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Bug#773178: marked as done (unblock: biomaj-watcher/1.2.2-2)

Your message dated Tue, 16 Dec 2014 23:10:11 +0000
with message-id <20141216231011.GS11902@lupin.home.powdarrmonkey.net>
and subject line Re: Bug#773178: unblock: biomaj-watcher/1.2.2-2
has caused the Debian Bug report #773178,
regarding unblock: biomaj-watcher/1.2.2-2
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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773178: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=773178
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--- Begin Message ---
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
X-CC: debian-med@lists.debian.org

Please unblock package biomaj-watcher

biomaj-watcher depended on tomcat6. Jessie uses Tomcat8 a,d biomaj-watcher does not work anymore. This fix release changes the package to use tomcat8 and fixes bug 769348


Here is debdiff:

diff -Nru biomaj-watcher-1.2.2/debian/changelog biomaj-watcher-1.2.2/debian/changelog
--- biomaj-watcher-1.2.2/debian/changelog 2014-06-23 09:13:13.000000000 +0200
+++ biomaj-watcher-1.2.2/debian/changelog 2014-12-15 11:26:27.000000000 +0100
@@ -1,3 +1,9 @@
+biomaj-watcher (1.2.2-2) unstable; urgency=medium
+
+  * Switch to Tomcat 8 (Closes: #769348). 
+
+ -- Olivier Sallou <osallou@debian.org>  Mon, 15 Dec 2014 08:03:09 +0100
+
 biomaj-watcher (1.2.2-1) unstable; urgency=medium
 
   * New usptream release:
diff -Nru biomaj-watcher-1.2.2/debian/control biomaj-watcher-1.2.2/debian/control
--- biomaj-watcher-1.2.2/debian/control 2014-06-23 09:13:56.000000000 +0200
+++ biomaj-watcher-1.2.2/debian/control 2014-12-15 08:04:53.000000000 +0100
@@ -21,7 +21,7 @@
 
 Package: biomaj-watcher
 Architecture: all
-Depends: ${misc:Depends}, default-jdk, tomcat6 (>=6.0.32-3), biomaj (>= 1.2.1), debconf,
+Depends: ${misc:Depends}, default-jdk, tomcat8 , biomaj (>= 1.2.1), debconf,
  liblog4j1.2-java, libjsch-java (>= 0.1.42),libjdom1-java (>= 1.1), libcommons-lang-java (>=2.4),
  libcommons-logging-java (>=1.1),libquartz-java(>=1.6),libxerces2-java, unzip, zip, libgnumail-java
 Description: biological data-bank updater - web interface
diff -Nru biomaj-watcher-1.2.2/debian/patches/series biomaj-watcher-1.2.2/debian/patches/series
--- biomaj-watcher-1.2.2/debian/patches/series 2014-01-09 16:25:31.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/patches/series 2014-12-15 10:37:02.000000000 +0100
@@ -1 +1,2 @@
 prevent_jobs_file_move
+use_tomcat8
diff -Nru biomaj-watcher-1.2.2/debian/patches/use_tomcat8 biomaj-watcher-1.2.2/debian/patches/use_tomcat8
--- biomaj-watcher-1.2.2/debian/patches/use_tomcat8 1970-01-01 01:00:00.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/patches/use_tomcat8 2014-12-15 10:40:03.000000000 +0100
@@ -0,0 +1,17 @@
+Subject: adapt xml for Tomcat8
+Description: use tomcat8, this impact the context descriptor
+Author: Olivier Sallou <osallou@debian.org>
+Last-Updated: 2014-12-15
+Forwarded: No
+--- a/usr/share/biomaj-watcher/bin/WatcherConfigurator.java
++++ b/usr/share/biomaj-watcher/bin/WatcherConfigurator.java
+@@ -45,7 +45,8 @@
+ PrintWriter pw = new PrintWriter(biomajConf + "/BmajWatcher.xml");
+
+ pw.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
+- pw.println("<Context path=\"/BmajWatcher\" docBase=\"/usr/share/java/webapps/biomaj-watcher\"  reloadable=\"false\" allowLinking=\"true\">");
++ pw.println("<Context path=\"/BmajWatcher\" docBase=\"/usr/share/java/webapps/biomaj-watcher\"  reloadable=\"false\" >");
++ pw.println("<Resources allowLinking=\"true\"/>");
+ 
+ pw.println("<Parameter name=\"ADMIN_LOGIN\" value=\"" + params.get("app_login") + "\" override=\"false\"/>");
+
diff -Nru biomaj-watcher-1.2.2/debian/postinst biomaj-watcher-1.2.2/debian/postinst
--- biomaj-watcher-1.2.2/debian/postinst 2014-01-09 16:25:31.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/postinst 2014-12-15 11:05:48.000000000 +0100
@@ -49,8 +49,8 @@
       ln -s /usr/share/java/gnumail.jar /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/gnumail.jar
 
       #cp /usr/share/biomaj/lib/biomaj.jar /var/lib/tomcat6/shared/
-      rm -f /var/lib/tomcat6/shared/biomaj.jar
-      cp /usr/share/biomaj/lib/biomaj.jar /var/lib/tomcat6/shared/biomaj.jar
+      rm -f /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/biomaj.jar
+      cp /usr/share/biomaj/lib/biomaj.jar /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/biomaj.jar
       # Install latest definition
       cp /usr/share/java/webapps/biomaj-watcher/jobs.xsd /etc/biomaj-watcher/jobs.xsd
 
