Mercurial > repos > melissacline > ucsc_xena_platform
annotate xena_delete.py @ 17:6785e729c7ad
Updated the xena jar to version 14, updated the URL of the Xena pages
| author | melissacline |
|---|---|
| date | Tue, 02 Jun 2015 14:54:24 -0700 |
| parents | 98b498545a52 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 | |
| 3 """ | |
| 4 xena_delete.py: delete a dataset from Xena | |
| 5 | |
| 6 Given the name of a Xena dataset, delete it from the local Xena database. | |
| 7 """ | |
| 8 | |
| 9 import argparse | |
| 10 import json | |
| 11 import os | |
| 12 import re | |
| 13 import shutil | |
| 14 import subprocess | |
| 15 import sys | |
| 16 import traceback | |
| 17 import xena_utils as xena | |
| 18 | |
| 19 def main(): | |
| 20 parser = argparse.ArgumentParser() | |
| 21 parser.add_argument("datasetName", type=str) | |
| 22 parser.add_argument("outfile", type=str) | |
| 23 args = parser.parse_args() | |
| 24 | |
| 25 fp2 = open(args.outfile, "w") | |
| 26 xenaFileDir = xena.fileDir() | |
| 27 | |
| 28 # Set up the xena delete comamnd and try to execute it. If an exception | |
| 29 # is generated, output a traceback and exit with nonzero status. If | |
| 30 # no exception was generated, indicate a successful import and exit | |
| 31 # with zero status. | |
|
2
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
32 xenaDeleteCmd = "java -jar %s --delete %s/%s -p %s" % (xena.jarPath(), |
|
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
33 xenaFileDir, |
|
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
34 args.datasetName, |
|
6eeb3ca663fb
Fixed dataset delete bugs (the full pathname was needed) plus changed xena_import to give a checkbox for turning on column normalization
melissacline
parents:
0
diff
changeset
|
35 xena.port()) |
| 0 | 36 try: |
| 37 subprocess.call(xenaDeleteCmd, shell=True) | |
| 38 except: | |
| 39 exc_type, exc_value, exc_traceback = sys.exc_info() | |
| 40 lines = traceback.format_exception(exc_type, exc_value, exc_traceback) | |
| 41 allLines = ''.join('!! ' + line for line in lines) | |
| 42 fp2.write("Unsuccessful: error %s\n" % allLines) | |
| 43 fp2.close() | |
| 44 sys.exit(-1) | |
| 45 else: | |
| 46 fp2.write( "Dataset %s deleted\n" % args.datasetName) | |
|
3
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
47 dataPathname = xenaFileDir + "/" + args.datasetName |
|
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
48 if os.path.exists(dataPathname): |
|
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
49 os.unlink(dataPathname) |
|
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
50 metadataPathname = dataPathname + ".json" |
|
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
51 if os.path.exists(metadataPathname): |
|
98b498545a52
Fixed xena_delete to delete the files from the Xena files directory as well as from the database
melissacline
parents:
2
diff
changeset
|
52 os.unlink(metadataPathname) |
| 0 | 53 fp2.close() |
| 54 sys.exit(0) | |
| 55 | |
| 56 | |
| 57 if __name__ == "__main__": | |
| 58 main() |