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Hanging on SQL Queries

Every now and again (1 in 3 times) Rapidminer will hang on an SQL query. Usually my process will take 5 minutes.

By hang I mean the timer just keeps going, for hours, it never resolves.

The data in the database is static, im not updating/writing new rows to it.

is this a common issue? Should I think about doing a large extract from the database to my local machine and working with that?

I sometimes get this: Feb 4, 2012 6:12:29 PM WARNING: Caught exception in concurrent execution of Read Database (Read Database): com.rapidminer.operator.UserError: Database error occurred: Operation not allowed after ResultSet closed

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haddock

Hi,
Please post the XML.

johnyma22


<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<process version="5.2.000">
  <context>
    <input/>
    <output/>
    <macros/>
  </context>
  <operator activated="true" class="process" compatibility="5.2.000" expanded="true" name="Process">
    <parameter key="parallelize_main_process" value="true"/>
    <process expanded="true" height="386" width="835">
      <operator activated="true" class="read_database" compatibility="5.2.000" expanded="true" height="60" name="Read Database (2)" width="90" x="45" y="30">
        <parameter key="connection" value="slave2"/>
        <parameter key="query" value="SELECT label, data, school_list_holiday_sources.id FROM school_list_holiday_data INNER JOIN school_list_holiday_sources ON school_list_holiday_data.id=school_list_holiday_sources.id WHERE school_list_holiday_sources.label = &quot;true&quot; OR isGood = -2 AND school_list_holiday_sources.label = &quot;false&quot; LIMIT 0,200"/>
        <enumeration key="parameters"/>
      </operator>
      <operator activated="true" class="nominal_to_text" compatibility="5.2.000" expanded="true" height="76" name="Nominal to Text" width="90" x="179" y="30">
        <parameter key="attribute_filter_type" value="single"/>
        <parameter key="attribute" value="data"/>
      </operator>
      <operator activated="true" class="text:process_document_from_data" compatibility="5.1.004" expanded="true" height="76" name="Process Documents from Data" width="90" x="313" y="30">
        <parameter key="keep_text" value="true"/>
        <parameter key="prune_method" value="absolute"/>
        <parameter key="prune_below_absolute" value="2"/>
        <parameter key="prune_above_absolute" value="999"/>
        <list key="specify_weights"/>
        <process expanded="true" height="480" width="815">
          <operator activated="true" class="web:extract_html_text_content" compatibility="5.1.004" expanded="true" height="60" name="Extract Content" width="90" x="45" y="120"/>
          <operator activated="true" class="text:transform_cases" compatibility="5.1.004" expanded="true" height="60" name="Transform Cases" width="90" x="179" y="120"/>
          <operator activated="true" class="text:tokenize" compatibility="5.1.004" expanded="true" height="60" name="Tokenize" width="90" x="313" y="120"/>
          <operator activated="true" class="text:filter_stopwords_english" compatibility="5.1.004" expanded="true" height="60" name="Filter Stopwords (English)" width="90" x="447" y="120"/>
          <operator activated="true" class="text:stem_snowball" compatibility="5.1.004" expanded="true" height="60" name="Stem (Snowball)" width="90" x="581" y="120"/>
          <operator activated="true" class="text:filter_by_length" compatibility="5.1.004" expanded="true" height="60" name="Filter Tokens (by Length)" width="90" x="715" y="120">
            <parameter key="min_chars" value="2"/>
          </operator>
          <connect from_port="document" to_op="Extract Content" to_port="document"/>
          <connect from_op="Extract Content" from_port="document" to_op="Transform Cases" to_port="document"/>
          <connect from_op="Transform Cases" from_port="document" to_op="Tokenize" to_port="document"/>
          <connect from_op="Tokenize" from_port="document" to_op="Filter Stopwords (English)" to_port="document"/>
          <connect from_op="Filter Stopwords (English)" from_port="document" to_op="Stem (Snowball)" to_port="document"/>
          <connect from_op="Stem (Snowball)" from_port="document" to_op="Filter Tokens (by Length)" to_port="document"/>
          <connect from_op="Filter Tokens (by Length)" from_port="document" to_port="document 1"/>
          <portSpacing port="source_document" spacing="90"/>
          <portSpacing port="sink_document 1" spacing="90"/>
          <portSpacing port="sink_document 2" spacing="0"/>
        </process>
      </operator>
      <operator activated="true" class="read_database" compatibility="5.2.000" expanded="true" height="60" name="Read Database" width="90" x="45" y="210">
        <parameter key="connection" value="slave2"/>
        <parameter key="query" value="SELECT data, label, isGood, school_list_holiday_sources.id FROM school_list_holiday_data INNER JOIN school_list_holiday_sources ON school_list_holiday_data.id=school_list_holiday_sources.id WHERE label != &quot;true&quot; AND isGood = 0 LIMIT 0,2000"/>
        <enumeration key="parameters"/>
      </operator>
      <operator activated="true" class="nominal_to_text" compatibility="5.2.000" expanded="true" height="76" name="Nominal to Text (2)" width="90" x="179" y="210">
