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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: Coils ############################  -->
    <bean id="jobCoils" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description" value="Prediction of Coiled Coil Regions in Proteins"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleaseCoils"/>
        <property name="doRunLocally" value="false"/>
        <property name="active" value="true" />
    </bean>

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

    <!-- STEP 1 -->
    <bean id="stepCoilsWriteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
          parent="abstractCoilsStep">
        <!-- 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_COILS"/>
    </bean>

    <!-- STEP 2 -->
    <bean id="stepCoilsRunBinary"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.coils.RunCoilsBinaryStep"
          parent="abstractCoilsStep">
        <!-- /ebi/sp/pro1/interpro/binaries/32_bit_Linux/ncoils -c -m /ebi/sp/pro1/interpro/data/members/coils/2.2/new_coil.mat <  -->
        <property name="dependsUpon" ref="stepCoilsWriteFastaFile"/>
        <property name="stepDescription" value="Run fingerprintscan Binary for selected proteins"/>
        <property name="fullPathToBinary" value="${binary.coils.path}"/>
        <property name="binarySwitches" value="${coils.binary.switches}"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="requiresDatabaseAccess" value="false"/>
    </bean>

    <bean id="stepCoilsDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractCoilsStep">
        <property name="dependsUpon" ref="stepCoilsRunBinary"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of FPS"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>

    <bean id="stepCoilsStoreFilteredMatches"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.coils.ParseCoilsOutputStep"
          parent="abstractCoilsStep">
        <property name="dependsUpon" ref="stepCoilsRunBinary"/>
        <property name="stepDescription" value="Parse the Coils binary output and store as Filtered matches."/>
        <property name="coilsOutputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.coils.CoilsMatchParser"/>
        </property>
        <property name="matchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.CoilsFilteredMatchDAOImpl">
                <constructor-arg ref="latestCoilsSignatureLibraryRelease"/>
            </bean>
        </property>
        <property name="serialGroup" value="PARSE_COILS"/>
    </bean>

    <bean id="stepCoilsDeleteRawOutput"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractCoilsStep">
        <property name="dependsUpon" ref="stepCoilsStoreFilteredMatches"/>
        <property name="stepDescription"
                  value="Delete the raw output file following successful parsing and persistence"/>
        <property name="fileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
    </bean>

    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: Coils !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
    <!-- ######################## Dependencies ############################  -->
    <bean id="signatureLibraryReleaseCoils" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
        <constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="COILS"/>
        <constructor-arg type="java.lang.String" ref="latestCoilsSignatureLibraryRelease"/>
    </bean>

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

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