# HG changeset patch
# User bernhardlutz
# Date 1396028482 14400
# Node ID 54358dfa62c0d7c8af2f0a57555fd34d02685162
# Parent 0bbb107a2cf2e3b35869d3b1e8e679cc6e5a1e27
Uploaded
diff -r 0bbb107a2cf2 -r 54358dfa62c0 readfile.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readfile.py Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,19 @@
+#!/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 0bbb107a2cf2 -r 54358dfa62c0 readfile.pyc
Binary file readfile.pyc has changed
diff -r 0bbb107a2cf2 -r 54358dfa62c0 rest_tool.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.py Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,54 @@
+#!/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 0bbb107a2cf2 -r 54358dfa62c0 rest_tool.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.xml Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,119 @@
+
+ Fetch pubchem data
+ echo "0.1.0"
+
+ REST_TOOL_SCRIPT_PATH
+
+
+ #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
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+**What it does**
+
+This tool fetches data from pubchem
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diff -r 0bbb107a2cf2 -r 54358dfa62c0 rest_tool_assay_by_activity_or_target.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_assay_by_activity_or_target.py Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,39 @@
+#!/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 0bbb107a2cf2 -r 54358dfa62c0 rest_tool_comp_for_assay.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,44 @@
+#!/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 0bbb107a2cf2 -r 54358dfa62c0 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,5 @@
+
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+ $REPOSITORY_INSTALL_DIR
+
+