| Previous changeset 2:a104cc98359c (2012-07-24) Next changeset 5:f798da48a30d (2013-07-22) |
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Commit message:
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added:
synapse_interface/._synapse_create.xml synapse_interface/._synapse_download.xml synapse_interface/._synapse_query.xml synapse_interface/synapse_create.xml synapse_interface/synapse_download.xml synapse_interface/synapse_query.xml |
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removed:
synapse_create.xml synapse_download.xml synapse_query.xml |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_create.xml --- a/synapse_create.xml Tue Jul 24 17:34:37 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,92 +0,0 @@ -<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="${outfile}"); - -""" - - -import tempfile -import os -import sys -import subprocess - -h, path = tempfile.mkstemp() -os.write(h,rcode) -os.close(h) - -proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE ) -(stdoutdata, stderrdata) = proc.communicate() -if proc.returncode: - sys.stderr.write(stderrdata) -sys.stdout.write(stdoutdata) -os.unlink(path) - -]]></configfile> - </configfiles> -</tool> |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_download.xml --- a/synapse_download.xml Tue Jul 24 17:34:37 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,74 +0,0 @@ -<tool id="synapse_download" name="Synapse Download" version="1.0"> - <description>Download Synapse Entity</description> - <command interpreter="python">$script_file -#if str( $user ) != '': - -u "$user" -#end if -#if str( $pass ) != '': - -p "$pass" -#end if --s $synid -$data_type --o $outfile - </command> - <inputs> - <param name="user" type="text" size="90" label="Username"/> - <param name="pass" type="text" size="90" label="Password"/> - <param name="synid" type="text" label="Synapse ID"/> - <param name="data_type" type="select" label="Data Type"> - <option value="-e">Affy Eset</option> - <option value="-a">Attachment</option> - </param> - </inputs> - <outputs> - <data format="txt" name="outfile" label="${synid}" /> - </outputs> - <configfiles> - <configfile name="script_file"><![CDATA[#!/usr/bin/env python -rcode = """ -library('getopt'); -library(affy) -require(synapseClient) - -opt = getopt(c( - 'user', 'u', 2, "character", - 'pass', 'p', 2, "character", - 'outfile', 'o', 2, "character", - 'synid', 's', 2, "character", - 'eset', 'e', 0, "logical", - 'attach', 'a', 0, "logical" -)); - -if ( !is.null(opt\$user) && !is.null(opt\$pass)) { - synapseLogin(username=user, password=pass) -} - -ent <- loadEntity(opt\$synid); - -if (!is.null(opt\$eset)) { - eset <- exprs(ent\$objects\$eset); - write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file=opt\$outfile) - write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE); -} -if (!is.null(opt\$attach)) { - fpath <- file.path(ent\$cacheDir, ent\$files[[1]]); - file.copy(fpath, opt\$outfile, overwrite=T); -} - -""" - -import tempfile -import os -import sys -import subprocess - -h, path = tempfile.mkstemp() -os.write(h,rcode) -os.close(h) - -print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT ) -os.unlink(path) - -]]></configfile> - </configfiles> -</tool> |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/._synapse_create.xml |
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| Binary file synapse_interface/._synapse_create.xml has changed |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/._synapse_download.xml |
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| Binary file synapse_interface/._synapse_download.xml has changed |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/._synapse_query.xml |
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| Binary file synapse_interface/._synapse_query.xml has changed |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/synapse_create.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_interface/synapse_create.xml Thu Oct 25 02:39:06 2012 -0400 |
