cdk and grails - why don't get they along. This time using maven for dependency management...

...

Recently I posted about grails2 and the CDK using the BuildConfig.groovy approach.

Now it's only fair that I show the maven approach as alternative. It's aint pretty...

But it works and allows you to build grails 2.1 project with the CDK. Now i just need to integrate scala into the mix...

<?xml version="1.0" encoding="utf-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <groupId>edu.ucdavis.fiehnlab.cts</groupId>
    <artifactId>cts</artifactId>
    <packaging>grails-app</packaging>
    <version>2.0-beta-2</version>
    <name>cts</name>
    <description>2.0-beta-2</description>

    <parent>
        <artifactId>web</artifactId>
        <groupId>edu.ucdavis.fiehnlab.cts.web</groupId>
        <version>1.0-SNAPSHOT</version>
    </parent>

    <dependencies>
        <dependency>
            <groupId>org.grails</groupId>
            <artifactId>grails-dependencies</artifactId>
            <version>${grails.version}</version>
            <type>pom</type>
        </dependency>

        <dependency>
            <groupId>org.grails</groupId>
            <artifactId>grails-test</artifactId>
            <version>${grails.version}</version>
            <type>pom</type>
        </dependency>


        <dependency>
            <groupId>org.grails</groupId>
            <artifactId>grails-plugin-testing</artifactId>
            <version>${grails.version}</version>
            <scope>test</scope>
        </dependency>


        <dependency>
            <groupId>net.sf.jni-inchi</groupId>
            <artifactId>jni-inchi</artifactId>
            <version>${jni.inchi.version}</version>
        </dependency>

        <dependency>

            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-inchi</artifactId>
            <version>${cdk.version}</version>

            <exclusions>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xmlParserAPIs</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xercesImpl</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xalan</groupId>
                    <artifactId>xalan</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>java3d</groupId>
                    <artifactId>vecmath</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xmlpull</groupId>
                    <artifactId>xmlpull</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>cml</groupId>
                    <artifactId>cmlxom</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xom</groupId>
                    <artifactId>xom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>jdom</groupId>
                    <artifactId>jdom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xpp3</groupId>
                    <artifactId>xpp3</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>jama</groupId>
                    <artifactId>jama</artifactId>
                </exclusion>

            </exclusions>
        </dependency>

        <dependency>

            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-fingerprint</artifactId>
            <version>${cdk.version}</version>

            <exclusions>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xmlParserAPIs</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xercesImpl</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xalan</groupId>
                    <artifactId>xalan</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>java3d</groupId>
                    <artifactId>vecmath</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xmlpull</groupId>
                    <artifactId>xmlpull</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>cml</groupId>
                    <artifactId>cmlxom</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xom</groupId>
                    <artifactId>xom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>jdom</groupId>
                    <artifactId>jdom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xpp3</groupId>
                    <artifactId>xpp3</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>jama</groupId>
                    <artifactId>jama</artifactId>
                </exclusion>

            </exclusions>
        </dependency>
        <dependency>

            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-renderawt</artifactId>
            <version>${cdk.version}</version>

            <exclusions>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xmlParserAPIs</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xercesImpl</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xalan</groupId>
                    <artifactId>xalan</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>java3d</groupId>
                    <artifactId>vecmath</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xmlpull</groupId>
                    <artifactId>xmlpull</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>cml</groupId>
                    <artifactId>cmlxom</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xom</groupId>
                    <artifactId>xom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>jdom</groupId>
                    <artifactId>jdom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xpp3</groupId>
                    <artifactId>xpp3</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>jama</groupId>
                    <artifactId>jama</artifactId>
                </exclusion>

            </exclusions>
        </dependency>


        <dependency>

            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-render</artifactId>
            <version>${cdk.version}</version>

            <scope>runtime</scope>


            <exclusions>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xmlParserAPIs</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xercesImpl</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xalan</groupId>
                    <artifactId>xalan</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>java3d</groupId>
                    <artifactId>vecmath</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xmlpull</groupId>
                    <artifactId>xmlpull</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>cml</groupId>
                    <artifactId>cmlxom</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xom</groupId>
                    <artifactId>xom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>jdom</groupId>
                    <artifactId>jdom</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xpp3</groupId>
                    <artifactId>xpp3</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>jama</groupId>
                    <artifactId>jama</artifactId>
                </exclusion>

            </exclusions>
        </dependency>


        <dependency>
            <groupId>org.codehaus.groovy.modules.http-builder</groupId>
            <artifactId>http-builder</artifactId>
            <version>0.5.2</version>
            <scope>runtime</scope>

            <exclusions>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xmlParserAPIs</artifactId>
                </exclusion>
                <exclusion>
                    <groupId>xerces</groupId>
                    <artifactId>xercesImpl</artifactId>
                </exclusion>

                <exclusion>
                    <groupId>xalan</groupId>
                    <artifactId>xalan</artifactId>
                </exclusion>
            </exclusions>
        </dependency>


        <dependency>
            <groupId>postgresql</groupId>
            <artifactId>postgresql</artifactId>
            <version>8.2-504.jdbc3</version>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>cache</artifactId>
            <version>1.0.1</version>
            <type>zip</type>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>jquery-ui</artifactId>
            <version>1.8.24</version>
            <type>zip</type>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>jquery</artifactId>
            <version>1.8.3</version>
            <type>zip</type>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>export</artifactId>
            <version>1.5</version>
            <type>zip</type>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>resources</artifactId>
            <version>1.1.6</version>
            <type>zip</type>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>jquery-ui-extensions</artifactId>
            <version>0.5.8</version>
            <type>zip</type>
        </dependency>

        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>hibernate</artifactId>
            <version>${grails.version}</version>
            <type>zip</type>

        </dependency>

        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>spock</artifactId>
            <version>0.6</version>
            <type>zip</type>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.spockframework</groupId>
            <artifactId>spock-grails-support</artifactId>
            <version>0.6-groovy-1.8</version>
            <scope>test</scope>
        </dependency>


        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>functional-test</artifactId>
            <version>1.2.7</version>
            <type>zip</type>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>webxml</artifactId>
            <version>1.4.1</version>
            <type>zip</type>
        </dependency>

        <dependency>
            <groupId>org.grails.plugins</groupId>
            <artifactId>tomcat</artifactId>
            <version>2.1.0</version>
            <type>zip</type>
            <scope>runime</scope>
        </dependency>


    </dependencies>

    <build>
        <pluginManagement/>

        <plugins>
            <!-- Disables the Maven surefire plugin for Grails applications, as we have our own test runner -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <configuration>
                    <skip>true</skip>
                </configuration>
                <executions>
                    <execution>
                        <id>surefire-it</id>
                        <phase>integration-test</phase>
                        <goals>
                            <goal>test</goal>
                        </goals>
                        <configuration>
                            <skip>false</skip>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-clean-plugin</artifactId>
                <version>2.4.1</version>
                <configuration>
                    <filesets>
                        <fileset>
                            <directory>plugins</directory>
                            <includes>
                                <include>**/*</include>
                            </includes>
                            <followSymlinks>false</followSymlinks>
                        </fileset>
                    </filesets>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.grails</groupId>
                <artifactId>grails-maven-plugin</artifactId>
                <version>${grails.version}</version>
                <configuration>
                    <!-- Whether for Fork a JVM to run Grails commands -->
                    <fork>true</fork>
                </configuration>
                <extensions>true</extensions>
            </plugin>
        </plugins>
    </build>

    <repositories>
        <repository>
            <id>grails</id>
            <name>grails</name>
            <url>http://repo.grails.org/grails/core</url>
        </repository>
        <repository>
            <id>grails-plugins</id>
            <name>grails-plugins</name>
            <url>http://repo.grails.org/grails/plugins</url>
        </repository>

        <repository>
            <id>ambit-public</id>
            <name>ambit-public</name>
            <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/public/</url>
        </repository>


