示例#1
0
    def test_addExternalResources(self):
        ds = DataSet()
        er1 = ExternalResource()
        er1.resourceId = "test1.bam"
        er2 = ExternalResource()
        er2.resourceId = "test2.bam"
        er3 = ExternalResource()
        er3.resourceId = "test1.bam"
        ds.addExternalResources([er1], updateCount=False)
        self.assertEquals(ds.numExternalResources, 1)
        # different resourceId: succeeds
        ds.addExternalResources([er2], updateCount=False)
        self.assertEquals(ds.numExternalResources, 2)
        # same resourceId: fails
        ds.addExternalResources([er3], updateCount=False)
        self.assertEquals(ds.numExternalResources, 2)
        for extRef in ds.externalResources:
            self.assertEqual(type(extRef).__name__, "ExternalResource")

        extRef = ds.externalResources[0]
        self.assertEqual(type(extRef).__name__, "ExternalResource")
        self.assertEqual(extRef.resourceId, 'test1.bam')

        extRef = ds.externalResources[1]
        self.assertEqual(type(extRef).__name__, "ExternalResource")
        self.assertEqual(extRef.resourceId, 'test2.bam')
示例#2
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    def test_addExternalResources(self):
        ds = DataSet()
        er1 = ExternalResource()
        er1.resourceId = "test1.bam"
        er2 = ExternalResource()
        er2.resourceId = "test2.bam"
        er3 = ExternalResource()
        er3.resourceId = "test1.bam"
        ds.addExternalResources([er1], updateCount=False)
        self.assertEquals(ds.numExternalResources, 1)
        # different resourceId: succeeds
        ds.addExternalResources([er2], updateCount=False)
        self.assertEquals(ds.numExternalResources, 2)
        # same resourceId: fails
        ds.addExternalResources([er3], updateCount=False)
        self.assertEquals(ds.numExternalResources, 2)
        for extRef in ds.externalResources:
            self.assertEqual(type(extRef).__name__, "ExternalResource")

        extRef = ds.externalResources[0]
        self.assertEqual(type(extRef).__name__, "ExternalResource")
        self.assertEqual(extRef.resourceId, 'test1.bam')

        extRef = ds.externalResources[1]
        self.assertEqual(type(extRef).__name__, "ExternalResource")
        self.assertEqual(extRef.resourceId, 'test2.bam')
示例#3
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def wrapNewResource(path):
    # filter out non-resource file types:
    for ext in FILE_INDICES.keys():
        if path.endswith(ext):
            log.debug('Index file {f} given as regular file, will be treated '
                      ' as an index file instead'.format(f=path))
            return
    extRes = ExternalResource()
    path = resolveLocation(path)
    extRes.resourceId = path
    index_files = [
        path + ext for ext in FILE_INDICES.keys() if os.path.exists(path + ext)
    ]
    if index_files:
        extRes.addIndices(index_files)

    # Check for sub resources:
    for ext in SUB_RESOURCES:
        filen = '.'.join(path.split('.')[:-2]) + ext
        # don't want to add e.g. scraps to scraps:
        if os.path.exists(filen) and path.endswith('subreads.bam'):
            log.debug("Adding {} as a subresource".format(filen))
            subres = wrapNewResource(filen)
            setattr(extRes, ext.split('.')[1], subres)
    return extRes
示例#4
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def wrapNewResource(path):
    possible_indices = [".fai", ".pbi", ".bai", ".metadata.xml"]
    for ext in possible_indices:
        if path.endswith(ext):
            log.debug(
                "Index file {f} given as regular file, will be treated " " as an index file instead".format(f=path)
            )
            return
    extRes = ExternalResource()
    path = resolveLocation(path)
    extRes.resourceId = path
    index_files = [path + ext for ext in possible_indices if os.path.exists(path + ext)]
    if index_files:
        extRes.addIndices(index_files)
    return extRes
示例#5
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def wrapNewResource(path):
    possible_indices = ['.fai', '.pbi', '.bai', '.metadata.xml']
    for ext in possible_indices:
        if path.endswith(ext):
            log.debug('Index file {f} given as regular file, will be treated '
                      ' as an index file instead'.format(f=path))
            return
    extRes = ExternalResource()
    path = resolveLocation(path)
    extRes.resourceId = path
    index_files = [
        path + ext for ext in possible_indices if os.path.exists(path + ext)
    ]
    if index_files:
        extRes.addIndices(index_files)
    return extRes
示例#6
0
def wrapNewResource(path):
    # filter out non-resource file types:
    for ext in FILE_INDICES:
        if path.endswith(ext):
            log.debug('Index file {f} given as regular file, will be treated '
                      ' as an index file instead'.format(f=path))
            return
    extRes = ExternalResource()
    path = resolveLocation(path)
    extRes.resourceId = path
    index_files = [path + ext for ext in FILE_INDICES if
                   os.path.exists(path + ext)]
    if index_files:
        extRes.addIndices(index_files)

    # Check for sub resources:
    for ext in SUB_RESOURCES:
        filen = '.'.join(path.split('.')[:-2]) + ext
        # don't want to add e.g. scraps to scraps:
        if os.path.exists(filen) and path.endswith('subreads.bam'):
            subres = wrapNewResource(filen)
            setattr(extRes, ext.split('.')[1], subres)
    return extRes