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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 common beans-->
<!--Old versions are switched off because they aren't in the database anymore-->
<import resource="jobCDD-context.xml"/>
<import resource="jobCoils-context.xml"/>
<import resource="jobGene3d-context.xml"/>
<import resource="jobHAMAP-context.xml"/>
<import resource="jobMobiDBLite-context.xml"/>
<import resource="jobPanther-context.xml"/>
<import resource="jobPIRSF-context.xml"/>
<import resource="jobPfam-context.xml"/>
<import resource="jobPhobius-context.xml"/>
<import resource="jobPrints-42.0-context.xml"/>
<import resource="jobProDom-2006.1-context.xml"/>
<import resource="jobPrositeProfiles-context.xml"/>
<import resource="jobPrositePatterns-context.xml"/>
<import resource="jobSFLD-context.xml"/>
<import resource="jobSignalP_EUK-context.xml"/>
<import resource="jobSignalP_GRAM_POSITIVE-context.xml"/>
<import resource="jobSignalP_GRAM_NEGATIVE-context.xml"/>
<import resource="jobSMART-context.xml"/>
<import resource="jobTIGRFAM-context.xml"/>
<import resource="jobSuperFamily-1.75-context.xml"/>
<import resource="jobTMHMM-context.xml"/>
<import resource="classpath:/spring/persistence/persistence-config-context.xml"/>
<import resource="classpath:/spring/uapro-db-access-context.xml"/>
<import resource="classpath:/spring/match-converter-context.xml"/>
<import resource="classpath:/spring/berkeley-oxm-context.xml"/>
<import resource="classpath:/spring/jobs/outputWriter/jobWriteOutput-context.xml"/>
<bean id="jobs" class="uk.ac.ebi.interpro.scan.management.model.Jobs">
<property name="jobList">
<list>
<ref bean="jobLoadFromFasta"/>
<ref bean="jobLoadNucleicAcidSequence"/>
<ref bean="jobLoadFromUniParc"/>
<ref bean="jobWriteOutput"/>
<!-- Analyses -->
<!--Old versions are not present because they aren't in the H2 database anymore-->
<ref bean="jobCDD"/>
<ref bean="jobCoils"/>
<ref bean="jobGene3d"/>
<ref bean="jobHAMAP"/>
<ref bean="jobMobiDBLite"/>
<ref bean="jobPanther"/>
<ref bean="jobPfam"/>
<ref bean="jobPhobius"/>
<ref bean="jobPIRSF" />
<ref bean="jobPRINTS-42.0"/>
<ref bean="jobProDom-2006.1"/>
<ref bean="jobPrositeProfiles"/>
<ref bean="jobPrositePatterns"/>
<ref bean="jobSFLD"/>
<ref bean="jobSignalP_EUK"/>
<ref bean="jobSignalP_GRAM_POSITIVE"/>
<ref bean="jobSignalP_GRAM_NEGATIVE"/>
<ref bean="jobSMART"/>
<ref bean="jobTIGRFAM"/>
<ref bean="jobSuperFamily-1.75"/>
<ref bean="jobTMHMM"/>
</list>
</property>
<property name="baseDirectoryTemporaryFiles" value="${temporary.file.directory}"/>
</bean>
<!-- String properties common to all jobs -->
<bean id="fastaFileNameTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND].fasta"/>
</bean>
<bean id="rawAnalaysisOutputFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND].raw.out"/>
</bean>
<bean id="rawAnalaysisOutputOneFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND]_one.raw.out"/>
</bean>
<bean id="rawAnalaysisOutputTwoFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND]_two.raw.out"/>
</bean>
<bean id="rawAnalaysisOutputThreeFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND]_three.raw.out"/>
</bean>
<bean id="rawAnalaysisOutputTbloutFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND].raw.tblout.out"/>
</bean>
<bean id="rawAnalaysisOutputDomTbloutFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND].raw.domtblout.out"/>
</bean>
<bean id="rawAnalaysisOutputAlignmentsFileTemplate" class="java.lang.String">
<constructor-arg value="[PROTSTART]_[PROTEND].raw.align.out"/>
</bean>
<bean id="clcMonitor" class="uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationMonitor">
<property name="binaryRunDelay" value="${binary.run.delay}"/>
<property name="checkForkInProgress" value="${check.fork.progress}"/>
<property name="verboseLog" value="${verbose.log}"/>
