comparison synapseGetDataset.py @ 37:e81019e3ac99

Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format

36:ab161b5ac9cc

#!/usr/bin/env python
"""Download a dataset from Synapse into Galaxy """

import argparse
import json
import synapseclient
import sys
import zipfile

class InputError(Exception):

    jsonMetadata = json.dumps(entityMetadata)
    fp.write("%s\n" % (jsonMetadata))
    fp.close()

def saveData(entity, dataPathname):
    if entity.properties['contentType'] == "application/zip":
        zf = zipfile.ZipFile(entity.path)
        if len(zf.namelist()) > 1:
            raise InputError(len(zf.namelist())), "Error: more than one input file"
        else:
            data = zf.read(zf.namelist()[0])

37:e81019e3ac99

#!/usr/bin/env python
"""Download a dataset from Synapse into Galaxy """

import argparse
import json
import re
import synapseclient
import sys
import zipfile

class InputError(Exception):

    jsonMetadata = json.dumps(entityMetadata)
    fp.write("%s\n" % (jsonMetadata))
    fp.close()

def saveData(entity, dataPathname):
    if re.search("\.zip$", entity.path):
        zf = zipfile.ZipFile(entity.path)
        if len(zf.namelist()) > 1:
            raise InputError(len(zf.namelist())), "Error: more than one input file"
        else:
            data = zf.read(zf.namelist()[0])