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| @@ -0,0 +1,138 @@ +<tool id="synapse_create" name="Synapse Create" version="2.0.0"> + <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="select" size="90" label="Name"> + <option value="name">Name</option> + <option value="parentId">ParentID</option> + <option value="description">Description</option> + <option value="species">Species</option> + <option value="numSamples">Number of Samples</option> + <option value="disease">Disease</option> + <option value="tissueType">Tissue Type</option> + </param> + <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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + </repeat> + + </inputs> + <outputs> + <data format="txt" name="outfile" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode=""" +require(synapseClient) + +galaxyClean <- function(x) { +y = gsub("__gt__", ">", x); +y = gsub("__lt__", "<", y ); +y = gsub("__sq__", "'", y); +y = gsub("__dq__", "\\"",y); +y = gsub("__ob__", "[", y); +y = gsub("__cb__", "]", y); +y = gsub("__oc__", "{", y); +y = gsub("__cc__", "}", y); +y = gsub("__at__", "@", y); +y = gsub("__cn__", "\\n", y); +y = gsub("__cr__", "\\r", y); +y = gsub("__tc__", "\\t", y); +y = gsub("__pd__", "#", y); +y = gsub("__at__", "@", y); +return(y); +} + +if (nchar("$user") && nchar("$pass")) { + synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass")) +} + + +ent <- ${etype}( list(name=galaxyClean("${name}")) ) + +#for $a in $annotations: +annotValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}") +#end for + +#for a in $properties: +propertyValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}") +#end for + +ent <- createEntity(ent) + +#if $attachment != 'None' +#if $attachment_name == '': +ent <- addFile(ent, galaxyClean("${attachment}")) +#else +ent <- addFile(ent, galaxyClean("${attachment}"), galaxyClean("${attachment_name}")) +#end if +#end if + +ent <- storeEntity(ent) + +write(properties(ent)\$id, file=galaxyClean("${outfile}")); + +""" + + +import tempfile +import os +import sys +import subprocess + +h, path = tempfile.mkstemp() +os.write(h,rcode) +os.close(h) + +proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE ) +(stdoutdata, stderrdata) = proc.communicate() +if proc.returncode: + sys.stderr.write(stderrdata) +sys.stdout.write(stdoutdata) +os.unlink(path) + +]]></configfile> + </configfiles> + <help> + +Install R SynapseClient: + source('http://depot.sagebase.org/CRAN.R') + pkgInstall("synapseClient") + +`To setup auto login (so you don't have to type in your password) <https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login>`_ + + </help> + +</tool> \ No newline at end of file |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/synapse_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_interface/synapse_download.xml Thu Oct 25 02:39:06 2012 -0400 |
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| @@ -0,0 +1,92 @@ +<tool id="synapse_download" name="Synapse Download" version="2.0.0"> + <description>Download Synapse Entity</description> + <command interpreter="python">$script_file</command> + <inputs> + <param name="user" type="text" size="90" label="Username"/> + <param name="pass" type="text" size="90" label="Password"/> + <param name="synid" type="text" label="Synapse ID"/> + <param name="data_type" type="select" label="Data Type"> + <option value="e">Affy Eset</option> + <option value="a">Attachment</option> + </param> + </inputs> + <outputs> + <data format="txt" name="outfile" label="${synid}" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode = """ +library(affy) +require(synapseClient) + +galaxyClean <- function(x) { +y = gsub("__gt__", ">", x); +y = gsub("__lt__", "<", y ); +y = gsub("__sq__", "'", y); +y = gsub("__dq__", "\\"",y); +y = gsub("__ob__", "[", y); +y = gsub("__cb__", "]", y); +y = gsub("__oc__", "{", y); +y = gsub("__cc__", "}", y); +y = gsub("__at__", "@", y); +y = gsub("__cn__", "\\n", y); +y = gsub("__cr__", "\\r", y); +y = gsub("__tc__", "\\t", y); +y = gsub("__pd__", "#", y); +y = gsub("__at__", "@", y); +return(y); +} + +if (nchar("$user") && nchar("$pass")) { + synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass")) +} + + +cat("Loading...") +ent <- loadEntity("$synid"); +cat("Done\n") + +if ("e" == "$data_type") { + eset <- exprs(ent\$objects\$eset); + write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file="$outfile") + write.table(eset, "$outfile", col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE); +} +if ("a" == "$data_type") { + fpath <- file.path(ent\$cacheDir, ent\$files[[1]]); + file.copy(fpath, "$outfile", overwrite=T); +} + +""" + +import tempfile +import os +import sys +import subprocess + +h, path = tempfile.mkstemp() +os.write(h,rcode) +os.close(h) + +cmd_args = ["R", "CMD", "BATCH", path ] +proc = subprocess.Popen(cmd_args, stderr=subprocess.PIPE) +stdout, stderr = proc.communicate() +if proc.poll() != 0: + sys.stderr.write(stderr) +os.unlink(path) +]]></configfile> + </configfiles> + <help> + +This tool current supports two types of data from Synapse: Affy eset data and attachment files. +For Affy eset data, it will attempt to turn the eset into a table and write a tab separated file. For attachment files, it will +save the first attached file as the output. + +Install R SynapseClient:: + + source('http://depot.sagebase.org/CRAN.R') + pkgInstall("synapseClient") + +`To setup auto login (so you don't have to type in your password) <https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login>`_ + + </help> +</tool> \ No newline at end of file |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_interface/synapse_query.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synapse_interface/synapse_query.xml Thu Oct 25 02:39:06 2012 -0400 |
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| @@ -0,0 +1,94 @@ +<tool id="synapse_query" name="Synapse Query" version="1.0"> + <description>Query Synapse</description> + <command interpreter="python">$script_file</command> + <inputs> + <param name="user" type="text" size="90" label="Username"/> + <param name="pass" type="text" size="90" label="Password"/> + <param name="query" type="text" area="True" size="5x35" label="Query"/> + + <!-- + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + <mapping initial="none"> + <add source=""" target="'"/> + </mapping> + </sanitizer> + </param> + --> + </inputs> + <outputs> + <data format="tabular" name="outfile" /> + </outputs> + <configfiles> + <configfile name="script_file"><![CDATA[#!/usr/bin/env python +rcode=""" +library(affy) +require(synapseClient) + +galaxyClean <- function(x) { +y = gsub("__gt__", ">", x); +y = gsub("__lt__", "<", y ); +y = gsub("__sq__", "'", y); +y = gsub("__dq__", "\\"",y); +y = gsub("__ob__", "[", y); +y = gsub("__cb__", "]", y); +y = gsub("__oc__", "{", y); +y = gsub("__cc__", "}", y); +y = gsub("__at__", "@", y); +y = gsub("__cn__", "\\n", y); +y = gsub("__cr__", "\\r", y); +y = gsub("__tc__", "\\t", y); +y = gsub("__pd__", "#", y); +y = gsub("__at__", "@", y); +return(y); +} + +if (nchar("$user") && nchar("$pass")) { + synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass")) +} + + + +query <- galaxyClean("${query}"); +cat(query) + +query.out <- synapseQuery(query); +write.table(query.out, quote=F, file="$outfile", row.name=F, sep="\\t") + +""" +import tempfile +import os +import sys +import subprocess + +h, path = tempfile.mkstemp(dir="/tmp") +os.write(h,rcode) +os.close(h) + +proc = subprocess.Popen( ["Rscript", path], 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> + <help> + +Install R SynapseClient:: + + source('http://depot.sagebase.org/CRAN.R') + pkgInstall("synapseClient") + +`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>`_ + +Example Query: + +select * from entity where parentId=="syn300013" + + </help> + +</tool> \ No newline at end of file |
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| diff -r a104cc98359c -r 2925d82b84fc synapse_query.xml --- a/synapse_query.xml Tue Jul 24 17:34:37 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,72 +0,0 @@ -<tool id="synapse_query" name="Synapse Query" version="1.0"> - <description>Query Synapse</description> - <command interpreter="python">$script_file -#if str( $user ) != '': - -u "$user" -#end if - -#if str( $pass ) != '': - -p "$pass" -#end if --o $outfile - </command> - <inputs> - <param name="user" type="text" size="90" label="Username"/> - <param name="pass" type="text" size="90" label="Password"/> - <param name="query" type="text" area="True" size="5x35" label="Query"> - <sanitizer> - <valid initial="string.printable"> - <remove value="""/> - </valid> - <mapping initial="none"> - <add source=""" target="'"/> - </mapping> - </sanitizer> - </param> - </inputs> - <outputs> - <data format="txt" name="outfile" /> - </outputs> - <configfiles> - <configfile name="script_file"><![CDATA[#!/usr/bin/env python -rcode=""" -library('getopt'); -library(affy) -require(synapseClient) - -opt = getopt(c( - 'user', 'u', 2, "character", - 'pass', 'p', 2, "character", - 'outfile', 'o', 2, "character" -)); - -query <- "${query}"; -cat(query) -if ( !is.null(opt\$user) && !is.null(opt\$pass)) { - synapseLogin(username=user, password=pass) -} - -query.out <- synapseQuery(query); -write.table(query.out, quote=F, file=opt\$outfile, row.name=F, sep="\\t") - -""" -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> |