[med-svn] r3019 - in trunk/packages/mlstdbnet/trunk/debian: . po template
tille at alioth.debian.org
tille at alioth.debian.org
Sun Jan 18 14:57:43 UTC 2009
Author: tille
Date: 2009-01-18 14:57:43 +0000 (Sun, 18 Jan 2009)
New Revision: 3019
Added:
trunk/packages/mlstdbnet/trunk/debian/README.source
trunk/packages/mlstdbnet/trunk/debian/TODO
trunk/packages/mlstdbnet/trunk/debian/apache.conf
trunk/packages/mlstdbnet/trunk/debian/compat
trunk/packages/mlstdbnet/trunk/debian/config
trunk/packages/mlstdbnet/trunk/debian/cron.daily
trunk/packages/mlstdbnet/trunk/debian/dirs
trunk/packages/mlstdbnet/trunk/debian/docs
trunk/packages/mlstdbnet/trunk/debian/examples
trunk/packages/mlstdbnet/trunk/debian/install
trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql
trunk/packages/mlstdbnet/trunk/debian/po/
trunk/packages/mlstdbnet/trunk/debian/po/POTFILES.in
trunk/packages/mlstdbnet/trunk/debian/po/templates.pot
trunk/packages/mlstdbnet/trunk/debian/postinst
trunk/packages/mlstdbnet/trunk/debian/postrm
trunk/packages/mlstdbnet/trunk/debian/prerm
trunk/packages/mlstdbnet/trunk/debian/rules
trunk/packages/mlstdbnet/trunk/debian/template/
trunk/packages/mlstdbnet/trunk/debian/template/footer.html
trunk/packages/mlstdbnet/trunk/debian/template/index.html
trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
trunk/packages/mlstdbnet/trunk/debian/templates
Modified:
trunk/packages/mlstdbnet/trunk/debian/README.Debian
Log:
Took over packaging stuff from agdbnet and tried a quite rude s/agdbnet/mlstdbnet/g which most probably does not lead to a workin package but seems to be a reasonable approach to finish the mlstdbnet packaging soon.
Modified: trunk/packages/mlstdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/README.Debian 2009-01-17 20:56:22 UTC (rev 3018)
+++ trunk/packages/mlstdbnet/trunk/debian/README.Debian 2009-01-18 14:57:43 UTC (rev 3019)
@@ -5,4 +5,4 @@
-----------------------------------
- -- Andreas Tille <tillea at rki.de>, Wed, 24 Sep 2008 14:23:04 +0200
+ -- Andreas Tille <tille at debian.org>, Wed, 24 Sep 2008 14:23:04 +0200
Added: trunk/packages/mlstdbnet/trunk/debian/README.source
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/README.source (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/README.source 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,16 @@
+README.source for mlstdbnet
+===========================
+
+The old and unreproducible tweaked java/Djalview.jar is removed from
+the upstream source because Upstream said:
+
+ Date: Wed, 14 Jan 2009 07:54:21 +0000
+ From: Keith Jolley <keith.jolley at zoo.ox.ac.uk>
+ To: Andreas Tille <tillea at rki.de>
+
+ The included jalview binary was modified quite a bit by Man-Suen Chan
+ (author of mlstdb) and Michele Clamp (original author of JalView version
+ 1). The functionality is not particularly useful and I've never liked
+ the way it spawned a Java program anyway, so I'd be happy to see it left out.
+
+ -- Andreas Tille <tille at debian.org>, Wed, 24 Sep 2008 14:23:04 +0200
Added: trunk/packages/mlstdbnet/trunk/debian/TODO
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/TODO (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/TODO 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,4 @@
+What is the sense of apache-modconf?
+The command
+ apache-modconf apache enable authn_anon
+does nothing and I have to manually do
Added: trunk/packages/mlstdbnet/trunk/debian/apache.conf
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/apache.conf (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/apache.conf 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,44 @@
+# agcurate default Apache configuration
+
+ScriptAlias /agcurate/ /usr/share/mlstdbnet/cgi-bin/
+<Directory "/usr/share/mlstdbnet/cgi-bin">
+ AllowOverride None
+ Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+
+ AuthName "Authentication for agcurator"
+ AuthType Basic
+
+ # This is a very simple Authentication method which in principle enables
+ # ANYBODY to authenticate successfully. This definitely should be changed
+ # to get a secure system.
