diff TrustStoreGalaxyBrowse.py @ 0:2a996fea49a3

Initial.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TrustStoreGalaxyBrowse.py	Thu May 07 12:34:06 2015 +1000
@@ -0,0 +1,134 @@
+from __future__ import division, absolute_import, print_function, unicode_literals
+import sys
+import shutil
+import gzip
+import tempfile
+import os
+from py_ts import TrustStoreClient, utils
+# from galaxy.datatypes.checkers import *
+
+def printNice(elem, f, depth):
+    try:
+        f.write('\t'*depth + elem.name + " (" + str(len(elem.fragments)) + " parts)\n")
+    except AttributeError:
+        f.write('\t'*depth + elem.name + "\n")
+        for child in elem.children:
+            printNice(child, f, depth+1)
+
+def check_gzip(file_path):
+    try:
+        temp = open( file_path, "U" )
+        magic_check = temp.read( 2 )
+        temp.close()
+        if magic_check != util.gzip_magic:
+            return ( False, False )
+    except:
+        return ( False, False )
+    return ( True, True )
+
+def ungzip(download, outputFile):
+    is_gzipped, is_valid = check_gzip(download)
+
+    if is_gzipped and not is_valid:
+        print "File is compressed (gzip) but not valid."
+        sys.exit(4)
+    elif is_gzipped and is_valid:
+        # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
+        CHUNK_SIZE = 2**20 # 1Mb
+        fd, uncompressed = tempfile.mkstemp(prefix='data_id_upload_gunzip_', dir=os.path.dirname(outputFile), text=False )
+        gzipped_file = gzip.GzipFile(download, 'rb')
+        while 1:
+            try:
+                chunk = gzipped_file.read(CHUNK_SIZE)
+            except IOError:
+                os.close(fd)
+                os.remove(uncompressed)
+                print 'Problem decompressing gzipped data', dataset, json_file
+                sys.exit(4)
+            if not chunk:
+                break
+            os.write(fd, chunk)
+        os.close(fd)
+        gzipped_file.close()
+
+        shutil.copy(uncompressed, outputFile)
+        try:
+            os.remove(uncompressed)
+            os.remove(download)
+        except OSError:
+                pass
+    else:
+        shutil.copy(download, outputFile)
+
+if __name__ == '__main__':
+
+    kms_url = "https://tstest-kms.it.csiro.au/kmscolab_3_0"
+    ims_url = "https://tstest-ims.it.csiro.au/ims_3_0/services/IMS"
+    username = sys.argv[1]
+    password = sys.argv[2]
+    client_key = "desktop"
+    client_secret = "cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg=="
+    storename = sys.argv[3]
+    path = sys.argv[4]
+    fileType = sys.argv[5]
+    filename = ""
+    outputFile = ""
+    if len(sys.argv) > 9:
+        filename = sys.argv[6]
+        outputFile = sys.argv[7]
+        outputFileId = sys.argv[8]
+        otherFilesDir = sys.argv[9]
+    else:
+        outputFile = sys.argv[6]
+
+    config = TrustStoreClient.Config(ims_url, kms_url, client_key, client_secret, tmpDir='/mnt/galaxy/tmp')
+    ts = TrustStoreClient.TrustStoreClient(headless=False, config=config)
+    try:
+        ts.authenticate(username, password)
+    except TrustStoreClient.TrustStoreClientAuthenticationException as e:
+        print e
+        sys.exit(5)
+    ts.getPrivateKey('privkey.pem')
+    listing = ts.listStores()
+    found = False
+    for store in listing:
+        if store.friendly_name == storename:
+            found = True
+            root = ts.listDirectory(store)
+            location = None
+            if path != "/":
+                location = ts_utils.ts_utils.dirAtPath(root, path)
+                if not location:
+                    print "Path not found"
+                    sys.exit(3)
+            else:
+                location = root
+            if filename and filename != "":
+                outputFileList = [outputFile]
+                inputFileList = None
+                if "," in filename: # we have multiple files guys.
+                    inputFileList = filename.split(",")
+                    for inputFile in inputFileList[1:]: # First file will be sent to outputFile.
+                        outName = "%s_%s_%s_%s_%s" % ('primary', outputFileId, inputFile.replace(".","-"), 'visible', fileType)
+                        outputFileList.append(os.path.join(otherFilesDir, outName))
+                else:
+                    inputFileList = [filename]
+                for inFile, outFile in zip(inputFileList, outputFileList):
+                    downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, inFile)
+                    if downloadMe:
+                        download = ts.getFile(store, downloadMe)
+                        ungzip(download, outFile)
+                    else:
+                        print "File %s not found" % inFile
+                        sys.exit(4)
+            else:
+                with open(outputFile, 'w+') as f:
+                    try:
+                        for child in root.children:
+                            printNice(child, f, 0)
+                    except AttributeError as e:
+                        print e
+                        print root
+    if not found:
+        print "Store %s not found" % storename
+        sys.exit(2)