[med-svn] r8819 - trunk/packages/ensembl/ensembl/trunk/debian

[Andreas Tille]

Author: tille
Date: 2011-12-07 19:57:13 +0000 (Wed, 07 Dec 2011)
New Revision: 8819

Modified:
   trunk/packages/ensembl/ensembl/trunk/debian/changelog
   trunk/packages/ensembl/ensembl/trunk/debian/control
   trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links
   trunk/packages/ensembl/ensembl/trunk/debian/rules
Log:
FOr security reasons use Debian packaged JavaScript library tinymce


Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-07 17:58:08 UTC (rev 8818)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-07 19:57:13 UTC (rev 8819)
@@ -22,6 +22,7 @@
     - move some cp statements to ensembl(-bin).install
     - remove some extra license files
     - fix some permissions
+    - use Debian packaged JavaScript library tinymce
   * debian/ensembl.dirs:
     - Do not create directories in /var/tmp which are created in postinst
       anyway

Modified: trunk/packages/ensembl/ensembl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-07 17:58:08 UTC (rev 8818)
+++ trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-07 19:57:13 UTC (rev 8819)
@@ -25,7 +25,8 @@
  libensembl-compara-perl (= ${source:Version}),
  libensembl-external-perl (= ${source:Version}),
  libensembl-variation-perl (= ${source:Version}),
- liblwp-parallel-perl, mysql-server, mysql-client, jalview, jemboss
+ liblwp-parallel-perl, mysql-server, mysql-client,
+ jalview, jemboss, tinymce
 Recommends: ttf-mscorefonts-installer, acedb-other-dotter, libcgi-ajax-perl,
  libcache-memcached-perl, libclass-dbi-sweet-perl, libclass-std-perl,
  libclass-std-utils-perl, libcompress-bzip2-perl, libfile-spec-perl,

Modified: trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links	2011-12-07 17:58:08 UTC (rev 8818)
+++ trunk/packages/ensembl/ensembl/trunk/debian/ensembl.links	2011-12-07 19:57:13 UTC (rev 8819)
@@ -1,5 +1,6 @@
 /usr/share/java/jalview.jar			/usr/share/ensembl/htdocs/jalview/jalview.jar
 /usr/share/EMBOSS/jemboss/lib/jalviewApplet.jar	/usr/share/ensembl/htdocs/jalview/jalviewApplet.jar
+/usr/share/tinymce/www				/usr/share/ensembl/public-plugins/admin/htdocs/tiny_mce
 #Commented because tried to do it here but didn't work, so
 # we are using postinst instead
 #/usr/share/ensembl/logs /var/log/ensembl

Modified: trunk/packages/ensembl/ensembl/trunk/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/rules	2011-12-07 17:58:08 UTC (rev 8818)
+++ trunk/packages/ensembl/ensembl/trunk/debian/rules	2011-12-07 19:57:13 UTC (rev 8819)
@@ -24,33 +24,6 @@
 override_dh_auto_install:
 	# do nothing
 
-remaining_stuff:
-	for p in core compara draw external functgenomics variation; do \
-		destdir="$(CURDIR)/debian/libensembl-$${p}-perl/usr/share/ensembl" ; \
-		if [ ! -d "$$destdir" ]; then mkdir -p "$$destdir"; fi ; \
-	done
-
-	from="debian/ensembl/usr/share/ensembl/ensembl" ; \
-	to="debian/libensembl-core-perl/usr/share/ensembl/" ; \
-	# echo "Renaming '$$from' to '$$to'.\n" ; \
-	mv "$$from" "$$to"
-
-	# move the remaining directories
-	sourcedir="$(CURDIR)/debian/ensembl/usr/share/ensembl" ; \
-	for p in compara draw external functgenomics variation; do \
-		destdir="$(CURDIR)/debian/libensembl-$${p}-perl/usr/share/ensembl/" ; \
-		echo "Moving '$$sourcedir/*-$$p' to '$$destdir'" ; \
-		mv $${sourcedir}/*-$$p $$destdir ; \
-	done
-
-	# some cleanup
-#	find debian -name Makefile.PL -o -name "*.tar.gz" | xargs -r rm -f
-
-
-	# install-indep: build-indep install-indep-copying
-#	find debian/ensembl -name config.guess -o -name config.sub -o -name configure -o \
-#		-name depcomp -o -name install-sh -o -name missing -o -name Makefile.PL | xargs -r rm
-
 override_dh_install:
 	# Several interpreterlines needs fixing and file permission needs changing
 	# To do so a fake installation to debian/tmp is done and the files there
@@ -68,6 +41,11 @@
 	#        should be fine because it is mentioned in the accompanied README
 	rm -rf $(TMPINSTDIR)/utils/static_content/doxygen
 
+	# Ensembl contains some JavaScript libraries which are packaged for Debian
+	# For security reasons it is strongly recommended to use the Debian packaged version
+	# and leave the updates of this to the security team
+	rm -rf $(TMPINSTDIR)/public-plugins/admin/htdocs/tiny_mce
+
 	# move binary code out of share
 	mkdir -p $(CURDIR)/debian/tmp/usr/bin
 	mv $(TMPINSTDIR)/ensembl-variation/C_code/calc_genotypes $(CURDIR)/debian/tmp/usr/bin