patch 2 seems to replace usage of Molecule with Molecule, rather than IMolecule

Now, this particularly problem was Eclipse being overly active cleaning up the imports, but we reached the point that it is actually interesting to have PMD warn about these issues. PMD is a cool piece of software used by the CDK project for a long time one. One particular cool thing is that you can write code warnings as XPath queries.

So, I promised Rajarshi to have a look at a custom rule to look at using IMolecule instead of Molecule. The code is actually pretty simple, using the aforementioned XPath feature:

<rule name="ReplaceMoleculeWithIMolecule"
      language="java"
      message="Use the IMolecule interfaces instead of the Molecule implementation"
      class="net.sourceforge.pmd.rules.XPathRule">
  <description>
      Programming against the CDK interfaces allows users to pick their favorite
      implementation (nonotify, datadebug).
  </description>
  <priority>3</priority>
  <properties>
    <property name="xpath">
      <value>
 <![CDATA[
   //Type/ReferenceType/ClassOrInterfaceType[@Image='Molecule']
 ]]>
      </value>
    </property>
  </properties>
    <example>
    <![CDATA[
      Molecule mol = builder.newInstance(IMolecule.class);
    ]]>
  </example>
</rule>

Patch pending…

Running the PMD tests from the command line

When you are writing patches for the CDK, you can run the PMD tests via an Ant file, for example via the command line:

$ ant -f pmd.xml

However, when working on a single file, you will likely appreciated running the tests against a single module. This can be done with (for the data module):

$ ant -f pmd.xml -Dpmd.test=custom -Dmodule=data test-module

The custom.xml defines the tests we normally run.

The pmd.xml does not create HTML pages, like Nightly does. Instead, an XML file is currently created. The xpath utility can be used to filter out the information we are interested in. For example, if we want to reports just about DefaultChemObjectBuilder, we issue:

$ xpath -e "//violation[@class='DefaultChemObjectBuilder']" \\
    reports/pmd/data.xml

The number of these false positives seems to be significant as the number of PMD violations for the CDK 1.2.x branch seems to have dropped about 1500! warnings :)