comparison TrustStoreGalaxyImport.py @ 20:b94a8f55b1da

Un-gzip.

19:1cae026e4dcd

import sys
import shutil
from py_ts import TrustStoreClient, ts_utils

def printNice(elem, f, depth):
    try:
        f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
    except AttributeError:

                location = root
            if filename and filename != "":
                downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, filename)
                if downloadMe:
                    download = ts.getFile(store, downloadMe)
                    shutil.copy(download, outputFile)
                else:
                    print "File not found"
                    sys.exit(4)
            else:
                with open(outputFile, 'w+') as f:

20:b94a8f55b1da

import sys
import shutil
import gzip
from py_ts import TrustStoreClient, ts_utils
from galaxy.datatypes.checkers import *

def printNice(elem, f, depth):
    try:
        f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
    except AttributeError:

                location = root
            if filename and filename != "":
                downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, filename)
                if downloadMe:
                    download = ts.getFile(store, downloadMe)
                    is_gzipped, is_valid = check_gzip(download)

                    if is_gzipped and not is_valid:
                        print "File is compressed (gzip) but not valid."
                        sys.exit(4)
                    elif is_gzipped and is_valid:
                        if link_data_only == 'copy_files':
                            # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
                            CHUNK_SIZE = 2**20 # 1Mb
                            fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False )
                            gzipped_file = gzip.GzipFile(download, 'rb')
                            while 1:
                                try:
                                    chunk = gzipped_file.read(CHUNK_SIZE)
                                except IOError:
                                    os.close(fd)
                                    os.remove(uncompressed)
                                    print 'Problem decompressing gzipped data', dataset, json_file
                                    sys.exit(4)
                                if not chunk:
                                    break
                                os.write(fd, chunk)
                            os.close(fd)
                            gzipped_file.close()

                        shutil.copy(uncompressed, outputFile)
                    else:
                        shutil.copy(download, outputFile)
                else:
                    print "File not found"
                    sys.exit(4)
            else:
                with open(outputFile, 'w+') as f: