debian package doesn't migrate sql files that are managed by flyway

CHANGELOG

+minerva (12.1.0~alpha.0) experimental; urgency=medium
+  * Feature: genome browser with gene variants
+  * Feature: support of all CellDesigner element modifications
+  * Feature: ldap authentication
+  * Feature: multicolored anchors for data overlays
+  * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
+    weren't provided properly
+  * Small improvement: annotations from RHEA are handled
+  * Small improvement: description of a grouped results in improved
+  * Small improvement: selection of required annotation on map upload improved
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 25 Jul 2018 10:00:00 +0200
+
 minerva (12.0.1) stable; urgency=medium
   * Bug fix: setting default zoom level on submap
   * Bug fix: opened submap had different background then current selection
@@ -8,7 +21,7 @@ minerva (12.0.1) stable; urgency=medium
   * Bug fix: map is repositioned when info window is outside of current view in
     OpenLayers library
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 22 Jul 2018 10:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
 
 minerva (12.0.0) stable; urgency=medium
   * Feature: There is alternative OpenLayers map engine available

debian/create-debian-pkg.sh

@@ -22,7 +22,7 @@ DOC_DIR=doc
 TOMCAT_FILE=web/target/web-1.0.war
 
 #Directory with database schema
-DB_SCHEMA_DIR=persist/src/db
+DB_SCHEMA_DIR=persist/src/main/resources/db/migration
 
 ROOT_DIR=`pwd`
 
@@ -46,7 +46,7 @@ cp $DB_SCHEMA_DIR/base.sql $SRC_DIR/db_0.sql
 
 #copy manual documentation
 cp $DOC_DIR/description.txt $SRC_DIR/minerva.txt
-gzip $SRC_DIR/minerva.txt
+gzip -n $SRC_DIR/minerva.txt
 
 #copy configuration of logrotate
 cp debian/logrotate/* $SRC_DIR/
@@ -58,16 +58,18 @@ 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
 
 echo "Current version: " $current_version
+echo "Flyway was introduced in version: " $MAX_DB_VERSION_FOR_MIGRTION
 
 # check if the changelog contains info about new version
 tmpVar=`cat debian/template/changelog | grep "minerva ($current_version)"|wc -l`
 if [ $tmpVar -eq "0" ] 
 then
 	echo "Invalid changelog file. Please modify debian/template/changelog to contain information about current version";
-	exit 1;
+	e-n xit 1;
 fi
 
 
@@ -120,6 +122,7 @@ sed -i "s/__DB_PORT__/$DB_PORT/g" common.sh
 sed -i "s/__DB_DATABASE_NAME__/$DB_DATABASE_NAME/g" common.sh
 sed -i "s/__DB_USERNAME__/$DB_USERNAME/g" common.sh
 sed -i "s/__DB_PASSWORD__/$DB_PASSWORD/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/postinst
 sed -i -e "1r common.sh" debian/postrm
@@ -132,12 +135,12 @@ sed -i -e "1r common.sh" debian/prerm
 #put scripts into $DB_SCRIPT_DIR (it's a bit different than varaiable because it's not
 #escaped
 echo db_0.sql /usr/share\/minerva/schema >> debian/install
-echo db_0_to_$current_version".sql" /usr/share/minerva/schema >> debian/install
+echo db_0_to_$MAX_DB_VERSION_FOR_MIGRTION".sql" /usr/share/minerva/schema >> debian/install
 for version in ${versions[*]}
 do
 	if [ "$version" != "$current_version" ]
 	then
-		echo db_"$version"_to_$current_version".sql" /usr/share/minerva/schema >> debian/install;
+		echo db_"$version"_to_$MAX_DB_VERSION_FOR_MIGRTION".sql" /usr/share/minerva/schema >> debian/install;
 	fi
 done
 
@@ -152,7 +155,8 @@ echo minerva.txt.gz /usr/share/doc/minerva/minerva.txt.gz >> debian/install;
 echo minerva /etc/logrotate.d >> debian/install;
 
 #remove some sample file
-rm debian/package.doc-base.EX
+rm debian/*.EX
+rm debian/*.ex
 
 #build debian package
 debuild -us -uc

debian/scripts/common.sh

@@ -5,6 +5,7 @@ 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__"

debian/template/control

 Source: minerva
 Priority: optional
 Maintainer: Piotr Gawron <piotr.gawron@uni.lu>
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
 #Vcs-Git: git://anonscm.debian.org/collab-maint/minerva.git
 #Vcs-Browser: http://anonscm.debian.org/?p=collab-maint/minerva.git;a=summary
 

debian/template/postinst

@@ -31,11 +31,15 @@ case "$1" in
 			#install base version of the framework
 			exec_sql_file "$DB_SCRIPT_DIR/db_0.sql"
 			#install patch to current version
-			exec_sql_file "$DB_SCRIPT_DIR/db_0_to_${CURRENT_VERSION}.sql"
+			exec_sql_file "$DB_SCRIPT_DIR/db_0_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql"
 
 		else
 			#if we update the package
-			exec_sql_file "$DB_SCRIPT_DIR/db_${OLD_VERSION}_to_${CURRENT_VERSION}.sql"
+			if [ -f $DB_SCRIPT_DIR/db_${OLD_VERSION}_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql ]; then
+				exec_sql_file "$DB_SCRIPT_DIR/db_${OLD_VERSION}_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql"
+			else
+				log "INFO: File doesn't exist: $DB_SCRIPT_DIR/db_${OLD_VERSION}_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql"
+			fi
 		fi
 
 		#print a disclaimer

management_scripts/db_schema_and_diff.sh

@@ -4,8 +4,9 @@
 # files)
 
 # Precondition: the following variables have to be correctly initialised
-# * DB_SCHEMA_DIR        set to the directory containing database initialisation and upgrade sql commands
-# * DBSCRIPT_DEST_DIR    set to the directory that will be populated with database upgrade scripts
+# * DB_SCHEMA_DIR                 set to the directory containing database initialisation and upgrade sql commands
+# * DBSCRIPT_DEST_DIR             set to the directory that will be populated with database upgrade scripts
+# * MAX_DB_VERSION_FOR_MIGRTION   set to the max version number that should be used for generating migration scripts; further version will be managed by flyway
 
 # Postcondition:
 # * versions is set to the available MINERVA versions (bash array)
@@ -20,12 +21,22 @@ versions=();
 current_version=-1;
 
 #find all available versions
+versionCompLte() {
+    [  "$1" = "`echo -e "$1\n$2" | sort -V | head -n1`" ]
+}
 
+
+versionCompLt() {
+    [ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
+}
 for version in `ls "$DB_SCHEMA_DIR" | sort -V`;
 do
 	if [ -d "$DB_SCHEMA_DIR/$version" ]
 	then
-		versions+=($version);
+		if versionCompLt $version $MAX_DB_VERSION_FOR_MIGRTION
+		then
+			versions+=($version);
+		fi
 		current_version=$version;
 	fi
 done
@@ -34,28 +45,24 @@ done
 # GENERATE DB schemas and diff files
 #--------------------------------------
 
-versionCompLte() {
-    [  "$1" = "`echo -e "$1\n$2" | sort -V | head -n1`" ]
-}
-
-
-versionCompLt() {
-    [ "$1" = "$2" ] && return 1 || versionCompLte $1 $2
-}
+for version_A in ${versions[*]}
+do
+	touch $DBSCRIPT_DEST_DIR/db_${version_A}_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql
+done
 
 #last version (used for generating db diff files)
 for version_A in ${versions[*]}
 do
 	#main update file (used to create this version - it's a diff
-	#between base.sql and current version)
-	update_file="$DBSCRIPT_DEST_DIR/db_0_to_${current_version}.sql";
+	#between base.sql and last version not managed by flyway)
+	update_file="$DBSCRIPT_DEST_DIR/db_0_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql";
 
 	#now iterate through all versions
 	for file in `ls "$DB_SCHEMA_DIR/$version_A" | sort -V`;
 	do
 		if [ -f "$DB_SCHEMA_DIR/$version_A/$file" ]
 		then
-			#add difference to current db schema diff
+			#add db schema diff to last version  not managed by flyway
 			printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$update_file";
 			cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$update_file";
 
@@ -67,7 +74,7 @@ do
 				#after #version_B (so version_A must be later)
 				if versionCompLt $version_B $version_A 
 				then
-					upd_file="$DBSCRIPT_DEST_DIR/db_${version_B}_to_${current_version}.sql";
+					upd_file="$DBSCRIPT_DEST_DIR/db_${version_B}_to_${MAX_DB_VERSION_FOR_MIGRTION}.sql";
 					printf "\n\n-- UPDATE $version_A/$file\n\n" >> "$upd_file";
 					cat "$DB_SCHEMA_DIR/$version_A/$file" >> "$upd_file";
 				fi