<property name="verboseLogLevel" value="${verbose.log.level}"/>
</bean>
<!--<import resource="all-jobs-context.xml"/>-->
<!-- ######################## JOB: job-load-from-fasta ############################ -->
<bean id="jobLoadFromFasta" class="uk.ac.ebi.interpro.scan.management.model.Job">
<property name="description" value="Load proteins from a fasta file and create required JobInstance objects"/>
<property name="analysis" value="false"/>
</bean>
<!-- STEP 1 -->
<bean id="stepLoadFromFasta"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep">
<property name="job" ref="jobLoadFromFasta"/>
<!-- This step has no dependencies, so will be scheduled first for its associated job. -->
<property name="stepDescription"
value="Load proteins from a fasta file and create required JobInstance objects"/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="2"/>
<property name="serialGroup" value="LOAD_PROTEINS"/>
<property name="fastaFileLoader" ref="proteinFastaFileLoader"/>
<property name="jobs" ref="jobs"/>
<property name="stepInstanceDAO" ref="stepInstanceDAO"/>
</bean>
<!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: jobLoadFromFasta !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ######################## JOB: jobLoadFromUniParc ############################ -->
<bean id="jobLoadFromUniParc" class="uk.ac.ebi.interpro.scan.management.model.Job">
<property name="description" value="Load proteins from UniParc and create required JobInstance objects"/>
<property name="analysis" value="false"/>
</bean>
<!-- STEP 1 -->
<bean id="stepLoadFromUniParc"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.UniparcProteinLoadStep">
<property name="job" ref="jobLoadFromUniParc"/>
<!-- This step has no dependencies, so will be scheduled first for its associated job. -->
<property name="stepDescription" value="Load proteins from UniParc and create required JobInstance objects"/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="2"/>
<property name="serialGroup" value="LOAD_PROTEINS"/>
<property name="uniparcLoader">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.uniparcdb.LoadUniParcFromDBImpl">
<property name="jdbcTemplate" ref="targetJdbcTemplate"/>
<property name="rowCallbackHandlerTemplate">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.uniparcdb.UniParcDBRowCallbackHandler">
<property name="proteinLoader" ref="proteinLoader"/>
<property name="sequenceLoadListener" ref="proteinLoadListener"/>
</bean>
</property>
<property name="maximumProteins" value="${ebi.uniparc.protein.load.size}"/>
<property name="xrefDao" ref="xrefDAO"/>
</bean>
</property>
</bean>
<!-- ######################## JOB: jobLoadNucleicAcidSequence ############################ -->
<bean id="jobLoadNucleicAcidSequence" class="uk.ac.ebi.interpro.scan.management.model.Job">
<property name="description"
value="Load nucleic acid sequence, run getOrf and load proteins to create required JobInstance objects"/>
<property name="analysis" value="false"/>
</bean>
<!-- STEP 1 -->
<bean id="stepLoadNucleicAcidFromFasta"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep">
<property name="job" ref="jobLoadNucleicAcidSequence"/>
<!-- This step has no dependencies, so will be scheduled first for its associated job. -->
<property name="stepDescription" value="Load nucleic acids from a fasta file"/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="2"/>
<property name="serialGroup" value="LOAD_NUCLEIC_ACID"/>
<property name="fastaFileLoader">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadNucleotideFastaFile">
<property name="sequenceLoader">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.NucleotideSequenceLoader">
<property name="sequenceInsertBatchSize" value="500"/>
<property name="nucleotideSequenceDAO" ref="nucleotideSequenceDAO"/>
<property name="nucleotideSequenceXrefDAO" ref="nucleotideSequenceXrefDAO"/>
</bean>
