comparison synapse_download.xml @ 3:93c4d2fad9af

Fixing bugs and bad code

2:a104cc98359c

<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

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>

3:93c4d2fad9af

<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

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) &lt;https://sagebionetworks.jira.com/wiki/display/SYNR/How+to+configure+automatic+login&gt;`_ 

	</help>
</tool>