Mercurial > repos > melissacline > ucsc_xena_platform
comparison getXenaData.py @ 52:bb840cc2603d
better error handling
| author | jingchunzhu |
|---|---|
| date | Thu, 13 Aug 2015 17:30:19 -0700 |
| parents | 3167c1a26101 |
| children |
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| 51:47926759295a | 52:bb840cc2603d |
|---|---|
| 1 # getXenaData.py | 1 #!/usr/bin/env python |
| 2 | |
| 2 import os, sys, string, json, csv | 3 import os, sys, string, json, csv |
| 3 import xena_query as xena | 4 import xena_query as xena |
| 4 | 5 |
| 5 if len(sys.argv[:])!=4: | 6 if len(sys.argv[:])!=5: |
| 6 print "python getXenaData.py hub datasetId outputfile\n" | 7 print "python getXenaData.py hub datasetId outputfile galaxy_url\n" |
| 7 sys.exit(1) | 8 sys.exit(2) |
| 8 | 9 |
| 9 def main(): | 10 def main(): |
| 10 url = sys.argv[1] | 11 url = sys.argv[1] |
| 11 dataset = sys.argv[2] | 12 dataset = sys.argv[2] |
| 12 output = sys.argv[3] | 13 output = sys.argv[3] |
| 14 GALAXY_URL = sys.argv[4] | |
| 13 | 15 |
| 14 fout = open(output,'w') | 16 fout = open(output,'w') |
| 15 | 17 |
| 16 contactUrl = url | 18 contactUrl = url |
| 17 if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1: | 19 if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1: |
| 20 #testing if the url is reachable | 22 #testing if the url is reachable |
| 21 try: | 23 try: |
| 22 r =json.loads(xena.post(contactUrl, "(+ 1 2)")) | 24 r =json.loads(xena.post(contactUrl, "(+ 1 2)")) |
| 23 | 25 |
| 24 if r!=3.0: | 26 if r!=3.0: |
| 25 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance." | 27 fout.write("There is an error\n\n") |
| 26 print "You entered hub: %s" % (url) | |
| 27 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 this galaxy instance.\n") | |
| 28 fout.write("You entered hub: %s\n" % (url)) | 28 fout.write("You entered hub: %s\n" % (url)) |
| 29 fout.write("Possible causes for error:\n") | |
| 30 fout.write("1. The hub is not running.\n") | |
| 31 fout.write("2. The hub is not accessible to this galaxy instance at: %s.\n" %(GALAXY_URL)) | |
| 32 fout.write("3. The hub url has a typo.\n") | |
| 29 fout.close() | 33 fout.close() |
| 30 sys.exit(1) | 34 sys.exit(1) |
| 31 | 35 |
| 32 except: | 36 except: |
| 33 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance." | 37 fout.write("There is an error\n\n") |
| 34 print "You entered hub: %s" % (url) | |
| 35 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 this galaxy instance.\n") | |
| 36 fout.write("You entered hub: %s\n" % (url)) | 38 fout.write("You entered hub: %s\n" % (url)) |
| 39 fout.write("Possible causes for error:\n") | |
| 40 fout.write("1. The hub is not running.\n") | |
| 41 fout.write("2. The hub is not accessible to this galaxy instance at: %s.\n" %(GALAXY_URL)) | |
| 42 fout.write("3. The hub url has a typo.\n") | |
| 37 fout.close() | 43 fout.close() |
| 38 sys.exit(1) | 44 sys.exit(1) |
| 39 | 45 |
| 40 samples = xena.dataset_samples (contactUrl, dataset) | 46 samples = xena.dataset_samples (contactUrl, dataset) |
| 41 if not samples: | 47 if not samples: |
| 42 print "Dataset does not exist" | 48 fout.write("There is an error\n\n") |
| 43 print "You entered dataset id: %s" % (dataset) | |
| 44 fout.write("Dataset does not exists\n") | |
| 45 fout.write("You entered dataset id: %s\n" % (dataset)) | 49 fout.write("You entered dataset id: %s\n" % (dataset)) |
| 50 fout.write("Possible causes for error:\n") | |
| 51 fout.write("1. Dataset does not exist.\n") | |
| 46 fout.close() | 52 fout.close() |
| 47 sys.exit(1) | 53 sys.exit(1) |
| 48 | 54 |
| 49 type = xena.dataset_type(contactUrl, dataset) | 55 type = xena.dataset_type(contactUrl, dataset) |
| 50 if type[0] not in ["genomicMatrix", "clinicalMatrix"]: | 56 if type[0] not in ["genomicMatrix", "clinicalMatrix"]: |
| 51 print "The type of data is not supported" | 57 fout.write("There is an error\n\n") |
| 52 print "datatype=%s" % (type[0]) | 58 fout.write("You entered dataset id: %s\n" % (dataset)) |
| 53 fout.write("The type of data is not supported\n") | 59 fout.write("It's datatype=%s\n" % (type[0])) |
| 54 fout.write("datatype=%s\n" % (type[0])) | 60 fout.write("This type of data is not supported yet.\n") |
| 55 fout.close() | 61 fout.close() |
| 56 sys.exit(1) | 62 sys.exit(1) |
| 57 | 63 |
| 58 writer = csv.writer(fout, delimiter='\t') | 64 writer = csv.writer(fout, delimiter='\t') |
| 59 writer.writerow(["sample"]+samples) | 65 writer.writerow(["sample"]+samples) |
| 69 if i+j == N: | 75 if i+j == N: |
| 70 break | 76 break |
| 71 writer.writerow([probes[i+j]]+results[j]) | 77 writer.writerow([probes[i+j]]+results[j]) |
| 72 | 78 |
| 73 fout.close() | 79 fout.close() |
| 74 print "done" | |
| 75 sys.exit(0) | 80 sys.exit(0) |
| 76 | |
| 77 | 81 |
| 78 if __name__ == "__main__": | 82 if __name__ == "__main__": |
| 79 main() | 83 main() |
| 80 | 84 |