        <parameter key="attribute_filter_type" value="single"/>
        <parameter key="attribute" value="data"/>
      </operator>
      <operator activated="true" class="text:process_document_from_data" compatibility="5.1.004" expanded="true" height="76" name="Process Documents from Data (2)" width="90" x="313" y="210">
        <parameter key="keep_text" value="true"/>
        <parameter key="prune_method" value="absolute"/>
        <parameter key="prune_below_absolute" value="2"/>
        <parameter key="prune_above_absolute" value="999"/>
        <list key="specify_weights"/>
        <process expanded="true" height="340" width="803">
          <operator activated="true" class="web:extract_html_text_content" compatibility="5.1.004" expanded="true" height="60" name="Extract Content (2)" width="90" x="45" y="30"/>
          <operator activated="true" class="text:transform_cases" compatibility="5.1.004" expanded="true" height="60" name="Transform Cases (2)" width="90" x="180" y="30"/>
          <operator activated="true" class="text:tokenize" compatibility="5.1.004" expanded="true" height="60" name="Tokenize (2)" width="90" x="315" y="30"/>
          <operator activated="true" class="text:filter_stopwords_english" compatibility="5.1.004" expanded="true" height="60" name="Filter Stopwords (2)" width="90" x="450" y="30"/>
          <operator activated="true" class="text:stem_snowball" compatibility="5.1.004" expanded="true" height="60" name="Stem (2)" width="90" x="585" y="30"/>
          <operator activated="true" class="text:filter_by_length" compatibility="5.1.004" expanded="true" height="60" name="Filter Tokens (2)" width="90" x="703" y="30">
            <parameter key="min_chars" value="2"/>
          </operator>
          <connect from_port="document" to_op="Extract Content (2)" to_port="document"/>
          <connect from_op="Extract Content (2)" from_port="document" to_op="Transform Cases (2)" to_port="document"/>
          <connect from_op="Transform Cases (2)" from_port="document" to_op="Tokenize (2)" to_port="document"/>
          <connect from_op="Tokenize (2)" from_port="document" to_op="Filter Stopwords (2)" to_port="document"/>
          <connect from_op="Filter Stopwords (2)" from_port="document" to_op="Stem (2)" to_port="document"/>
          <connect from_op="Stem (2)" from_port="document" to_op="Filter Tokens (2)" to_port="document"/>
          <connect from_op="Filter Tokens (2)" from_port="document" to_port="document 1"/>
          <portSpacing port="source_document" spacing="0"/>
          <portSpacing port="sink_document 1" spacing="0"/>
          <portSpacing port="sink_document 2" spacing="0"/>
        </process>
      </operator>
      <operator activated="true" class="set_role" compatibility="5.2.000" expanded="true" height="76" name="Set Role (2)" width="90" x="447" y="210">
        <parameter key="name" value="label"/>
        <parameter key="target_role" value="label"/>
        <list key="set_additional_roles"/>
      </operator>
      <operator activated="true" class="set_role" compatibility="5.2.000" expanded="true" height="76" name="Set Role" width="90" x="447" y="30">
        <parameter key="name" value="label"/>
        <parameter key="target_role" value="label"/>
        <list key="set_additional_roles"/>
      </operator>
      <operator activated="true" class="naive_bayes" compatibility="5.2.000" expanded="true" height="76" name="Naive Bayes" width="90" x="581" y="30">
        <parameter key="laplace_correction" value="false"/>
      </operator>
      <operator activated="true" class="apply_model" compatibility="5.2.000" expanded="true" height="76" name="Apply Model (2)" width="90" x="715" y="120">
        <list key="application_parameters"/>
      </operator>
      <connect from_op="Read Database (2)" from_port="output" to_op="Nominal to Text" to_port="example set input"/>
      <connect from_op="Nominal to Text" from_port="example set output" to_op="Process Documents from Data" to_port="example set"/>
      <connect from_op="Process Documents from Data" from_port="example set" to_op="Set Role" to_port="example set input"/>
      <connect from_op="Process Documents from Data" from_port="word list" to_op="Process Documents from Data (2)" to_port="word list"/>
      <connect from_op="Read Database" from_port="output" to_op="Nominal to Text (2)" to_port="example set input"/>
      <connect from_op="Nominal to Text (2)" from_port="example set output" to_op="Process Documents from Data (2)" to_port="example set"/>
      <connect from_op="Process Documents from Data (2)" from_port="example set" to_op="Set Role (2)" to_port="example set input"/>
      <connect from_op="Set Role (2)" from_port="example set output" to_op="Apply Model (2)" to_port="unlabelled data"/>
      <connect from_op="Set Role" from_port="example set output" to_op="Naive Bayes" to_port="training set"/>
      <connect from_op="Naive Bayes" from_port="model" to_op="Apply Model (2)" to_port="model"/>
      <connect from_op="Apply Model (2)" from_port="labelled data" to_port="result 1"/>
      <connect from_op="Apply Model (2)" from_port="model" to_port="result 2"/>
      <portSpacing port="source_input 1" spacing="0"/>
      <portSpacing port="sink_result 1" spacing="90"/>
      <portSpacing port="sink_result 2" spacing="0"/>
      <portSpacing port="sink_result 3" spacing="0"/>
    </process>
  </operator>
</process>

