<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>BioSQL.BioSeqDatabase.DBServer</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.BioSeqDatabase-module.html">Module BioSeqDatabase</a> ::
Class DBServer
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="BioSQL.BioSeqDatabase.DBServer-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DBServer</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer">source code</a></span></p>
<p>Represents a BioSQL database continaing namespaces
(sub-databases).</p>
<p>This acts like a Python dictionary, giving access to each namespace
(defined by a row in the biodatabase table) as a BioSeqDatabase
object.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">conn</span>,
<span class="summary-sig-arg">module</span>,
<span class="summary-sig-arg">module_name</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__repr__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__getitem__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Number of namespaces (sub-databases) in this database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__len__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__contains__"></a><span class="summary-sig-name">__contains__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span><br />
Check if a namespace (sub-database) in this database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__contains__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__iter__"></a><span class="summary-sig-name">__iter__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over namespaces (sub-databases) in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__iter__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="iterkeys"></a><span class="summary-sig-name">iterkeys</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over namespaces (sub-databases) in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.iterkeys">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="itervalues"></a><span class="summary-sig-name">itervalues</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over BioSeqDatabase objects in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.itervalues">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="iteritems"></a><span class="summary-sig-name">iteritems</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over (namespace, BioSeqDatabase) in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.iteritems">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="keys"></a><span class="summary-sig-name">keys</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of namespaces (sub-databases) in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.keys">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="values"></a><span class="summary-sig-name">values</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of BioSeqDatabase objects in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.values">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="items"></a><span class="summary-sig-name">items</span>(<span class="summary-sig-arg">self</span>)</span><br />
List of (namespace, BioSeqDatabase) for entries in the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.items">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__delitem__"></a><span class="summary-sig-name">__delitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span><br />
Remove a namespace and all its entries.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.__delitem__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.DBServer-class.html#remove_database" class="summary-sig-name">remove_database</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">db_name</span>)</span><br />
Remove a namespace and all its entries (OBSOLETE).</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.remove_database">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="new_database"></a><span class="summary-sig-name">new_database</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">db_name</span>,
<span class="summary-sig-arg">authority</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">description</span>=<span class="summary-sig-default">None</span>)</span><br />
Add a new database to the server and return it.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.new_database">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.DBServer-class.html#load_database_sql" class="summary-sig-name">load_database_sql</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql_file</span>)</span><br />
Load a database schema into the given database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.load_database_sql">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="commit"></a><span class="summary-sig-name">commit</span>(<span class="summary-sig-arg">self</span>)</span><br />
Commits the current transaction to the database.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.commit">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="rollback"></a><span class="summary-sig-name">rollback</span>(<span class="summary-sig-arg">self</span>)</span><br />
Rolls backs the current transaction.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.rollback">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.DBServer-class.html#close" class="summary-sig-name">close</a>(<span class="summary-sig-arg">self</span>)</span><br />
Close the connection.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.close">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="remove_database"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">remove_database</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">db_name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.remove_database">source code</a></span>
</td>
</tr></table>
<p>Remove a namespace and all its entries (OBSOLETE).</p>
<p>Try to remove all references to items in a database.</p>
<p>server.remove_database(name)</p>
<p>In keeping with the dictionary interface, you can now do this:</p>
<p>del server[name]</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="load_database_sql"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">load_database_sql</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sql_file</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.load_database_sql">source code</a></span>
</td>
</tr></table>
<p>Load a database schema into the given database.</p>
<p>This is used to create tables, etc when a database is first created.
sql_file should specify the complete path to a file containing SQL
entries for building the tables.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="close"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">close</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#DBServer.close">source code</a></span>
</td>
</tr></table>
<p>Close the connection. No further activity possible.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:17 2011
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