+ AuthBasicProvider anon
+ # A detailed description of Apache authentication mechanisms is given at
+ # http://httpd.apache.org/docs/2.2/howto/auth.html
+ # We recommend at least file authentication which is described here
+ # http://httpd.apache.org/docs/2.2/mod/mod_authn_file.html
+ # and could be configured like this:
+ # AuthBasicProvider file
+ # AuthUserFile /etc/mlstdbnet/htpasswd
+ # Alternatively you might have an LDAP directory for your local users
+ # which can be used with Apache LDAP athentication which is described here
+ # http://httpd.apache.org/docs/2.2/mod/mod_authnz_ldap.html
+ # Setting up this is quite comfortable for your users because they do
+ # not need to remember just another password for agcurator but can use
+ # the same as for local network authentication
+ #
+ # I repeat: CHANGE THE AUTHENTICATION METHOD TO SOMETHING MORE SECURE
+ # BECAUSE EVERYBODY WHO KNOWS YOUR NAME AND E_MAIL ADDRESS MIGHT CURATE
+ # YOUR mlstdbnet DATABASE OTHERWISE.
+
+ Anonymous_NoUserID off
+ Anonymous_MustGiveEmail on
+ Anonymous_VerifyEmail on
+ Anonymous_LogEmail on
+ # Accepts any user name and valid e-mail address combination
+ Anonymous "*"
+
+ Order Deny,Allow
+ Allow from all
+
+ Require valid-user
+</Directory>
Added: trunk/packages/mlstdbnet/trunk/debian/compat
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/compat (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/compat 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1 @@
+7
Added: trunk/packages/mlstdbnet/trunk/debian/config
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/config (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/config 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,127 @@
+#!/bin/sh
+set -e
+
+# export should ensure that pkg is available in the template
+export pkg=mlstdbnet
+
+DEBCONF_DEBUG=developer
+
+. /usr/share/debconf/confmodule
+db_version 2.0
+
+# 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/mlstdbnet/${xmlname}
+# and thus we have to look first, where the config items are stored.
+# Then we can read out the remaining config items from the apropriate
+# config file
+
+db_get ${pkg}/xmlname || true
+XMLNAME=$RET
+
+# Verify the existence of a /etc/${pkg}/${XMLNAME}.xml file
+if [ -e /etc/${pkg}/${XMLNAME}.xml ] ; then
+ confavail="true"
+else
+ confavail="false"
+ # Verify whether there are other potential XML conffiles
+ if [ -d /etc/${pkg} ] ; then
+ if grep -q "<mlstdb>" /etc/${pkg}/*.xml 2> /dev/null ; then
+ # use first potential conffile
+ confxml=`grep -l "<mlstdb>" /etc/${pkg}/*.xml | head -1`
+ confxml=`basename ${confxml} .xml`
+ fi
+ fi
+fi
+
+if [ "$XMLNAME" = "" ] ; then
+ if [ "$confavail" = "false" -a "$confxml" != "" ] ; then
+ XMLNAME="$confxml"
+ fi
+fi
+
+db_set ${pkg}/xmlname "$XMLNAME"
+db_input high ${pkg}/xmlname || true
+db_go || true
+
+# Verify whether config file might contain values different from
+# debconf database and set these values
+if [ -s /etc/${pkg}/${XMLNAME}.xml ] ; then
+ ## According to upstream pathogen is not used ... can be removed
+ ## PATOGEN=`grep '</system>' /etc/${pkg}/${XMLNAME}.xml | sed 's?\([^>]\+\)</system>.*?\1?'`
+ ## # verify whether Pathogen is set in config file
+ ## if [ "$PATOGEN" != "##Pathogen##" -a "$PATOGEN" != "" ] ; then
+ ## db_set ${pkg}/pathogen "$PATOGEN"
+ ## fi
+ DESCRIPTION=`grep 'description="' /etc/${pkg}/${XMLNAME}.xml | sed 's/.*description="\([^"]*\)".*/\1/'`
+ # verify whether description is set in config file
+ if [ "$DESCRIPTION" != "##Description##" -a "$DESCRIPTION" != "" ] ; then
+ db_set ${pkg}/description "$DESCRIPTION"
+ fi
+ LOCUSFULLNAME=`grep '<locus fullname=' /etc/${pkg}/${XMLNAME}.xml | sed 's/.*<locus fullname="\([^"]*\)".*/\1/'`
+ # verify whether LocusFullName is set in config file
+ if [ "$LOCUSFULLNAME" != "##LocusFullName##" -a "$LOCUSFULLNAME" != "" ] ; then
