def test_view(self): """ Test the view method """ data = { "profiles.csv": [{"PROJECTID": "ENCODE", "project_id": "ENCODE", "ANNOTATION": ""}], "annotations.csv": [{}], "genomes.csv": [], "accessions.csv": [ { "project_id": "ENCODE", "accession_id": "ABCD", "species": "H**o sapiens", "cell": "cell", "readType": "1x70D", "type": "type", "qualities": "qualities", "dataType": "dataType", "rnaExtract": "rnaExtract", "localization": "localization", "lab": "lab", } ], "runs.csv": [{"project_id": "ENCODE", "run_id": "run_id", "read_length": 70}], "files.csv": [ {"project_id": "ENCODE", "accession_id": "ABCD", "type": "fastq", "file_location": "myfile.fastq.gz"} ], } view.main(data, SANDBOX)
def install(self): workspace = self.buildout['extract']['workspace'] staging = self.options['staging'] if not os.path.exists(staging): os.makedirs(staging) data = {} for source in [f for f in glob.glob(os.path.join(workspace, '*.csv'))]: file_name = os.path.split(source)[-1] target = os.path.join(staging, file_name) shutil.copyfile(source, target) data[file_name] = read_csv(target) accessions.main(data, staging) annotations.main(data, staging) files.main(data, staging) genomes.main(data, staging) profiles.main(data) experiments.main(data, staging) read_length.main(data, staging) view.main(data, staging)
def test_view(self): """ Test the view method """ data = { 'profiles.csv': [{ 'PROJECTID': 'ENCODE', 'project_id': 'ENCODE', 'ANNOTATION': '' }], 'annotations.csv': [{}], 'genomes.csv': [], 'accessions.csv': [{ 'project_id': 'ENCODE', 'accession_id': 'ABCD', 'species': 'H**o sapiens', 'cell': 'cell', 'readType': '1x70D', 'type': 'type', 'qualities': 'qualities', 'dataType': 'dataType', 'rnaExtract': 'rnaExtract', 'localization': 'localization', 'lab': 'lab' }], 'runs.csv': [{ 'project_id': 'ENCODE', 'run_id': 'run_id', 'read_length': 70 }], 'files.csv': [{ 'project_id': 'ENCODE', 'accession_id': 'ABCD', 'type': 'fastq', 'file_location': 'myfile.fastq.gz' }], } view.main(data, SANDBOX)