[med-svn] r2557 - in trunk/packages/agdbnet/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Sep 29 14:23:10 UTC 2008
Author: tille
Date: 2008-09-29 14:23:09 +0000 (Mon, 29 Sep 2008)
New Revision: 2557
Modified:
trunk/packages/agdbnet/trunk/debian/README.Debian
trunk/packages/agdbnet/trunk/debian/changelog
trunk/packages/agdbnet/trunk/debian/install
trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
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/postinst
trunk/packages/agdbnet/trunk/debian/postrm
Log:
Several adaptations to new upstream version
Modified: trunk/packages/agdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-29 14:23:09 UTC (rev 2557)
@@ -127,7 +127,7 @@
http://httpd.apache.org/docs/2.2/howto/auth.html
For the sake of simplicity and to get something working fast the
-most simple method "anonymous" was choosen for this Debian package.
+most simple method "anonymous" was chosen for this Debian package.
This methods provides nearly non security for your agdbnet database
because everybaody who is able to guess the name of a user who is
registered as a curator and just uses any email-ish string as
@@ -154,6 +154,6 @@
apache-modconf apache enable authnz_ldap
but in my tests this did not worked unfortunately so the method to
-place the symlinks manually should be prefered for the moment.
+place the symlinks manually should be preferred for the moment.
-- Andreas Tille <tillea at rki.de>, Wed, 24 Sep 2008 14:23:04 +0200
Modified: trunk/packages/agdbnet/trunk/debian/changelog
===================================================================
--- trunk/packages/agdbnet/trunk/debian/changelog 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/changelog 2008-09-29 14:23:09 UTC (rev 2557)
@@ -1,5 +1,5 @@
-agdbnet (1.0.0-1) unstable; urgency=low
+agdbnet (1.0.4-1) UNRELEASED; urgency=low
* Initial release (Closes: #500106)
- -- Andreas Tille <tille at debian.org> Thu, 25 Sep 2008 08:51:47 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 29 Sep 2008 13:30:39 +0200
Modified: trunk/packages/agdbnet/trunk/debian/install
===================================================================
--- trunk/packages/agdbnet/trunk/debian/install 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/install 2008-09-29 14:23:09 UTC (rev 2557)
@@ -4,3 +4,4 @@
scripts/*.pl usr/share/agdbnet
stylesheets/stylesheet.css usr/share/agdbnet/template
debian/mlstdbnet.conf etc/agdbnet
+images usr/share/agdbnet
Modified: trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch 2008-09-29 14:23:09 UTC (rev 2557)
@@ -1,42 +1,56 @@
In Debian configuration files have to be located in /etc and not in
the same directory as the cgi script as upstream suggests.
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -35,7 +35,7 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
+@@ -33,13 +33,10 @@
######################################################
-
###########Local configuration########################
--local ( our $configfile = '/usr/local/agdbnet/agdbnet.conf' );
-+local ( our $configfile = '/etc/agdbnet/agdbnet.conf' );
+ local ( our $configfile );
+-if ( -e '/usr/local/agdbnet/agdbnet.conf' ) {
+- $configfile = '/usr/local/agdbnet/agdbnet.conf';
++if ( -e '/etc/agdbnet/agdbnet.conf' ) {
++ $configfile = '/etc/agdbnet/agdbnet.conf';
+ } else {
+-
+-#use mlstdbnet conf file if agdbnet one not available - useful for auto-updating mirrors where
+-#agdbnet not previously installed
+- $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf';
++ die "Cannot open config file '/etc/agdbnet/agdbnet.conf'";
+ }
#######End Local configuration########################
-
local (
-@@ -134,7 +134,7 @@
+@@ -128,7 +125,10 @@
+ $parser->parse( Source => { SystemId => "$1/$instance" } );
}
- }
- else {
+ } else {
- $parser->parse( Source => { SystemId => $instance } );
-+ $parser->parse( Source => { SystemId => "/etc/agdbnet/$instance" } );
++ my $xmlinstance = `pwd`."/$instance";
