Merge branch '1464-build-issue' into 'master'

Resolve "remove support for upgrade from versions before 12.1"

Closes #1464

See merge request !1292

.gitlab-ci.yml

@@ -524,7 +524,7 @@ test_deploy_with_db_without_superadmin_rights:
   script:
     - apt-get update
     - DEBIAN_FRONTEND=noninteractive apt-get install -y postgresql-client
-    - mkdir /etc/minerva
+    - mkdir -p /etc/minerva
     - echo "database.uri=jdbc:postgresql://postgres:5432/test" > /etc/minerva/db.properties
     - echo "database.username=test" >> /etc/minerva/db.properties
     - echo "database.password=test" >> /etc/minerva/db.properties

CHANGELOG

-minerva (16.0.0~alpha.1) stable; urgency=medium
+minerva (16.0.0~alpha.2) stable; urgency=medium
+  * Backward incompatibility: debian package cannot be upgraded from version
+    prior to 12.1.0 (#1464)
   * Small improvement: homomultimer information is provided in API (#1468)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 19 Mar 2021 10:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Mar 2021 10:00:00 +0200
 
 minerva (16.0.0~alpha.1) stable; urgency=medium
   * Backward incompatibility: deprecated columns in data overlays are no longer

CellDesigner-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>CellDesigner-plugin</artifactId>
 	<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>

annotation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>annotation</artifactId>
 	<name>Annotation module</name>
@@ -18,7 +18,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer dao -->
@@ -26,7 +26,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer cell designer parser (we need access 
@@ -34,13 +34,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->

build.xml

@@ -64,7 +64,7 @@
 	</target>
 
 
-	<target name="maven-build" depends="gitversion, maven-build-windows, maven-build-unix" />
+	<target name="maven-build" depends="maven-build-windows, maven-build-unix" />
 
 	<target name="maven-build-windows" if="isWindows">
 		<exec dir="." executable="cmd">
@@ -78,7 +78,7 @@
 		</exec>
 	</target>
 
-	<target name="maven-build-with-doc" depends="gitversion, maven-build-with-doc-windows, maven-build-with-doc-unix" />
+	<target name="maven-build-with-doc" depends="maven-build-with-doc-windows, maven-build-with-doc-unix" />
 
 	<target name="maven-build-with-doc-windows" if="isWindows">
 		<exec dir="." executable="cmd">
@@ -108,32 +108,6 @@
 		</exec>
 	</target>
 
-	<target name="deployMapFiles">
-		<copy todir="${tomcat.deploy.dir}/map_images">
-			<fileset dir="map_images" />
-		</copy>
-	</target>
-
-
-	<target name="gitversion">
-		<exec executable="git" outputproperty="gitversion">
-			<arg value="rev-parse" />
-			<arg value="HEAD" />
-		</exec>
-
-		<tstamp>
-			<format property="build.time" pattern="dd/MM/yyyy HH:mm" unit="hour" />
-		</tstamp>
-		<echo>GIT Version: ${gitversion}
-            Build timestamp: ${build.time}
-        </echo>
-
-		<echo file="web/src/main/webapp/version.txt">${gitversion}
-            ${build.time}
-        </echo>
-		<copy file="CHANGELOG" tofile="web/src/main/webapp/CHANGELOG" overwrite="true" />
-	</target>
-
 	<target name="debian-pkg" depends="maven-build">
 		<exec executable="debian/create-debian-pkg.sh" />
 	</target>

commons/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>commons</artifactId>
 	<name>Mapviewer commons</name>

commons/src/main/java/lcsb/mapviewer/common/Configuration.java

@@ -3,6 +3,7 @@ package lcsb.mapviewer.common;
 import java.io.*;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.jar.Manifest;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -215,25 +216,17 @@ public final class Configuration {
     systemBuildVersion = "Unknown";
     systemBuildTime = "Unknown";
     systemVersion = "Unknown";
-    File buildVersionFile = null;
-    File changelogFile = null;
+    File manifestFile = null;
     if (baseDir == null) {
-      buildVersionFile = new File("version.txt");
-      changelogFile = new File("CHANGELOG");
+      manifestFile = new File("META-INF/MANIFEST.MF");
     } else {
-      buildVersionFile = new File(baseDir + "version.txt");
-      changelogFile = new File(baseDir + "CHANGELOG");
+      manifestFile = new File(baseDir + "MANIFEST.MF");
     }
-    if (buildVersionFile.exists()) {
-      loadSystemBuildVersion(buildVersionFile);
+    if (manifestFile.exists()) {
+      loadSystemBuildVersion(manifestFile);
     } else {
-      logger.error(buildVersionFile.getAbsoluteFile() + " doesn't exist.");
-    }
-
-    if (changelogFile.exists()) {
-      loadSystemVersion(changelogFile);
-    } else {
-      logger.error(changelogFile.getAbsoluteFile() + " doesn't exist.");
+      
+      logger.error(manifestFile.getAbsoluteFile() + " doesn't exist.", new Exception());
     }
   }
 