        <repository>
            <id>ambit-thirdparty</id>
            <name>ambit-thirdparty</name>
            <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty/</url>
        </repository>


        <repository>
            <id>codehaus</id>
            <name>codehaus</name>
            <url>http://snapshots.repository.codehaus.org</url>
        </repository>


    </repositories>
</project>

scala yield vs map which is nicer?

currently I'm playing a bit more with scala in an attempt to leverage the power of my new pair of radeon 7970 for GPU calculations and I'm a touch unsure, which syntax I prefer and is easier to read.

example a:


scala> 1 to 10 map ( _ * 2)
res4: scala.collection.immutable.IndexedSeq[Int] = Vector(2, 4, 6, 8, 10, 12, 14, 16, 18, 20)


versus example b:

scala> for (i <- 10="" 1="" 2="" i="" nbsp="" to="" yield="">
res5: scala.collection.immutable.IndexedSeq[Int] = Vector(2, 4, 6, 8, 10, 12, 14, 16, 18, 20)


They both produce the same result, but I feel the b is easier to understand from a none scala perspective. But a. Is shorter and somewhat clearer

Now if we change this to:


scala> val result  = 1 to 10 map ( _ * 2)
result: scala.collection.immutable.IndexedSeq[Int] = Vector(2, 4, 6, 8, 10, 12, 14, 16, 18, 20)

and

scala> val result = for (i <- 10="" 1="" 2="" i="" nbsp="" to="" yield="">
result: scala.collection.immutable.IndexedSeq[Int] = Vector(2, 4, 6, 8, 10, 12, 14, 16, 18, 20)

now the first version seems to make a lot more sense and the second looks unwieldy complicated.

cdk and grails, why don't they get along...

so apperently the cdk depends on some xml libaries, which causes us all kind of error messages like this in grails:

| Loading Grails 2.1.0
| Configuring classpath
| Error Error executing script Help: loader constraint violation: when resolving overridden method "org.apache.tools.ant.helper.ProjectHelper2$RootHandler.setDocumentLocator(Lorg/xml/sax/Locator;)V" the class loader (instance of org/codehaus/groovy/grails/cli/support/GrailsRootLoader) of the current class, org/apache/tools/ant/helper/ProjectHelper2$RootHandler, and its superclass loader (instance of ), have different Class objects for the type org/xml/sax/Locator used in the signature (Use --stacktrace to see the full trace)

IDEA hook: Grails not found!
| Error java.lang.NullPointerException
| Error  at org.jetbrains.groovy.grails.rt.Agent$2.run(Agent.java:135)
| Error  at java.lang.Thread.run(Thread.java:680)

which are rather annoying since all the mailing list say, to just run the dependency report to see what causes this problem. Great idea exact that grails crashes before it can generate the report...

So after a while of searching and goggling and shouting random words at my imac, I found an ugly solution which works rather well for now.
Basically make your BuildConfig.groovy file look like this and it should fix your current issues...

    dependencies {
        
        runtime 'postgresql:postgresql:8.2-504.jdbc3'

        compile('xmlpull:xmlpull:1.1.3.1')

        compile('org.openscience.cdk:cdk-fingerprint:1.4.16') {
            transitive = false
        }
        compile('org.openscience.cdk:cdk-inchi:1.4.16') {
            transitive = false
        }
        compile('org.openscience.cdk:cdk-standard:1.4.16')
        compile('org.openscience.cdk:cdk-interfaces:1.4.16')
        compile('org.openscience.cdk:cdk-annotation:1.4.16')
        compile('org.openscience.cdk:cdk-io:1.4.16')
        compile('org.openscience.cdk:cdk-isomorphism:1.4.16')
        compile('org.openscience.cdk:cdk-render:1.4.16')
        compile('org.openscience.cdk:cdk-renderbasic:1.4.16')
        compile('org.openscience.cdk:cdk-renderawt:1.4.16')
        compile('org.openscience.cdk:cdk-smarts:1.4.16')  {
            transitive = false
        }
        compile('org.openscience.cdk:cdk-extra:1.4.16')  {
            transitive = false
        }
        compile('org.openscience.cdk:cdk-dict:1.4.16')  {
            transitive = false
        }
        compile('jama:jama:1.0.2')  {
            transitive = false
        }
        compile('org.openscience.cdk:cdk-formula:1.4.16')
        compile('org.openscience.cdk:cdk-smsd:1.4.16')
        compile('xpp3:xpp3:1.1.4c')
        compile('java3d:vecmath:1.3.1')
        compile('net.sf.jni-inchi:jni-inchi:0.7')
    }

