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<a href="BioSQL-module.html">Package BioSQL</a> ::
Module DBUtils
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<h1 class="epydoc">Source Code for <a href="BioSQL.DBUtils-module.html">Module BioSQL.DBUtils</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Andrew Dalke. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Revisions 2007-2008 by Peter Cock.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Note that BioSQL (including the database schema and scripts) is</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># available and licensed separately. Please consult www.biosql.org</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable BioSQL.DBUtils._dbutils=BioSQL.DBUtils-module.html#_dbutils"><a title="BioSQL.DBUtils._dbutils" class="py-name" href="#" onclick="return doclink('link-0', '_dbutils', 'link-0');">_dbutils</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="Generic_dbutils"></a><div id="Generic_dbutils-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="Generic_dbutils-toggle" onclick="return toggle('Generic_dbutils');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.DBUtils.Generic_dbutils-class.html">Generic_dbutils</a><tt class="py-op">:</tt> </tt>
</div><div id="Generic_dbutils-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Generic_dbutils-expanded"><a name="Generic_dbutils.__init__"></a><div id="Generic_dbutils.__init__-def"><a name="L13"></a><tt class="py-lineno"> 13</tt> <a class="py-toggle" href="#" id="Generic_dbutils.__init__-toggle" onclick="return toggle('Generic_dbutils.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Generic_dbutils-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Generic_dbutils.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Generic_dbutils.__init__-expanded"><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="Generic_dbutils.tname"></a><div id="Generic_dbutils.tname-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="Generic_dbutils.tname-toggle" onclick="return toggle('Generic_dbutils.tname');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Generic_dbutils-class.html#tname">tname</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Generic_dbutils.tname-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Generic_dbutils.tname-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-1" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-1', 'table', 'link-1');">table</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">'biosequence'</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt id="link-2" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-2', 'table', 'link-1');">table</a></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-string">'bioentry'</tt> </tt>
</div><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"># Disabled: better safe than sorry</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## def next_id(self, cursor, table):</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # XXX brain-dead! Hopefully, the database will enforce PK unicity..</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## table = self.tname(table)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## sql = r"select 1+max(%s_id) from %s" % (table, table)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## cursor.execute(sql)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## rv = cursor.fetchone()</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return rv[0]</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Generic_dbutils.last_id"></a><div id="Generic_dbutils.last_id-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="Generic_dbutils.last_id-toggle" onclick="return toggle('Generic_dbutils.last_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Generic_dbutils-class.html#last_id">last_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Generic_dbutils.last_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Generic_dbutils.last_id-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-comment"># XXX: Unsafe without transactions isolation</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-3" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-3', 'table', 'link-1');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method BioSQL.DBUtils.Generic_dbutils.tname()=BioSQL.DBUtils.Generic_dbutils-class.html#tname"><a title="BioSQL.DBUtils.Generic_dbutils.tname" class="py-name" href="#" onclick="return doclink('link-4', 'tname', 'link-4');">tname</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-5', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select max(%s_id) from %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-6', 'table', 'link-1');">table</a></tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-7', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt id="link-8" class="py-name" targets="Method Bio.DocSQL.Query.cursor()=Bio.DocSQL.Query-class.html#cursor,Method Bio.DocSQL.QuerySingle.cursor()=Bio.DocSQL.QuerySingle-class.html#cursor"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-8', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-9', 'execute', 'link-9');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-10', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="Generic_dbutils.autocommit"></a><div id="Generic_dbutils.autocommit-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="Generic_dbutils.autocommit-toggle" onclick="return toggle('Generic_dbutils.autocommit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Generic_dbutils-class.html#autocommit">autocommit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">conn</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Generic_dbutils.autocommit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Generic_dbutils.autocommit-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-comment"># Let's hope it was not really needed</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="Mysql_dbutils"></a><div id="Mysql_dbutils-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="Mysql_dbutils-toggle" onclick="return toggle('Mysql_dbutils');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.DBUtils.Mysql_dbutils-class.html">Mysql_dbutils</a><tt class="py-op">(</tt><tt