| Next changeset 1:7a60e992bfb0 (2012-07-24) |
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Commit message:
Uploaded |
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added:
synapse_create.xml |
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| diff -r 000000000000 -r 83173eca36b7 synapse_create.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_create.xml Tue Jul 24 17:33:11 2012 -0400 |
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| @@ -0,0 +1,92 @@ +<tool id="synapse_create" name="Synapse Create" version="1.0"> + <description>Create Synapse</description> + <command interpreter="python">$script_file</command> + <inputs> + <param name="user" type="text" size="90" label="Username"/> + <param name="pass" type="text" size="90" label="Password"/> + <param name="name" type="text" size="90" label="Name"/> + <param name="attachment" type="data" optional="true" label="Attachment"/> + <param name="attachment_name" type="text" size="90" optional="true" label="Attachment Name"/> + <param name="etype" type="select" label="Entity Type"> + <option value="Project">Project</option> + <option value="Study">Study</option> + <option value="Data">Data</option> + </param> + <repeat name="properties" title="Properties"> + <param name="name" type="text" size="90" label="Name"/> + <param name="value" type="text" size="90" label="Value"> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + </repeat> + + <repeat name="annotations" title="Annotations"> + <param name="name" type="text" size="90" label="Name"/> + <param name="value" type="text" size="90" label="Value"/> + </repeat> + + </inputs> + <outputs> + <data format="txt" name="outfile" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode=""" +require(synapseClient) + +if (nchar("$user") > 0 && nchar("$pass") > 0) { + synapseLogin(username="$user", password="$pass") +} + +ent <- ${etype}( list(name="${name}") ) + +#for $a in $annotations: +annotValue(ent, "${a.name}") <- "${a.value}" +#end for + +#for a in $properties: +propertyValue(ent, "${a.name}") <- "${a.value}" +#end for + +ent <- createEntity(ent) + +#if $attachment != 'None' +#if $attachment_name == '': +ent <- addFile(ent, "${attachment}") +#else +ent <- addFile(ent, "${attachment}", "${attachment_name}") +#end if +#end if + +ent <- storeEntity(ent) + +write(properties(ent)\$id, file="${outfile}"); + +""" + + +import tempfile +import os +import sys +import subprocess + +h, path = tempfile.mkstemp() +os.write(h,rcode) +os.close(h) + +proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE ) +(stdoutdata, stderrdata) = proc.communicate() +if proc.returncode: + sys.stderr.write(stderrdata) +sys.stdout.write(stdoutdata) +os.unlink(path) + +]]></configfile> + </configfiles> +</tool> |