Mercurial > repos > melissacline > ucsc_xena_platform
changeset 43:78d6e6772e30
more reliable
| author | jingchunzhu <jingchunzhu@gmail.com> |
|---|---|
| date | Mon, 27 Jul 2015 12:21:55 -0700 |
| parents | bc9784300015 |
| children | da86478b1d64 |
| files | getXenaData.py xenaGetDataset.xml |
| diffstat | 2 files changed, 18 insertions(+), 11 deletions(-) [+] |
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--- a/getXenaData.py Mon Jul 27 12:01:42 2015 -0700 +++ b/getXenaData.py Mon Jul 27 12:21:55 2015 -0700 @@ -16,22 +16,29 @@ url = "https://galaxyxena.soe.ucsc.edu:443/xena" #testing if the url is reachable -#try: -r =json.loads(xena.post(url, "(+ 1 2)")) -if r!=3.0: - print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you." - print "You entered hub: %s" % (url) - fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you.\n") - fout.write("You entered hub: %s\n" % (url)) - fout.close() - sys.exit(1) +try: + r =json.loads(xena.post(url, "(+ 1 2)")) + if r!=3.0: + print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you." + print "You entered hub: %s" % (url) + fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you.\n") + fout.write("You entered hub: %s\n" % (url)) + fout.close() + sys.exit(1) +except: + print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you." + print "You entered hub: %s" % (url) + fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you.\n") + fout.write("You entered hub: %s\n" % (url)) + fout.close() + sys.exit(1) samples = xena.dataset_samples (url, dataset) if not samples: print "Dataset does not exist" print "You entered dataset id: %s" % (dataset) fout.write("Dataset does not exists\n") - fout.wriet("You entered dataset id: %s\n" % (dataset)) + fout.write("You entered dataset id: %s\n" % (dataset)) fout.close() sys.exit(1)
--- a/xenaGetDataset.xml Mon Jul 27 12:01:42 2015 -0700 +++ b/xenaGetDataset.xml Mon Jul 27 12:21:55 2015 -0700 @@ -29,7 +29,7 @@ </inputs> <outputs> <!-- <data format="txt" name="metadataFile" label="${dataset}.json"/> --> - <data format="tabular" name="dataFile" label="${dataset}" /> + <data format="txt" name="dataFile" label="${dataset}" /> </outputs> <help> Given the data hub name and the dataset id, download the dataset into this Galaxy. Xena dataset id can be obtained through the Explore Data in Xena tool.