Author: tille
Date: 2008-09-19 08:25:21 +0000 (Fri, 19 Sep 2008)
New Revision: 2509
Added:
trunk/packages/agdbnet/trunk/debian/cron.daily
trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
trunk/packages/agdbnet/trunk/debian/template/banner.html
trunk/packages/agdbnet/trunk/debian/template/footer.html
trunk/packages/agdbnet/trunk/debian/template/header.html
Removed:
trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
trunk/packages/agdbnet/trunk/debian/patches/10_conf_location.patch
trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
Modified:
trunk/packages/agdbnet/trunk/debian/README.Debian
trunk/packages/agdbnet/trunk/debian/examples
trunk/packages/agdbnet/trunk/debian/install
trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
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
trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml
Log:
Let ident authentication work, make use of layout templates, cron job for refs
database, updated README.Debian
Modified: trunk/packages/agdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-18 07:59:19 UTC
(rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-19 08:25:21 UTC
(rev 2509)
@@ -5,4 +5,20 @@
enable you to do the final steps to run agdbnet. Here are the last
steps from installation manual that have to be done.
+PubMed references
+-----------------
+
+According to item 6. of the original installation manual (see
+installation.html) the confiuration file has to be adjusted to
+enable obtaining PubMed references. You can find the original
+getrefs.conf example file in the examples directory. The data
+in this example file correspond to the configuration file example
+poravr.xml. Please adapt this to your own needs and finally copy
+a working getrefs.conf file into the directory /etc/agdbnet.
+Once you have done this the cron job in /etc/cron.daily/agdbnet
+will fetch the references once a day. It is strongly advised
+to call /etc/cron.daily/agdbnet manually for testing proper
+opperation.
+
+
-- Andreas Tille <[EMAIL PROTECTED]> Fri, 05 Sep 2008 11:07:50 +0200
Added: trunk/packages/agdbnet/trunk/debian/cron.daily
===================================================================
--- trunk/packages/agdbnet/trunk/debian/cron.daily
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/cron.daily 2008-09-19 08:25:21 UTC
(rev 2509)
@@ -0,0 +1,17 @@
+#!/bin/sh
+# populate the refs database once isolate databases have been set up
+#
+# The config file
+CONFFILE=/etc/agdbnet/getrefs.conf
+# is not installed at package installation time because the information
+# in this file has to be edited manually before reasonable operation can
+# be accomplished. So this cron job does not do anything until a valid
+# $CONFFILE exists.
+#
+# See /usr/share/agdbnet/README.Debian for more detailed information
+
+PROG=/usr/share/agdbnet/getrefs.pl
+
+if [ -x $PROG -a -s $CONFFILE ] ; then
+ su - --command "$PROG $CONFFILE" www-data
+fi
Modified: trunk/packages/agdbnet/trunk/debian/examples
===================================================================
--- trunk/packages/agdbnet/trunk/debian/examples 2008-09-18 07:59:19 UTC
(rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/examples 2008-09-19 08:25:21 UTC
(rev 2509)
@@ -1 +1,2 @@
examples/*
+scripts/getrefs.conf
Modified: trunk/packages/agdbnet/trunk/debian/install
===================================================================
--- trunk/packages/agdbnet/trunk/debian/install 2008-09-18 07:59:19 UTC (rev
2508)
+++ trunk/packages/agdbnet/trunk/debian/install 2008-09-19 08:25:21 UTC (rev
2509)
@@ -1,2 +1,4 @@
-cgi-bin usr/lib
-debian/template usr/share/agdbnet
+cgi-bin usr/lib
+debian/template usr/share/agdbnet
+scripts/*.pl usr/share/agdbnet
+stylesheets/stylesheet.css usr/share/agdbnet/template
Deleted: trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
2008-09-18 07:59:19 UTC (rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_apache_is_web-data.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -1,76 +0,0 @@
-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";
Deleted: trunk/packages/agdbnet/trunk/debian/patches/10_conf_location.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_conf_location.patch
2008-09-18 07:59:19 UTC (rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_conf_location.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -1,11 +0,0 @@
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl.orig
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -35,7 +35,7 @@
- ######################################################
-
- ###########Local configuration########################
--local ( our $configfile = '/usr/local/agdbnet/agdbnet.conf' );
-+local ( our $configfile = '/etc/agdbnet/agdbnet.conf' );
- #######End Local configuration########################
-
- local (
Modified: trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
2008-09-18 07:59:19 UTC (rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -1,3 +1,14 @@
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl.orig
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -35,7 +35,7 @@
+ ######################################################
+
+ ###########Local configuration########################
+-local ( our $configfile = '/usr/local/agdbnet/agdbnet.conf' );
++local ( our $configfile = '/etc/agdbnet/agdbnet.conf' );
+ #######End Local configuration########################
+
+ local (
--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
@@ -125,7 +125,8 @@
Deleted: trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
2008-09-18 07:59:19 UTC (rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -1,23 +0,0 @@
---- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
-+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
-@@ -129,7 +129,7 @@
- print $q->header;
- if ($invalidXML) {
- print $q->start_html( -title => "Invalid XML file" );
-- print "<p>Invalid (or no) database description file
specified!</p>";
-+ print "<p>Invalid (or no) database description file
specified!<br />Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.</p>";
- print $q->end_html;
- return;
- }
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -198,7 +198,8 @@
- }
- if ($invalidXML) {
- print $q->start_html( -title => "Invalid XML file" );
-- print "<p>Invalid (or no) database description file
specified!</p>";
-+ print "<p>Invalid (or no) database description file specified!
