# HG changeset patch
# User Catherine Wise <catherine.wise@csiro.au>
# Date 1386825463 -39600
# Node ID 159d2159e745605b972cb3e97c69c5c00b792fc5
# Parent  32d9b3343955dfbdbf905c3d17ee0d627ed40610
Add list files.

diff -r 32d9b3343955 -r 159d2159e745 TrustStoreGalaxyImport.py
--- a/TrustStoreGalaxyImport.py	Thu Dec 12 13:07:45 2013 +1100
+++ b/TrustStoreGalaxyImport.py	Thu Dec 12 16:17:43 2013 +1100
@@ -2,6 +2,14 @@
 import shutil
 from py_ts import TrustStoreClient, ts_utils
 
+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)
+
 if __name__ == '__main__':
 
     kms_url = sys.argv[1]
@@ -12,8 +20,13 @@
     client_secret = sys.argv[6]
     storename = sys.argv[7]
     path = sys.argv[8]
-    filename = sys.argv[9]
-    outputFile = sys.argv[10]
+    filename = ""
+    outputFile = ""
+    if len(sys.argv) > 10:
+        filename = sys.argv[9]
+        outputFile = sys.argv[10]
+    else:
+        outputFile = sys.argv[9]
 
     config = TrustStoreClient.Config(ims_url, kms_url, client_key, client_secret)
     ts = TrustStoreClient.TrustStoreClient(headless=True, config=config)
@@ -37,13 +50,22 @@
                     sys.exit(3)
             else:
                 location = root
-            downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, filename)
-            if downloadMe:
-                download = ts.getFile(store, downloadMe)
-                shutil.copy(download, outputFile)
+            if filename and filename != "":
+                downloadMe = ts_utils.ts_utils.recurseToChildNamed(location, filename)
+                if downloadMe:
+                    download = ts.getFile(store, downloadMe)
+                    shutil.copy(download, outputFile)
+                else:
+                    print "File not found"
+                    sys.exit(4)
             else:
-                print "File not found"
-                sys.exit(4)
+                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 not found"
         sys.exit(2)
diff -r 32d9b3343955 -r 159d2159e745 TrustStoreGalaxyImport.xml
--- a/TrustStoreGalaxyImport.xml	Thu Dec 12 13:07:45 2013 +1100
+++ b/TrustStoreGalaxyImport.xml	Thu Dec 12 16:17:43 2013 +1100
@@ -9,6 +9,7 @@
     <command interpreter="python">TrustStoreGalaxyImport.py https://tstest-kms.it.csiro.au/kmscolab_3_0 https://tstest-ims.it.csiro.au/ims_3_0/services/IMS $username $password desktop cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg== $storename $path $filename $output</command>
     <inputs>
         <param name="file_type" type="select" label="File Format" help="Which format is the data you're downloading?">
+            <option value="just list files"/>
             <option value="ab1"/>
             <option value="axt"/>
             <option value="bam"/>
@@ -42,7 +43,7 @@
         </param>
         <!-- <param name="kms_url" type="text" label="kms url" help="the remote url for your key management service" value="http://localhost:8080/TSSKeyManagementService-Collaboration" size="200" />
         <param name="ims_url" type="text" label="ims url" help="the remote url for your integrity management service" value="http://localhost:8080/TSSIntegrityManagementService/services/IMS" size="200" /> -->
-        <param name="username" type="text" label="username" help="kms username" value="user" size="20" >
+        <param name="username" type="text" label="Username" help="Your KMS username, e.g. jo.blogs@workplace.com" value="user" size="20" >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -52,7 +53,7 @@
                 </mapping>
             </sanitizer>
         </param>
-        <param name="password" type="text" label="password" help="kms password" value="password" size="1">
+        <param name="password" type="text" label="Password" help="Your KMS password" value="password" size="1">
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -65,11 +66,11 @@
         <!-- <param name="client_key" type="text" label="client key" help="kms client name" value="my-trusted-client-with-secret" size="20" /> -->
         <!-- <param name="client_secret" type="text" label="client secret" help="kms client secret" value="somesecret" size="20" /> -->
         <param name="storename" type="text" label="Store Name" help="e.g.: My Galaxy Store" value="galaxy" size="20" />
-        <param name="path" type="text" label="Path in store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" />
-        <param name="filename" type="text" label="File name" help="e.g.: export1.bam" value="1.png" size="20" />
+        <param name="path" type="text" label="Path in Store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" />
+        <param name="filename" type="text" label="Filename" help="e.g.: export1.bam. Leave empty if 'just list files' is chosen above." value="" size="20" />
     </inputs>
     <outputs>
-        <data name="output" format="ab1">
+        <data name="output" format="txt">
             <change_format>
                 <when input="file_type" value="ab1" format="ab1" />
                 <when input="file_type" value="axt" format="axt" />
@@ -101,6 +102,7 @@
                 <when input="file_type" value="txt" format="txt" />
                 <when input="file_type" value="wig" format="wig" />
                 <when input="file_type" value="xml" format="xml" />
+                <when input="file_type" value="just list files" format="txt"/>
             </change_format>
         </data>
     </outputs>