Skip to content

Commit

Permalink
Updates for v4.1_20200615 release
Browse files Browse the repository at this point in the history
  • Loading branch information
@easaki
easaki committed Jun 28, 2020
1 parent c01210d commit 99b0d20
Show file tree
Hide file tree
Showing 3 changed files with 117 additions and 1 deletion.
3 changes: 3 additions & 0 deletions admin/src/main/resources/META-INF/spring/admin.properties
View file
Original file line number Diff line number Diff line change
Expand Up @@ -220,6 +220,9 @@ ucsf.gorlin.nes.cell.tumor.formation.data.location=file:${CTD2_DATA_HOME}/submis
ucsf.gse1.tumor.formation.data.location=file:${CTD2_DATA_HOME}/submissions/20200303-ucsf_gse1_tumor_formation/20200303-ucsf_gse1_tumor_formation.txt
ucsf.mycn.transformation.data.location=file:${CTD2_DATA_HOME}/submissions/20200303-ucsf_mycn_transformation/20200303-ucsf_mycn_transformation.txt
broad.por.data.location=file:${CTD2_DATA_HOME}/submissions/20200422-broad_por/20200422-broad_por.txt
dfci.creb5.data.locaton=file:${CTD2_DATA_HOME}/submissions/20200528-dfci_creb5/20200528-dfci_creb5.txt
dfci.mrt.vulnerablility.data.location=file:${CTD2_DATA_HOME}/submissions/20200601-dfci_mrt_vulnerability/20200601-dfci_mrt_vulnerability.txt
dfci.shoc2.data.location=file:${CTD2_DATA_HOME}/submissions/20200601-dfci_shoc2/20200601-dfci_shoc2.txt



Expand Down
29 changes: 29 additions & 0 deletions admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1766,4 +1766,33 @@
</property>
</bean>


<bean name="dfciCreb5DataLocatonReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
<property name="resources" value="${dfci.creb5.data.locaton}"/>
<property name="delegate">
<bean class="org.springframework.batch.item.file.FlatFileItemReader">
<property name="lineMapper" ref="dfciCreb5DataLocatonLineMapper" />
<property name="linesToSkip" value="7" />
</bean>
</property>
</bean>
<bean name="dfciMrtVulnerablilityDataLocationReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
<property name="resources" value="${dfci.mrt.vulnerablility.data.location}" />
<property name="delegate">
<bean class="org.springframework.batch.item.file.FlatFileItemReader">
<property name="lineMapper" ref="dfciMrtVulnerablilityDataLocationLineMapper" />
<property name="linesToSkip" value="7" />
</bean>
</property>
</bean>
<bean name="dfciShoc2DataLocationReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
<property name="resources" value="${dfci.shoc2.data.location}" />
<property name="delegate">
<bean class="org.springframework.batch.item.file.FlatFileItemReader">
<property name="lineMapper" ref="dfciShoc2DataLocationLineMapper" />
<property name="linesToSkip" value="7" />
</bean>
</property>
</bean>

</beans>
86 changes: 85 additions & 1 deletion admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -982,11 +982,26 @@
<batch:chunk reader="ucsfMycnTransformationReader" processor="observationDataProcessor" writer="observationDataWriter"/>
</batch:tasklet>
</batch:step>
<batch:step id="broadPorStep" parent="observationDataStep">
<batch:step id="broadPorStep" parent="observationDataStep" next="dfciCreb5DataLocatonStep">
<batch:tasklet>
<batch:chunk reader="broadPorReader" processor="observationDataProcessor" writer="observationDataWriter"/>
</batch:tasklet>
</batch:step>
<batch:step id="dfciCreb5DataLocatonStep" parent="observationDataStep" next="dfciShoc2DataLocationStep">
<batch:tasklet>
<batch:chunk reader="dfciCreb5DataLocatonReader" processor="observationDataProcessor" writer="observationDataWriter"/>
</batch:tasklet>
</batch:step>
<batch:step id="dfciShoc2DataLocationStep" parent="observationDataStep" next="dfciMrtVulnerablilityDataLocationStep">
<batch:tasklet>
<batch:chunk reader="dfciShoc2DataLocationReader" processor="observationDataProcessor" writer="observationDataWriter"/>
</batch:tasklet>
</batch:step>
<batch:step id="dfciMrtVulnerablilityDataLocationStep" parent="observationDataStep" >
<batch:tasklet>
<batch:chunk reader="dfciMrtVulnerablilityDataLocationReader" processor="observationDataProcessor" writer="observationDataWriter"/>
</batch:tasklet>
</batch:step>



