diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7ec9a8b0510be2f3b25b65c99513f0750656d7ef..2ad4c0b4229bf1f9db62b1509b2f930d6e23649a 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/CHANGELOG b/CHANGELOG
index d134921f33ac51f00f8b8107847408795823efad..e072471c5c77f6af3ac0a06a8a841a49d5886eaa 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,11 +1,18 @@
+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)
diff --git a/debian/logrotate/minerva b/debian/logrotate/minerva
index f9f1ada6d09567a1e3992604dfb468901343d399..709458b86b5ae6b6443d2e0949f3dac21bb8bfc8 100644
--- a/debian/logrotate/minerva
+++ b/debian/logrotate/minerva
@@ -1,4 +1,4 @@
-/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
}
diff --git a/debian/scripts/common.sh b/debian/scripts/common.sh
index ccaa42f66f256bc7118854f1e8b5bd371c2007d5..d8c9bc6f911a7e0413716ceb46fee1e0b58dfe9f 100644
--- a/debian/scripts/common.sh
+++ b/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")
diff --git a/debian/template/control b/debian/template/control
index 0409a218fa411e9b6a627410b298c0098ec65efb..e4d12c6446c267ffb6fd1c3f7ba7946150ed7dee 100644
--- a/debian/template/control
+++ b/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
diff --git a/debian/template/minerva.1.xml b/debian/template/minerva.1.xml
index 0c54fcbed21df13b34bd83cab64db1c86e86ab10..e9e22a86a078857369288a44fcb42a24a442f3cc 100644
--- a/debian/template/minerva.1.xml
+++ b/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>
diff --git a/debian/template/postinst b/debian/template/postinst
index 016862312efc8431812e4f24218d2e73a1d699de..cc0055554f0fb88ea54b47f10ca3314de2bb0811 100644
--- a/debian/template/postinst
+++ b/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