+ db_set ${pkg}/locusfullname "$LOCUSFULLNAME"
+ fi
+ LOCUS=`grep '<locus fullname=' /etc/${pkg}/${XMLNAME}.xml | sed 's/.*<locus fullname="[^"]*">\([^<]\+\)/\1/'`
+ # verify whether Locus is set in config file
+ if [ "$LOCUS" != "##Locus##" -a "$LOCUS" != "" ] ; then
+ db_set ${pkg}/locus "$LOCUS"
+ fi
+fi
+
+## db_input high ${pkg}/pathogen || true
+db_input high ${pkg}/description || true
+db_input high ${pkg}/locusfullname || true
+db_input high ${pkg}/locus || true
+db_input high ${pkg}/note || true
+
+## Now configure a curator for the agcurator.pl cgi script
+## values are stored in
+CURATORCONF=/etc/${pkg}/agcurator.conf
+
+parse_config_string () {
+ grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"
+ return 0
+}
+
+if [ -s "$CURATORCONF" ] ; then
+ USERNAME=`parse_config_string USERNAME`
+ if [ "$USERNAME" != "" ] ; then
+ db_set ${pkg}/curator/username "$USERNAME"
+ fi
+ SURNAME=`parse_config_string SURNAME`
+ if [ "$SURNAME" != "" ] ; then
+ db_set ${pkg}/curator/surname "$SURNAME"
+ fi
+ FIRSTNAME=`parse_config_string FIRSTNAME`
+ if [ "$FIRSTNAME" != "" ] ; then
+ db_set ${pkg}/curator/firstname "$FIRSTNAME"
+ fi
+ EMAIL=`parse_config_string EMAIL`
+ if [ "$EMAIL" != "" ] ; then
+ db_set ${pkg}/curator/email "$EMAIL"
+ fi
+fi
+
+db_input high ${pkg}/curator/username || true
+db_input high ${pkg}/curator/surname || true
+db_input high ${pkg}/curator/firstname || true
+db_input high ${pkg}/curator/email || true
+
+# 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
Added: trunk/packages/mlstdbnet/trunk/debian/cron.daily
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/cron.daily (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/cron.daily 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,17 @@
+#!/bin/sh
+# populate the refs database once isolate databases have been set up
+#
+# The config file
+CONFFILE=/etc/mlstdbnet/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/doc/mlstdbnet/README.Debian for more detailed information
+
+PROG=/usr/share/mlstdbnet/getrefs.pl
+
+if [ -x $PROG -a -s $CONFFILE ] ; then
+ su - --command "$PROG $CONFFILE" www-data
+fi
Added: trunk/packages/mlstdbnet/trunk/debian/dirs
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/dirs (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/dirs 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,3 @@
+etc/mlstdbnet
+etc/apache2/conf.d
+usr/share/dbconfig-common/data/mlstdbnet/install
Added: trunk/packages/mlstdbnet/trunk/debian/docs
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/docs (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/docs 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,2 @@
+debian/mlstdbnet_xml2sql
+
Added: trunk/packages/mlstdbnet/trunk/debian/examples
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/examples (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/examples 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1 @@
+example_xmlfiles/*
Added: trunk/packages/mlstdbnet/trunk/debian/install
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/install (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/install 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,9 @@
+cgi-bin/mlstdbnet.pl usr/lib/cgi-bin
+cgi-bin/curate.pl usr/share/mlstdbnet/cgi-bin
+cgi-bin/lib usr/share/perl5/mlstdbnet
+cgi-bin/Plugins usr/share/perl5/mlstdbnet
+debian/template usr/share/mlstdbnet
+scripts/*.pl usr/share/mlstdbnet
+css/stylesheet.css usr/share/mlstdbnet/template
+conf/* etc/mlstdbnet
+images usr/share/mlstdbnet
Added: trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,75 @@
+#!/bin/sh -e
+pkg=mlstdbnet
+SQLDIR="/var/lib/${pkg}"
+
+if [ "$1" != "" ] ; then
+ XML="/etc/${pkg}/$1"
+ if [ ! -s "$XML" ] ; then
+ XML="/etc/${pkg}/$1.xml"
+ if [ ! -s "$XML" ] ; then
+ echo "$0: File /etc/${pkg}/$1 or $XML not found."
