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InterProScan JMS Implementation Module
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<?xml version="1.0" encoding="UTF-8" ?>
<beans xmlns="http://www.springframework.org/schema/beans"
       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:schemaLocation="http://www.springframework.org/schema/beans
                           http://www.springframework.org/schema/beans/spring-beans-4.2.xsd">

    <import resource="../persistence/persistence-config-context.xml"/>

    <!-- ######################## JOB: CDD ############################  -->
    <bean id="jobCDD" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description" value="Prediction of CDD domains in Proteins"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleaseCDD"/>
        <property name="doRunLocally" value="true"/>
        <property name="active" value="true" />
    </bean>

    <bean id="abstractCDDStep" abstract="true" class="uk.ac.ebi.interpro.scan.management.model.Step">
        <property name="job" ref="jobCDD"/>
        <property name="maxProteins" value="${analysis.max.sequence.count.CDD}"/>
        <property name="createStepInstancesForNewProteins" value="true"/>
        <property name="retries" value="0"/>
        <property name="nfsDelayMilliseconds" value="${nfs.delay.milliseconds}"/>
    </bean>

    <!-- STEP 1 -->
    <bean id="stepCDDWriteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractCDDStep">
        <!-- This step has no dependencies, so will be scheduled first for its associated job. -->
        <property name="stepDescription" value="Create fasta file."/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="proteinDAO" ref="proteinDAO"/>
        <property name="serialGroup" value="WRITE_FASTA_CDD"/>
    </bean>

    <!-- STEP 2 -->
    <bean id="stepCDDRunBinaryRPSblast"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.cdd.RunCDDRPSBlastStep"
          parent="abstractCDDStep">
        <!-- rpsblast - options  -->
        <property name="dependsUpon" ref="stepCDDWriteFastaFile"/>
        <property name="stepDescription" value="Run CDD Binary for selected proteins"/>
        <property name="fullPathToBinary" value="${binary.rpsblast.path}"/>
        <property name="libraryPath" value="${cdd.library.path}"/>
        <property name="binarySwitches" value="${rpsblast.switches.cdd}"/>
        <property name="outputFileNameTemplate" value="[PROTSTART]_[PROTEND].blast.raw.out"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <!-- STEP 3 -->
    <bean id="stepCDDRunPostBlastProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.cdd.RunCDDPostBlastUtilityStep"
          parent="abstractCDDStep">
        <!-- cmd -options   -->
        <property name="dependsUpon" ref="stepCDDRunBinaryRPSblast"/>
        <property name="stepDescription" value="Run CDD Binary rpsbproc. for selected proteins"/>
        <property name="fullPathToBinary" value="${binary.rpsbproc.path}"/>
        <property name="binarySwitches" value="${rpsbproc.switches.cdd}"/>
        <property name="cddDataPath" value="${cdd.data.path}"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" value="[PROTSTART]_[PROTEND].blast.raw.out"/>
        <property name="retries" value="3"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <!-- STEP 4 -->
    <bean id="stepCDDDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractCDDStep">
        <property name="dependsUpon" ref="stepCDDRunPostBlastProcessing"/>
        <property name="deleteWorkingDirectoryOnCompletion" value="${delete.temporary.directory.on.completion}"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of CDD"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>

    <!-- STEP 5 -->
    <bean id="stepCDDParsePostBlastProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.cdd.ParseCDDOutputStep"
          parent="abstractCDDStep">
        <property name="dependsUpon" ref="stepCDDRunPostBlastProcessing"/>
        <property name="stepDescription" value="Parse the CDD binary output and store as Filtered matches."/>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.cdd.CDDMatchParser">
                <property name="signatureLibraryRelease" ref="cddSignatureLibraryRelease"/>
            </bean>
        </property>
        <property name="excludeSites" value="${exclude.sites.from.output}"/>
        <property name="rawMatchDAO"  ref="cddRawMatchDAO"/>
        <property name="rawSiteDAO"  ref="cddRawSiteDAO"/>
        <property name="serialGroup" value="PARSE_CDD"/>
    </bean>

    <!-- STEP 6 -->

    <bean id="stepCDDDeleteRawOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractCDDStep">
        <property name="dependsUpon" ref="stepCDDParsePostBlastProcessing"/>
        <property name="stepDescription"
                  value="Delete the raw output file following successful parsing and persistence"/>
        <property name="fileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="deleteWorkingDirectoryOnCompletion" value="${delete.temporary.directory.on.completion}"/>
    </bean>

    <!-- STEP 7 -->

    <bean id="stepCDDPostProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.cdd.CDDPostProcessingStep"
          parent="abstractCDDStep">
        <property name="dependsUpon" ref="stepCDDParsePostBlastProcessing"/>
        <property name="serialGroup" value="RPSBLAST_POST_PROCESSING"/>
        <property name="stepDescription" value="Filter CDD matches and persist filtered results"/>
        <property name="signatureLibraryRelease" ref="cddSignatureLibraryRelease"/>
        <property name="postProcessor">
            <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.cdd.CDDPostProcessing">
                <property name="hitTypes">
                    <list>
                        <value>SPECIFIC</value>
                    </list>
                </property>
            </bean>
        </property>
        <property name="filteredMatchAndSiteDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.CDDFilteredMatchDAOImpl"/>
        </property>
        <property name="excludeSites" value="${exclude.sites.from.output}"/>
        <property name="rawMatchDAO" ref="cddRawMatchDAO"/>
        <property name="rawSiteDAO" ref="cddRawSiteDAO"/>
    </bean>


    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: CDD !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
    <!-- ######################## Dependencies ############################  -->

    <bean id="cddRawMatchDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">
        <constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.CDDRawMatch"/>
    </bean>

    <bean id="cddRawSiteDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.RawSiteDAOImpl">
        <constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.CDDRawSite"/>
    </bean>

    <bean id="signatureLibraryReleaseCDD" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="CDD"/>
        <constructor-arg type="java.lang.String" ref="cddSignatureLibraryRelease"/>
    </bean>

    <bean id="cddSignatureLibraryRelease" class="java.lang.String">
        <constructor-arg value="${cdd.signature.library.release}"/>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
</beans>