Mercurial > repos > bernhardlutz > rest_tool

--- a/rest_tool.py	Mon Mar 24 14:00:06 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-#!/usr/bin/env python
-# Aufruf convert_graph.py --type type --operation op --id id --outformat format --outfile outfile
-
-import sys, os
-import networkx as nx
-import argparse
-import urllib2
-
-#supported graph_types
-output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
-
-
-def getresult(url):
-    try:
-        connection = urllib2.urlopen(url)
-    except urllib2.HTTPError, e:
-        return ""
-    else:
-        return connection.read().rstrip()
-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/"
-    url+=args.id+"/"+args.operation+"/"+args.outformat
-    print(url)
-    print(args.type)
-    data=getresult(url)
-    file=args.outfile
-    file.write(data)
-    file.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('--outformat', type=str,
-        help="Specify the format of the output", choices = output_types)
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify one output file")
-    if len(sys.argv) < 8:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )
--- a/rest_tool.xml	Mon Mar 24 14:00:06 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +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
-            --id $choose_action.id
-            --type $choose_action.input_type
-            --outformat $choose_action.output_format
-
-            --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 --aid $choose_action.aid --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 BioAssay IDs with Compound IDs</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>
-                <param format="txt" name="id" type="text" label="Specify the ID" />
-                <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>
-                <param name="output_format" type="select" label="Output Format">
-                <option value="tsv">tsv</option>
-                <option value="csv">csv</option>
-                <option value="txt">txt</option>
-                <option value="png">png</option>
-                <option value="json">json</option>
-                <option value="xml">xml</option>
-                </param>
-            </when>
-            <when value="compounds_for_assay">
-                <param format="txt" name="aid" type="text" label="Specify the ID of BioAssay" />
-            </when>
-
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="csv" name="output">
-            <change_format>
-                <when input="output_format" value="tsv" format="tsv" />
-                <when input="output_format" value="png" format="png" />
-                <when input="output_format" value="csv" format="csv" />
-                <when input="output_format" value="txt" format="txt" />
-                <when input="output_format" value="json" format="json" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-**What it does**
-
-This tool fetches data from pubchem
-    </help>
-</tool>
--- a/rest_tool_comp_for_assay.py	Mon Mar 24 14:00:06 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +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
-
-#supported graph_types
-#output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
-
-
-def getresult(url):
-    try:
-        connection = urllib2.urlopen(url)
-    except urllib2.HTTPError, e:
-        return ""
-    else:
-        return connection.read().rstrip()
-
-
-def getresultPost(url, aidList):
-    values={'aids': ",".join(aidList)}
-    data=urllib.urlencode(values)
-    print(data)
-
-    headers = {"Content-type": "application/x-www-form-urlencoded"}
-    conn = httplib.HTTPConnection("pubchem.ncbi.nlm.nih.gov")
-    conn.request("POST", "/rest/pug/assay/aid/aids/csv", data, headers)
-    response = conn.getresponse()
-    conn.close()
-    return response.read()
-
-
-
-#get the cids for bioassay aid
-def getCompoundList(aid):
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aid+"/cids/txt"
-    data=getresult(url)
-    return data
-
-def main(args):
-    cids=getCompoundList(args.aid)
-    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('--aid-from-file', 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 )
--- a/tool_dependencies.xml	Mon Mar 24 14:00:06 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>