Maybe this help someone, who has the same issues with old XML-Apis and Xerces and so

Lift - getting access to a database

Since I recently started to play more and more with lift. I discovered that it's not always as easy as you think it is and once you find a solution it was easy indeed.

For example I want to connect to my database server, but have no desire to actually use any form of OR mapping.

So after googleing a bit and woundering how todo this. It's all rather simple.

In your Boot.scala file

def boot {
    // where to search snippet
    LiftRules.addToPackages("code")

    // Build SiteMap
    LiftRules.setSiteMap(sitemap)

    //rest based stuff

    /**
     * connection url for lift
     */
    val vendor = new StandardDBVendor("org.postgresql.Driver","jdbc:postgresql://****/****",Full("username"),Full("password")) with ProtoDBVendor{
      override def maxPoolSize = 100
      override def doNotExpandBeyond = 200
    }
    
    DB.defineConnectionManager(DefaultConnectionIdentifier, vendor)

  }

This basically defines what to connect to and a connection pool with a max of 100 connections.

To actually access this connection and todo something with it, well this is remarkable easy.

          DB.performQuery("select * from data")

scala + lift + json

So since I really really really dislike soap and Java, I decided to play a bit more with scala and rest based web services. Basically parse some JSON strings with scala.

Now after browsing countless articles and remembering the JSON structure, I finally found the 'lift-json' project, which simplifies my live as busy developer a bit.

How to parse JSON with scala?

package edu.ucdavis.fiehnlab.alchemy.core.communication.services.reader

import edu.ucdavis.fiehnlab.alchemy.core.process.types.LibrarySpectra

import net.liftweb.json.parse

import net.liftweb.json.DefaultFormats

/**

 * connects to the alchemy webservice and fetches all registered co

 */

class WebserviceLibraryReader {

  /**

   * internal converter class to simplify things

   */

  case class JsonCompound(name: String, inchikey: String, retentiontime: Double, theoretical: Double, massspectra: String)

  case class CompoundWapper(compound: Array[JsonCompound])

  implicit val formats = DefaultFormats

  /**

   * downloads the compounds for the given URL and returns it as a set of library spectra

   */

  def fetchCompounds(url: String): Set[LibrarySpectra] = {

    val compounds: CompoundWapper = parse("""

        

        {"compound":[{"name":"test","inchikey":"ADVPTQAUNPRNPO-UHFFFAOYSA-N","retentiontime":11111,"theoretical":11,"massspectra":"111:1 112:2 113:3"},{"name":"test","inchikey":"ADVPTQAUNPRNPO-UHFFFAOYSA-N","retentiontime":11111,"theoretical":11,"massspectra":"111:1 112:2 113:3"}]}

        

        """).extract[CompoundWapper]

    compounds.compound.foreach { x: JsonCompound =>

      println(x)

    }

    

    

    null

  }

}

object WebserviceLibraryReader {

  def main(ars: Array[String]) = {

    println(new WebserviceLibraryReader().fetchCompounds("http://localhost:8080/alchemy-admin/services/queryAllCompoundsForMethod/test"))

  }

}

The complete tutorial can be found here

using ssd's in a raid0 over 4 drives.

Recently I played a bit more with ssd's, since frankly they are getting affordable enough to use as scratch drives for our new software product.

