[med-svn] r2508 - in trunk/packages/agdbnet/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Sep 18 07:59:20 UTC 2008
Author: tille
Date: 2008-09-18 07:59:19 +0000 (Thu, 18 Sep 2008)
New Revision: 2508
Added:
trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
trunk/packages/agdbnet/trunk/debian/prerm
Modified:
trunk/packages/agdbnet/trunk/debian/config
trunk/packages/agdbnet/trunk/debian/control
trunk/packages/agdbnet/trunk/debian/dirs
trunk/packages/agdbnet/trunk/debian/patches/series
trunk/packages/agdbnet/trunk/debian/postinst
trunk/packages/agdbnet/trunk/debian/postrm
trunk/packages/agdbnet/trunk/debian/rules
Log:
Use dbconfig-common to install references database
Modified: trunk/packages/agdbnet/trunk/debian/config
===================================================================
--- trunk/packages/agdbnet/trunk/debian/config 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/config 2008-09-18 07:59:19 UTC (rev 2508)
@@ -9,6 +9,23 @@
. /usr/share/debconf/confmodule
db_version 2.0
+# Try to enforce a yes to first question whether we want dbconfig-common
+# automatism, because we really want it ...
+db_set ${pkg}/dbconfig-install "true" || true
+db_go || true
+# unfortunately neither this nor setting dbc_authmethod_user
+# prevents dbconfig-common from asking about these values again :-((
+
+dbc_dbuser='www-data'
+dbc_dbname='refs'
+dbc_authmethod_user="ident"
+
+# source dbconfig-common shell library, and call the hook function
+if [ -f /usr/share/dbconfig-common/dpkg/config.pgsql ]; then
+ . /usr/share/dbconfig-common/dpkg/config.pgsql
+ dbc_go ${pkg} $@
+fi
+
# Check whether there is an xmlname stored in debconf database
# Yes, debconf is no registry, but the real place of the real
# information is stored in the configfile /etc/agdbnet/${xmlname}
Modified: trunk/packages/agdbnet/trunk/debian/control
===================================================================
--- trunk/packages/agdbnet/trunk/debian/control 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/control 2008-09-18 07:59:19 UTC (rev 2508)
@@ -13,7 +13,7 @@
Package: agdbnet
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, blast2, postgresql-8.3,
- libcgi-pm-perl, libdbd-pg-perl, libxml-perl
+ libcgi-pm-perl, libdbd-pg-perl, libxml-perl, dbconfig-common
Description: antigen sequence database software for web-based bacterial typing
AgdbNet facilitates simultaneous BLAST querying of multiple loci using
either nucleotide or peptide sequences. Databases are described by XML
Modified: trunk/packages/agdbnet/trunk/debian/dirs
===================================================================
--- trunk/packages/agdbnet/trunk/debian/dirs 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/dirs 2008-09-18 07:59:19 UTC (rev 2508)
@@ -1 +1,2 @@
-/etc/agdbnet
+etc/agdbnet
+usr/share/dbconfig-common/data/agdbnet/install
Added: trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch 2008-09-18 07:59:19 UTC (rev 2508)
@@ -0,0 +1,76 @@
+Apache runs as user www-data on Debian systems - so replace any
+occurence of system user apache by www-data
+--- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
+@@ -80,7 +80,7 @@
+ $system{'port'} = 5432;
+ }
+ if ( !$system{'user'} ) {
+- $system{'user'} = 'apache';
++ $system{'user'} = 'www-data';
+ }
+ if ( !$system{'pass'} ) {
+ $system{'pass'} = 'remote';
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -157,7 +157,7 @@
+ $system{'port'} = 5432;
+ }
+ if ( !$system{'user'} ) {
+- $system{'user'} = 'apache';
++ $system{'user'} = 'www-data';
+ }
+ if ( !$system{'pass'} ) {
+ $system{'pass'} = 'remote';
+--- agdbnet_v1.0.0.orig/examples/poravr.xml
++++ agdbnet_v1.0.0/examples/poravr.xml
+@@ -131,7 +131,7 @@
+ <field type="text" length="256">description</field>
+ </auxtable>
+
+-<extisolates dbase="nm_isolates" host="localhost" port="5432" user="apache" pass="remote" view="isolates" fullname="PubMLST isolates" url="http://pubmlst.org/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-nm_isolates.xml&page=straininfo&id=\?">PubMLST
++<extisolates dbase="nm_isolates" host="localhost" port="5432" user="www-data" pass="remote" view="isolates" fullname="PubMLST isolates" url="http://pubmlst.org/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-nm_isolates.xml&page=straininfo&id=\?">PubMLST
+ <field type="int" length="5" userupdate="no" comments="primary key">id</field>
+ <field type="text" length="20" comments="Original strain name as supplied by sender">strain</field>
+ <field type="text" required="no" maindisplay="no" length="20"
+--- agdbnet_v1.0.0.orig/installation.html
++++ agdbnet_v1.0.0/installation.html
+@@ -38,9 +38,9 @@
+ <li>Create the SQL file to generate the database using the xml2sql.pl script found in the scripts directory. First make sure that the XML has a valid syntax by running the script as below:<br />
+ <p />
+ <p class="code">./xml2sql.pl database.xml</p>
+-where 'database.xml' is the XML file you created above (change the filename as appropriate). If the script does not produce an error message, generate your SQL file as follows - substitute the name of the web server user account for 'apache':<br />
++where 'database.xml' is the XML file you created above (change the filename as appropriate). If the script does not produce an error message, generate your SQL file as follows - substitute the name of the web server user account for 'www-data':<br />
+ <p />
+-<p class="code">./xml2sql.pl -u apache database.xml > database.sql</p></li>
++<p class="code">./xml2sql.pl -u www-data database.xml > database.sql</p></li>
+ <li>Create the database - you may need to log in with an account with permissions to create new databases, e.g. 'postgres':<br />
+ <p />
+ <p class="code">createdb database</p>
+@@ -60,4 +60,4 @@
+ </ol>
+
+ </body>
+-</html>
+\ No newline at end of file
++</html>
+--- agdbnet_v1.0.0.orig/scripts/xml2sql.pl
++++ agdbnet_v1.0.0/scripts/xml2sql.pl
+@@ -45,7 +45,7 @@
+ $webuser = $opts{'u'};
+ }
+ else {
+- $webuser = 'apache';
++ $webuser = 'www-data';
+ }
+ my $instance = $ARGV[0];
+ if ( !$instance ) {
+--- agdbnet_v1.0.0.orig/setup/refs.sql
++++ agdbnet_v1.0.0/setup/refs.sql
+@@ -23,4 +23,4 @@
+ PRIMARY KEY (pmid)
+ );
+
+-GRANT SELECT ON authors,refs TO apache;
+\ No newline at end of file
++GRANT SELECT ON authors,refs TO "www-data";
Modified: trunk/packages/agdbnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-18 07:59:19 UTC (rev 2508)
@@ -3,3 +3,4 @@
10_preconf.patch
10_moreinfo.patch
10_config_location.patch
+10_apache_is_web-data.patch
Modified: trunk/packages/agdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postinst 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/postinst 2008-09-18 07:59:19 UTC (rev 2508)
@@ -1,7 +1,5 @@
#!/bin/sh
# postinst script for agdbnet
-#
-# see: dh_installdeb(1)
set -e
@@ -11,6 +9,12 @@
. /usr/share/debconf/confmodule
db_version 2.0
+# source dbconfig-common shell library, and call the hook function
+if [ -f /usr/share/dbconfig-common/dpkg/postinst.pgsql ]; then
+ . /usr/share/dbconfig-common/dpkg/postinst.pgsql
+ dbc_go ${pkg} $@
+fi
+
db_get ${pkg}/xmlname
XMLNAME=${RET}
Modified: trunk/packages/agdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postrm 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/postrm 2008-09-18 07:59:19 UTC (rev 2508)
@@ -1,12 +1,19 @@
#!/bin/sh
# postrm script for agdbnet
-#
-# see: dh_installdeb(1)
set -e
pkg=agdbnet
+. /usr/share/debconf/confmodule
+db_version 2.0
+
+# source dbconfig-common shell library, and call the hook function
+if [ -f /usr/share/dbconfig-common/dpkg/postrm.pgsql ]; then
+ . /usr/share/dbconfig-common/dpkg/postrm.pgsql
+ dbc_go ${pkg} $@
+fi
+
case "$1" in
purge)
# remove all potential config files and dirs in /var/www
Added: trunk/packages/agdbnet/trunk/debian/prerm
===================================================================
--- trunk/packages/agdbnet/trunk/debian/prerm (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/prerm 2008-09-18 07:59:19 UTC (rev 2508)
@@ -0,0 +1,19 @@
+#!/bin/sh
+# prerm script for agdbnet
+
+set -e
+
+pkg=agdbnet
+
+. /usr/share/debconf/confmodule
+db_version 2.0
+
+# source dbconfig-common shell library, and call the hook function
+if [ -f /usr/share/dbconfig-common/dpkg/config.pgsql ]; then
+ . /usr/share/dbconfig-common/dpkg/config.pgsql
+ dbc_go ${pkg} $@
+fi
+
+#DEBHELPER#
+
+exit 0
Modified: trunk/packages/agdbnet/trunk/debian/rules
===================================================================
--- trunk/packages/agdbnet/trunk/debian/rules 2008-09-17 17:11:13 UTC (rev 2507)
+++ trunk/packages/agdbnet/trunk/debian/rules 2008-09-18 07:59:19 UTC (rev 2508)
@@ -12,6 +12,10 @@
common-binary-post-install-arch::
# Directory conf has to be copied to /etc/agdbnet
cp -a conf/* debian/$(pkg)/etc/$(pkg)
+
+ # copy script to setup PubMed reference fields into
+ # apropriate dbconfig-common dir
+ cp -a setup/refs.sql debian/$(pkg)/usr/share/dbconfig-common/data/${pkg}/install/pgsql
# To update po files as recommended in po-debconf(7)
clean::
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