| Previous changeset 2:a104cc98359c (2012-07-24) Next changeset 7:353be5809eeb (2014-01-27) |
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Commit message:
Fixing bugs and bad code |
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modified:
synapse_create.xml synapse_download.xml synapse_query.xml |
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| diff -r a104cc98359c -r 93c4d2fad9af synapse_create.xml --- a/synapse_create.xml Tue Jul 24 17:34:37 2012 -0400 +++ b/synapse_create.xml Wed Oct 24 23:31:13 2012 -0700 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="synapse_create" name="Synapse Create" version="1.0"> +<tool id="synapse_create" name="Synapse Create" version="2.0.0"> <description>Create Synapse</description> <command interpreter="python">$script_file</command> <inputs> @@ -13,6 +13,28 @@ <option value="Data">Data</option> </param> <repeat name="properties" title="Properties"> + <param name="name" type="select" size="90" label="Name"> + <option value="name">Name</option> + <option value="parentId">ParentID</option> + <option value="description">Description</option> + <option value="species">Species</option> + <option value="numSamples">Number of Samples</option> + <option value="disease">Disease</option> + <option value="tissueType">Tissue Type</option> + </param> + <param name="value" type="text" size="90" label="Value"> + <sanitizer> + <valid initial="string.printable"> + <remove value="""/> + </valid> + <mapping initial="none"> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </param> + </repeat> + + <repeat name="annotations" title="Annotations"> <param name="name" type="text" size="90" label="Name"/> <param name="value" type="text" size="90" label="Value"> <sanitizer> @@ -26,11 +48,6 @@ </param> </repeat> - <repeat name="annotations" title="Annotations"> - <param name="name" type="text" size="90" label="Name"/> - <param name="value" type="text" size="90" label="Value"/> - </repeat> - </inputs> <outputs> <data format="txt" name="outfile" /> @@ -40,33 +57,52 @@ rcode=""" require(synapseClient) -if (nchar("$user") > 0 && nchar("$pass") > 0) { - synapseLogin(username="$user", password="$pass") +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); } -ent <- ${etype}( list(name="${name}") ) +if (nchar("$user") && nchar("$pass")) { + synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass")) +} + + +ent <- ${etype}( list(name=galaxyClean("${name}")) ) #for $a in $annotations: -annotValue(ent, "${a.name}") <- "${a.value}" +annotValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}") #end for #for a in $properties: -propertyValue(ent, "${a.name}") <- "${a.value}" +propertyValue(ent, galaxyClean("${a.name}")) <- galaxyClean("${a.value}") #end for ent <- createEntity(ent) #if $attachment != 'None' #if $attachment_name == '': -ent <- addFile(ent, "${attachment}") +ent <- addFile(ent, galaxyClean("${attachment}")) #else -ent <- addFile(ent, "${attachment}", "${attachment_name}") +ent <- addFile(ent, galaxyClean("${attachment}"), galaxyClean("${attachment_name}")) #end if #end if ent <- storeEntity(ent) -write(properties(ent)\$id, file="${outfile}"); +write(properties(ent)\$id, file=galaxyClean("${outfile}")); """ @@ -89,4 +125,14 @@ ]]></configfile> </configfiles> -</tool> + <help> + +Install R SynapseClient: + source('http://depot.sagebase.org/CRAN.R') + pkgInstall("synapseClient") + +`To setup auto login (so you don't have to type in your password) <https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login>`_ + + </help> + +</tool> \ No newline at end of file |
| b |
| diff -r a104cc98359c -r 93c4d2fad9af synapse_download.xml --- a/synapse_download.xml Tue Jul 24 17:34:37 2012 -0400 +++ b/synapse_download.xml Wed Oct 24 23:31:13 2012 -0700 |
| [ |
| @@ -1,23 +1,13 @@ -<tool id="synapse_download" name="Synapse Download" version="1.0"> +<tool id="synapse_download" name="Synapse Download" version="2.0.0"> <description>Download Synapse Entity</description> - <command interpreter="python">$script_file -#if str( $user ) != '': - -u "$user" -#end if -#if str( $pass ) != '': - -p "$pass" -#end if --s $synid -$data_type --o $outfile - </command> + <command interpreter="python">$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> + <option value="e">Affy Eset</option> + <option value="a">Attachment</option> </param> </inputs> <outputs> @@ -26,33 +16,44 @@ <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) +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); } -ent <- loadEntity(opt\$synid); +if (nchar("$user") && nchar("$pass")) { + synapseLogin(username=galaxyClean("$user"), password=galaxyClean("$pass")) +} + -if (!is.null(opt\$eset)) { +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=opt\$outfile) - write.table(eset, opt\$outfile, col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE); + write(paste(c("PROBE", colnames(eset)), collapse="\\t"), file="$outfile") + write.table(eset, "$outfile", col.names=FALSE, sep="\\t", quote=FALSE, append=TRUE); } -if (!is.null(opt\$attach)) { +if ("a" == "$data_type") { fpath <- file.path(ent\$cacheDir, ent\$files[[1]]); - file.copy(fpath, opt\$outfile, overwrite=T); + file.copy(fpath, "$outfile", overwrite=T); } """ @@ -66,9 +67,26 @@ os.write(h,rcode) os.close(h) -print subprocess.check_output( ["Rscript", path] + sys.argv[1:], stderr=subprocess.STDOUT ) +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> -</tool> + <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 93c4d2fad9af synapse_query.xml --- a/synapse_query.xml Tue Jul 24 17:34:37 2012 -0400 +++ b/synapse_query.xml Wed Oct 24 23:31:13 2012 -0700 |
| [ |
| @@ -1,19 +1,12 @@ <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 $outfile - </command> + <command interpreter="python">$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"> + <param name="query" type="text" area="True" size="5x35" label="Query"/> + + <!-- <sanitizer> <valid initial="string.printable"> <remove value="""/> @@ -22,32 +15,47 @@ <add source=""" target="'"/> </mapping> </sanitizer> - </param> + </param> + --> </inputs> <outputs> - <data format="txt" name="outfile" /> + <data format="tabular" 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 <- "${query}"; -cat(query) -if ( !is.null(opt\$user) && !is.null(opt\$pass)) { - synapseLogin(username=user, password=pass) +galaxyClean <- function(x) { +y = gsub("__gt__", ">", x); +y = gsub("__lt__", "<", y ); +y = gsub("__sq__", "'", y); +y = gsub("__dq__", "\\"",y); +y = gsub("__ob__", "[", y); +y = gsub("__cb__", "]", y); +y = gsub("__oc__", "{", y); +y = gsub("__cc__", "}", y); +y = gsub("__at__", "@", y); +y = gsub("__cn__", "\\n", y); +y = gsub("__cr__", "\\r", y); +y = gsub("__tc__", "\\t", y); +y = gsub("__pd__", "#", y); +y = gsub("__at__", "@", y); +return(y); } +if (nchar("$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=opt\$outfile, row.name=F, sep="\\t") +write.table(query.out, quote=F, file="$outfile", row.name=F, sep="\\t") """ import tempfile @@ -55,18 +63,32 @@ import sys import subprocess -h, path = tempfile.mkstemp() +h, path = tempfile.mkstemp(dir="/tmp") os.write(h,rcode) os.close(h) -proc = subprocess.Popen( ["Rscript", path] + sys.argv[1:], stderr=subprocess.PIPE, stdout=subprocess.PIPE ) +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> -</tool> + <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 |