@@ -62,24 +62,17 @@
       # Update logs
       set_perms /var/log/biomaj
 
-      #chown -R tomcat6 /etc/biomaj/db_properties
-      chown -R tomcat6 /usr/share/java/webapps/biomaj-watcher
-      #chmod -R 775 /etc/biomaj/db_properties
-      #chown -R tomcat6 /var/log/biomaj
-      #chmod -R 775 /var/log/biomaj
-      #chown -R tomcat6 /var/lib/biomaj
-      #chmod -R 775 /var/lib/biomaj
-      chown -R tomcat6 /etc/biomaj-watcher
+      chown -R tomcat8 /usr/share/java/webapps/biomaj-watcher
+      chown -R tomcat8 /etc/biomaj-watcher
       # Update context
       java -cp $biomajwatcher_root/bin UpdateToBiomaj1_2 /usr/share/java/webapps/biomaj-watcher admin
-      chown -R tomcat6 /etc/biomaj-watcher
-      #cp /etc/biomaj-watcher/BmajWatcher*.xml /var/lib/tomcat6/conf/Catalina/localhost/
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher.xml
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher#logs.xml
-      ln -s /etc/biomaj-watcher/BmajWatcher.xml /etc/tomcat6/Catalina/localhost/BmajWatcher.xml
-      ln -s /etc/biomaj-watcher/BmajWatcher#logs.xml /etc/tomcat6/Catalina/localhost/BmajWatcher#logs.xml
+      chown -R tomcat8 /etc/biomaj-watcher
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher.xml
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher#logs.xml
+      ln -s /etc/biomaj-watcher/BmajWatcher.xml /etc/tomcat8/Catalina/localhost/BmajWatcher.xml
+      ln -s /etc/biomaj-watcher/BmajWatcher#logs.xml /etc/tomcat8/Catalina/localhost/BmajWatcher#logs.xml
 
-      invoke-rc.d tomcat6 restart
+      invoke-rc.d tomcat8 restart
 
 
     ;;
diff -Nru biomaj-watcher-1.2.2/debian/postrm biomaj-watcher-1.2.2/debian/postrm
--- biomaj-watcher-1.2.2/debian/postrm 2014-01-09 16:25:31.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/postrm 2014-12-15 11:24:50.000000000 +0100
@@ -14,21 +14,23 @@
     ;;
     remove|failed-upgrade|abort-install|abort-upgrade|disappear)
 
-      if [ -e /var/lib/tomcat6/shared/biomaj.jar ]; then
-        rm  /var/lib/tomcat6/shared/biomaj.jar
-      fi
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher.xml
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher#logs.xml
+      #if [ -e /var/lib/tomcat6/shared/biomaj.jar ]; then
+      #  rm  /var/lib/tomcat6/shared/biomaj.jar
+      #fi
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher.xml
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher#logs.xml
       rm -f /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/*.jar
+      rm -rf /usr/share/java/webapps/biomaj-watcher
     ;;
 
     purge)
-      if [ -e /var/lib/tomcat6/shared/biomaj.jar ]; then
-        rm  /var/lib/tomcat6/shared/biomaj.jar
-      fi
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher.xml
-      rm -f /etc/tomcat6/Catalina/localhost/BmajWatcher#logs.xml
+      #if [ -e /var/lib/tomcat6/shared/biomaj.jar ]; then
+      #  rm  /var/lib/tomcat6/shared/biomaj.jar
+      #fi
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher.xml
+      rm -f /etc/tomcat8/Catalina/localhost/BmajWatcher#logs.xml
       rm -f /usr/share/java/webapps/biomaj-watcher/WEB-INF/lib/*.jar
+      rm -rf /usr/share/java/webapps/biomaj-watcher
       rm -rf /etc/biomaj-watcher
 
     ;;
diff -Nru biomaj-watcher-1.2.2/debian/README.Debian biomaj-watcher-1.2.2/debian/README.Debian
--- biomaj-watcher-1.2.2/debian/README.Debian 2014-01-09 16:25:31.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/README.Debian 2014-12-15 08:05:09.000000000 +0100
@@ -10,4 +10,4 @@
  http://gwt-google-apis.googlecode.com/svn/tags/visualization/1.1.1
 
 
- Biomaj watcher updates the access rights of most of Biomaj directories to add write access to the user tomcat6. Indeed, all configuration and bank updates will be done via the Tomcat application. Those modifications are needed only while biomaj-watcher is installed.
+ Biomaj watcher updates the access rights of most of Biomaj directories to add write access to the user tomcat8. Indeed, all configuration and bank updates will be done via the Tomcat application. Those modifications are needed only while biomaj-watcher is installed.
diff -Nru biomaj-watcher-1.2.2/debian/setperms.sh biomaj-watcher-1.2.2/debian/setperms.sh
--- biomaj-watcher-1.2.2/debian/setperms.sh 2014-01-09 16:25:31.000000000 +0100
+++ biomaj-watcher-1.2.2/debian/setperms.sh 2014-12-15 08:08:21.000000000 +0100
@@ -2,8 +2,8 @@
 
 if ! dpkg-statoverride --list "$1" >/dev/null; then
   if [ "$1" == "/etc/biomaj/db_properties/global.properties" ]; then
-    dpkg-statoverride --update --add tomcat6 root 0660  $1
+    dpkg-statoverride --update --add tomcat8 root 0660  $1
   else
-    dpkg-statoverride --update --add tomcat6 root 0775  $1
+    dpkg-statoverride --update --add tomcat8 root 0775  $1
   fi
 fi

--- End Message ---
--- Begin Message --- 
On Tue, Dec 16, 2014 at 08:13:29PM +0000, olivier sallou wrote:
> Yep, remove/purge cleans files. New tomcat8 modifications mainly changes
> configuration context file and modifies directories.

Excellent, unblocked.

-- 
Jonathan Wiltshire                                      jmw@debian.org
Debian Developer                         http://people.debian.org/~jmw

4096R: 0xD3524C51 / 0A55 B7C5 1223 3942 86EC  74C3 5394 479D D352 4C51

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