Hi Galaxy-team,<div><br></div><div>I&#39;m running Galaxy on my local system, but recently get an coding error. The database I&#39;m using is postgresql, I also modified part of the code, hope that will not make things complex.<div>

<br></div><div>Looks like the tool generate a pdf file, and a geek of the file contains some binary code which is failed to store into the database.</div><div><br></div><div>Below is the error message. Appreciate for suggestions.</div>

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<p class="p1"></p><p class="p1">galaxy.jobs.runners.local ERROR 2012-10-30 10:47:28,855 Job wrapper finish method failed</p><p class="p1">Traceback (most recent call last):</p><p class="p1">  File &quot;/data/CistromeAP/lib/galaxy/jobs/runners/local.py&quot;, line 133, in run_job</p>

<p class="p1">    job_wrapper.finish( stdout, stderr )</p><p class="p1">  File &quot;/data/CistromeAP/lib/galaxy/jobs/__init__.py&quot;, line 454, in finish</p><p class="p1">    tool=self.tool, stdout=stdout, stderr=stderr )</p>

<p class="p1">  File &quot;/data/CistromeAP/lib/galaxy/tools/__init__.py&quot;, line 2207, in call_hook</p><p class="p1">    return code( *args, **kwargs )</p><p class="p1">  File &quot;./tools/expression/norm_code.py&quot;, line 103, in exec_after_process</p>

<p class="p1">    app.model.context.flush()</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py&quot;, line 127, in do</p><p class="p1">    return getattr(self.registry(), name)(*args, **kwargs)</p>

<p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py&quot;, line 1356, in flush</p><p class="p1">    self._flush(objects)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py&quot;, line 1434, in _flush</p>

<p class="p1">    flush_context.execute()</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 261, in execute</p><p class="p1">    UOWExecutor().execute(self, tasks)</p>

<p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 753, in execute</p><p class="p1">    self.execute_save_steps(trans, task)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 773, in execute_save_steps</p>

<p class="p1">    self.execute_cyclical_dependencies(trans, task, False)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 789, in execute_cyclical_dependencies</p>

<p class="p1">    self.execute(trans, [t], isdelete)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 753, in execute</p><p class="p1">    self.execute_save_steps(trans, task)</p>

<p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 768, in execute_save_steps</p><p class="p1">    self.save_objects(trans, task)</p><p class="p1">

  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py&quot;, line 759, in save_objects</p><p class="p1">    task.mapper._save_obj(task.polymorphic_tosave_objects, trans)</p>
<p class="p1">
  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py&quot;, line 1424, in _save_obj</p><p class="p1">    c = connection.execute(statement.values(value_params), params)</p><p class="p1">

  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py&quot;, line 824, in execute</p><p class="p1">    return Connection.executors[c](self, object, multiparams, params)</p><p class="p1">

  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py&quot;, line 874, in _execute_clauseelement</p><p class="p1">    return self.__execute_context(context)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py&quot;, line 896, in __execute_context</p>

<p class="p1">    self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py&quot;, line 952, in _cursor_execute</p>

<p class="p1">    self._handle_dbapi_exception(e, statement, parameters, cursor, context)</p><p class="p1">  File &quot;/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py&quot;, line 933, in _handle_dbapi_exception</p>

