Mercurial > repos > kellrott > nosql_interface
comparison mongo_client.xml @ 1:bda961c955d5 draft
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| author | kellrott |
|---|---|
| date | Tue, 24 Jul 2012 17:40:44 -0400 |
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| 0:907b95ba9cf7 | 1:bda961c955d5 |
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| 1 <tool id="mongo_client" name="Mongo Client" version="1.0.0"> | |
| 2 <description>Mongo Client</description> | |
| 3 <command interpreter="python">$scriptfile</command> | |
| 4 <inputs> | |
| 5 <param name="server" type="text" size="52" label="Server address"/> | |
| 6 <param name="port" type="integer" label="Server Port" value="27017"/> | |
| 7 <param name="db" type="text" size="32" label="Database"/> | |
| 8 <param name="collection" type="text" size="32" label="Collection"/> | |
| 9 <param name="query" type="text" area="True" size="5x25" label="Query"> | |
| 10 <sanitizer> | |
| 11 <valid initial="string.printable"/> | |
| 12 <mapping initial="none"> | |
| 13 <add source=" " target="__cn__"/> | |
| 14 <add source=""" target="__dq__"/> | |
| 15 </mapping> | |
| 16 </sanitizer> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="output" format="txt"/> | |
| 21 </outputs> | |
| 22 <configfiles> | |
| 23 | |
| 24 <configfile name="scriptfile"><![CDATA[#!/usr/bin/env python | |
| 25 import pymongo | |
| 26 import json | |
| 27 import galaxy.eggs | |
| 28 import galaxy.util | |
| 29 | |
| 30 query=galaxy.util.restore_text("""$query""") | |
| 31 | |
| 32 conn = pymongo.Connection(galaxy.util.restore_text("$server"), $port) | |
| 33 db = conn[galaxy.util.restore_text('$db')] | |
| 34 collection = db[galaxy.util.restore_text('$collection')] | |
| 35 | |
| 36 qObj = None | |
| 37 if len(query): | |
| 38 qObj = json.loads(query) | |
| 39 | |
| 40 handle = open(galaxy.util.restore_text("$output"), "w") | |
| 41 for row in collection.find(qObj): | |
| 42 handle.write("%s\n" % (json.dumps(row))) | |
| 43 handle.close() | |
| 44 | |
| 45 ]]></configfile> | |
| 46 </configfiles> | |
| 47 <help> | |
| 48 | |
| 49 Info about the Mongo Query Syntax: | |
| 50 - `Mongo Query Language <http://www.mongodb.org/display/DOCS/Mongo+Query+Language>`_ | |
| 51 - `Advanced Queries <http://www.mongodb.org/display/DOCS/Advanced+Queries>`_ | |
| 52 | |
| 53 </help> | |
| 54 </tool> |