@@ -245,35 +238,27 @@ public final class Configuration {
    */
   protected static void loadSystemBuildVersion(File file) {
     try {
-      BufferedReader reader = new BufferedReader(new FileReader(file));
-      systemBuildVersion = reader.readLine().trim();
-      systemBuildTime = reader.readLine().trim();
-      reader.close();
-    } catch (IOException e) {
-      logger.error(e);
-    }
-  }
-
-  /**
-   * Loads system version from debian changelog file.
-   * 
-   * @param file
-   *          debian changelog file
-   */
-  protected static void loadSystemVersion(File file) {
-    try {
-      BufferedReader reader = new BufferedReader(new FileReader(file));
-      String line = reader.readLine();
-
-      int startIndex = line.indexOf("(");
-      int endIndex = line.indexOf(")");
-
-      if (startIndex >= 0 && endIndex >= 0) {
-        systemVersion = line.substring(startIndex + 1, endIndex);
-      } else {
-        logger.error("Invalid CHANGELOG file. Cannot find system version in line: " + line);
+      boolean problem = false;
+      Manifest manifest = new Manifest(new FileInputStream(file));
+      systemBuildTime = manifest.getMainAttributes().getValue("git-timestamp");
+      if (systemBuildTime == null) {
+        systemBuildTime = "Unknown";
+        problem = true;
+      }
+      systemBuildVersion = manifest.getMainAttributes().getValue("git-version");
+      if (systemBuildVersion == null) {
+        systemBuildVersion = "Unknown";
+        problem = true;
+      }
+      systemVersion = manifest.getMainAttributes().getValue("version");
+      if (systemVersion == null) {
+        systemVersion = "Unknown";
+        problem = true;
+      }
+      
+      if (problem) {
+        logger.warn("MANIFEST.MF file does not contain required information.");
       }
-      reader.close();
     } catch (IOException e) {
       logger.error(e);
     }

commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java

@@ -42,7 +42,7 @@ public class ConfigurationTest extends CommonTestFunctions {
   @Test
   public void testLoadSystemBuildVersion2() {
     Configuration.loadSystemVersion((String) null);
-    Configuration.loadSystemVersion(new File("unknown.xxx"));
+    Configuration.loadSystemVersion("/tmp");
     assertEquals("Unknown", Configuration.getSystemBuildVersion(null));
     assertEquals("Unknown", Configuration.getSystemBuild(null));
     assertEquals("Unknown", Configuration.getSystemVersion(null));
@@ -50,15 +50,15 @@ public class ConfigurationTest extends CommonTestFunctions {
 
   @Test
   public void testGetSystemBuildVersion() {
-    assertEquals("100", Configuration.getSystemBuildVersion("testFiles/version/", true));
-    assertEquals("100", Configuration.getSystemBuildVersion(null, false));
-    assertEquals("101", Configuration.getSystemVersion("testFiles/version/", true));
+    assertEquals("78606521500fd349b603a77e9f64cfe57517c1a6", Configuration.getSystemBuildVersion("testFiles/version/", true));
+    assertEquals("78606521500fd349b603a77e9f64cfe57517c1a6", Configuration.getSystemBuildVersion(null, false));
+    assertEquals("16.0.0~alpha.2", Configuration.getSystemVersion("testFiles/version/", true));
   }
 
   @Test
   public void testGetSystemBuild() {
-    assertEquals("102", Configuration.getSystemBuild("testFiles/version/", true));
-    assertEquals("102", Configuration.getSystemBuild(null, false));
+    assertEquals("2021-03-29T08:44:16+0200", Configuration.getSystemBuild("testFiles/version/", true));
+    assertEquals("2021-03-29T08:44:16+0200", Configuration.getSystemBuild(null, false));
   }
 
   @Test
@@ -83,9 +83,12 @@ public class ConfigurationTest extends CommonTestFunctions {
   }
 
   @Test
-  public void testLoadInvalidSystemVersion() {
-    Configuration.loadSystemVersion(new File("testFiles/version/INVALID_CHANGELOG"));
-    assertEquals(1, super.getErrors().size());
+  public void testLoadMissingSystemVersion() {
+    FrameworkVersion version = Configuration.getFrameworkVersion("testFiles/invalid_version/");
+    assertEquals("Unknown", version.getGitVersion());
+    assertEquals("Unknown", version.getTime());
+    assertEquals("Unknown", version.getVersion());
+    assertEquals(1, super.getWarnings().size());
   }
 
   @Test

commons/testFiles/invalid_version/MANIFEST.MF

+Manifest-Version: 1.0
+Created-By: Apache Maven 3.6.3
+Built-By: gawi
+Build-Jdk: 11.0.10

commons/testFiles/version/CHANGELOG

-minerva (101) stable; urgency=medium
-
-  * Initial release 
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
- 
\ No newline at end of file

commons/testFiles/version/INVALID_CHANGELOG

-blablabla
\ No newline at end of file

commons/testFiles/version/MANIFEST.MF

+Manifest-Version: 1.0
+Created-By: Apache Maven 3.6.3
+Built-By: gawi
+Build-Jdk: 11.0.10
+git-timestamp: 2021-03-29T08:44:16+0200
+git-version: 78606521500fd349b603a77e9f64cfe57517c1a6
+version: 16.0.0~alpha.2

commons/testFiles/version/version.txt

-100
- 102
\ No newline at end of file

converter-CellDesigner/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>converter-CellDesigner</artifactId>
 	<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->

converter-SBGNML/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>converter-SBGNML</artifactId>
 