class="py-base-class">Generic_dbutils</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Mysql_dbutils-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Mysql_dbutils-expanded"><a name="Mysql_dbutils.last_id"></a><div id="Mysql_dbutils.last_id-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="Mysql_dbutils.last_id-toggle" onclick="return toggle('Mysql_dbutils.last_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Mysql_dbutils-class.html#last_id">last_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Mysql_dbutils.last_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Mysql_dbutils.last_id-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-comment">#This worked on older versions of MySQL</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-11" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-11', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">insert_id</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-comment">#See bug 2390</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Google suggests this is the new way,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#same fix also suggested by Eric Gibert:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-12" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-12', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">lastrowid</tt> </tt>
</div></div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt id="link-13" class="py-name"><a title="BioSQL.DBUtils._dbutils" class="py-name" href="#" onclick="return doclink('link-13', '_dbutils', 'link-0');">_dbutils</a></tt><tt class="py-op">[</tt><tt class="py-string">"MySQLdb"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Class BioSQL.DBUtils.Mysql_dbutils=BioSQL.DBUtils.Mysql_dbutils-class.html"><a title="BioSQL.DBUtils.Mysql_dbutils" class="py-name" href="#" onclick="return doclink('link-14', 'Mysql_dbutils', 'link-14');">Mysql_dbutils</a></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="Psycopg_dbutils"></a><div id="Psycopg_dbutils-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="Psycopg_dbutils-toggle" onclick="return toggle('Psycopg_dbutils');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.DBUtils.Psycopg_dbutils-class.html">Psycopg_dbutils</a><tt class="py-op">(</tt><tt class="py-base-class">Generic_dbutils</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Psycopg_dbutils-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Psycopg_dbutils-expanded"><a name="Psycopg_dbutils.next_id"></a><div id="Psycopg_dbutils.next_id-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="Psycopg_dbutils.next_id-toggle" onclick="return toggle('Psycopg_dbutils.next_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Psycopg_dbutils-class.html#next_id">next_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Psycopg_dbutils.next_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Psycopg_dbutils.next_id-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-15" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-15', 'table', 'link-1');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="BioSQL.DBUtils.Generic_dbutils.tname" class="py-name" href="#" onclick="return doclink('link-16', 'tname', 'link-4');">tname</a></tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-17', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select nextval('%s_pk_seq')"</tt> <tt class="py-op">%</tt> <tt id="link-18" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-18', 'table', 'link-1');">table</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-19', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-20', 'execute', 'link-9');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-21', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="Psycopg_dbutils.last_id"></a><div id="Psycopg_dbutils.last_id-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="Psycopg_dbutils.last_id-toggle" onclick="return toggle('Psycopg_dbutils.last_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Psycopg_dbutils-class.html#last_id">last_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Psycopg_dbutils.last_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Psycopg_dbutils.last_id-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-22', 'table', 'link-1');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="BioSQL.DBUtils.Generic_dbutils.tname" class="py-name" href="#" onclick="return doclink('link-23', 'tname', 'link-4');">tname</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-24', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select currval('%s_pk_seq')"</tt> <tt class="py-op">%</tt> <tt id="link-25" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-25', 'table', 'link-1');">table</a></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-26', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-27', 'execute', 'link-9');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-28', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="Psycopg_dbutils.autocommit"></a><div id="Psycopg_dbutils.autocommit-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="Psycopg_dbutils.autocommit-toggle" onclick="return toggle('Psycopg_dbutils.autocommit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Psycopg_dbutils-class.html#autocommit">autocommit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">conn</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-29', 'True', 'link-29');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Psycopg_dbutils.autocommit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Psycopg_dbutils.autocommit-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">conn</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.autocommit()=BioSQL.BioSeqDatabase.Adaptor-class.html#autocommit,Method BioSQL.DBUtils.Generic_dbutils.autocommit()=BioSQL.DBUtils.Generic_dbutils-class.html#autocommit,Method BioSQL.DBUtils.Pgdb_dbutils.autocommit()=BioSQL.DBUtils.Pgdb_dbutils-class.html#autocommit,Method BioSQL.DBUtils.Psycopg_dbutils.autocommit()=BioSQL.DBUtils.Psycopg_dbutils-class.html#autocommit"><a title="BioSQL.BioSeqDatabase.Adaptor.autocommit
BioSQL.DBUtils.Generic_dbutils.autocommit
BioSQL.DBUtils.Pgdb_dbutils.autocommit