++ if ( ! -e $xmlinstance ) { $xmlinstance = "/etc/agdbnet/$instance"; }
++ else { $xmlinstance = $instance ; }
++ $parser->parse( Source => { SystemId => $xmlinstance } );
}
};
if ($@) {
---- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
-+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
-@@ -30,7 +30,7 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.4/cgi-bin/agcurate.pl
+@@ -29,7 +29,7 @@
+ use XML::Parser::PerlSAX;
use strict;
-
###########Local configuration########################
--local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
-+local ( our $configfile = '/etc/agdbnet/mlstdbnet.conf' );
+-local ( our $configfile = '/usr/local/agdbnet/agdbnet.conf' );
++local ( our $configfile = '/etc/agdbnet/agdbnet.conf' );
#######End Local configuration########################
-
- local (our (
-@@ -64,7 +64,7 @@
+ local (
+ our (
+@@ -69,7 +69,10 @@
if ( $q->param('file') =~ /^([\w\d\-_]+\.xml)$/ ) {
$instance = $1;
}
- eval { $parser->parse( Source => { SystemId => $instance } ); };
-+ eval { $parser->parse( Source => { SystemId => "/etc/agdbnet/$instance" } ); };
++ my $xmlinstance = `pwd`."/$instance";
++ if ( ! -e $xmlinstance ) { $xmlinstance = "/etc/agdbnet/$instance" ; }
++ else { $xmlinstance = $instance ; }
++ eval { $parser->parse( Source => { SystemId => $xmlinstance } ); };
if ($@) {
$invalidXML = 1;
}
Modified: trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/patches/11_moreinfo.patch 2008-09-29 14:23:09 UTC (rev 2557)
@@ -1,20 +1,20 @@
Provide some more information to the user if the initialisation of
the web page fails by pointing to README.Debian which might contain
hints about things to do next.
---- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
-+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
-@@ -129,7 +129,7 @@
- print $q->header;
+--- agdbnet_v1.0.4.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.4/cgi-bin/agcurate.pl
+@@ -145,7 +145,7 @@
+ print $q->header ( -charset => 'UTF-8' );
if ($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!<br />Please follow the instructions at /usr/share/doc/agdbnet/README.Debian to get a running system.</p>";
- print $q->end_html;
+ print $q->end_html;
return;
}
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -198,7 +198,7 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
+@@ -339,7 +339,7 @@
}
if ($invalidXML) {
print $q->start_html( -title => "Invalid XML file" );
Modified: trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/patches/12_apache_is_web-data.patch 2008-09-29 14:23:09 UTC (rev 2557)
@@ -3,9 +3,9 @@
Attention: The '"' around www-data in the GRANT SQL statement
are important to make sure the '-' in the name will not be
interpreted by the SQL parser.
---- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
-+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
-@@ -80,7 +80,7 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.4/cgi-bin/agcurate.pl
+@@ -87,7 +87,7 @@
$system{'port'} = 5432;
}
if ( !$system{'user'} ) {
@@ -14,9 +14,9 @@
}
if ( !$system{'pass'} ) {
$system{'pass'} = 'remote';
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -156,7 +156,7 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
+@@ -146,7 +146,7 @@
$system{'port'} = 5432;
}
if ( !$system{'user'} ) {
@@ -25,8 +25,8 @@
}
if ( !$system{'pass'} ) {
$system{'pass'} = 'remote';
---- agdbnet_v1.0.0.orig/examples/poravr.xml
-+++ agdbnet_v1.0.0/examples/poravr.xml
+--- agdbnet_v1.0.4.orig/examples/poravr.xml
++++ agdbnet_v1.0.4/examples/poravr.xml
@@ -131,7 +131,7 @@
<field type="text" length="256">description</field>
</auxtable>
@@ -34,10 +34,10 @@
-<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" length="20" comments="Original strain name as supplied by sender">isolate</field>
<field type="text" required="no" maindisplay="no" length="20"
---- agdbnet_v1.0.0.orig/installation.html
-+++ agdbnet_v1.0.0/installation.html
