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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: SMART ############################  -->
    <bean id="jobSMART" class="uk.ac.ebi.interpro.scan.management.model.Job">
        <property name="description"
                  value="SMART allows the identification and analysis of domain architectures based on Hidden Markov Models or HMMs"/>
        <property name="analysis" value="true"/>
        <property name="libraryRelease" ref="signatureLibraryReleaseSmart"/>
        <property name="mandatoryParameters">
            <map key-type="java.lang.String" value-type="java.lang.String">
                <entry key="smart.hmm.bin.path" value-ref="fullPathToHmmFile"/>
                <!-- NOTE: SMART "overlapping" and "THRESHOLDS" files are required to perform full SMART post processing,
                but are licensed therefore cannot be included with InterProScan -->
            </map>
        </property>
        <property name="active" value="true" />
    </bean>

    <bean id="fullPathToHmmFile" class="java.lang.String">
        <constructor-arg value="${smart.hmm.bin.path}"/>
    </bean>

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

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


    <!--TODO - The run binary step for HMMER should choose between search or scan, depending
        TODO - upon the number of proteins being searched.  True for both HMMER2 & 3.
        TODO - PROBLEM - HMMER2 hmmsearch ONLY ACCEPTS ONE MODEL AT A TIME. -->

    <!-- STEP 2 -->
    <bean id="stepSMARTRunBinary"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.smart.RunSmartBinaryStep"
          parent="abstractSMARTStep">
        <!-- In example command line below, replace _ with -
        hmmpfam _-cpu 1 _-acc -A 0 smart.HMMs.bin  XXX.fasta -->
        <property name="dependsUpon" ref="stepSMARTWriteFastaFile"/>
        <property name="stepDescription" value="Run HMM on selected proteins"/>

        <property name="fullPathToHmmsearchBinary" value="${binary.hmmer2.hmmpfam.path}"/>
        <property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
        <property name="binarySwitches" value="${hmmer2.hmmpfam.switches.smart} ${hmmer2.hmmpfam.cpu.switch.smart}"/>
        <property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
        <property name="retries" value="3"/>
        <property name="fullPathToHmmFile" ref="fullPathToHmmFile"/>
        <property name="requiresDatabaseAccess" value="false"/>
        <property name="smartResourceManager" ref="smartResourceManager"/>
    </bean>

    <bean id="smartResourceManager" class="uk.ac.ebi.interpro.scan.business.postprocessing.smart.SmartResourceManager">
        <property name="overlappingFileResource" value="file:${smart.overlapping.path}"/>
        <property name="thresholdFileResource" value="file:${smart.threshold.path}"/>
    </bean>

    <bean id="stepSMARTDeleteFastaFile"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
          parent="abstractSMARTStep">
        <property name="dependsUpon" ref="stepSMARTRunBinary"/>
        <property name="stepDescription" value="Delete the fasta file following successful run of HMMER2"/>
        <property name="fileNameTemplate" ref="fastaFileNameTemplate"/>
    </bean>

    <bean id="stepSMARTStoreRawMatches"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.smart.ParseSmartHmmpfamOutputStep"
          parent="abstractSMARTStep">
        <property name="dependsUpon" ref="stepSMARTRunBinary"/>
        <property name="stepDescription" value="Parse the HMMER2 output and store as Filtered matches."/>
        <property name="outputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
        <property name="rawMatchDAO" ref="smartRawMatchDAO"/>
        <property name="serialGroup" value="PARSE_SMART"/>
        <property name="parser">
            <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer2.HmmPfamParser">
                <property name="signatureLibrary" value="SMART"/>
                <property name="signatureLibraryRelease" ref="smartSignatureLibraryReleaseVersion"/>
                <property name="hmmer2ParserSupport">
                    <bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer2.SmartHmmer2ParserSupport">
                        <property name="signatureLibraryRelease" ref="smartSignatureLibraryReleaseVersion"/>
                    </bean>
                </property>
            </bean>
        </property>
    </bean>

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

    <bean id="stepSmartPostProcessing"
          class="uk.ac.ebi.interpro.scan.management.model.implementations.smart.SmartPostProcessingStep"
          parent="abstractSMARTStep">
        <property name="dependsUpon" ref="stepSMARTStoreRawMatches"/>
        <property name="stepDescription" value="Performs post processing and Match persistence on SMART data"/>
        <property name="postProcessor">
            <bean class="uk.ac.ebi.interpro.scan.business.postprocessing.smart.SmartPostProcessing">
                <property name="smartResourceManager" ref="smartResourceManager"/>
                <property name="overlappingFileParser">
                    <bean class="uk.ac.ebi.interpro.scan.io.smart.SmartOverlappingFileParser"/>
                </property>
                <property name="thresholdFileParser">
                    <bean class="uk.ac.ebi.interpro.scan.io.smart.SmartThresholdFileParser"/>
                </property>
                <property name="proteinDAO" ref="proteinDAO"/>
            </bean>
        </property>
        <property name="serialGroup" value="HMMER2_POST_PROCESSING"/>
        <property name="signatureLibraryRelease" ref="smartSignatureLibraryReleaseVersion"/>
        <property name="rawMatchDAO" ref="smartRawMatchDAO"/>
        <property name="filteredMatchDAO">
            <bean class="uk.ac.ebi.interpro.scan.persistence.SmartFilteredMatchDAOImpl"/>
        </property>
    </bean>
    <!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: SMART !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->

    <!-- ######################## Dependencies ############################  -->
    <bean id="smartRawMatchDAO"
          class="uk.ac.ebi.interpro.scan.persistence.raw.SmartHmmer2RawMatchDAOImpl">
    </bean>

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

    <bean id="smartSignatureLibraryReleaseVersion" class="java.lang.String">
        <constructor-arg value="${smart.signature.library.release}"/>
    </bean>
    <!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!!  -->
</beans>