+ exit 66 # EX_NOINPUT
+ fi
+ fi
+else
+ if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 1 ] ; then
+ XML=`grep -l "<mlstdb>" /etc/${pkg}/*.xml`
+ else
+ if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 0 ] ; then
+ echo "$0: There are no valid XML configuration files for ${pkg} available in /etc/${pkg}"
+ exit 66 # EX_NOINPUT
+ else
+ cat <<EOT
+Usage: $0 [${pkg}.xml]
+ There are more than one XML files available.
+ You need to specify the one which should be used to create the database.
+EOT
+ grep -l "<mlstdb>" /etc/${pkg}/*.xml
+ exit 64 # EX_USAGE
+ fi
+ fi
+fi
+
+XMLNAME=`basename $XML .xml`
+
+if [ -e "$SQLDIR"/"$XMLNAME".sql ] ; then
+ mv "$SQLDIR"/"$XMLNAME".sql "$SQLDIR"/"$XMLNAME".sql~
+fi
+/usr/share/${pkg}/xml2sql.pl -u 'www-data' "$XML" > "$SQLDIR"/"$XMLNAME".sql
+
+if psql -l | grep -wq "$XMLNAME" ; then
+ cat <<EOT
+$0: The database $XMLNAME just exists.
+ You might like to manually drop this database and populate a newly created
+ one with the data in "$SQLDIR"/"$XMLNAME".sql.
+EOT
+ exit 0
+fi
+
+createdb "$XMLNAME"
+psql "$XMLNAME" < "$SQLDIR"/"$XMLNAME".sql
+
+# try to set curator information
+CURATORCONF=/etc/${pkg}/agcurator.conf
+
+parse_config_string () {
+ RET=`grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"`
+ if [ "$RET" = "" ] ; then
+ echo "Unable to find value $1 in $CURATORCONF. Curator information can not be set."
+ return -1
+ fi
+ echo "$RET"
+ return 0
+}
+
+if [ -s "$CURATORCONF" ] ; then
+ USERNAME=`parse_config_string USERNAME`
+ SURNAME=`parse_config_string SURNAME`
+ FIRSTNAME=`parse_config_string FIRSTNAME`
+ EMAIL=`parse_config_string EMAIL`
+fi
+
+set -x
+psql "$XMLNAME" <<EOT
+ INSERT INTO users VALUES (1, '$USERNAME', '$SURNAME', '$FIRSTNAME', '$EMAIL', '', 'curator', now(), '') ;
+EOT
Added: trunk/packages/mlstdbnet/trunk/debian/po/POTFILES.in
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/po/POTFILES.in (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/po/POTFILES.in 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1 @@
+[type: gettext/rfc822deb] templates
Added: trunk/packages/mlstdbnet/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/po/templates.pot (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/po/templates.pot 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,279 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL at ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"Report-Msgid-Bugs-To: mlstdbnet at packages.debian.org\n"
+"POT-Creation-Date: 2009-01-18 15:52+0100\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
+"Language-Team: LANGUAGE <LL at li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=CHARSET\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid "Name of the mlstdbnet database:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid ""
+"The package mlstdbnet is using a configuration file which stores the name of "
+"the database. The configuration file should have the same name. The "
+"database specific configuration items will be stored in the file /etc/"
+"mlstdbnet/<name_you_input_here>.xml and can be adjusted there."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid ""
+"It is suggested to use a characteristical lower-case character name which is "
+"handy for file names for instance. A shortcut for the pathogen that will be "
+"typed by mlstdbnet makes perfectly sense."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"mlstdbnet/attributes.shtml . See the description of the attribute \"longcode"
+"\" for the \"<system>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:2001
+msgid "Database description:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:2001
+msgid ""
+"Each mlstdbnet database should have a description which includes the "
+"pathogen name and genetic locus/loci that the database holds. It is used as "
+"<h1> heading and <title> of the generated HTML pages. The description will "
+"be stored in the configuration file in /etc/mlstdbnet and can be changed "
+"there if needed."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:2001
+msgid ""
+"Resonable values for such a short description are something like:\n"
+" * Campylobacter jejuni FlaA\n"
+" * Neisseria meningitidis FetA variable region\n"
+" * Streptococcus equi seM"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:2001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"mlstdbnet/attributes.shtml . See the description of the attribute "
+"\"description\" for the \"<system>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:3001
+msgid "Full name of locus:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:3001
+msgid ""
+"A locus describes a genetic locus (gene, partial gene fragment, operon etc.) "