</property>
<property name="inputType" value="NucleotideSequence"/>
</bean>
</property>
<!-- Don't need the following two properties, that have been copied from load Protein fasta file above.-->
<property name="jobs" ref="jobs"/>
</bean>
<!-- STEP 2 -->
<bean id="stepRunGetOrf"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.nucleotide.RunGetOrfStep">
<!--Abstract parameter-->
<property name="job" ref="jobLoadNucleicAcidSequence"/>
<property name="stepDescription" value="Run GetOrf to predict open reading frames from nucleic acid sequence"/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="1"/>
<!-- Need to consider this parameter "outputFileNameTemplate"- this is normally the output from the binary
but in this case
the output is defined as a parameter (fastaFileNameTemplate). This may contain error messages,
so needs to be handled in some way.-->
<property name="outputFileNameTemplate" value="getorf.err.txt"/>
<!--More specific parameter-->
<property name="fullPathToBinary" value="${binary.getorf.path}"/>
<property name="fastaFilePath" ref="getOrfResultFile"/>
<property name="minSize" value="${getorf.minsize}"/>
</bean>
<!-- STEP 3 -->
<bean id="stepRunParseGetOrf"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.nucleotide.RunGetOrfParserStep">
<!--Abstract parameter-->
<property name="job" ref="jobLoadNucleicAcidSequence"/>
<property name="stepDescription" value="Run GetOrf to predict open reading frames from nucleic acid sequence"/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="dependsUpon">
<list>
<ref bean="stepRunGetOrf"/>
</list>
</property>
<property name="fullPathToPython" value="${python3.command}"/>
<property name="fullPathToBinary" value="${binary.getorf.parser.path}"/>
<property name="orfsFilterSize" value="${binary.getorf.parser.filtersize}"/>
<property name="binarySwitches" value="${getorf.parser.binary.switches}"/>
<property name="orfsFilePath" ref="getOrfResultFile"/>
<property name="fastaFilePath" ref="getOrfParserResultFile"/>
<property name="retries" value="3"/>
<property name="requiresDatabaseAccess" value="false"/>
</bean>
<!-- STEP 3 (depends on both Step 1 and 2) -->
<bean id="stepLoadOrfFromFasta"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep">
<!--Abstract parameter-->
<property name="job" ref="jobLoadNucleicAcidSequence"/>
<!-- This step has no dependencies, so will be scheduled first for its associated job. -->
<property name="stepDescription"
value="Load proteins from a fasta file generated by GetOrf and create required JobInstance objects. Also creates OpenReadingFrame records to connect the proteins to the NucleicAcid records."/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="2"/>
<property name="serialGroup" value="LOAD_PROTEINS"/>
<property name="dependsUpon">
<list>
<ref bean="stepLoadNucleicAcidFromFasta"/>
<ref bean="stepRunParseGetOrf"/>
</list>
</property>
<!--More specific parameter-->
<property name="fastaFileLoader">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadProteinFastaFile">
<property name="sequenceLoader">
<bean class="uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader">
<property name="proteinPrecalcLookupBatchSize" value="50"/>
<!-- MUST NOT EXCEED 1000 ?? maybe need to revise this after more testing : gift -->
<property name="proteinInsertBatchSize" value="${precalculated.match.protein.insert.batch.size}"/>
<property name="proteinInsertBatchSizeNoLookup" value="${precalculated.match.protein.insert.batch.size.nolookup}"/>
<property name="proteinDAO" ref="proteinDAO"/>
<property name="proteinLookup" ref="precalculatedLookup"/>
<property name="getOrfOutput" value="true"/>
<property name="nucleotideSequenceDAO" ref="nucleotideSequenceDAO"/>
<property name="openReadingFrameDAO" ref="openReadingFrameDAO"/>
<property name="descriptionLineParser" ref="getOrfDescriptionLineParser"/>
</bean>
