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comparison synapse_create.xml @ 0:83173eca36b7

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author kellrott
date Tue, 24 Jul 2012 17:33:11 -0400
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children 93c4d2fad9af
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-1:000000000000 0:83173eca36b7
1 <tool id="synapse_create" name="Synapse Create" version="1.0">
2 <description>Create Synapse</description>
3 <command interpreter="python">$script_file</command>
4 <inputs>
5 <param name="user" type="text" size="90" label="Username"/>
6 <param name="pass" type="text" size="90" label="Password"/>
7 <param name="name" type="text" size="90" label="Name"/>
8 <param name="attachment" type="data" optional="true" label="Attachment"/>
9 <param name="attachment_name" type="text" size="90" optional="true" label="Attachment Name"/>
10 <param name="etype" type="select" label="Entity Type">
11 <option value="Project">Project</option>
12 <option value="Study">Study</option>
13 <option value="Data">Data</option>
14 </param>
15 <repeat name="properties" title="Properties">
16 <param name="name" type="text" size="90" label="Name"/>
17 <param name="value" type="text" size="90" label="Value">
18 <sanitizer>
19 <valid initial="string.printable">
20 <remove value="&quot;"/>
21 </valid>
22 <mapping initial="none">
23 <add source="&quot;" target="\&quot;"/>
24 </mapping>
25 </sanitizer>
26 </param>
27 </repeat>
28
29 <repeat name="annotations" title="Annotations">
30 <param name="name" type="text" size="90" label="Name"/>
31 <param name="value" type="text" size="90" label="Value"/>
32 </repeat>
33
34 </inputs>
35 <outputs>
36 <data format="txt" name="outfile" />
37 </outputs>
38 <configfiles>
39 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
40 rcode="""
41 require(synapseClient)
42
43 if (nchar("$user") > 0 && nchar("$pass") > 0) {
44 synapseLogin(username="$user", password="$pass")
45 }
46
47 ent <- ${etype}( list(name="${name}") )
48
49 #for $a in $annotations:
50 annotValue(ent, "${a.name}") <- "${a.value}"
51 #end for
52
53 #for a in $properties:
54 propertyValue(ent, "${a.name}") <- "${a.value}"
55 #end for
56
57 ent <- createEntity(ent)
58
59 #if $attachment != 'None'
60 #if $attachment_name == '':
61 ent <- addFile(ent, "${attachment}")
62 #else
63 ent <- addFile(ent, "${attachment}", "${attachment_name}")
64 #end if
65 #end if
66
67 ent <- storeEntity(ent)
68
69 write(properties(ent)\$id, file="${outfile}");
70
71 """
72
73
74 import tempfile
75 import os
76 import sys
77 import subprocess
78
79 h, path = tempfile.mkstemp()
80 os.write(h,rcode)
81 os.close(h)
82
83 proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
84 (stdoutdata, stderrdata) = proc.communicate()
85 if proc.returncode:
86 sys.stderr.write(stderrdata)
87 sys.stdout.write(stdoutdata)
88 os.unlink(path)
89
90 ]]></configfile>
91 </configfiles>
92 </tool>