+"or a gene product (protein/peptide)."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:3001
+msgid ""
+"The preconfiguration of this Debian package has a template for one <locus> "
+"element which is the minimal required number. If you need more loci you have "
+"to edit the XML file manually as it is described later."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:3001
+msgid "Reasonable values might be: variable region <number>."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:3001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"mlstdbnet/attributes.shtml . See the description of the attribute \"fullname"
+"\" for the \"<locus>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:4001
+msgid "Locus abbreviation:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:4001
+msgid ""
+"Within the locus element you must have either a nucleotide or a peptide "
+"element (or both if you have tables defined for both). The generated XML "
+"file in /etc/mlstdbnet contains templates for both and you have to edit this "
+"manually as described later."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:4001
+msgid ""
+"The abbreviation should be short and describe only the locus - for instance "
+"for \"variable region 1\" the abbreviation 'VR1' is fine or 'flaA' for "
+"\"Campylobacter jejuni FlaA\". The name here is used throughout the website "
+"- including the name of sequences when you download in FASTA format. It "
+"should definitely be short."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:4001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"mlstdbnet/attributes.shtml . The value here corresponds to the man attribute "
+"of the \"<locus>\" element."
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:5001
+msgid "Hint about configuration of the PubMed reference database"
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:5001
+msgid ""
+"You are now finished with the mlstdbnet configuration. Please read more "
+"about mlstdbnet configuration at\n"
+" http://pubmlst.org/software/database/mlstdbnet/xml.shtml and\n"
+" http://pubmlst.org/software/database/mlstdbnet/attributes.shtml\n"
+"and review the XML file in /etc/mlstdbnet and make sure that all values are "
+"reasonable. The database is not created automatically and you have to "
+"follow the procedure described in /usr/share/doc/mlstdbnet/README.Debian to "
+"finish the installation process."
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:5001
+msgid ""
+"The following questions concern the creation of the database for PubMed "
+"references. It should be safe to use always default values (just <Enter>)."
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:5001
+msgid ""
+"To enable daily updates of PubMed references you have to create\n"
+" /etc/mlstdbnet/getrefs.conf\n"
+"according to the template in examples. It is strongly recommended to read\n"
+" /usr/share/doc/mlstdbnet/README.Debian\n"
+"how to create this file."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:6001
+msgid "Username of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:6001
+msgid ""
+"Curators of agdbnat are people who are allowed to insert new sequences into "
+"the database which can be used to compare with user provided sequences in "
+"mlstdbnet. Curators should be knowledged administrators of the database and "
+"need to authenticate themself before they will be able to manage database "
+"information. You have to provide a username, real name information and a "
+"valid e-mail address."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:6001
+msgid ""
+"Attention: The method currently used for authentication is insecure. Please "
+"read /usr/share/doc/mlstdbnet/README.Debian how to change this to a secure "
+"method."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:6001
+msgid ""
+"Please input the login username for one curator now. Others can be added "
+"later."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid "Surname of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid ""
+"Please input the surname of the person which should work as a curator for "
+"mlstdbnet."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:8001
+msgid "First name of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:8001
+msgid ""
+"Please input the first name of the person which should work as a curator for "
+"mlstdbnet."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:9001
+msgid "E-mail address of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:9001
+msgid ""
+"Please input the e-mail address of the person which should work as a 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."