haddock

Hi there,

You're getting an SQL error - "Operation not allowed after ResultSet closed" - the question is why? I Googled that error and followed this link

http://stackoverflow.com/questions/5840866/getting-java-sql-sqlexception-operation-not-allowed-after-resultset-closed

The bit that caught my eye was..

A ResultSet object is automatically closed when the Statement object that generated it is closed, re-executed, or used to retrieve the next result from a sequence of multiple results.

because there is a fair amount of common ground between the two SQL statements. I could imagine scenarios where the second request kicks off at the wrong time, especially if the main process is parallelised http://rapid-i.com/rapidforum/index.php/topic,2162.msg8510.html#msg8510.

As an aside, if we look at the SQL..

SELECT label, data, school_list_holiday_sources.id FROM school_list_holiday_data INNER JOIN school_list_holiday_sources ON school_list_holiday_data.id=school_list_holiday_sources.id WHERE school_list_holiday_sources.label = &quot;true&quot; OR isGood = -2 AND school_list_holiday_sources.label = &quot;false&quot; LIMIT 0,200"/>

SELECT data, label, isGood, school_list_holiday_sources.id FROM school_list_holiday_data INNER JOIN school_list_holiday_sources ON school_list_holiday_data.id=school_list_holiday_sources.id WHERE label != &quot;true&quot; AND isGood = 0 LIMIT 0,2000"/>

In each you are joining the same two tables, in the same way , on school_list_holiday_data.id=school_list_holiday_sources.id ; that could therefore be done in one statement, because you can filter out your training and test sets explicitly in RM. In fact this is a pretty good example of how it is easier to debug SQL using el rapido. Actually I'd do the join in RM as well 8)

johnyma22

Ahhh, okay.. Well I will try to figure out how to filter out my training data. Any pointers?

haddock

Don't want to sound grumpy, but you really need to work through help->tutorial.

johnyma22

Agreed. I hadn't spotted this before, just the Video tutorials. I have the book to read next week when I'm on holiday. Will go through these tomorrow. Good shout!

haddock

Cool.