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 <[EMAIL PROTECTED]>, 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 <[EMAIL PROTECTED]> Thu, 25 Sep 2008 08:51:47 +0200 + -- Andreas Tille <[EMAIL PROTECTED]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