+msgstr ""
Added: trunk/packages/mlstdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/postinst (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/postinst 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,169 @@
+#!/bin/sh
+# postinst script for mlstdbnet
+
+set -e
+
+pkg=mlstdbnet
+
+DEBCONF_DEBUG=developer
+. /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}
+
+db_get ${pkg}/description
+DESCRIPTION=${RET}
+
+## According to upstream pathogen is not used any more
+## db_get ${pkg}/pathogen
+## PATHOGEN=${RET}
+
+db_get ${pkg}/locusfullname
+LOCUSFULLNAME=${RET}
+
+db_get ${pkg}/locus
+LOCUS=${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/##Description##/${DESCRIPTION}/g" \
+ -e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
+ -e "s/##Locus##/${LOCUS}/g" \
+ /usr/share/${pkg}/template/${pkg}.xml > \
+ "$XMLOUT"
+else
+ cp -a "$XMLOUT" "$XMLOUT".old
+ sed -i \
+ -e "s/longcode=\"[^\"]\+\"/longcode=\"${XMLNAME}\"/g" \
+ -e "s/description=\"[^\"]\+\"/description=\"${DESCRIPTION}\"/g" \
+ -e "s/<locus fullname=\"[^\"]*\">[^<]\+/<locus fullname=\"${LOCUSFULLNAME}\">${LOCUS}/" \
+ "$XMLOUT"
+fi
+
+# All files that might influence the layout of the web site are
+# considered config files and stored into /etc/${pkg}/${XMLNAME}
+# If such files do not exist they will be created from a simple
+# template.
+STYLEDIR=/etc/${pkg}/"$XMLNAME"
+mkdir -p ${STYLEDIR}
+for style in `ls /usr/share/${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/##LocusFullName##/${LOCUSFULLNAME}/g" \
+ -e "s/##Locus##/${LOCUS}/g" \
+ "$style" > "$STYLEDIR/$confstyle"
+ else
+ cp -a "$style" "$STYLEDIR/$confstyle"
+ fi
+ fi
+done
+
+# Finally a link is put into place to enable mlstdbnet to find these files.
+mkdir -p /var/www/${pkg}
+if [ ! -L "/var/www/${pkg}/$XMLNAME" -a ! -d "/var/www/${pkg}/$XMLNAME" ] ; then
+ ln -s "$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}
+
+db_get ${pkg}/curator/surname
+SURNAME=${RET}
+
+db_get ${pkg}/curator/firstname
+FIRSTNAME=${RET}
+
+db_get ${pkg}/curator/email
+EMAIL=${RET}
+
+CURATORCONF=/etc/${pkg}/agcurator.conf
+if [ ! -s "$CURATORCONF" ] ; then
+ cat > "$CURATORCONF" <<EOT
+# This file is used when creating the mlstdbnet database to add an initial curator
+# Please read /usr/share/${pkg}/README.Debian for further information.
+USERNAME=${USERNAME}
+SURNAME=${SURNAME}
+FIRSTNAME=${FIRSTNAME}
+EMAIL=${EMAIL}
+EOT
+else
+ sed -i~ -e "s/^\([[:space:]]*USERNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${USERNAME}/" \
+ -e "s/^\([[:space:]]*SURNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${SURNAME}/" \
+ -e "s/^\([[:space:]]*FIRSTNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${FIRSTNAME}/" \
+ -e "s/^\([[:space:]]*EMAIL[[:space:]]*=[[:space:]]*\)[^#]\+/\1${EMAIL}/" \
+ "$CURATORCONF"
+fi
+
+TMPDIR="/var/www/${pkg}/temporary"
+SQLDIR="/var/lib/${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
+ # Here the SQL code which is created by xml2sql.pl from config
+ # file is stored. It is world writable because a normal user
+ # with proper postgresql permissions should be enabled to create the
+ # database.
+ chmod 777 ${SQLDIR}
+ /usr/share/${pkg}/xml2sql.pl -u '"www-data"' "$XMLOUT" > "$SQLDIR"/"$XMLNAME".sql
+ chmod 666 "$SQLDIR"/"$XMLNAME".sql
+
+ # Enable Apache anonymous authentication for agcurate.pl
+ # script
+ # apache-modconf apache enable authn_anon
+ # I have no idea for what purpose apache-modconf exists -
+ # at least it does not set the necessary link - so do it
+ # manually here ...
+ 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
+ invoke-rc.d apache2 reload 3>/dev/null || true
+ else
+ /etc/init.d/apache2 reload 3>/dev/null || true
+ fi
+ else
+ echo "Your apache2 configuration is broken, so we're not restarting it for you."
