From c4d75bb7959f7c0a24dda8d055ecc986875a3991 Mon Sep 17 00:00:00 2001
From: Yiwen He <yiwenhe@gmail.com>
Date: Wed, 24 Feb 2021 09:51:19 -0500
Subject: [PATCH] Updates for v4.3.1_20210214 release

---
 .../META-INF/spring/admin.properties          |  1 +
 .../observationDataApplicationContext.xml     |  9 ++++++
 ...bservationDataSharedApplicationContext.xml | 31 +++++++++++++++++--
 3 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/admin/src/main/resources/META-INF/spring/admin.properties b/admin/src/main/resources/META-INF/spring/admin.properties
index 998c2ab6..daa7e13d 100644
--- a/admin/src/main/resources/META-INF/spring/admin.properties
+++ b/admin/src/main/resources/META-INF/spring/admin.properties
@@ -227,6 +227,7 @@ ucsf1.kras.sl.drug.screen.data.location=file:${CTD2_DATA_HOME}/submissions/20200
 columbia.oncosig.ppi.networks.data.location=file:${CTD2_DATA_HOME}/submissions/20201028-columbia_oncosig_ppi_networks/20201028-columbia_oncosig_ppi_networks.txt
 columbia.oncosig.shrna.knockdown.data.location=file:${CTD2_DATA_HOME}/submissions/20201028-columbia_oncosig_shrna_knockdown/20201028-columbia_oncosig_shrna_knockdown.txt
 dfci.creb5.story.data.location=file:${CTD2_DATA_HOME}/submissions/20201111-dfci_creb5_story/20201111-dfci_creb5_story.txt
+broad.peroxisome.data.location=file:${CTD2_DATA_HOME}/submissions/20210108-broad_peroxisome/20210108-broad_peroxisome.txt
 
 
 
diff --git a/admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml b/admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml
index 3a0775a1..3e882721 100644
--- a/admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml
+++ b/admin/src/main/resources/META-INF/spring/observationDataApplicationContext.xml
@@ -1828,4 +1828,13 @@
             </bean>
         </property>
     </bean>
+    <bean name="broadPeroxisomeReader" class="org.springframework.batch.item.file.MultiResourceItemReader">
+        <property name="resources" value="${broad.peroxisome.data.location}" />
+        <property name="delegate">
+            <bean class="org.springframework.batch.item.file.FlatFileItemReader">
+                <property name="lineMapper" ref="broadPeroxisomeLineMapper" />
+                <property name="linesToSkip" value="7" />
+            </bean>
+        </property>
+    </bean>
 </beans>
diff --git a/admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml b/admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml
index f2b727be..888fca0a 100644
--- a/admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml
+++ b/admin/src/main/resources/META-INF/spring/observationDataSharedApplicationContext.xml
@@ -1017,11 +1017,16 @@
                 <batch:chunk reader="columbiaOncosigShrnaKnockdownReader" processor="observationDataProcessor" writer="observationDataWriter"/>
 	    </batch:tasklet>
 	</batch:step>
-	<batch:step id="dfciCreb5StoryStep" parent="observationDataStep">
+	<batch:step id="dfciCreb5StoryStep" parent="observationDataStep" next="broadPeroxisomeStep">
 	    <batch:tasklet>
                 <batch:chunk reader="dfciCreb5StoryReader" processor="observationDataProcessor" writer="observationDataWriter"/>
 	    </batch:tasklet>
 	</batch:step>
+	<batch:step id="broadPeroxisomeStep" parent="observationDataStep">
+	    <batch:tasklet>
+                <batch:chunk reader="broadPeroxisomeReader" processor="observationDataProcessor" writer="observationDataWriter"/>
+	    </batch:tasklet>
+	</batch:step>
     </batch:job>
 
     <bean id="observationDataStep" class="org.springframework.batch.core.step.item.SimpleStepFactoryBean" abstract="true">
@@ -2848,7 +2853,14 @@
         <property name="names" value="dummy,submission_name,submission_date,template_name,gene_1,disease_1,drug_1,gene_2,publication_reference,story_location,evidence_ontology_1,evidence_ontology_2,evidence_ontology_3,evidence_ontology_4,evidence_ontology_5"/>
     </bean>
 
-
+    <bean name="broadPeroxisomeLineMapper" class="org.springframework.batch.item.file.mapping.DefaultLineMapper">
+        <property name="fieldSetMapper" ref="observationDataMapper" />
+        <property name="lineTokenizer" ref="broadPeroxisomeLineTokenizer" />
+    </bean>
+    <bean name="broadPeroxisomeLineTokenizer" class="org.springframework.batch.item.file.transform.DelimitedLineTokenizer" >
+        <property name="delimiter" value="&#9;"/>
+        <property name="names" value="dummy,submission_name,submission_date,template_name,disease_1,disease_2,cell_line_1,cell_line_2,gene_1,gene_2,gene_3,gene_4,gene_5,gene_6,story_location,reference_1,reference_2,reference_3"/>
+    </bean>
 
     <!-- shared helper beans -->
     <bean name="observationTemplateMap" class="java.util.HashMap">
@@ -4903,7 +4915,20 @@
 		<entry key="ucsf1_kras_sl_drug_screen:cell_line" value="subject:findCellLineByName" />
 		<entry key="ucsf1_kras_sl_drug_screen:percent_change_auc" value="evidence:readDouble:createObservedNumericEvidence" />
 		<entry key="ucsf1_kras_sl_drug_screen:reference" value="evidence:readString:createObservedUrlEvidence" />
-
+		<entry key="broad_peroxisome:disease_1" value="subject:findTissueSampleByName" />
+		<entry key="broad_peroxisome:disease_2" value="subject:findTissueSampleByName" />
+		<entry key="broad_peroxisome:cell_line_1" value="subject:findCellLineByName" />
+		<entry key="broad_peroxisome:cell_line_2" value="subject:findCellLineByName" />
+		<entry key="broad_peroxisome:gene_1" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:gene_2" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:gene_3" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:gene_4" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:gene_5" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:gene_6" value="subject:findGenesBySymbol" />
+		<entry key="broad_peroxisome:story_location" value="evidence:readString:createObservedFileEvidence" />
+		<entry key="broad_peroxisome:reference_1" value="evidence:readString:createObservedUrlEvidence" />
+		<entry key="broad_peroxisome:reference_2" value="evidence:readString:createObservedUrlEvidence" />
+		<entry key="broad_peroxisome:reference_3" value="evidence:readString:createObservedUrlEvidence" />
             </map>
         </constructor-arg>
     </bean>