Author: tille
Date: 2009-01-23 07:30:47 +0000 (Fri, 23 Jan 2009)
New Revision: 3040
Added:
trunk/packages/mlstdbnet/trunk/debian/patches/13_ident_authentication.patch
Modified:
trunk/packages/mlstdbnet/trunk/debian/config
trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
trunk/packages/mlstdbnet/trunk/debian/patches/series
trunk/packages/mlstdbnet/trunk/debian/po/templates.pot
trunk/packages/mlstdbnet/trunk/debian/postinst
trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
trunk/packages/mlstdbnet/trunk/debian/templates
Log:
Enhanced configuration issues
Modified: trunk/packages/mlstdbnet/trunk/debian/config
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/config 2009-01-23 04:24:07 UTC
(rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/config 2009-01-23 07:30:47 UTC
(rev 3040)
@@ -54,7 +54,7 @@
db_set ${pkg}/description "$DESCRIPTION"
fi
PUBLICDESCRIPTION=`grep 'description="' /etc/${pkg}/${XMLNAME}.xml | sed
's/.*description="[^"]\+">\([^<]\+\)<.*/\1/'`
- # verify whether description is set in config file
+ # verify whether public description is set in config file
if [ "$PUBLICDESCRIPTION" != "##PublicDescription##" -a
"$PUBLICDESCRIPTION" != "" ] ; then
db_set ${pkg}/publicdescription "$PUBLICDESCRIPTION"
fi
@@ -68,6 +68,19 @@
if [ "$LOCUS" != "##Locus##" -a "$LOCUS" != "" ] ; then
db_set ${pkg}/locus "$LOCUS"
fi
+ WEBROOT=`grep 'webroot="' /etc/${pkg}/${XMLNAME}.xml | sed
's/.*webroot="[^"]\+">\([^<]\+\)<.*/\1/'`
+ # verify whether webroot is set in config file
+ if [ "$WEBROOT" != "##webroot##" -a "$WEBROOT" != "" ] ; then
+ db_set ${pkg}/webroot "$WEBROOT"
+ else
+ # set database name as default webroot
+ db_set ${pkg}/webroot "/${XMLNAME}"
+ fi
+ DBPROF=`grep 'dbprof="' /etc/${pkg}/${XMLNAME}.xml | sed
's/.*dbprof="[^"]\+">\([^<]\+\)<.*/\1/'`
+ # verify whether DPPROF is set in config file
+ if [ "$DBPROF" != "##dbprofiles##" -a "$DBPROF" != "" ] ; then
+ db_set ${pkg}/dbprof "$DBPROF"
+ fi
fi
## db_input high ${pkg}/pathogen || true
@@ -76,6 +89,11 @@
db_input high ${pkg}/locus || true
db_input high ${pkg}/note || true
+# set database name as default webroot
+db_set ${pkg}/webroot "/${XMLNAME}"
+# set database name as default dbprof
+db_set ${pkg}/dbprof "${XMLNAME}"
+
## Now configure a curator for the curator.pl cgi script
## values are stored in
CURATORCONF=/etc/${pkg}/curator.conf
Modified: trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
2009-01-23 04:24:07 UTC (rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
2009-01-23 07:30:47 UTC (rev 3040)
@@ -1,3 +1,5 @@
+In Debian configuration files have to be located in /etc and not in
+the same directory as the cgi script as upstream suggests.
--- mlstdbnet_v2.0.0.orig/cgi-bin/mlstdbnet.pl
+++ mlstdbnet_v2.0.0/cgi-bin/mlstdbnet.pl
@@ -29,9 +29,11 @@
@@ -46,3 +48,25 @@
if ($@) {
warn $@ if $config{'debug'};
$invalidXML = 1;
+--- mlstdbnet_v2.0.0.orig/cgi-bin/curate.pl
++++ mlstdbnet_v2.0.0/cgi-bin/curate.pl
+@@ -26,7 +26,7 @@
+ #E-mail: [email protected]
+
+ ###########Local configuration########################
+-local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
++local ( our $configfile = '/etc/mlstdbnet/mlstdbnet.conf' );
+ #######End Local configuration########################
+ use CGI;
+ use DBI;
+@@ -69,7 +69,9 @@
+ if ( $q->param('file') =~ /^([\w\d\-_]+\.xml)$/ ) {
+ $instance = $1;
+ }
+- eval { $parser->parse( Source => { SystemId => $instance } ); };
++ my $xmlinstance = $instance;
++ if ( ! -e $xmlinstance ) { $xmlinstance = "/etc/mlstdbnet/$instance" ; }
++ eval { $parser->parse( Source => { SystemId => $xmlinstance } ); };
+ if ($@) {
+ $invalidXML = 1;
+ }
Modified: trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
2009-01-23 04:24:07 UTC (rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/10_preconf.patch
2009-01-23 07:30:47 UTC (rev 3040)
@@ -1,3 +1,5 @@
+This patch adjust some pathes in the upstream suggestion for a
+configuration file to the locations in Debian.
--- mlstdbnet_v2.0.0.orig/conf/mlstdbnet.conf
+++ mlstdbnet_v2.0.0/conf/mlstdbnet.conf
@@ -1,11 +1,11 @@
Added:
trunk/packages/mlstdbnet/trunk/debian/patches/13_ident_authentication.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/13_ident_authentication.patch
(rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/13_ident_authentication.patch
2009-01-23 07:30:47 UTC (rev 3040)
@@ -0,0 +1,52 @@
+On Debian GNU Linux systems the suggested way to authenticate to
+a PostgreSQL server on local host is ident authentication. This
+authentication method requires that the host parameter is left out,
+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'.