<p class="p1">    raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)</p><p class="p1">DataError: (&#39;E&#39;, &#39;r&#39;, &#39;r&#39;, &#39;o&#39;, &#39;r&#39;, &#39; &#39;, &#39;i&#39;, &#39;n&#39;, &#39; &#39;, &quot;&#39;&quot;, &#39;G&#39;, &#39;e&#39;, &#39;n&#39;, &#39;e&#39;, &#39; &#39;, &#39;e&#39;, &#39;x&#39;, &#39;p&#39;, &#39;r&#39;, &#39;e&#39;, &#39;s&#39;, &#39;s&#39;, &#39;i&#39;, &#39;o&#39;, &#39;n&#39;, &#39; &#39;, &#39;i&#39;, &#39;n&#39;, &#39;d&#39;, &#39;e&#39;, &#39;x&#39;, &quot;&#39;&quot;, &#39; &#39;, &#39;h&#39;, &#39;o&#39;, &#39;o&#39;, &#39;k&#39;, &#39; &#39;, &quot;&#39;&quot;, &#39;e&#39;, &#39;x&#39;, &#39;e&#39;, &#39;c&#39;, &#39;_&#39;, &#39;a&#39;, &#39;f&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;_&#39;, &#39;p&#39;, &#39;r&#39;, &#39;o&#39;, &#39;c&#39;, &#39;e&#39;, &#39;s&#39;, &#39;s&#39;, &quot;&#39;&quot;, &#39;,&#39;, &#39; &#39;, &#39;o&#39;, &#39;r&#39;, &#39;i&#39;, &#39;g&#39;, &#39;i&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;, &#39; &#39;, &#39;m&#39;, &#39;e&#39;, &#39;s&#39;, &#39;s&#39;, &#39;a&#39;, &#39;g&#39;, &#39;e&#39;, &#39;:&#39;, &#39; &#39;, &#39;(&#39;, &#39;D&#39;, &#39;a&#39;, &#39;t&#39;, &#39;a&#39;, &#39;E&#39;, &#39;r&#39;, &#39;r&#39;, &#39;o&#39;, &#39;r&#39;, &#39;)&#39;, &#39; &#39;, &#39;i&#39;, &#39;n&#39;, &#39;v&#39;, &#39;a&#39;, &#39;l&#39;, &#39;i&#39;, &#39;d&#39;, &#39; &#39;, &#39;b&#39;, &#39;y&#39;, &#39;t&#39;, &#39;e&#39;, &#39; &#39;, &#39;s&#39;, &#39;e&#39;, &#39;q&#39;, &#39;u&#39;, &#39;e&#39;, &#39;n&#39;, &#39;c&#39;, &#39;e&#39;, &#39; &#39;, &#39;f&#39;, &#39;o&#39;, &#39;r&#39;, &#39; &#39;, &#39;e&#39;, &#39;n&#39;, &#39;c&#39;, &#39;o&#39;, &#39;d&#39;, &#39;i&#39;, &#39;n&#39;, &#39;g&#39;, &#39; &#39;, &#39;&quot;&#39;, &#39;U&#39;, &#39;T&#39;, &#39;F&#39;, &#39;8&#39;, &#39;&quot;&#39;, &#39;:&#39;, &#39; &#39;, &#39;0&#39;, &#39;x&#39;, &#39;8&#39;, &#39;1&#39;, &#39;\n&#39;, &#39;H&#39;, &#39;I&#39;, &#39;N&#39;, &#39;T&#39;, &#39;:&#39;, &#39; &#39;, &#39; &#39;, &#39;T&#39;, &#39;h&#39;, &#39;i&#39;, &#39;s&#39;, &#39; &#39;, &#39;e&#39;, &#39;r&#39;, &#39;r&#39;, &#39;o&#39;, &#39;r&#39;, &#39; &#39;, &#39;c&#39;, &#39;a&#39;, &#39;n&#39;, &#39; &#39;, &#39;a&#39;, &#39;l&#39;, &#39;s&#39;, &#39;o&#39;, &#39; &#39;, &#39;h&#39;, &#39;a&#39;, &#39;p&#39;, &#39;p&#39;, &#39;e&#39;, &#39;n&#39;, &#39; &#39;, &#39;i&#39;, &#39;f&#39;, &#39; &#39;, &#39;t&#39;, &#39;h&#39;, &#39;e&#39;, &#39; &#39;, &#39;b&#39;, &#39;y&#39;, &#39;t&#39;, &#39;e&#39;, &#39; &#39;, &#39;s&#39;, &#39;e&#39;, &#39;q&#39;, &#39;u&#39;, &#39;e&#39;, &#39;n&#39;, &#39;c&#39;, &#39;e&#39;, &#39; &#39;, &#39;d&#39;, &#39;o&#39;, &#39;e&#39;, &#39;s&#39;, &#39; &#39;, &#39;n&#39;, &#39;o&#39;, &#39;t&#39;, &#39; &#39;, &#39;m&#39;, &#39;a&#39;, &#39;t&#39;, &#39;c&#39;, &#39;h&#39;, &#39; &#39;, &#39;t&#39;, &#39;h&#39;, &#39;e&#39;, &#39; &#39;, &#39;e&#39;, &#39;n&#39;, &#39;c&#39;, &#39;o&#39;, &#39;d&#39;, &#39;i&#39;, &#39;n&#39;, &#39;g&#39;, &#39; &#39;, &#39;e&#39;, &#39;x&#39;, &#39;p&#39;, &#39;e&#39;, &#39;c&#39;, &#39;t&#39;, &#39;e&#39;, &#39;d&#39;, &#39; &#39;, &#39;b&#39;, &#39;y&#39;, &#39; &#39;, &#39;t&#39;, &#39;h&#39;, &#39;e&#39;, &#39; &#39;, &#39;s&#39;, &#39;e&#39;, &#39;r&#39;, &#39