Merge pull request #1437 from EBISPOT/2.x-dev

2.x dev
EBISPOT · Sep 19, 2024 · 5e338ab · 5e338ab
2 parents 787e10b + 3b30055
commit 5e338ab
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Showing 4 changed files with 97 additions and 13 deletions.
diff --git a/goci-dependencies/pom.xml b/goci-dependencies/pom.xml
@@ -348,18 +348,39 @@
 
 
     <repositories>
-   	    <repository>
-   	        <id>nexus-public</id>
-   	        <name>Public Repository</name>
-   	        <url>https://www.ebi.ac.uk/spot/nexus/repository/maven-public/</url>
-   	        <releases>
-   	            <enabled>true</enabled>
-   	        </releases>
-   	        <snapshots>
-   	            <enabled>true</enabled>
-   	        </snapshots>
-   	    </repository>
-   	</repositories>
+        <repository>
+            <id>spot-releases</id>
+            <name>Releases</name>
+            <url>https://wwwdev.ebi.ac.uk/gwas/nexus/repository/maven-releases/</url>
+            <releases>
+                <enabled>true</enabled>
+            </releases>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+        </repository>
+        <repository>
+            <id>spot-snapshots</id>
+            <name>Snapshot</name>
+            <url>https://wwwdev.ebi.ac.uk/gwas/nexus/repository/maven-snapshots/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+
+        <!--  <repository>
+              <id>central</id>
+              <name>Maven Central</name>
+              <layout>default</layout>
+              <url>https://repo1.maven.org/maven2</url>
+              <snapshots>
+                  <enabled>false</enabled>
+              </snapshots>
+          </repository>-->
+    </repositories>
 
     <!--<repositories>-->
         <!--<repository>-->

diff --git a/goci-parent/pom.xml b/goci-parent/pom.xml
@@ -145,6 +145,32 @@
         <tag>HEAD</tag>
     </scm>
 
+    <pluginRepositories>
+        <pluginRepository>
+            <id>spot-releases</id>
+            <name>Releases</name>
+            <url>https://wwwdev.ebi.ac.uk/gwas/nexus/repository/maven-releases/</url>
+        </pluginRepository>
+        <pluginRepository>
+            <id>spot-snapshots</id>
+            <name>Snapshot</name>
+            <url>https://wwwdev.ebi.ac.uk/gwas/nexus/repository/maven-snapshots/</url>
+        </pluginRepository>
+    </pluginRepositories>
+
+
+
+        <!--  <repository>
+              <id>central</id>
+              <name>Maven Central</name>
+              <layout>default</layout>
+              <url>https://repo1.maven.org/maven2</url>
+              <snapshots>
+                  <enabled>false</enabled>
+              </snapshots>
+          </repository>-->
+
+
     <!-- Maven repository and site deployment -->
     <!-- TODO: Set this up to work with GitHub repo -->
     <!--<distributionManagement>-->

diff --git a/...oci-public-data-export/src/main/java/uk/ac/ebi/spot/goci/service/DataDeletionService.java b/...oci-public-data-export/src/main/java/uk/ac/ebi/spot/goci/service/DataDeletionService.java
@@ -4,6 +4,8 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 import uk.ac.ebi.spot.goci.model.Ancestry;
 import uk.ac.ebi.spot.goci.model.Association;
 import uk.ac.ebi.spot.goci.model.Publication;
@@ -63,10 +65,11 @@ public void deleteNonPublicStudies(){
     }
 
 
+    @Transactional
     public void deletePublicationsWithoutStudies() {
         List<Publication>  pubs = publicationService.findAll();
         pubs.forEach(pub ->  {
-            if(pub.getStudies().isEmpty()) {
+            if(pub.getStudies() != null && pub.getStudies().isEmpty()) {
                 getLog().info(" Deleting Pmid without studies {}",pub.getPubmedId());
                 publicationService.deletePublicationWithoutStudies(pub);
             }

diff --git a/goci-tools/goci-public-data-export/src/main/resources/logback-local.xml b/goci-tools/goci-public-data-export/src/main/resources/logback-local.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+    <!--<property name="LOG_FILE" value="data_export.log" />-->
+    <property name="LOG_PATTERN" value=" %d{yyyy-MM-dd HH:mm:ss} [%thread] %-5level %logger{36} - %msg%n" />
+    <include resource="org/springframework/boot/logging/logback/defaults.xml" />
+    <include resource="org/springframework/boot/logging/logback/console-appender.xml" />
+
+    <appender name="Console"
+              class="ch.qos.logback.core.ConsoleAppender">
+        <layout class="ch.qos.logback.classic.PatternLayout">
+            <Pattern>
+                %d{yyyy-MM-dd HH:mm:ss} [%thread] %-5level %logger{36} - %msg%n
+            </Pattern>
+        </layout>
+    </appender>
+
+    <appender name="CONSOLE" class="ch.qos.logback.core.ConsoleAppender">
+        <!-- <filter class="ch.qos.logback.classic.filter.LevelFilter">
+             <level>WARN</level>
+             <onMatch>DENY</onMatch>
+         </filter>-->
+        <encoder>
+            <pattern>${LOG_PATTERN}</pattern>
+        </encoder>
+    </appender>
+
+    <root level="DEBUG">
+        <appender-ref ref="CONSOLE" />
+        <!--   <appender-ref ref="FILE" /> -->
+       </root>
+    <logger name="uk.ac.ebi.spot.gwas" level="DEBUG" additivity="false">
+        <appender-ref ref="CONSOLE"/>
+    </logger>
+   </configuration>