Merge branch '879-add-support-for-debian-buster' into 'master'

Resolve "add support for debian:buster"

Closes #828, #77, and #879

See merge request minerva/core!871

.gitlab-ci.yml

@@ -325,7 +325,7 @@ build_debian_package:
     - debian/create-debian-pkg.sh
 
 test_upgrade_debian_package:
-  image: debian:stretch
+  image: debian
   stage: test
   only:
     - tags
@@ -376,7 +376,7 @@ test_upgrade_debian_package:
      - test 1 = $(cat configuration.json| grep $version | wc -l)
 
 test_install_debian_package:
-  image: debian:stretch
+  image: debian
   stage: test
   only:
     - tags

CHANGELOG

+minerva (14.0.0~alpha.1) unstable; urgency=low
+  * Small improvement: debian package can be installed on debian:buster (#879)
+  * Feature removal: support for tomcat7 removed (#828)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 12 Aug 2019 10:00:00 +0200
+
 minerva (14.0.0~alpha.0) unstable; urgency=low
-  * Feature: security layer redesigned - privilge types and scope changed 
+  * Feature: security layer redesigned - privilege types and scope changed 
     (#636, #624)
   * Feature: log4j is replaced with log4j2 logging mechanism (#291)
   * Feature: database installed via debian package is done via dbconfig-commons
     (#469)
   * Feature: Replaced connection pool manager C3P0 with better maintained
-    Hikari (#564)
+    Hikari - restart of postgresql database doesn't require restart of tomcat 
+    (#564)
   * Feature removal: BioCompendium annotator removed (#32)
   * Small improvement: anonymous login is no longer required - each API query 
     outside session is authorized with anonymous user privileges (#629)
@@ -24,7 +31,7 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
     overlay is now deprecated (#850)
   * Small improvement: information about deprecated columns in data overlay is 
     visible in overlay list (#838)
-  * Small improvement: publication list is resizable (#740)
+  * Small improvement: publication list is resizeable (#740)
   * Small improvement: user list on project edit dialog is sortable (#808)
   * Bug fix: export to CellDesigner of reaction with two modifiers connected
     with boolean operator resulted was skipping some layout information
@@ -39,14 +46,14 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
   * Bug fix: Search drug by target element did not return values when this
     element was annotated automatically (#216)
 
- -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 09 Aug 2019 10:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 09 Aug 2019 10:00:00 +0200
 
 minerva (13.1.2) stable; urgency=medium
   * Bug fix: Information about problematic zip file is more specific (#865)
   * Bug fix: Url didn't contain list of opened plugins and they weren't reload
     automatically on refresh (#866)
 
- -- Piotr Gawron <piotr.gawron@uni.lu> Mon, 22 Jul 2019 17:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
 
 minerva (13.1.1) stable; urgency=medium
   * Bug fix: adding gene mapping before the genome caused an error (#835)

debian/logrotate/minerva

-/var/log/tomcat7/minerva.txt {
+/var/log/tomcat8/minerva.txt {
   copytruncate
   size 32k
   weekly
@@ -6,5 +6,5 @@
   rotate 52
   compress
   missingok
-  create 640 tomcat7 adm
+  create 640 tomcat8 adm
 }

debian/scripts/common.sh

@@ -18,16 +18,17 @@ then
 fi
 
 TOMCAT_PACKAGE="";
-TOMCAT7_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat7|grep "install ok installed")
 TOMCAT8_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat8|grep "install ok installed")
-if [ "$TOMCAT7_OK" != "" ];
-then
-  TOMCAT_PACKAGE='tomcat7'
-fi
+TOMCAT9_OK=$(dpkg-query -W --showformat='${Status}\n' tomcat9|grep "install ok installed")
 if [ "$TOMCAT8_OK" != "" ];
 then
   TOMCAT_PACKAGE='tomcat8'
 fi
 
+if [ "$TOMCAT9_OK" != "" ];
+then
+  TOMCAT_PACKAGE='tomcat9'
+fi
+
 POSTGRES_OK=$(dpkg-query -W --showformat='${Status}\n' postgresql|grep "install ok installed")
 

debian/template/control

@@ -3,7 +3,7 @@ Priority: optional
 Maintainer: Piotr Gawron <piotr.gawron@uni.lu>
 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
+Vcs-Browser: https://git-r3lab.uni.lu/minerva/core
 
 Package: minerva
 Description: Standalone web application for visualization, exploration and 
@@ -15,4 +15,5 @@ Description: Standalone web application for visualization, exploration and
 Section: science
 Homepage: http://r3lab.uni.lu/web/minerva-website/
 Recommends: postgresql (>=9.3)
-Depends: ${misc:Depends}, openjdk-8-jre-headless, dbconfig-pgsql | dbconfig-no-thanks, tomcat7 | tomcat8
+Breaks: tomcat7
+Depends: ${misc:Depends}, openjdk-8-jre-headless | openjdk-11-jre-headless, web | dbconfig-no-thanks, tomcat8 |tomcat9

debian/template/minerva.1.xml

@@ -50,7 +50,7 @@ man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
   <!-- dhusername could also be set to "&dhfirstname; &dhsurname;". -->
   <!ENTITY dhusername  "Piotr Gawron">
   <!ENTITY dhemail     "piotr.gawron@uni.lu">
-  <!ENTITY dhhomepage  "http://r3lab.uni.lu/web/minerva-website/">
+  <!ENTITY dhhomepage  "https://minerva.pages.uni.lu/doc/">
   <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
        allowed: see man(7), man(1) and
        http://www.tldp.org/HOWTO/Man-Page/q2.html. -->
@@ -135,9 +135,15 @@ man(1), man(7), http://www.tldp.org/HOWTO/Man-Page/
     <title>FILES</title>
     <variablelist>
       <varlistentry>
-        <term><filename>/var/lib/tomcat7/webapps/minerva.war</filename></term>
+        <term><filename>/var/lib/tomcat9/webapps/minerva.war</filename></term>
         <listitem>
-          <para>Deployable web application for <application>tomcat7</application>.</para>
+          <para>Deployable web application for <application>tomcat9</application>.</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><filename>/var/lib/tomcat8/webapps/minerva.war</filename></term>
+        <listitem>
+          <para>Deployable web application for <application>tomcat8</application>.</para>
         </listitem>
       </varlistentry>
     </variablelist>

debian/template/postinst

@@ -82,6 +82,19 @@ case "$1" in
     rm -rf /var/lib/$TOMCAT_PACKAGE/webapps/minerva
     ln -sf /usr/share/minerva/minerva.war /var/lib/$TOMCAT_PACKAGE/webapps/minerva.war
     invoke-rc.d $TOMCAT_PACKAGE start
+
+    
+    #minerva prior to 14.0 could be installed on tomcat7, we need to migrate files from such version to current one
+    if [ -d "/var/lib/tomcat7/webapps/map_images/" ]; then
+      log "moving '/var/lib/tomcat7/webapps/map_images/' -> '/var/lib/$TOMCAT_PACKAGE/webapps/map_images/'";
+      mv /var/lib/tomcat7/webapps/map_images/ /var/lib/$TOMCAT_PACKAGE/webapps/map_images/
+      chown -R $TOMCAT_PACKAGE:$TOMCAT_PACKAGE /var/lib/$TOMCAT_PACKAGE/webapps/map_images/
+    fi
+    if [ -d "/var/lib/tomcat7/webapps/minerva-big/" ]; then
+      log "moving '/var/lib/tomcat7/webapps/minerva-big/' -> '/var/lib/$TOMCAT_PACKAGE/webapps/minerva-big/'";
+      mv /var/lib/tomcat7/webapps/minerva-big/ /var/lib/$TOMCAT_PACKAGE/webapps/minerva-big/
+      chown -R $TOMCAT_PACKAGE:$TOMCAT_PACKAGE /var/lib/$TOMCAT_PACKAGE/webapps/minerva-big/
+    fi
     ;;
     *)
         echo "postinst called with unknown argument \`$1'" >&2