Mercurial > repos > kellrott > synapse_interface

comparison synapse_create.xml @ 3:93c4d2fad9af

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixing bugs and bad code
author Kyle Ellrott <kellrott@gmail.com>
date Wed, 24 Oct 2012 23:31:13 -0700
parents 83173eca36b7
children
comparison
equal deleted inserted replaced
2:a104cc98359c 3:93c4d2fad9af
1 <tool id="synapse_create" name="Synapse Create" version="1.0"> 1 <tool id="synapse_create" name="Synapse Create" version="2.0.0">
2 <description>Create Synapse</description> 2 <description>Create Synapse</description>
3 <command interpreter="python">$script_file</command> 3 <command interpreter="python">$script_file</command>
4 <inputs> 4 <inputs>
5 <param name="user" type="text" size="90" label="Username"/> 5 <param name="user" type="text" size="90" label="Username"/>
6 <param name="pass" type="text" size="90" label="Password"/> 6 <param name="pass" type="text" size="90" label="Password"/>
11 <option value="Project">Project</option> 11 <option value="Project">Project</option>
12 <option value="Study">Study</option> 12 <option value="Study">Study</option>
13 <option value="Data">Data</option> 13 <option value="Data">Data</option>
14 </param> 14 </param>
15 <repeat name="properties" title="Properties"> 15 <repeat name="properties" title="Properties">
16 <param name="name" type="select" size="90" label="Name">
17 <option value="name">Name</option>
18 <option value="parentId">ParentID</option>
19 <option value="description">Description</option>
20 <option value="species">Species</option>
21 <option value="numSamples">Number of Samples</option>
22 <option value="disease">Disease</option>
23 <option value="tissueType">Tissue Type</option>
24 </param>
25 <param name="value" type="text" size="90" label="Value">
26 <sanitizer>
27 <valid initial="string.printable">
28 <remove value="&quot;"/>
29 </valid>
30 <mapping initial="none">
31 <add source="&quot;" target="\&quot;"/>
32 </mapping>
33 </sanitizer>
34 </param>
35 </repeat>
36
37 <repeat name="annotations" title="Annotations">
16 <param name="name" type="text" size="90" label="Name"/> 38 <param name="name" type="text" size="90" label="Name"/>
17 <param name="value" type="text" size="90" label="Value"> 39 <param name="value" type="text" size="90" label="Value">
18 <sanitizer> 40 <sanitizer>
19 <valid initial="string.printable"> 41 <valid initial="string.printable">
20 <remove value="&quot;"/> 42 <remove value="&quot;"/>
24 </mapping> 46 </mapping>
25 </sanitizer> 47 </sanitizer>
26 </param> 48 </param>
27 </repeat> 49 </repeat>
28 50
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> 51 </inputs>
35 <outputs> 52 <outputs>
36 <data format="txt" name="outfile" /> 53 <data format="txt" name="outfile" />
37 </outputs> 54 </outputs>
38 <configfiles> 55 <configfiles>
39 <configfile name="script_file"><![CDATA[#!/usr/bin/env python 56 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
40 rcode=""" 57 rcode="""
41 require(synapseClient) 58 require(synapseClient)
42 59
43 if (nchar("$user") > 0 && nchar("$pass") > 0) { 60 galaxyClean <- function(x) {
44 synapseLogin(username="$user", password="$pass") 61 y = gsub("__gt__", ">", x);
62 y = gsub("__lt__", "<", y );
63 y = gsub("__sq__", "'", y);
64 y = gsub("__dq__", "\\"",y);
65 y = gsub("__ob__", "[", y);
66 y = gsub("__cb__", "]", y);
67 y = gsub("__oc__", "{", y);
68 y = gsub("__cc__", "}", y);
69 y = gsub("__at__", "@", y);
70 y = gsub("__cn__", "\\n", y);
71 y = gsub("__cr__", "\\r", y);
72 y = gsub("__tc__", "\\t", y);
73 y = gsub("__pd__", "#", y);
74 y = gsub("__at__", "@", y);
75 return(y);
45 } 76 }
46 77
47 ent <- ${etype}( list(name="${name}") ) 78 if (nchar("$user") && nchar("$pass")) {
79 synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
80 }
81
82
83 ent <- ${etype}( list(name=galaxyClean("${name}")) )
48 84
49 #for $a in $annotations: 85 #for $a in $annotations:
50 annotValue(ent, "${a.name}") <- "${a.value}" 86 annotValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}")
51 #end for 87 #end for
52 88
53 #for a in $properties: 89 #for a in $properties:
54 propertyValue(ent, "${a.name}") <- "${a.value}" 90 propertyValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}")
55 #end for 91 #end for
56 92
57 ent <- createEntity(ent) 93 ent <- createEntity(ent)
58 94
59 #if $attachment != 'None' 95 #if $attachment != 'None'
60 #if $attachment_name == '': 96 #if $attachment_name == '':
61 ent <- addFile(ent, "${attachment}") 97 ent <- addFile(ent, galaxyClean("${attachment}"))
62 #else 98 #else
63 ent <- addFile(ent, "${attachment}", "${attachment_name}") 99 ent <- addFile(ent, galaxyClean("${attachment}"), galaxyClean("${attachment_name}"))
64 #end if 100 #end if
65 #end if 101 #end if
66 102
67 ent <- storeEntity(ent) 103 ent <- storeEntity(ent)
68 104
69 write(properties(ent)\$id, file="${outfile}"); 105 write(properties(ent)\$id, file=galaxyClean("${outfile}"));
70 106
71 """ 107 """
72 108
73 109
74 import tempfile 110 import tempfile
87 sys.stdout.write(stdoutdata) 123 sys.stdout.write(stdoutdata)
88 os.unlink(path) 124 os.unlink(path)
89 125
90 ]]></configfile> 126 ]]></configfile>
91 </configfiles> 127 </configfiles>
128 <help>
129
130 Install R SynapseClient:
131 source('http://depot.sagebase.org/CRAN.R')
132 pkgInstall("synapseClient")
133
134 `To setup auto login (so you don't have to type in your password) &lt;https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login&gt;`_
135
136 </help>
137
92 </tool> 138 </tool>