(agdbnet.pl) Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.
($system{'webroot'}/$system{'longcode'})</p>";
-+ print $system{'webroot'} . "//" . $system{'longcode'};
- print $q->end_html;
- return;
- }
Added: trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -0,0 +1,22 @@
+--- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
+@@ -129,7 +129,7 @@
+ print $q->header;
+ if ($invalidXML) {
+ print $q->start_html( -title => "Invalid XML file" );
+- print "<p>Invalid (or no) database description file
specified!</p>";
++ print "<p>Invalid (or no) database description file
specified!<br />Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.</p>";
+ print $q->end_html;
+ return;
+ }
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -198,7 +198,7 @@
+ }
+ if ($invalidXML) {
+ print $q->start_html( -title => "Invalid XML file" );
+- print "<p>Invalid (or no) database description file
specified!</p>";
++ print "<p>Invalid (or no) database description file
specified!<br />Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.</p>";
+ print $q->end_html;
+ return;
+ }
Added: trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -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";
Added: trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
2008-09-19 08:25:21 UTC (rev 2509)
@@ -0,0 +1,23 @@
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -168,10 +168,19 @@
+ }
+
+ sub dbconnect {
+- $db = DBI->connect(
++ # On Debian GNU/Linux we use ident authentication if host=localhost
which
++ # needs and empty string for user and password ...
++ if ( $system{'host'} =~ /^localhost$/ ) {
++ $db = DBI->connect(
++"DBI:Pg:dbname=$system{'longcode'}",
++ '', '', { AutoCommit => 0 }
++ );
++ } else {
++ $db = DBI->connect(
+ "DBI:Pg:host=$system{'host'};port=$system{'port'};dbname=$system{'longcode'}",
+ "$system{'user'}", "$system{'pass'}", { AutoCommit => 0 }
+ );
++ }
+ }
+
+ sub dbdisconnect {
Modified: trunk/packages/agdbnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-18 07:59:19 UTC
(rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-19 08:25:21 UTC
(rev 2509)
@@ -1,6 +1,6 @@
-10_conf_location.patch
+10_config_location.patch
10_bioperl.patch
10_preconf.patch
-10_moreinfo.patch
-10_config_location.patch
-10_apache_is_web-data.patch
+11_moreinfo.patch
+12_apache_is_web-data.patch
+13_ident_authentication.patch
Modified: trunk/packages/agdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postinst 2008-09-18 07:59:19 UTC
(rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/postinst 2008-09-19 08:25:21 UTC
(rev 2509)
@@ -52,29 +52,45 @@
"$XMLOUT"
fi
-HTMLOUT=/etc/${pkg}/"$XMLNAME".html
-# if no HTML file exists, just create one from the template
-if [ ! -s "$HTMLOUT" ] ; then
- sed -e "s/##database##/${XMLNAME}/g" \
- -e "s/##Description##/${DESCRIPTION}/g" \
- -e "s/##Pathogen##/${PATHOGEN}/g" \
- -e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
- -e "s/##Locus##/${LOCUS}/g" \
- /usr/share/${pkg}/template/index.html > \
- "$HTMLOUT"
-fi
+# All files that might influence the layout of the web site are
+# considered config files and stored into /etc/${pkg}/${XMLNAME}
+# If such files do not exist they will be created from a simple
+# template. Finally links are putted into place to enable
+# agdbnet to find these files.
+STYLEDIR=/etc/${pkg}/"$XMLNAME"
+mkdir -p ${STYLEDIR}
mkdir -p /var/www/${pkg}/"$XMLNAME"
-if [ ! -s /var/www/${pkg}/"$XMLNAME"/index.html ] ; then
- ln -s "$HTMLOUT" /var/www/${pkg}/"$XMLNAME"/index.html
-fi
+for style in `ls /usr/share/${pkg}/template/*.css
/usr/share/${pkg}/template/*.html` ; do
+ confstyle=`basename $style`
+ if [ ! -s "$STYLEDIR/$confstyle" ] ; then
+ if [ "$confstyle" = "index.html" ] ; then
+ sed -e "s/##database##/${XMLNAME}/g" \
+ -e "s/##Description##/${DESCRIPTION}/g" \
+ -e "s/##Pathogen##/${PATHOGEN}/g" \
+ -e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
+ -e "s/##Locus##/${LOCUS}/g" \
+ "$style" > "$STYLEDIR/$confstyle"
+ else
+ cp -a "$style" "$STYLEDIR/$confstyle"
+ fi
+ fi
+ if [ ! -s "/var/www/${pkg}/$XMLNAME/$confstyle" ] ; then
+ ln -s "$STYLEDIR/$confstyle" "/var/www/${pkg}/$XMLNAME/$confstyle"
+ fi
+done
TMPDIR="/var/www/${pkg}/tmp"
+SQLDIR="/var/lib/${pkg}"
case "$1" in
configure)
[ -d ${TMPDIR} ] || mkdir -p ${TMPDIR}
chgrp www-data ${TMPDIR}
chmod g+w ${TMPDIR}
+
+ # create SQL script from config file
+ mkdir -p $SQLDIR
+ /usr/share/${pkg}/xml2sql.pl -u '"www-data"' "$XMLOUT" >
"$SQLDIR"/"$XMLNAME".sql
;;
abort-upgrade|abort-remove|abort-deconfigure)
Modified: trunk/packages/agdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postrm 2008-09-18 07:59:19 UTC (rev
2508)
+++ trunk/packages/agdbnet/trunk/debian/postrm 2008-09-19 08:25:21 UTC (rev
2509)
@@ -21,8 +21,11 @@
for confxml in `grep -l "<agdb>" /etc/${pkg}/*.xml` ; do
XMLNAME=`basename ${confxml} .xml`
- rm -f /etc/${pkg}/"$XMLNAME".xml /etc/${pkg}/"$XMLNAME".html
- rm -f /etc/${pkg}/"$XMLNAME".xml.old
+ rm -f /etc/${pkg}/"$XMLNAME".xml
+ rm -f /etc/${pkg}/"$XMLNAME".xml.old
+ # remove style files
+ rm -rf /etc/${pkg}/"$XMLNAME"
+ # remove static files and links which were created in postinst
rm -rf /var/www/${pkg}/"$XMLNAME"
done
fi
@@ -30,10 +33,16 @@
# If package should be purged also purge temporary web directory
rm -rf /var/www/${pkg}/tmp
- # finally remove web directory
+ # finally remove web directory
if [ -d /var/www/${pkg} ] ; then
- rmdir /var/www/${pkg}
+ rmdir --ignore-fail-on-non-empty /var/www/${pkg}
fi
+
+ # Remove directory with SQL scripts
+ if [ -d /var/lib/${pkg} ] ; then
+ rm -f /var/lib/${pkg}/"$XMLNAME".sql
+ rmdir --ignore-fail-on-non-empty /var/lib/${pkg}
+ fi
;;
remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
Modified: trunk/packages/agdbnet/trunk/debian/rules
===================================================================
--- trunk/packages/agdbnet/trunk/debian/rules 2008-09-18 07:59:19 UTC (rev
2508)
+++ trunk/packages/agdbnet/trunk/debian/rules 2008-09-19 08:25:21 UTC (rev
2509)
@@ -16,6 +16,8 @@
# copy script to setup PubMed reference fields into
# apropriate dbconfig-common dir
cp -a setup/refs.sql
debian/$(pkg)/usr/share/dbconfig-common/data/${pkg}/install/pgsql
+ # keep lintian silent ...
+ chmod 644
debian/$(pkg)/usr/share/dbconfig-common/data/${pkg}/install/pgsql
# To update po files as recommended in po-debconf(7)
clean::
Modified: trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml
===================================================================
--- trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml 2008-09-18
07:59:19 UTC (rev 2508)
+++ trunk/packages/agdbnet/trunk/debian/template/agdbnet.xml 2008-09-19
08:25:21 UTC (rev 2509)
@@ -11,7 +11,7 @@
<!-- _______________________________________________________ -->
<system
- longcode="##database##" webroot="/agdbnet/##database##" indexpage=""
+ longcode="##database##" webroot="/agdbnet" indexpage=""
description="##Description##"
downloadFASTAonly="yes"
>
Added: trunk/packages/agdbnet/trunk/debian/template/banner.html
===================================================================
--- trunk/packages/agdbnet/trunk/debian/template/banner.html
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/template/banner.html 2008-09-19
08:25:21 UTC (rev 2509)
@@ -0,0 +1,2 @@
+<!-- This html snippet will be included on top of the agdbnet script index -->
+<p>This is the banner.html file.</p>
Added: trunk/packages/agdbnet/trunk/debian/template/footer.html
===================================================================
--- trunk/packages/agdbnet/trunk/debian/template/footer.html
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/template/footer.html 2008-09-19
08:25:21 UTC (rev 2509)
@@ -0,0 +1,3 @@
+<!-- This html snippet will be included after the output of the agdbnet --
+ -- cgi script -->
+<p>This is the footer.html file.</p>
Added: trunk/packages/agdbnet/trunk/debian/template/header.html
===================================================================
--- trunk/packages/agdbnet/trunk/debian/template/header.html
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/template/header.html 2008-09-19
08:25:21 UTC (rev 2509)
@@ -0,0 +1,3 @@
+<!-- This html snippet will be included before the output of the agdbnet --
+ -- cgi script -->
+<p>This is the header.html file.</p>
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