# HG changeset patch
# User bernhardlutz
# Date 1395684006 14400
# Node ID d3f9c70919dc297c242ae4a8df2689d9906d1264
# Parent 954a489c1606e32c8b54d960f395e32cbc0e6d6f
Uploaded
diff -r 954a489c1606 -r d3f9c70919dc rest_tool.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.py Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,53 @@
+#!/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 )
diff -r 954a489c1606 -r d3f9c70919dc rest_tool.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.xml Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,85 @@
+
+ Fetch pubchem data
+ echo "0.1.0"
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+ REST_TOOL_SCRIPT_PATH
+
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+ #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
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+**What it does**
+
+This tool fetches data from pubchem
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diff -r 954a489c1606 -r d3f9c70919dc rest_tool_comp_for_assay.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,59 @@
+#!/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 )
diff -r 954a489c1606 -r d3f9c70919dc tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,5 @@
+
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+ $REPOSITORY_INSTALL_DIR
+
+