# HG changeset patch
# User bernhardlutz
# Date 1396522250 14400
# Node ID 1ad35668671798d92e0c2210e2b4fc0e609d31fb
# Parent  54358dfa62c0d7c8af2f0a57555fd34d02685162
Deleted selected files

diff -r 54358dfa62c0 -r 1ad356686717 readfile.py
--- a/readfile.py	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-#!/usr/bin/env python
-
-import io
-import urllib2, urllib, httplib
-def getListFromFile(file):
-    idlist=[]
-    for line in file:
-        if int(line):
-            idlist.append(line.strip())
-    return idlist
-
-def getresult(url):
-    try:
-        connection = urllib2.urlopen(url)
-    except urllib2.HTTPError, e:
-        return ""
-    else:
-        return connection.read().rstrip()
-        
diff -r 54358dfa62c0 -r 1ad356686717 readfile.pyc
Binary file readfile.pyc has changed
diff -r 54358dfa62c0 -r 1ad356686717 rest_tool.py
--- a/rest_tool.py	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-#!/usr/bin/env python
-# Aufruf convert_graph.py --type type --operation op --id id --outfile outfile
-
-import sys, os
-import argparse
-
-import readfile
-
-txt_output=["cids", "summary", "synonyms" ]
-
-def main(args):
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
-    if args.type == "assay":
-        url+="aid/"
-    elif args.type == "compound":
-        url+="cid/"
-    elif args.type == "substance":
-        url+="sid/"
-    if args.idfile is None:
-        idstring=str(args.id)
-    else:
-        idlist=readfile.getListFromFile(args.idfile)
-        idstring=",".join(idlist)
-    url+=idstring+"/"+args.operation+"/"
-    if args.operation in txt_output:
-        url+="txt"
-    else:
-        url+="csv"
-    print(url)
-    data=readfile.getresult(url)
-    outfile=args.outfile
-    outfile.write(data)
-    outfile.close()
-    
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--type', type=str,
-        help="That you want BioAssay Compund ...")
-    parser.add_argument('--id', type=str,
-        help="Specify the ID")
-    parser.add_argument('--operation', type=str,
-        help="Specify the operation")
-    parser.add_argument('--property-value', type=str,
-        help="Specify the property")
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify one output file")
-    parser.add_argument('--idfile', type=argparse.FileType('r'),
-        help="Specify a file with a list of ids, one per line")
-    if len(sys.argv) < 8:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )
diff -r 54358dfa62c0 -r 1ad356686717 rest_tool.xml
--- a/rest_tool.xml	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-<tool id="rest_tool" name="Fetch Data from pubchem" version="0.1.0">
-    <description>Fetch pubchem data</description>
-    <version_command>echo "0.1.0"</version_command>
-    <requirements>
-        <requirement type="set_environment">REST_TOOL_SCRIPT_PATH</requirement>
-    </requirements>
-    <command interpreter="python">
-        #if $choose_action.action == 'specific_data':
-        rest_tool.py
-            #if $choose_action.field_or_file1.field_or_file1 == 'field':
-            --id $choose_action.field_or_file1.id1 
-            #else:
-            --idfile $choose_action.field_or_file1.file_ids_1
-            #end if
-            --type $choose_action.input_type 
-            
-            --operation $choose_action.operation_property.operation
-            #if $choose_action.operation_property.operation == 'property':
-                --property-value $choose_action.operation_property.property
-            #end if
-            
-            --outfile $output
-        #elif $choose_action.action == 'compounds_for_assay':
-            rest_tool_comp_for_assay.py
-            #if $choose_action.field_or_file2.field_or_file2 == 'field':
-            --aid $choose_action.field_or_file2.id2 
-            #else:
-            --aidfile $choose_action.field_or_file2.file_ids_2
-            #end if
-            --outfile $output
-        #elif $choose_action.action == 'assays_by_activity':
-            rest_tool_assay_by_activity_or_target.py --activity $choose_action.activity --outfile $output
-        #elif $choose_action.action == 'assays_by_targets':
-            rest_tool_assay_by_activity_or_target.py --targettype $choose_action.target_identifier_type --targetid $choose_action.target_id --outfile $output
-        #end if
-    </command>
-
-    <inputs>
-        <conditional name="choose_action">
-            <param name="action" multiple="false" type="select" label="Choose action">
-                <option value="specific_data">Get Data for specific Assay/Compound/Substance</option>
-                <option value="compounds_for_assay">Get all compound IDs to given BioAssays</option>
-                <option value="all_assay_with_compounds">Get all BioAssay IDs with Compound IDs</option>
-                <option value="assays_by_activity">Get BioAssays for activity</option>
-                <option value="assays_by_targets">Get BioAssays for targets</option>
-            </param>
-            <when value="specific_data">
-                <param name="input_type" multiple="false" type="select" label="Input Type">
-                    <option value="assay">BioAssay</option>
-                    <option value="compound">Compound</option>
-                    <option value="substance">Substance</option>
-                </param>
-                <conditional name="field_or_file1">
-                    <param name="field_or_file1" multiple="false" type="select" label="Specify the ID by">
-                        <option value="field">Textfield</option>
-                        <option value="file">File</option>
-                    </param>
-                    <when value="field">
-                        <param format="txt" name="id1" type="text" label="Enter the ID(s)" />
-                    </when>
-                    <when value="file">
-                        <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" />
-                    </when>
-                </conditional>
-                
-                <conditional name="operation_property">
-                    <param name="operation" type="select" multiple="false" label="Operation">
-                    <option value="synonyms">Synonyms</option>
-                    <option value="cids">CIDs</option>
-                    <option value="property">Property</option>
-                    <option value="xrefs">XRefs</option>
-                    <option value="description">Discription</option>
-                    <option value="summary">Summary</option>
-                    </param>
-                    <when value="property">
-                        <param name="property" label="Specify Property" type="text" />
-                    </when>
-                </conditional>
-
-            </when>
-            <when value="compounds_for_assay">
-                <conditional name="field_or_file2">
-                    <param name="field_or_file2" multiple="false" type="select" label="Specify the ID by">
-                        <option value="field">Textfield</option>
-                        <option value="file">File</option>
-                    </param>
-                    <when value="field">
-                        <param format="txt" name="id2" type="text" label="Enter the ID(s)" />
-                    </when>
-                    <when value="file">
-                        <param format="txt,csv" name="file_ids_2" type="data" label="Give the file" />
-                    </when>
-                </conditional>
-            </when>
-            <when value="assays_by_activity">
-                <param format="txt" name="activity" type="text" label="Enter the activity " />
-            </when>
-            <when value="assays_by_targets">
-                <param name="target_identifier_type" multiple="false" type="select" label="Choose target identifier">
-                    <option value="gi">GI</option>
-                    <option value="geneid">Gene ID</option>
-                    <option value="genesymbol">Gene Symbol</option>
-                </param>
-                <param format="txt" name="target_id" type="text" label="Enter the target" />
-            </when>
-            
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="csv" name="output" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-**What it does**
-
-This tool fetches data from pubchem
-    </help>
-</tool>
diff -r 54358dfa62c0 -r 1ad356686717 rest_tool_assay_by_activity_or_target.py
--- a/rest_tool_assay_by_activity_or_target.py	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-#!/usr/bin/env python
-# Aufruf convert_graph.py --aid list of ids --aid-from-file file
-
-import sys, os
-import argparse
-
-
-import readfile
-
-def main(args):
-    #search for acitivity or target
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/"
-    if args.activity is None:
-        #target
-        url+="target/"+args.targettype+"/"+args.targetid
-    else:
-        url+="activity/"+args.activity
-    url+="/aids/txt"
-    data=readfile.getresult(url)
-    args.outfile.write(data)
-    args.outfile.close()
-    
-    
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--activity', type=str,
-        help="Activities you are looking for")
-    parser.add_argument('--targettype', type=str,
-        help="The target identifier type")
-    parser.add_argument('--targetid', type=str,
-        help="The specific target")
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify output file")
-    if len(sys.argv) < 2:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )
diff -r 54358dfa62c0 -r 1ad356686717 rest_tool_comp_for_assay.py
--- a/rest_tool_comp_for_assay.py	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-#!/usr/bin/env python
-# Aufruf convert_graph.py --aid list of ids --aid-from-file file
-
-import sys, os
-import networkx as nx
-import argparse
-import urllib2, urllib, httplib
-
-import readfile
-#supported graph_types
-#output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
-
-        
-#get the cids for bioassay aid
-def getCompoundList(aidlist):
-    aidliststring=",".join(aidlist)
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/txt"
-    data=readfile.getresult(url)
-    return data
-        
-def main(args):
-    if args.aidfile is None:
-        aidlist=args.aid.split(",")
-    else:
-        aidlist=readfile.getListFromFile(args.aidfile)
-    cids=getCompoundList(aidlist)
-    args.outfile.write(cids)
-    args.outfile.close()
-    
-    
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--aid', type=str,
-        help="AIDs of the BioAssay")
-    parser.add_argument('--aidfile', type=argparse.FileType('r'),
-        help="Specify a file with a list of aids, one per line")
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify output file")
-    if len(sys.argv) < 2:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )
diff -r 54358dfa62c0 -r 1ad356686717 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 28 13:41:22 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="REST_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-</tool_dependency>