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