Basically I was wondering, if a raid0 over 4 ssd's is fast enough for us, or if I should use a PCI-Express card.



root@****:/mnt/luna/scratch/gert# dd if=/dev/zero of=/mnt/scratch/bs.img bs=8048 count=81920
81920+0 records in
81920+0 records out
659292160 bytes (659 MB) copied, 0.529044 s, 1.2 GB/s
root@****:/mnt/luna/scratch/gert# dd of=/dev/null if=/mnt/scratch/bs.img bs=8048 count=81920
81920+0 records in
81920+0 records out
659292160 bytes (659 MB) copied, 0.129838 s, 5.1 GB/s


Sure the sample size is not perfect, but for a first test I'm rather surprised by this result and looking forward, if the speed keeps up like this.

grails 1.3.8 and java 1.6

since we still have a lot of grails 1.3.8 application, we are forced to use them and apparently sometimes all the test fail with the following exception:


java.lang.IllegalAccessError: tried to access class org.apache.xml.serializer.XSLOutputAttributes from class org.apache.xalan.transformer.TransformerImpl at org.apache.xalan.transformer.TransformerImpl.executeChildTemplates(TransformerImpl.java:2387) at org.apache.xalan.transformer.TransformerImpl.executeChildTemplates(TransformerImpl.java:2255) at org.apache.xalan.lib.Redirect.write(Redirect.java:212) at org.apache.xalan.extensions.ExtensionHandlerJavaClass.processElement(ExtensionHandlerJavaClass.java:495) at org.apache.xalan.templates.ElemExtensionCall.execute(ElemExtensionCall.java:230) at org.apache.xalan.templates.ElemApplyTemplates.transformSelectedNodes(ElemApplyTemplates.java:395) at org.apache.xalan.templates.ElemApplyTemplates.execute(ElemApplyTemplates.java:177) at org.apache.xalan.transformer.TransformerImpl.executeChildTemplates(TransformerImpl.java:2336) at org.apache.xalan.transformer.TransformerImpl.applyTemplateToNode(TransformerImpl.java:2202) at org.apache.xalan.transformer.TransformerImpl.transformNode(TransformerImpl.java:1276) at org.apache.xalan.transformer.TransformerImpl.transform(TransformerImpl.java:673) at org.apache.xalan.transformer.TransformerImpl.transform(TransformerImpl.java:1192) at org.apache.xalan.transformer.TransformerImpl.transform(TransformerImpl.java:1170) at org.apache.tools.ant.taskdefs.optional.TraXLiaison.transform(TraXLiaison.java:187) at org.apache.tools.ant.taskdefs.XSLTProcess.process(XSLTProcess.java:709) at org.apache.tools.ant.taskdefs.XSLTProcess.execute(XSLTProcess.java:333) at org.apache.tools.ant.taskdefs.optional.junit.AggregateTransformer.transform(AggregateTransformer.java:264) at org.apache.tools.ant.taskdefs.optional.junit.XMLResultAggregator.execute(XMLResultAggregator.java:158) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at _GrailsEvents_groovy$_run_closure5.doCall(_GrailsEvents_groovy:58) at _GrailsEvents_groovy$_run_closure5.call(_GrailsEvents_groovy) at _GrailsTest_groovy$_run_closure1.doCall(_GrailsTest_groovy:199) at TestApp$_run_closure1.doCall(TestApp:82) at gant.Gant$_dispatch_closure5.doCall(Gant.groovy:381) at gant.Gant$_dispatch_closure7.doCall(Gant.groovy:415) at gant.Gant$_dispatch_closure7.doCall(Gant.groovy) at gant.Gant.withBuildListeners(Gant.groovy:427) at gant.Gant.this$2$withBuildListeners(Gant.groovy) at gant.Gant$this$2$withBuildListeners.callCurrent(Unknown Source) at gant.Gant.dispatch(Gant.groovy:415) at gant.Gant.this$2$dispatch(Gant.groovy) at gant.Gant.invokeMethod(Gant.groovy) at gant.Gant.executeTargets(Gant.groovy:590)
fix in the BuildConfig.groovy file:


inherits("global") { // uncomment to disable ehcache // excludes 'ehcache' excludes 'serializer' }