Mercurial > repos > cathywise > truststore_import
comparison TrustStoreGalaxyImport.py @ 21:8cf18ca6f13f
ugh.
| author | Catherine Wise <catherine.wise@csiro.au> |
|---|---|
| date | Mon, 13 Jan 2014 09:10:44 +1100 |
| parents | b94a8f55b1da |
| children | 1179f6e90e78 |
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| 20:b94a8f55b1da | 21:8cf18ca6f13f |
|---|---|
| 60 | 60 |
| 61 if is_gzipped and not is_valid: | 61 if is_gzipped and not is_valid: |
| 62 print "File is compressed (gzip) but not valid." | 62 print "File is compressed (gzip) but not valid." |
| 63 sys.exit(4) | 63 sys.exit(4) |
| 64 elif is_gzipped and is_valid: | 64 elif is_gzipped and is_valid: |
| 65 if link_data_only == 'copy_files': | 65 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format |
| 66 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format | 66 CHUNK_SIZE = 2**20 # 1Mb |
| 67 CHUNK_SIZE = 2**20 # 1Mb | 67 fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False ) |
| 68 fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False ) | 68 gzipped_file = gzip.GzipFile(download, 'rb') |
| 69 gzipped_file = gzip.GzipFile(download, 'rb') | 69 while 1: |
| 70 while 1: | 70 try: |
| 71 try: | 71 chunk = gzipped_file.read(CHUNK_SIZE) |
| 72 chunk = gzipped_file.read(CHUNK_SIZE) | 72 except IOError: |
| 73 except IOError: | 73 os.close(fd) |
| 74 os.close(fd) | 74 os.remove(uncompressed) |
| 75 os.remove(uncompressed) | 75 print 'Problem decompressing gzipped data', dataset, json_file |
| 76 print 'Problem decompressing gzipped data', dataset, json_file | 76 sys.exit(4) |
| 77 sys.exit(4) | 77 if not chunk: |
| 78 if not chunk: | 78 break |
| 79 break | 79 os.write(fd, chunk) |
| 80 os.write(fd, chunk) | 80 os.close(fd) |
| 81 os.close(fd) | 81 gzipped_file.close() |
| 82 gzipped_file.close() | |
| 83 | 82 |
| 84 shutil.copy(uncompressed, outputFile) | 83 shutil.copy(uncompressed, outputFile) |
| 85 else: | 84 else: |
| 86 shutil.copy(download, outputFile) | 85 shutil.copy(download, outputFile) |
| 87 else: | 86 else: |