BioSQL.DBUtils.Psycopg_dbutils.autocommit" class="py-name" href="#" onclick="return doclink('link-30', 'autocommit', 'link-30');">autocommit</a></tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt id="link-31" class="py-name"><a title="BioSQL.DBUtils._dbutils" class="py-name" href="#" onclick="return doclink('link-31', '_dbutils', 'link-0');">_dbutils</a></tt><tt class="py-op">[</tt><tt class="py-string">"psycopg"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name" targets="Class BioSQL.DBUtils.Psycopg_dbutils=BioSQL.DBUtils.Psycopg_dbutils-class.html"><a title="BioSQL.DBUtils.Psycopg_dbutils" class="py-name" href="#" onclick="return doclink('link-32', 'Psycopg_dbutils', 'link-32');">Psycopg_dbutils</a></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="Pgdb_dbutils"></a><div id="Pgdb_dbutils-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="Pgdb_dbutils-toggle" onclick="return toggle('Pgdb_dbutils');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.DBUtils.Pgdb_dbutils-class.html">Pgdb_dbutils</a><tt class="py-op">(</tt><tt class="py-base-class">Generic_dbutils</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pgdb_dbutils-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Pgdb_dbutils-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""Add support for pgdb in the PyGreSQL database connectivity package.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Pgdb_dbutils.next_id"></a><div id="Pgdb_dbutils.next_id-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="Pgdb_dbutils.next_id-toggle" onclick="return toggle('Pgdb_dbutils.next_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Pgdb_dbutils-class.html#next_id">next_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pgdb_dbutils.next_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pgdb_dbutils.next_id-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-33', 'table', 'link-1');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="BioSQL.DBUtils.Generic_dbutils.tname" class="py-name" href="#" onclick="return doclink('link-34', 'tname', 'link-4');">tname</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-35', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select nextval('%s_pk_seq')"</tt> <tt class="py-op">%</tt> <tt id="link-36" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-36', 'table', 'link-1');">table</a></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-37', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-38', 'execute', 'link-9');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-39', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="Pgdb_dbutils.last_id"></a><div id="Pgdb_dbutils.last_id-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="Pgdb_dbutils.last_id-toggle" onclick="return toggle('Pgdb_dbutils.last_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Pgdb_dbutils-class.html#last_id">last_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">cursor</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pgdb_dbutils.last_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pgdb_dbutils.last_id-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt id="link-40" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-40', 'table', 'link-1');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="BioSQL.DBUtils.Generic_dbutils.tname" class="py-name" href="#" onclick="return doclink('link-41', 'tname', 'link-4');">tname</a></tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-42', 'table', 'link-1');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"select currval('%s_pk_seq')"</tt> <tt class="py-op">%</tt> <tt id="link-43" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-43', 'table', 'link-1');">table</a></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-44', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-45', 'execute', 'link-9');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-46', 'cursor', 'link-8');">cursor</a></tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="Pgdb_dbutils.autocommit"></a><div id="Pgdb_dbutils.autocommit-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="Pgdb_dbutils.autocommit-toggle" onclick="return toggle('Pgdb_dbutils.autocommit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils.Pgdb_dbutils-class.html#autocommit">autocommit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">conn</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-47', 'True', 'link-29');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pgdb_dbutils.autocommit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pgdb_dbutils.autocommit-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"pgdb does not support this!"</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt id="link-48" class="py-name"><a title="BioSQL.DBUtils._dbutils" class="py-name" href="#" onclick="return doclink('link-48', '_dbutils', 'link-0');">_dbutils</a></tt><tt class="py-op">[</tt><tt class="py-string">"pgdb"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name" targets="Class BioSQL.DBUtils.Pgdb_dbutils=BioSQL.DBUtils.Pgdb_dbutils-class.html"><a title="BioSQL.DBUtils.Pgdb_dbutils" class="py-name" href="#" onclick="return doclink('link-49', 'Pgdb_dbutils', 'link-49');">Pgdb_dbutils</a></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="get_dbutils"></a><div id="get_dbutils-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="get_dbutils-toggle" onclick="return toggle('get_dbutils');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.DBUtils-module.html#get_dbutils">get_dbutils</a><tt class="py-op">(</tt><tt class="py-param">module_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="get_dbutils-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_dbutils-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-50" class="py-name"><a title="BioSQL.DBUtils._dbutils" class="py-name" href="#" onclick="return doclink('link-50', '_dbutils', 'link-0');">_dbutils</a></tt><tt class="py-op">[</tt><tt class="py-name">module_name</tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-51" class="py-name" targets="Class BioSQL.DBUtils.Generic_dbutils=BioSQL.DBUtils.Generic_dbutils-class.html"><a title="BioSQL.DBUtils.Generic_dbutils" class="py-name" href="#" onclick="return doclink('link-51', 'Generic_dbutils', 'link-51');">Generic_dbutils</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt><script type="text/javascript">
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