.
test_getMetadata <- function(){
    filters <- NULL ## IOW: no filters
    snapUrl <- snapshotUrl()
    res <- AnnotationHub:::.metadata(snapUrl,filters)
    checkTrue(dim(res)[1] > 1) ## should give multiple records 
    ## check that we can get filtered metadata
    filters <- list(TaxonomyId="9606",
        SourceFile=sampleSource)
    res <- AnnotationHub:::.metadata(snapUrl,filters)
    checkTrue(dim(res)[1] == 1)  ## should only match one record
}



## I think that I just need to simplify this function.
## Now that metadata is smarter it doesn't need to be so smart.
## test_getNewPathsBasedOnFilters <- function(){
## }



## test that this thing respects merging of values.  If values are
## repeated, they should not end up repeated in the result etc.
test_replaceFilter <- function(){
    filters(x) <- NULL ## null out filters
    checkTrue(length(filters(x))==0)
    x <- AnnotationHub:::.replaceFilter(x,list(TaxonomyId="9606"))
    checkTrue(length(filters(x))==1)
    ## now place a bigger filter on there
    filters <- list(TaxonomyId="9606",
        SourceFile=sampleSource)
    x <- AnnotationHub:::.replaceFilter(x,filters)
    checkTrue(length(filters(x))==2)  ## TaxonomyId should not repeat.
}



## does this work as expected?  (it should respect the filter values)
test_metadata <- function(){
    filters(x) <- NULL ## null out filters
    resFull <- metadata(x)
    ## Now apply filters
    filters(x) <- list(TaxonomyId="9606",
        SourceFile=sampleSource)
    resPartial <- metadata(x)
    checkTrue(dim(resFull)[2] == dim(resPartial)[2])
    checkTrue(dim(resFull)[1] != dim(resPartial)[1])

    ## does cols argument work?
    resPartial2 <- metadata(x, cols="TaxonomyId")
    checkTrue(dim(resPartial2)[2] == 1)
    
    resPartial3 <- metadata(x, cols=c("Title","TaxonomyId"))
    checkTrue(dim(resPartial3)[2] == 2)

    ## spot check that a data file has correct metadata values
    filters(x) <- NULL
    filters(x) <- list(RDataPath=sampleFile)
    resPartial4 <- metadata(x)

    ## this will change soon:
    checkEquals(resPartial4$Tags[[1]][11], "GSM1022658")
    checkTrue(as.character(resPartial4$Species) == "Homo sapiens")    
}



## TODO: simplify getNewPathsBasedOnFilters()
## TODO: solve bug that prevents the using of multi-valued keys in the
## filter lists.



## TODO: add tests for:
## versionDate etc.  (make sure they are returning correct things).


## Add tests for caching (test to make sure caching works, and that my helpers to test if cache is present etc. are working)


## some debugging code for caching:


##  system.time(a <- x$pub.databases.ensembl.encode.supplementary.integration_data_jan2011.byDataType.footprints.jan2011.all.footprints_0.0.1.RData)  



## 
test_caching <- function(){
    ## set to just the one file
    filters(x) <- list(RDataPath=sampleFile)
    ## now "get" the file
    x[[sampleFileDot]]
    
    ## now it *should* exist here:
    path <- hubResource(x)    
    ## so we should not be able to test if the file exists here or not.
    checkTrue(file.exists(file.path(path, sampleFile)))
}


##  FOR testing the caching. the test code should look at the dir that
##  is generated (we have helper for this), and see if the appropriate
##  dirs and files are being generated when code is run.





## more testing

## library(AnnotationHub); x = AnnotationHub(); filters(x) <- list(TaxonomyId="9606")





########################################################################
## TODO: add tests for: caching 










##########################################################################
## OTHER ISSUES:
##

## PROBLEM: this filter breaks things (x$ no longer works after:)
## filters(x) <- list(Title="Fake versioned data")

## But this one DOES work (maybe because of whitespace?)
## filters(x) <- list(RDataPath="fakedata/data.bed_0.0.3.RData")

## NOTE: fakeData is being removed.



## this one just runs this to make sure we can run the help display.
## would be nice if I could trap the output...
test_info <- function(){
    path = "goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak_0.0.1.RData"
    ## this is the real reason for this test
    res <- ahinfo(x, path) ## should return a list
    checkTrue(is(res[[1]],"ahinfoList")) ## just verify that it ran
}