+--- agdbnet_v1.0.4.orig/installation.html
++++ agdbnet_v1.0.4/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 />
@@ -57,8 +57,8 @@
-</html>
\ No newline at end of file
+</html>
---- agdbnet_v1.0.0.orig/scripts/xml2sql.pl
-+++ agdbnet_v1.0.0/scripts/xml2sql.pl
+--- agdbnet_v1.0.4.orig/scripts/xml2sql.pl
++++ agdbnet_v1.0.4/scripts/xml2sql.pl
@@ -45,7 +45,7 @@
$webuser = $opts{'u'};
}
@@ -68,12 +68,39 @@
}
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)
+@@ -85,7 +85,7 @@
+ PRIMARY KEY (id)
);
--GRANT SELECT ON authors,refs TO apache;
+-GRANT SELECT,UPDATE,INSERT,DELETE ON users TO $webuser;
++GRANT SELECT,UPDATE,INSERT,DELETE ON users TO "$webuser";
+
+ USERS
+
+@@ -128,7 +128,7 @@
+ CREATE INDEX i_pmid ON refs (pmid);
+ CREATE INDEX i_id ON refs (id);
+
+-GRANT SELECT,UPDATE,INSERT,DELETE ON refs TO apache;
++GRANT SELECT,UPDATE,INSERT,DELETE ON refs TO "www-data";
+ REFS
+
+ sub printtable {
+@@ -178,7 +178,7 @@
+ }
+ print $buffer;
+ print "\n);\n";
+- print "\nGRANT SELECT,UPDATE,INSERT,DELETE ON $table TO $webuser;\n";
++ print "\nGRANT SELECT,UPDATE,INSERT,DELETE ON $table TO \"$webuser\";\n";
+ }
+
+ sub locustype {
+--- agdbnet_v1.0.4.orig/setup/refs.sql
++++ agdbnet_v1.0.4/setup/refs.sql
+@@ -28,4 +28,4 @@
+ CONSTRAINT author FOREIGN KEY (author) references authors ON DELETE NO ACTION ON UPDATE CASCADE
+ );
+
+-GRANT SELECT ON authors,refs,refauthors TO apache;
\ No newline at end of file
-+GRANT SELECT ON authors,refs TO "www-data";
++GRANT SELECT ON authors,refs,refauthors TO "www-data";
Modified: trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/patches/13_ident_authentication.patch 2008-09-29 14:23:09 UTC (rev 2557)
@@ -4,9 +4,9 @@
i.e. if you specify the host localhost password authentication
is automatically used. This patch removes host and port from
the connection string if $host == 'localhost'.
---- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
-+++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
-@@ -167,10 +167,19 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.4/cgi-bin/agdbnet.pl
+@@ -208,10 +208,19 @@
}
sub dbconnect {
@@ -27,9 +27,9 @@
}
sub dbdisconnect {
---- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
-+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
-@@ -107,10 +107,19 @@
+--- agdbnet_v1.0.4.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.4/cgi-bin/agcurate.pl
+@@ -122,10 +122,19 @@
}
sub dbconnect {
Modified: trunk/packages/agdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postinst 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/postinst 2008-09-29 14:23:09 UTC (rev 2557)
@@ -81,6 +81,11 @@
ln -s "$STYLEDIR" "/var/www/${pkg}/$XMLNAME"
fi
+# Link to image directory
+if [ ! -e "/var/www/${pkg}/images" ] ; then
+ ln -s "/usr/share/${pkg}/images" "/var/www/${pkg}"
+fi
+
# Obtaining user information for agcurator and write this to the config file
db_get ${pkg}/curator/username
USERNAME=${RET}
@@ -137,7 +142,9 @@
# I have no idea for what purpose apache-modconf exists -
# at least it does not set the necessary link - so do it
# manually here ...
- ln -s ../mods-available/authn_anon.load /etc/apache2/mods-enabled
+ if [ ! -L /etc/apache2/mods-enabled/authn_anon.load ] ; then
+ ln -s ../mods-available/authn_anon.load /etc/apache2/mods-enabled
+ fi
# Restart Apache to register configuration for agcurator
if apache2ctl configtest 2>/dev/null; then
if [ -x /usr/sbin/invoke-rc.d ]; then
Modified: trunk/packages/agdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postrm 2008-09-29 13:00:08 UTC (rev 2556)
+++ trunk/packages/agdbnet/trunk/debian/postrm 2008-09-29 14:23:09 UTC (rev 2557)
@@ -25,6 +25,7 @@
rm -f /etc/${pkg}/"$XMLNAME".xml.old
# remove style files
rm -rf /etc/${pkg}/"$XMLNAME"
+ rm -rf /etc/${pkg}/images
# remove link from /var/www to /etc which was created in postinst
rm -rf /var/www/${pkg}/"$XMLNAME"
done
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