</property>
</bean>
</property>
<property name="overridingFastaFileName" ref="getOrfParserResultFile"/>
<property name="jobs" ref="jobs"/>
<property name="stepInstanceDAO" ref="stepInstanceDAO"/>
</bean>
<!-- STEP 4 - cleanup (depends on step 3) -->
<bean id="stepDeleteGetOrfOutput"
class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep">
<!--Abstract parameter-->
<property name="job" ref="jobLoadNucleicAcidSequence"/>
<property name="stepDescription"
value="Delete the GetOrf output fasta file following successful loading of the proteins."/>
<property name="createStepInstancesForNewProteins" value="false"/>
<property name="retries" value="1"/>
<property name="dependsUpon" ref="stepLoadOrfFromFasta"/>
<!--More specific parameter-->
<property name="fileNameTemplate">
<list>
<ref bean="getOrfResultFile"/>
<ref bean="getOrfErrorFile"/>
</list>
</property>
</bean>
<!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: jobLoadNucleicAcidSequence !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: jobLoadFromUniParc !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ######################## Dependencies ############################ -->
<bean id="getOrfResultFile" class="java.lang.String">
<constructor-arg value="orfs.fasta"/>
</bean>
<bean id="getOrfParserResultFile" class="java.lang.String">
<constructor-arg value="orfs.filtered.fasta"/>
</bean>
<bean id="getOrfErrorFile" class="java.lang.String">
<constructor-arg value="getorf.err.txt"/>
</bean>
<bean id="outputResultDevNullFile" class="java.lang.String">
<constructor-arg value="devnull.txt"/>
</bean>
<bean id="getOrfDescriptionLineParser"
class="uk.ac.ebi.interpro.scan.io.getorf.GetOrfDescriptionLineParser"/>
<bean id="proteinFastaFileLoader" class="uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadProteinFastaFile">
<property name="sequenceLoader" ref="proteinLoader"/>
<property name="inputType" value="Protein"/>
</bean>
<bean id="precalculatedLookup" class="uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup">
<property name="interproscanVersion" value="${i5.version}"/>
<property name="preCalcMatchClient" ref="preCalcMatchClient"/>
<property name="lookupStoreToI5ModelDAO" ref="lookupStoreToI5ModelDAO"/>
</bean>
<bean id="preCalcMatchClient" class="uk.ac.ebi.interpro.scan.precalc.client.MatchHttpClient">
<constructor-arg ref="berkeleyUnmarshaller"/>
<property name="url" value="${precalculated.match.lookup.service.url}"/>
<property name="proxyHost" value="${precalculated.match.lookup.service.proxy.host}"/>
<property name="proxyPort" value="${precalculated.match.lookup.service.proxy.port}"/>
</bean>
<bean id="proteinLoader" class="uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader">
<property name="proteinPrecalcLookupBatchSize" value="${precalculated.match.protein.lookup.batch.size}"/>
<!-- MUST NOT EXCEED 1000 -->
<!-- maybe the comment above only applies to when using the lookup match service : gn-->
<property name="proteinInsertBatchSize" value="${precalculated.match.protein.insert.batch.size}"/>
<property name="proteinInsertBatchSizeNoLookup" value="${precalculated.match.protein.insert.batch.size.nolookup}"/>
<property name="proteinDAO" ref="proteinDAO"/>
<property name="proteinLookup" ref="precalculatedLookup"/>
<property name="getOrfOutput" value="false"/>
</bean>
<bean id="proteinLoadListener"
class="uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.StepCreationSequenceLoadListener">
<property name="stepInstanceDAO" ref="stepInstanceDAO"/>
<property name="completionJob" ref="jobWriteOutput"/>
<property name="jobs" ref="jobs"/>
</bean>
<bean id="sequenceTypes" class="java.util.HashSet">
<constructor-arg>
<set>
<value>p</value>
<value>n</value>
</set>
</constructor-arg>
</bean>
<!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
</beans>
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