+--- mlstdbnet_v2.0.0.orig/cgi-bin/curate.pl
++++ mlstdbnet_v2.0.0/cgi-bin/curate.pl
+@@ -133,10 +133,19 @@
+ }
+
+ 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 {
+--- mlstdbnet_v2.0.0.orig/cgi-bin/mlstdbnet.pl
++++ mlstdbnet_v2.0.0/cgi-bin/mlstdbnet.pl
+@@ -376,10 +376,19 @@
+
+ ##################DATABASE CONNECTION########################
+ sub db_connect {
+- $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 }
+ );
++ }
+ $db->do("SET session CHARACTERISTICS AS TRANSACTION READ ONLY");
+ $db->commit();
+ if ( !$profiledb && !$system{'nomlst'} ) {
Modified: trunk/packages/mlstdbnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/series 2009-01-23
04:24:07 UTC (rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/series 2009-01-23
07:30:47 UTC (rev 3040)
@@ -1,2 +1,3 @@
10_preconf.patch
10_config_location.patch
+13_ident_authentication.patch
Modified: trunk/packages/mlstdbnet/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/po/templates.pot 2009-01-23
04:24:07 UTC (rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/po/templates.pot 2009-01-23
07:30:47 UTC (rev 3040)
@@ -8,7 +8,7 @@
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: [email protected]\n"
-"POT-Creation-Date: 2009-01-20 14:54+0100\n"
+"POT-Creation-Date: 2009-01-22 17:45+0100\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <em...@address>\n"
"Language-Team: LANGUAGE <[email protected]>\n"
@@ -305,3 +305,31 @@
"mail address, but once you want to log in as curator only strings containing "
"at least one '@' and a '.' will be accepted."
msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:11001
+msgid "Root directory on webserver"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:11001
+msgid ""
+"Please input the directory where the mlstdbnet CGI script should be "
+"located. By default this is the same as the database name."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:12001
+msgid "Database profile"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:12001
+msgid ""
+"MlstDBNet accepts a database profile. By default this is the same as the "
+"database name."
+msgstr ""
Modified: trunk/packages/mlstdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/postinst 2009-01-23 04:24:07 UTC
(rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/postinst 2009-01-23 07:30:47 UTC
(rev 3040)
@@ -34,13 +34,20 @@
db_get ${pkg}/locus
LOCUS=${RET}
+db_get ${pkg}/webroot
+WEBROOT=${RET}
+db_get ${pkg}/dbprof
+DBPROF=${RET}
+
# Substitute the value ##variables## in the templates and move them
# right into place
XMLOUT=/etc/${pkg}/"$XMLNAME".xml
# if no config file exists, just create one from the template
if [ ! -e "$XMLOUT" ] ; then
sed -e "s/##database##/${XMLNAME}/g" \
+ -e "s/##dbprofiles##/${DBPROF}/g" \
+ -e "s?##webroot##?/${DBPROF}?g" \
-e "s/##Description##/${DESCRIPTION}/g" \
-e "s/##PublicDescription##/${PUBLICDESCRIPTION}/g" \
-e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
@@ -51,6 +58,8 @@
cp -a "$XMLOUT" "$XMLOUT".old
sed -i \
-e "s/longcode=\"[^\"]\+\"/longcode=\"${XMLNAME}\"/g" \
+ -e "s/dbprof=\"[^\"]\+\"/dbprof=\"${DBPROF}\"/g" \
+ -e "s?webroot=\"[^\"]\+\"?webroot=\"${WEBROOT}\"?g" \
-e "s/description=\"[^\"]\+\"/description=\"${DESCRIPTION}\"/g" \
-e "s/\(description=\"[^\"]\+\">\)[^<]\+/\1${PUBLICDESCRIPTION}/g" \
-e "s/<locus fullname=\"[^\"]*\">[^<]\+/<locus
fullname=\"${LOCUSFULLNAME}\">${LOCUS}/" \
Modified: trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
2009-01-23 04:24:07 UTC (rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
2009-01-23 07:30:47 UTC (rev 3040)
@@ -16,7 +16,7 @@
webroot="##webroot##"
indexpage=""
dbprof="##dbprofiles##"
- profhome="/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-##dbprofiles##.xml"
+ profhome="/cgi-bin/mlstdbnet.pl?file=pub-##dbprofiles##.xml"
noshow="other_name,Z_number,region"
view="isolates" dbtype="st"
description="##Description##">##PublicDescription##</system>
Modified: trunk/packages/mlstdbnet/trunk/debian/templates
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/templates 2009-01-23 04:24:07 UTC
(rev 3039)
+++ trunk/packages/mlstdbnet/trunk/debian/templates 2009-01-23 07:30:47 UTC
(rev 3040)
@@ -149,3 +149,15 @@
curator for mlstdbnet. Please not that your input is not verified now
for a valid e-mail address, but once you want to log in as curator
only strings containing at least one '@' and a '.' will be accepted.
+
+Template: mlstdbnet/webroot
+Type: string
+_Description: Root directory on webserver
+ Please input the directory where the mlstdbnet CGI script should
+ be located. By default this is the same as the database name.
+
+Template: mlstdbnet/dbprof
+Type: string
+_Description: Database profile
+ MlstDBNet accepts a database profile. By default this is the same
+ as the database name.
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