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yiwenheyiwenhe
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Updates for v5.5_20220906 release
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-2
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3 files changed

+69
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‎admin/src/main/resources/META-INF/spring/admin.properties‎

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@@ -237,7 +237,8 @@ fhcrc1.OCCC.dependencies.data.location=file:${CTD2_DATA_HOME}/submissions/202106
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emory.hypomorph.SMAD4.SMAD3.PPI.inducer.discovery.data.location=file:${CTD2_DATA_HOME}/submissions/20210806-emory_hypomorph_SMAD4_SMAD3_PPI_inducer_discovery/20210806-emory_hypomorph_SMAD4_SMAD3_PPI_inducer_discovery.txt
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stanford.arid1a.story.data.location=file:${CTD2_DATA_HOME}/submissions/20210818-stanford_arid1a_story/20210818-stanford_arid1a_story.txt
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emory.hypomorph.SMAD4.SMAD3.PPI.inducer.discovery.story.data.location=file:${CTD2_DATA_HOME}/submissions/20210831-emory_hypomorph_SMAD4_SMAD3_PPI_inducer_discovery_story/20210831-emory_hypomorph_SMAD4_SMAD3_PPI_inducer_discovery_story.txt
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fhcrc1.KRAS.mutant.PDAC.dependencies.data.location=file:${CTD2_DATA_HOME}/submissions/20220805-fhcrc1_KRAS_mutant_PDAC_dependencies/20220805-fhcrc1_KRAS_mutant_PDAC_dependencies.txt
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emory.mutation.directed.neo.ppi.data.location=file:${CTD2_DATA_HOME}/submissions/20220831-emory_mutation_directed_neo_ppi/20220831-emory_mutation_directed_neo_ppi.txt
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‎admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml‎

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@@ -1909,4 +1909,22 @@
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</bean>
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</property>
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</bean>
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<bean name="fhcrc1KRASMutantPDACDependenciesReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
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<property name="resources" value="${fhcrc1.KRAS.mutant.PDAC.dependencies.data.location}" />
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<property name="delegate">
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<bean class="org.springframework.batch.item.file.FlatFileItemReader">
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<property name="lineMapper" ref="fhcrc1KRASMutantPDACDependenciesLineMapper" />
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<property name="linesToSkip" value="7" />
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</bean>
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</property>
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</bean>
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<bean name="emoryMutationDirectedNeoPpiReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
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<property name="resources" value="${emory.mutation.directed.neo.ppi.data.location}" />
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<property name="delegate">
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<bean class="org.springframework.batch.item.file.FlatFileItemReader">
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<property name="lineMapper" ref="emoryMutationDirectedNeoPpiLineMapper" />
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<property name="linesToSkip" value="7" />
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</bean>
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</property>
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</bean>
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</beans>

‎admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml‎

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@@ -1060,11 +1060,21 @@
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<batch:chunk reader="stanfordArid1aStoryReader" processor="observationDataProcessor" writer="observationDataWriter"/>
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</batch:tasklet>
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</batch:step>
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<batch:step id="emoryHypomorphSMAD4SMAD3PPIinducerDiscoveryStoryStep" parent="observationDataStep">
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<batch:step id="emoryHypomorphSMAD4SMAD3PPIinducerDiscoveryStoryStep" parent="observationDataStep" next="fhcrc1KRASMutantPDACDependenciesStep">
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<batch:tasklet>
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<batch:chunk reader="emoryHypomorphSMAD4SMAD3PPIinducerDiscoveryStoryReader" processor="observationDataProcessor" writer="observationDataWriter"/>
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</batch:tasklet>
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</batch:step>
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<batch:step id="fhcrc1KRASMutantPDACDependenciesStep" parent="observationDataStep" next="emoryMutationDirectedNeoPpiStep">
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<batch:tasklet>
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<batch:chunk reader="fhcrc1KRASMutantPDACDependenciesReader" processor="observationDataProcessor" writer="observationDataWriter"/>
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</batch:tasklet>
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</batch:step>
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<batch:step id="emoryMutationDirectedNeoPpiStep" parent="observationDataStep">
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<batch:tasklet>
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<batch:chunk reader="emoryMutationDirectedNeoPpiReader" processor="observationDataProcessor" writer="observationDataWriter"/>
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</batch:tasklet>
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</batch:step>
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</batch:job>
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<bean id="observationDataStep" class="org.springframework.batch.core.step.item.SimpleStepFactoryBean" abstract="true">
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<property name="names" value="dummy,submission_name,submission_date,template_name,compound_name1,gene1,gene2,gene3,compound_name2,ec50_1,reference,story_location,ec50_2,data_portal"/>
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</bean>
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<bean name="fhcrc1KRASMutantPDACDependenciesLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
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<property name="fieldSetMapper" ref="observationDataMapper" />
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<property name="lineTokenizer" ref="fhcrc1KRASMutantPDACDependenciesLineTokenizer" />
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</bean>
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<bean name="fhcrc1KRASMutantPDACDependenciesLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
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<property name="delimiter" value="&#9;"/>
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<property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,gene_2,gene_3,drug_1,drug_2,drug_3,perturbagen_1,gene_4,disease_1,evidence_1,evidence_2,evidence_3,evidence_4,evidence_5,story_location"/>
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</bean>
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<bean name="emoryMutationDirectedNeoPpiLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
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<property name="fieldSetMapper" ref="observationDataMapper" />
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<property name="lineTokenizer" ref="emoryMutationDirectedNeoPpiLineTokenizer" />
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</bean>
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<bean name="emoryMutationDirectedNeoPpiLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
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<property name="delimiter" value="&#9;"/>
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<property name="names" value="dummy,submission_name,submission_date,template_name,protein_1,protein_2,differential_score,ds_qvalue,reference,mutation"/>
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</bean>
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<!-- shared helper beans -->
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<bean name="observationTemplateMap" class="java.util.HashMap">
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<entry key="stanford_arid1a_story:story_location" value="evidence:readString:createObservedFileEvidence" />
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<entry key="stanford_arid1a_story:reference_1" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="stanford_arid1a_story:reference_2" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="emory_mutation_directed_neo_ppi:protein_1" value="subject:findGenesBySymbol" />
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<entry key="emory_mutation_directed_neo_ppi:protein_2" value="subject:findGenesBySymbol" />
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<entry key="emory_mutation_directed_neo_ppi:differential_score" value="evidence:readDouble:createObservedNumericEvidence" />
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<entry key="emory_mutation_directed_neo_ppi:ds_qvalue" value="evidence:readDouble:createObservedNumericEvidence" />
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<entry key="emory_mutation_directed_neo_ppi:reference" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="emory_mutation_directed_neo_ppi:mutation" value="evidence:readString:createObservedLabelEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:gene_1" value="subject:findGenesBySymbol" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:gene_2" value="subject:findGenesBySymbol" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:gene_3" value="subject:findGenesBySymbol" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:drug_1" value="subject:findCompoundsByName" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:drug_2" value="subject:findCompoundsByName" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:drug_3" value="subject:findCompoundsByName" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:perturbagen_1" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:gene_4" value="subject:findGenesBySymbol" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:disease_1" value="subject:findTissueSampleByName" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:evidence_1" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:evidence_2" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:evidence_3" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:evidence_4" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:evidence_5" value="evidence:readString:createObservedUrlEvidence" />
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<entry key="fhcrc1_KRAS_mutant_PDAC_dependencies:story_location" value="evidence:readString:createObservedFileEvidence" />
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</map>
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</constructor-arg>

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