;v&#39;, &#39;e&#39;, &#39;r&#39;, &#39;,&#39;, &#39; &#39;, &#39;w&#39;, &#39;h&#39;, &#39;i&#39;, &#39;c&#39;, &#39;h&#39;, &#39; &#39;, &#39;i&#39;, &#39;s&#39;, &#39; &#39;, &#39;c&#39;, &#39;o&#39;, &#39;n&#39;, &#39;t&#39;, &#39;r&#39;, &#39;o&#39;, &#39;l&#39;, &#39;l&#39;, &#39;e&#39;, &#39;d&#39;, &#39; &#39;, &#39;b&#39;, &#39;y&#39;, &#39; &#39;, &#39;&quot;&#39;, &#39;c&#39;, &#39;l&#39;, &#39;i&#39;, &#39;e&#39;, &#39;n&#39;, &#39;t&#39;, &#39;_&#39;, &#39;e&#39;, &#39;n&#39;, &#39;c&#39;, &#39;o&#39;, &#39;d&#39;, &#39;i&#39;, &#39;n&#39;, &#39;g&#39;, &#39;&quot;&#39;, &#39;.&#39;, &#39;\n&#39;) &#39;INSERT INTO history_dataset_association (id, history_id, dataset_id, create_time, update_time, state, copied_from_history_dataset_association_id, copied_from_library_dataset_dataset_association_id, hid, name, info, blurb, peek, tool_version, extension, metadata, parent_id, designation, deleted, purged, visible) VALUES (%(id)s, %(history_id)s, %(dataset_id)s, %(create_time)s, %(update_time)s, %(_state)s, %(copied_from_history_dataset_association_id)s, %(copied_from_library_dataset_dataset_association_id)s, %(hid)s, %(name)s, %(info)s, %(blurb)s, %(peek)s, %(tool_version)s, %(extension)s, %(_metadata)s, %(parent_id)s, %(designation)s, %(deleted)s, %(purged)s, %(visible)s)&#39; {&#39;info&#39;: &#39;makeAffyBatch, Normalized_rma_Raw_Plots.pdf&#39;, &#39;peek&#39;: &quot;%PDF-1.4\n%\x81\xe2\x81\xe3\x81\xcf\x81\xd3\\r\n1 0 obj\n&lt;&lt;\n/CreationDate (D:20121030103557)\n/ModDate (D:20121030103557)\n/Title (R Graphics Output)\n/Producer (R 2.15.1)\n/Creator (R)\n&gt;&gt;\nendobj\n2 0 obj\n&lt;&lt; /Type /Catalog /Pages 3 0 R &gt;&gt;\nendobj\n7 0 obj\n&lt;&lt; /Type /Page /Parent 3 0 R /Contents 8 0 R /Resources 4 0 R &gt;&gt;\nendobj\n8 0 obj\n&lt;&lt;\n/Length 990 /Filter /FlateDecode\n&gt;&gt;\nstream\nx\x9c\xa5W\xcb\x8eT9\x0c\xdd\xe7+\xbc\xec^\x10\x928\xcf--\x06\xa9\x05HP%\xb1@,\x80\x194B]\xbc\x1a\t&gt;\x1f&#39;vr\x1f}\x9b\xaaRon\xe9D\xc7&#39;\xceI\xe2\xb8,\\\x83\x85\xcf\xf0]\xbd\x82\xef`\x8d\xd71\x83\xf3Nc\x06o\xbdN\x0e0Y\x1d\x1c\xfc\xf8\x0f\xde\xc0\x17\xf5\xf8\xf6\xf5\xb3&#39;p\xb5SF\x1bc`\xfe\xdd]\xbdTN\xbb\x00\xbf\xd4\xdbw`\xe0_e\xe0Z\x91\xba\xb2\x95\x00/\x94uQ{\x0f\xe8H\x18\xe1\x006%\x1d\x07\xbe\x81\xaa\x9aZ&lt;4!$\xc4J\xb6*\x05\xa7\x8d\x07\x97\x8a\xb6\xb6F3&quot;, &#39;update_time&#39;: datetime.datetime(2012, 10, 30, 14, 36, 51, 684), &#39;name&#39;: &#39;Normalized_rma_Raw_Plots.pdf&#39;, &#39;extension&#39;: &#39;pdf&#39;, &#39;tool_version&#39;: None, &#39;deleted&#39;: False, &#39;history_id&#39;: None, &#39;copied_from_library_dataset_dataset_association_id&#39;: None, &#39;_state&#39;: None, &#39;designation&#39;: None, &#39;purged&#39;: False, &#39;parent_id&#39;: None, &#39;create_time&#39;: datetime.datetime(2012, 10, 30, 14, 36, 51, 587), &#39;hid&#39;: None, &#39;_metadata&#39;: &lt;psycopg2._psycopg.Binary object at 0x49231b8&gt;, &#39;visible&#39;: True, &#39;dataset_id&#39;: 727L, &#39;id&#39;: 739L, &#39;blurb&#39;: None, &#39;copied_from_history_dataset_association_id&#39;: None}</p>

<p class="p1"><br></p><p class="p1"><br></p><p></p></div>-- <br>best，<br><br>Jian Ma,<br><div><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br>

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