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2
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1 <tool id="synapse_query" name="Synapse Query" version="1.0">
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2 <description>Query Synapse</description>
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3
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3 <command interpreter="python">$script_file</command>
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2
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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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3
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7 <param name="query" type="text" area="True" size="5x35" label="Query"/>
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8
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9 <!--
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2
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10 <sanitizer>
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11 <valid initial="string.printable">
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12 <remove value="""/>
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13 </valid>
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14 <mapping initial="none">
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15 <add source=""" target="'"/>
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16 </mapping>
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17 </sanitizer>
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3
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18 </param>
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19 -->
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2
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20 </inputs>
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21 <outputs>
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3
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22 <data format="tabular" name="outfile" />
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2
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23 </outputs>
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24 <configfiles>
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25 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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26 rcode="""
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27 library(affy)
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28 require(synapseClient)
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29
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3
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30 galaxyClean <- function(x) {
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31 y = gsub("__gt__", ">", x);
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32 y = gsub("__lt__", "<", y );
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33 y = gsub("__sq__", "'", y);
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34 y = gsub("__dq__", "\\"",y);
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35 y = gsub("__ob__", "[", y);
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36 y = gsub("__cb__", "]", y);
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37 y = gsub("__oc__", "{", y);
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38 y = gsub("__cc__", "}", y);
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39 y = gsub("__at__", "@", y);
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40 y = gsub("__cn__", "\\n", y);
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41 y = gsub("__cr__", "\\r", y);
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42 y = gsub("__tc__", "\\t", y);
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43 y = gsub("__pd__", "#", y);
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44 y = gsub("__at__", "@", y);
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45 return(y);
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2
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46 }
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47
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3
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48 if (nchar("$user") && nchar("$pass")) {
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49 synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass"))
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50 }
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51
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52
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53
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54 query <- galaxyClean("${query}");
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55 cat(query)
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56
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2
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57 query.out <- synapseQuery(query);
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3
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58 write.table(query.out, quote=F, file="$outfile", row.name=F, sep="\\t")
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2
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59
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60 """
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61 import tempfile
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62 import os
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63 import sys
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64 import subprocess
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65
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66 h, path = tempfile.mkstemp(dir="/tmp")
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67 os.write(h,rcode)
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68 os.close(h)
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69
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70 proc = subprocess.Popen( ["Rscript", path], stderr=subprocess.PIPE, stdout=subprocess.PIPE )
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71 (stdoutdata, stderrdata) = proc.communicate()
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72 if proc.returncode:
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73 sys.stderr.write(stderrdata)
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74 sys.stdout.write(stdoutdata)
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75 os.unlink(path)
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76
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77 ]]></configfile>
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78 </configfiles>
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3
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79 <help>
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80
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81 Install R SynapseClient::
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82
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83 source('http://depot.sagebase.org/CRAN.R')
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84 pkgInstall("synapseClient")
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85
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86 `To setup auto login (so you don't have to type in your password) <https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login>`_
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87
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88 Example Query:
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89
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90 select * from entity where parentId=="syn300013"
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91
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92 </help>
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93
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94 </tool> |