@@ -20,26 +20,26 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 			<scope>test</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>

converter-graphics/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>converter-graphics</artifactId>
 	<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- Log4J2-->

converter-sbml/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~alpha.1</version>
+		<version>16.0.0~alpha.2</version>
 	</parent>
 	<artifactId>converter-sbml</artifactId>
 	<name>converter-sbml</name>
@@ -40,22 +40,22 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->
@@ -154,7 +154,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.0~alpha.1</version>
+			<version>16.0.0~alpha.2</version>
 			<scope>test</scope>
 		</dependency>
 

converter/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>16.0.0~alpha.1</version>
+    <version>16.0.0~alpha.2</version>
   </parent>
   
   <artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>16.0.0~alpha.1</version>
+      <version>16.0.0~alpha.2</version>
     </dependency>
 		<dependency>
 			<groupId>xerces</groupId>

debian/create-debian-pkg.sh

@@ -9,23 +9,15 @@ versionCompLt() {
     [ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
 }
 
-# file with bash code generating DB schema diffs for different versions
-dbschemadiff=management_scripts/db_schema_and_diff.sh
-
 #Where source file of the debian package should be placed
 SRC_DIR=debian/src
 
 #File that should be deployed on tomcat
 TOMCAT_FILE=web/target/*.war
 
-#Directory with database schema
-DB_SCHEMA_DIR=persist/src/main/resources/db/migration/postgres
-
 ROOT_DIR=`pwd`
 
-
 # where dn script files should be stored on the debian system
-DB_SCRIPT_DIR="\/usr\/share\/minerva\/schema"
 LOG_FILE="\/var\/log\/minerva-install.log"
 
 #clean build directories
@@ -52,20 +44,9 @@ cp debian/scripts/common.sh $SRC_DIR/
 #copy changelog file
 cp CHANGELOG $ROOT_DIR/debian/template/changelog
 
-# set $versions and $current_version; generate upgrade scripts in SRC_DIR
-DBSCRIPT_DEST_DIR=$SRC_DIR
-MAX_DB_VERSION_FOR_MIGRTION=12.1.0~alpha
-source $dbschemadiff
-
 current_version=`cat CHANGELOG |grep minerva |head -1 | cut -f2 -d'(' | cut -f1 -d')'`
 
 echo "Current version: " $current_version
-echo "Flyway was introduced in version: " $MAX_DB_VERSION_FOR_MIGRTION
-
-#------------------------------------------
-# Now we have all db schema diff files. Let's start preparing 
-# debian package
-#------------------------------------------
 
 #dh_make requires directory name to be like <package>-<version>
 # this points to the directory
@@ -92,11 +73,6 @@ find -name '*.ex' ! -name 'minerva*' -type f -exec rm -f {} +
 
 sed -i "s/__CURRENT_VERSION__/$current_version/g" common.sh
 sed -i "s/__LOG_FILE__/$LOG_FILE/g" common.sh
-#__DB_SCRIPT_DIR__ in our scripts points to place where db schema files are placed
-#in the filesystem where package is installed
-sed -i "s/__DB_SCRIPT_DIR__/$DB_SCRIPT_DIR/g" common.sh
-
-sed -i "s/__MAX_DB_VERSION_FOR_MIGRTION__/$MAX_DB_VERSION_FOR_MIGRTION/g" common.sh
 
 sed -i -e "1r common.sh" debian/config
 sed -i -e "1r common.sh" debian/postinst
@@ -107,14 +83,6 @@ sed -i -e "1r common.sh" debian/prerm
 
 
 
-#put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
-#escaped
-echo db_0_to_$MAX_DB_VERSION_FOR_MIGRTION".sql" /usr/share/minerva/schema >> debian/install
-for version in ${versions[*]}
-do
-	echo db_"$version"_to_$MAX_DB_VERSION_FOR_MIGRTION".sql" /usr/share/minerva/schema >> debian/install;
-done
-
 #set proper architecture
 arch=`dpkg --print-architecture`
 echo "Architecture: $arch" >>debian/control

debian/scripts/common.sh

@@ -4,9 +4,6 @@ log(){
 }
 LOG_FILE="__LOG_FILE__"
 
-DB_SCRIPT_DIR="__DB_SCRIPT_DIR__"
-MAX_DB_VERSION_FOR_MIGRTION="__MAX_DB_VERSION_FOR_MIGRTION__"
-
 #new (current) version of the package
 CURRENT_VERSION="__CURRENT_VERSION__"
 #if we update package then this will be the old version of the package