From 71cfd27015a7c044470db9543ba22dc9a0909801 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Wed, 29 May 2024 09:55:21 +0200
Subject: [PATCH] test: modify the file configuration.test.yaml used by the
 JUnit tets to update it with CellBase MongoDB configuration specified from
 the command line

On branch TASK-6026
Changes to be committed:
	modified:   cellbase-lib/pom.xml
	modified:   cellbase-lib/src/test/resources/configuration.test.yaml
	modified:   pom.xml
---
 cellbase-lib/pom.xml                          | 18 +++++++++++++
 .../test/resources/configuration.test.yaml    | 26 +++++++++----------
 pom.xml                                       |  9 +++++++
 3 files changed, 40 insertions(+), 13 deletions(-)

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 64c5a27a22..bfb68c86c0 100644
--- 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
index 1322d2fa52..e1750e7b4b 100644
--- a/cellbase-lib/src/test/resources/configuration.test.yaml
+++ b/cellbase-lib/src/test/resources/configuration.test.yaml
@@ -7,24 +7,24 @@ 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: "${JUNIT.CELLBASE.DB.PASSWORD}"
 defaultOutdir: "/tmp"
 download:
   ensembl:
@@ -32,7 +32,7 @@ download:
       host: ensembldb.ensembl.org:3306
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensembl.org/pub
   ensemblGenomes:
@@ -40,7 +40,7 @@ download:
       host: mysql-eg-publicsql.ebi.ac.uk:4157
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensemblgenomes.org/pub
   geneUniprotXref:
diff --git a/pom.xml b/pom.xml
index 0f729c9d0d..61e1f1d7fa 100644
--- 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>