changeset 50:3167c1a26101

fix

--- a/getXenaData.py	Sun Aug 09 23:23:58 2015 -0700
+++ b/getXenaData.py	Wed Aug 12 16:38:12 2015 -0700
@@ -6,66 +6,75 @@
   print "python getXenaData.py hub datasetId outputfile\n"
   sys.exit(1)
 
-url = sys.argv[1]
-dataset = sys.argv[2]
-output = sys.argv[3]
+def main():
+  url = sys.argv[1]
+  dataset = sys.argv[2]
+  output = sys.argv[3]
 
-fout = open(output,'w')
+  fout = open(output,'w')
 
-if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1:
-  url = "https://galaxyxena.soe.ucsc.edu:443/xena"
+  contactUrl = url
+  if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1:
+    contactUrl = "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."
+  #testing if the url is reachable
+  try:
+    r =json.loads(xena.post(contactUrl, "(+ 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 this galaxy instance."
+      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 this galaxy instance.\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 this galaxy instance."
     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("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")
     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.write("You entered dataset id: %s\n" % (dataset))
-  fout.close()
-  sys.exit(1)
+  samples = xena.dataset_samples (contactUrl, dataset)
+  if not samples:
+    print "Dataset does not exist"
+    print "You entered dataset id: %s" % (dataset)
+    fout.write("Dataset does not exists\n")
+    fout.write("You entered dataset id: %s\n" % (dataset))
+    fout.close()
+    sys.exit(1)
 
-type = xena.dataset_type(url, dataset)
-if type[0] not in ["genomicMatrix", "clinicalMatrix"]:
-  print "The type of data is not supported"
-  print "datatype=%s" % (type[0])
-  fout.write("The type of data is not supported\n")
-  fout.write("datatype=%s\n" % (type[0]))
-  fout.close()
-  sys.exit(1)
+  type = xena.dataset_type(contactUrl, dataset)
+  if type[0] not in ["genomicMatrix", "clinicalMatrix"]:
+    print "The type of data is not supported"
+    print "datatype=%s" % (type[0])
+    fout.write("The type of data is not supported\n")
+    fout.write("datatype=%s\n" % (type[0]))
+    fout.close()
+    sys.exit(1)
+
+  writer = csv.writer(fout, delimiter='\t')
+  writer.writerow(["sample"]+samples)
 
-writer = csv.writer(fout, delimiter='\t')
-writer.writerow(["sample"]+samples)
+  probes = xena.dataset_field(contactUrl, dataset)
+  start=0
+  size =100
+  N= len(probes)
+  for i in range (start, N,size):
+    results = xena.dataset_probe_values (contactUrl, dataset, samples, probes[i:i+size])
+    print ".",
+    for j in range (0, size):
+      if i+j == N:
+        break
+      writer.writerow([probes[i+j]]+results[j])
 
-probes = xena.dataset_field(url, dataset)
-start=0
-size =100
-N= len(probes)
-for i in range (start, N,size):
-  results = xena.dataset_probe_values (url, dataset, samples, probes[i:i+size])
-  print ".",
-  for j in range (0, size):
-    if i+j == N:
-      break
-    writer.writerow([probes[i+j]]+results[j])
+  fout.close()
+  print "done"
+  sys.exit(0)
 
-fout.close()
-print "done"
-sys.exit(0)
+
+if __name__ == "__main__":
+    main()
+

--- a/xenaGetDataset.py	Sun Aug 09 23:23:58 2015 -0700
+++ b/xenaGetDataset.py	Wed Aug 12 16:38:12 2015 -0700
@@ -9,26 +9,25 @@
     parser = argparse.ArgumentParser()
     parser.add_argument("dataHub", type=str)
     parser.add_argument("datasetId", type=str)
-    #parser.add_argument("metadatafile", type=str)
     parser.add_argument("datafile", type=str)
     args = parser.parse_args()
 
     datasetUrlHost = re.sub("/proj/", "/download/", args.dataHub)
     datasetIdTokens = re.split("/", args.datasetId)
     datasetUrl = datasetUrlHost + "/" + "/".join(datasetIdTokens[1:])
-    print datasetUrl
-    """
-    metadataUrl = datasetUrl + ".json"
-    mm = urllib2.urlopen(metadataUrl)
-    with open(args.metadatafile, "w") as metadata:
-        metadata.write(mm.read())
-    mm.close()
-    """
-    dd = urllib2.urlopen(datasetUrl)
-    with open(args.datafile, "w") as data:
+
+    data = open(args.datafile, "w")
+
+    try:
+        dd = urllib2.urlopen(datasetUrl)
         data.write(dd.read())
-    dd.close()
-
+        dd.close()
+        data.close()
+    except:
+        data.wriet("You entered dataset id: %s\n" % (args.datasetId))
+        data.write("Dataset does not exist. check typo.")
+        data.close()
+        sys.exit(1)
 
 if __name__ == "__main__":
     main()