# HG changeset patch
# User bernhardlutz
# Date 1396028473 14400
# Node ID 0bbb107a2cf2e3b35869d3b1e8e679cc6e5a1e27
# Parent d3f9c70919dc297c242ae4a8df2689d9906d1264
Deleted selected files
diff -r d3f9c70919dc -r 0bbb107a2cf2 rest_tool.py
--- 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 )
diff -r d3f9c70919dc -r 0bbb107a2cf2 rest_tool.xml
--- 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 @@
-
- Fetch pubchem data
- echo "0.1.0"
-
- 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 d3f9c70919dc -r 0bbb107a2cf2 rest_tool_comp_for_assay.py
--- 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 )
diff -r d3f9c70919dc -r 0bbb107a2cf2 tool_dependencies.xml
--- 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 @@
-
-
- $REPOSITORY_INSTALL_DIR
-
-