Merge pull request #692 from opencb/TASK-6026

TASK-6026 - Refactor the build.sh, test.sh, and run.sh scripts to remove commands and unify the scripts
opencb · Jun 19, 2024 · 4ecad11 · 4ecad11
2 parents 0a15bef + cd1e418
commit 4ecad11
Show file tree

Hide file tree

Showing 3 changed files with 40 additions and 13 deletions.
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
@@ -187,4 +187,22 @@
         </dependency>
 
     </dependencies>
+
+    <build>
+        <testResources>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <excludes>
+                    <exclude>configuration.test.yaml</exclude>
+                </excludes>
+            </testResource>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <includes>
+                    <include>configuration.test.yaml</include>
+                </includes>
+                <filtering>true</filtering>
+            </testResource>
+        </testResources>
+    </build>
 </project>
diff --git a/cellbase-lib/src/test/resources/configuration.test.yaml b/cellbase-lib/src/test/resources/configuration.test.yaml
@@ -7,40 +7,40 @@ maintainerContact: joaquin.tarraga@zettagenomics.com
 secretKey: "xPacig89igHSieEnveJEi4KCfdEslhmssC3vui1JJQGgDQ0y8v"
 databases:
   mongodb:
-    host: localhost:27017
-    user: 'cellbase'
-    password: 'cellbase'
+    host: "${JUNIT.CELLBASE.DB.MONGODB.HOST}"
+    user: "${JUNIT.CELLBASE.DB.USER}"
+    password: "${JUNIT.CELLBASE.DB.PASSWORD}"
     options:
-      authenticationDatabase: 'admin'
-      authenticationMechanism: 'SCRAM-SHA-256'
+      authenticationDatabase: "${JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE}"
+      authenticationMechanism: "${JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM}"
       readPreference: ''
       replicaSet: ''
       connectionsPerHost: 20
   neo4j:
     hsapiens:
-      host: "${CELLBASE.DB.NEO4J.HOST}"
-      user: "${CELLBASE.DB.USER}"
-      password: "${CELLBASE.DB.PASSWORD}"
+      host: "${JUNIT.CELLBASE.DB.NEO4J.HOST}"
+      user: "${JUNIT.CELLBASE.DB.USER}"
+      password: "${JUNIT.CELLBASE.DB.PASSWORD}"
     mmusculus:
-      host: "${CELLBASE.DB.NEO4J.HOST}"
-      user: "${CELLBASE.DB.USER}"
-      password: "${CELLBASE.DB.PASSWORD}"
+      host: "${JUNIT.CELLBASE.DB.NEO4J.HOST}"
+      user: "${JUNIT.CELLBASE.DB.USER}"
+      password: "${JUNIT.CELLBASE.DB.PASSWORD}"
 defaultOutdir: "/tmp"
 download:
   ensembl:
     database:
       host: ensembldb.ensembl.org:3306
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensembl.org/pub
   ensemblGenomes:
     database:
       host: mysql-eg-publicsql.ebi.ac.uk:4157
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensemblgenomes.org/pub
   geneUniprotXref:

diff --git a/pom.xml b/pom.xml
@@ -615,6 +615,15 @@
                 <CELLBASE.DB.MONGODB.READPREFERENCE>secondaryPreferred</CELLBASE.DB.MONGODB.READPREFERENCE>
                 <CELLBASE.SERVER.REST.PORT>9090</CELLBASE.SERVER.REST.PORT>
                 <CELLBASE.MONITOR.AGENT></CELLBASE.MONITOR.AGENT>
+
+                <!--
+                Configuration for JUnit tets (using the file configuration.test.yaml)
+                -->
+                <JUNIT.CELLBASE.DB.MONGODB.HOST>localhost:27017</JUNIT.CELLBASE.DB.MONGODB.HOST>
+                <JUNIT.CELLBASE.DB.USER>cellbase</JUNIT.CELLBASE.DB.USER>
+                <JUNIT.CELLBASE.DB.PASSWORD>cellbase</JUNIT.CELLBASE.DB.PASSWORD>
+                <JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>admin</JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>
+                <JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM>SCRAM-SHA-256</JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM>
             </properties>
         </profile>