Mercurial > repos > bernhardlutz > rest_tool

--- a/rest_tool_alt.xml	Thu Apr 03 06:50:57 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +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 a/some Assay/Compound/Substance</option>
-                <option value="compounds_for_assay">Get all compound IDs to given BioAssay IDs</option>
-                <option value="assays_by_activity">Get BioAssay IDs with compound IDs given activity/target</option>
-            </param>
-            <when value="specific_data">
-                <conditional name="choose_acs">
-                    <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>
-                    <when value="assay">
-                    <conditional name="field_or_file1">
-                        <param name="field_or_file1" multiple="false" type="select" label="Specify the ID by">
-                            <option value="field" selected="True">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="assay">
-                            <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" />
-                        </when>
-                    </conditional>
-                    </when>
-                    <when value="assay">
-                        <conditional name="operation_property">
-                            <param name="operation" type="select" multiple="false" label="Operation">
-                                <option value="cids">CIDs</option>
-                                <option value="sids">SIDs</option>
-                                <option value="record">Record</option>
-                                <option value="classification">Classification</option>
-                                <option value="property">Property</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="compound">
-                        <conditional name="operation_property">
-                            <param name="operation" type="select" multiple="false" label="Operation">
-                                <option value="aids">AIDs</option>
-                                <option value="sids">SIDs</option>
-                                <option value="assaysummary">Assaysummary</option>
-                                <option value="synonyms">Synonyms</option>
-                                <option value="record">Record</option>
-                                <option value="classification">Classification</option>
-                                <option value="property">Property</option>
-                                <option value="description">Discription</option>
-                            </param>
-                            <when value="property">
-                                <param name="property" label="Specify Property" type="text" />
-                            </when>
-                        </conditional>
-                    </when>
-                    <when value="substance">
-                        <conditional name="operation_property">
-                            <param name="operation" type="select" multiple="false" label="Operation">
-                                <option value="cids">CIDs</option>
-                                <option value="sids">SIDs</option>
-                                <option value="assaysummary">Assaysummary</option>
-                                <option value="synonyms">Synonyms</option>
-                                <option value="record">Record</option>
-                                <option value="classification">Classification</option>
-                                <option value="property">Property</option>
-                                <option value="description">Discription</option>
-                            </param>
-                            <when value="property">
-                                <param name="property" label="Specify Property" type="text" />
-                            </when>
-                        </conditional>
-                    </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>
--- a/rest_tool_assays_with_cids_given_target.py	Thu Apr 03 06:50:57 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-#!/usr/bin/env python
-
-
-import sys, os
-import argparse
-import readfile
-
-#get every aid as a list
-#returns a dictionary with aid as key and as value the list of cids
-def getAllAssayIDs():
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/all/aids/TXT"
-    data=readfile.getresult(url)
-    aidlist=readfile.getListFromString(data)
-    return aidlist
-
-
-def getIDofLine(line):
-    arr=line.split(">")
-    if len(arr) > 1:
-        aid=arr[1].split("<")[0]
-        return aid
-    else:
-        return "-1"
-
-#get xml of all aids with cids for an activity
-def getAllCidsForAssayActivity(activity):
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/activity/"+activity+"/aids/txt?list_return=listkey"
-    listkey=readfile.getresult(url)
-#    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/listkey/"+listkey+"/cids/xml"
-    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/25425,12345/cids/xml"
-    print("url: "+url)
-    xml=readfile.getresult(url)
-
-    #init parser
-    handler = DictHandler()
-    parser = sax.make_parser()
-    parser.setContentHandler(handler)
-
-    tempfile=open("tempfile","w")
-    #handle the last line, there is sometimes some random output
-    lastline_arr=xml.split("\n")
-    #print(lastline_arr)
-
-    print("l: ")
-    print(len(lastline_arr))
-    lastline=lastline_arr[len(lastline_arr)-1]
-    print("lastline: "+lastline)
-    print("lastline-2: "+lastline_arr[len(lastline_arr)-2])
-    cidlastline=getIDofLine(lastline)
-    aidkey="-1"
-    if cidlastline != "-1":
-        i=len(lastline_arr)-2
-        #search for nex aid entry
-        while i >= 0 and "AID" not in lastline_arr[i]:
-            i-=1
-        if i >= 0:
-            aid=getIDofLine(lastline_arr[i])
-            if aid != "-1":
-                aidkey=aid
-    #remove the last line and put the array back together
-
-    lastline_arr_list=list(lastline_arr)
-    #lastline_arr_list.remove(lastline)
-    xml2="\n".join(lastline_arr_list)
-    tempfile.write(xml2)
-    #add the last tags
-    #tempfile.write("</Information></InformationList>")
-    tempfile.close()
-    parser.parse(open("tempfile","r"))
-    dic=handler.ergebnis
-
-    #add the last line
-    #if cidlastline != "-1":
-    #    dic[aidkey].append(cidlastline)
-    return dic
-
-
-def main(args):
-    aid_cid_dict=getAllCidsForAssayActivity(args.target)
-    write_to_csv(aid_cid_dict, args.outfile)
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify output file")
-    parser.add_argument('--target', type=str,
-        help="Specify output file")
-    if len(sys.argv) < 2:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )