Mercurial > repos > kellrott > nosql_interface
changeset 1:bda961c955d5 draft
Uploaded
| author | kellrott |
|---|---|
| date | Tue, 24 Jul 2012 17:40:44 -0400 |
| parents | 907b95ba9cf7 |
| children | 1fce03693725 |
| files | mongo_client.xml |
| diffstat | 1 files changed, 54 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mongo_client.xml Tue Jul 24 17:40:44 2012 -0400 @@ -0,0 +1,54 @@ +<tool id="mongo_client" name="Mongo Client" version="1.0.0"> + <description>Mongo Client</description> + <command interpreter="python">$scriptfile</command> + <inputs> + <param name="server" type="text" size="52" label="Server address"/> + <param name="port" type="integer" label="Server Port" value="27017"/> + <param name="db" type="text" size="32" label="Database"/> + <param name="collection" type="text" size="32" label="Collection"/> + <param name="query" type="text" area="True" size="5x25" label="Query"> + <sanitizer> + <valid initial="string.printable"/> + <mapping initial="none"> + <add source=" " target="__cn__"/> + <add source=""" target="__dq__"/> + </mapping> + </sanitizer> + </param> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <configfiles> + + <configfile name="scriptfile"><![CDATA[#!/usr/bin/env python +import pymongo +import json +import galaxy.eggs +import galaxy.util + +query=galaxy.util.restore_text("""$query""") + +conn = pymongo.Connection(galaxy.util.restore_text("$server"), $port) +db = conn[galaxy.util.restore_text('$db')] +collection = db[galaxy.util.restore_text('$collection')] + +qObj = None +if len(query): + qObj = json.loads(query) + +handle = open(galaxy.util.restore_text("$output"), "w") +for row in collection.find(qObj): + handle.write("%s\n" % (json.dumps(row))) +handle.close() + +]]></configfile> + </configfiles> +<help> + +Info about the Mongo Query Syntax: + - `Mongo Query Language <http://www.mongodb.org/display/DOCS/Mongo+Query+Language>`_ + - `Advanced Queries <http://www.mongodb.org/display/DOCS/Advanced+Queries>`_ + +</help> +</tool>