def test_extract_bam(self):
self.call_extract_metadata_for_bam(inObjPathParam=self.BAM_OBJ_PATH,
inFilePathParam=self.BAM_FILE_PATH)
# '-d' option is used when metadatas are get from a file and not a collection
rule_output = imeta_ls('-d', self.BAM_FILE_NAME)
self.assertNotEqual(rule_output,
self.IMETA_LS_NONE.format(self.BAM_FILE_NAME))
def test_extract_jpeg(self):
self.call_extract_metadata_for_jpeg(
inObjPathParam=self.JPEG_OBJ_PATH,
inFilePathParam=self.JPEG_FILE_PATH
)
# '-d' option is used when metadatas are get from a file and not a collection
rule_output = imeta_ls('-d', self.JPEG_FILE_NAME)
self.assertNotEqual(rule_output, self.IMETA_LS_NONE.format(self.JPEG_FILE_NAME))
def test_manifest(self):
self.call_manifest_rule(obj_path=self.obj_path,
file_path=self.file_path,
manifest_path=self.file_path)
imeta_output = imeta_ls('-d', self.obj_path)
self.assertIsNotNone(imeta_output)
self.assertNotEqual(imeta_output,
self.IMETA_LS_NONE.format(self.obj_path))
def test_manifest(self):
self.call_manifest_rule(
obj_path=self.obj_path,
file_path=self.file_path,
manifest_path=self.file_path
)
imeta_output = imeta_ls('-d', self.obj_path)
self.assertIsNotNone(imeta_output)
self.assertNotEqual(imeta_output, self.IMETA_LS_NONE.format(self.obj_path))
def test_extract_illumina(self):
illumina_args = {'objPath': self.ILLUMINA_OBJ_PATH,
'targetPath': self.IRODS_HOME_PATH,
'destResc': self.IRODS_RESC}
if not self.IRODS_42:
illumina_args['status'] = 'null'
self.call_extract_metadata_for_illumina(**illumina_args)
# '-d' option is used when metadatas are get from a file and not a collection
rule_output = imeta_ls('-d', self.ILLUMINA_METADATA_FILE)
self.assertNotEqual(rule_output, self.IMETA_LS_NONE.format(self.ILLUMINA_METADATA_FILE))
def test_extract_illumina(self):
illumina_args = {
'objPath': self.ILLUMINA_OBJ_PATH,
'targetPath': self.IRODS_HOME_PATH,
'destResc': self.IRODS_RESC
}
if not self.IRODS_42:
illumina_args['status'] = 'null'
self.call_extract_metadata_for_illumina(**illumina_args)
# '-d' option is used when metadatas are get from a file and not a collection
rule_output = imeta_ls('-d', self.ILLUMINA_METADATA_FILE)
self.assertNotEqual(
rule_output,
self.IMETA_LS_NONE.format(self.ILLUMINA_METADATA_FILE))
def test_populate(self):
self.call_populate_metadata_rule(obj_path=self.obj_path)
imeta_output = imeta_ls('-d', self.obj_path)
self.assertIn("ATTRIBUTE01", imeta_output)
self.assertIn("VALUE1", imeta_output)
self.assertIn("chars", imeta_output)
self.assertIn("ATTRIBUTE02", imeta_output)
self.assertIn("2", imeta_output)
self.assertIn("ints", imeta_output)
self.assertIn("ATTRIBUTE03", imeta_output)
self.assertIn("2, 3, 4, 5", imeta_output)
self.assertIn("ATTRIBUTE04", imeta_output)
self.assertIn("VALUE-1235", imeta_output)
self.assertIn("ATTRIBUTE05", imeta_output)
self.assertIn("1865", imeta_output)
self.assertIn("bytes", imeta_output)
self.assertIn("ATTRIBUTE06", imeta_output)
self.assertIn("False", imeta_output)
self.assertIn("bool", imeta_output)
self.assertIn("ATTRIBUTE07", imeta_output)
self.assertIn("_TAG-12342_", imeta_output)
self.assertIn("ATTRIBUTE08", imeta_output)
self.assertIn("['value1', 'value2, 'value3']", imeta_output)
self.assertIn("as", imeta_output)
self.assertIn("ATTRIBUTE09", imeta_output)
self.assertIn("MLX", imeta_output)
self.assertIn("ATTRIBUTE10", imeta_output)
self.assertIn("NULL", imeta_output)
def test_populate(self):
self.call_populate_metadata_rule(obj_path=self.obj_path)
imeta_output = imeta_ls('-d', self.obj_path)
self.assertIn("ATTRIBUTE01", imeta_output)
self.assertIn("VALUE1", imeta_output)
self.assertIn("chars", imeta_output)
self.assertIn("ATTRIBUTE02", imeta_output)
self.assertIn("2", imeta_output)
self.assertIn("ints", imeta_output)
self.assertIn("ATTRIBUTE03", imeta_output)
self.assertIn("2, 3, 4, 5", imeta_output)
self.assertIn("ATTRIBUTE04", imeta_output)
self.assertIn("VALUE-1235", imeta_output)
self.assertIn("ATTRIBUTE05", imeta_output)
self.assertIn("1865", imeta_output)
self.assertIn("bytes", imeta_output)
self.assertIn("ATTRIBUTE06", imeta_output)
self.assertIn("False", imeta_output)
self.assertIn("bool", imeta_output)
self.assertIn("ATTRIBUTE07", imeta_output)
self.assertIn("_TAG-12342_", imeta_output)
self.assertIn("ATTRIBUTE08", imeta_output)
self.assertIn("['value1', 'value2, 'value3']", imeta_output)
self.assertIn("as", imeta_output)
self.assertIn("ATTRIBUTE09", imeta_output)
self.assertIn("MLX", imeta_output)
self.assertIn("ATTRIBUTE10", imeta_output)
self.assertIn("NULL", imeta_output)