Expand Down Expand Up @@ -2749,6 +2764,30 @@
<property name="delimiter" value="&#9;"/>
<property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,gene_2,cell_line_1,cell_line_2,disease_1,disease_2,story_location,reference_1,reference_2,evidence_ontology"/>
</bean>
<bean name="dfciCreb5DataLocatonLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
<property name="fieldSetMapper" ref="observationDataMapper" />
<property name="lineTokenizer" ref="dfciCreb5DataLocatonLineTokenizer" />
</bean>
<bean name="dfciCreb5DataLocatonLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
<property name="delimiter" value="&#9;"/>
<property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,disease_1,drug_1,gene_2,ref_1,figure_1,figure_2,figure_5,evidence_ontology_1,evidence_ontology_2,evidence_ontology_3,evidence_ontology_4,evidence_ontology_5"/>
</bean>
<bean name="dfciShoc2DataLocationLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
<property name="fieldSetMapper" ref="observationDataMapper" />
<property name="lineTokenizer" ref="dfciShoc2DataLocationLineTokenizer" />
</bean>
<bean name="dfciShoc2DataLocationLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
<property name="delimiter" value="&#9;"/>
<property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,disease_1,disease_2,drug_1,gene_2,gene_3,gene_4,gene_5,ref_1,figure_1,figure_4,figure_5,evidence_ontology_1,evidence_ontology_2,evidence_ontology_3,evidence_ontology_4"/>
</bean>
<bean name="dfciMrtVulnerablilityDataLocationLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
<property name="fieldSetMapper" ref="observationDataMapper" />
<property name="lineTokenizer" ref="dfciMrtVulnerablilityDataLocationLineTokenizer" />
</bean>
<bean name="dfciMrtVulnerablilityDataLocationLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
<property name="delimiter" value="&#9;"/>
<property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,gene_2,gene_3,disease,gene_4,drug_1,drug_2,reference,figure_2,evidence_ontology_1,evidence_ontology_2,evidence_ontology_3,evidence_ontology_4,evidence_ontology_5,figure_4,figure_1"/>
</bean>


<!-- shared helper beans -->
Expand Down Expand Up @@ -4724,6 +4763,51 @@
<entry key="ucsf_mycn_transformation:evidence_ontology_term" value="evidence:readString:createObservedUrlEvidence" />
<entry key="ucsf_mycn_transformation:figure_1" value="evidence:readString:createObservedFileEvidence" />

<entry key="dfci_creb5:gene_1" value="subject:findGenesBySymbol" />
<entry key="dfci_creb5:disease_1" value="subject:findTissueSampleByName" />
<entry key="dfci_creb5:drug_1" value="subject:findCompoundsByName" />
<entry key="dfci_creb5:gene_2" value="subject:findGenesBySymbol" />
<entry key="dfci_creb5:ref_1" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_creb5:figure_1" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_creb5:figure_2" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_creb5:figure_5" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_creb5:evidence_ontology_1" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_creb5:evidence_ontology_2" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_creb5:evidence_ontology_3" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_creb5:evidence_ontology_4" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_creb5:evidence_ontology_5" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:gene_1" value="subject:findGenesBySymbol" />
<entry key="dfci_mrt_vulnerability:gene_2" value="subject:findGenesBySymbol" />
<entry key="dfci_mrt_vulnerability:gene_3" value="subject:findGenesBySymbol" />
<entry key="dfci_mrt_vulnerability:disease" value="subject:findTissueSampleByName" />
<entry key="dfci_mrt_vulnerability:gene_4" value="subject:findGenesBySymbol" />
<entry key="dfci_mrt_vulnerability:drug_1" value="subject:findCompoundsByName" />
<entry key="dfci_mrt_vulnerability:drug_2" value="evidence:readString:createObservedLabelEvidence" />
<entry key="dfci_mrt_vulnerability:reference" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:figure_2" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_mrt_vulnerability:evidence_ontology_1" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:evidence_ontology_2" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:evidence_ontology_3" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:evidence_ontology_4" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:evidence_ontology_5" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_mrt_vulnerability:figure_4" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_mrt_vulnerability:figure_1" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_shoc2:gene_1" value="subject:findGenesBySymbol" />
<entry key="dfci_shoc2:disease_1" value="subject:findTissueSampleByName" />
<entry key="dfci_shoc2:disease_2" value="subject:findTissueSampleByName" />
<entry key="dfci_shoc2:drug_1" value="subject:findCompoundsByName" />
<entry key="dfci_shoc2:gene_2" value="subject:findGenesBySymbol" />
<entry key="dfci_shoc2:gene_3" value="subject:findGenesBySymbol" />
<entry key="dfci_shoc2:gene_4" value="subject:findGenesBySymbol" />
<entry key="dfci_shoc2:gene_5" value="subject:findGenesBySymbol" />
<entry key="dfci_shoc2:ref_1" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_shoc2:figure_1" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_shoc2:figure_4" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_shoc2:figure_5" value="evidence:readString:createObservedFileEvidence" />
<entry key="dfci_shoc2:evidence_ontology_1" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_shoc2:evidence_ontology_2" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_shoc2:evidence_ontology_3" value="evidence:readString:createObservedUrlEvidence" />
<entry key="dfci_shoc2:evidence_ontology_4" value="evidence:readString:createObservedUrlEvidence" />


</map>
Expand Down

0 comments on commit 99b0d20

Please sign in to comment.