+ fi
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/mlstdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/postrm (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/postrm 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,63 @@
+#!/bin/sh
+# postrm script for mlstdbnet
+
+set -e
+
+pkg=mlstdbnet
+
+. /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 "$1" in
+ purge)
+ # remove all potential config files and dirs in /var/www
+ if ls /etc/${pkg}/*.xml 1>/dev/null 2>/dev/null ; then
+ for confxml in `grep -l "<mlstdb>" /etc/${pkg}/*.xml` ; do
+ XMLNAME=`basename ${confxml} .xml`
+
+ rm -f /etc/${pkg}/"$XMLNAME".xml
+ rm -f /etc/${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
+ fi
+
+ # If package should be purged also purge temporary web directory
+ rm -rf /var/www/${pkg}/temporary
+
+ # finally remove web directory
+ if [ -d /var/www/${pkg} ] ; then
+ 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/${pkg}
+ fi
+
+ # Remove configuration for curator
+ rm -f /etc/${pkg}/agcurator.conf
+ ;;
+
+ remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+ ;;
+
+ *)
+ echo "postrm called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/mlstdbnet/trunk/debian/prerm
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/prerm (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/prerm 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,19 @@
+#!/bin/sh
+# prerm script for mlstdbnet
+
+set -e
+
+pkg=mlstdbnet
+
+. /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} $@
+fi
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/mlstdbnet/trunk/debian/rules
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/rules (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/rules 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+# debian/rules for mlstdbnet
+# Andreas Tille <tille at debian.org>; GPL
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+
+pkg=mlstdbnet
+
+DEB_COMPRESS_EXCLUDE := .xml
+
+common-binary-post-install-arch::
+ # Directory conf has to be copied to /etc/$(pkg)
+ 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
+ # keep lintian silent ...
+ chmod 644 debian/$(pkg)/usr/share/dbconfig-common/data/${pkg}/install/pgsql
+
+ # Apache configuration for agcurator.pl
+ cp -a debian/apache.conf debian/$(pkg)/etc/apache2/conf.d/$(pkg)
+
+# To update po files as recommended in po-debconf(7)
+clean::
+ @debconf-updatepo
+
+get-orig-source:
+ sh debian/get-orig-source
Property changes on: trunk/packages/mlstdbnet/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/mlstdbnet/trunk/debian/template/footer.html
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/template/footer.html (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/template/footer.html 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,3 @@
+<!-- This html snippet will be included after the output of the mlstdbnet --
+ -- cgi script -->
+<p>This is the footer.html file.</p>
Added: trunk/packages/mlstdbnet/trunk/debian/template/index.html
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/template/index.html (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/template/index.html 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,18 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" >
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" >
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <title>##Description##</title>
+
+ <meta name="description" content="##Description##" />
+ <meta name="keywords" content="mlstdbnet" />
+ <meta http-equiv="content-language" content="en" />
+ <meta name="language" content="en" />
+</head>
+<body>
+
+##Description##: <a href="http://localhost/cgi-bin/mlstdbnet.pl?file=##database##.xml">##database##</a><br />
+##LocusFullName##
+
+</body>
+</html>
Added: trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<mlstdb>
+
+<!-- _______________________________________________________ -->
+<!-- Before you start -->
+<!-- ________________ -->
+<!-- As long as there are values marked like ##this## the -->
+<!-- XML file is not usable -->
+<!-- Make sure you read /usr/share/doc/mlstdbnet/README.Debian -->
+<!-- to learn what has to be done! -->
+<!-- _______________________________________________________ -->
+
+<system
+ longcode="##database##" webroot="/mlstdbnet" indexpage=""
+ description="##Description##"
+ downloadFASTAonly="yes"
+>
+</system>
+
+<!-- LOCI -->
+<locus fullname="##LocusFullName##">##Locus##
+<nucleotide>
+<field type="int" length="##?##" userupdate="no" comments="primary key">id</field>
+<field type="text" length="##?##" width="30" maindisplay="no">sequence</field>
+<field type="int" length="##?##" comments="foreign key to peptide table">peptide_id</field>
+<field type="text" length="##?##" required="no" maindisplay="no">genbank</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference1</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference2</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference3</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference4</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference5</field>
+<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
+<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date last modified">datestamp</field>
+<field type="int" maindisplay="no" userupdate="no" length="4" comments="curator who entered data,link to users">curator</field>
+</nucleotide>
+
+<peptide>
+<field type="int" length="##?##" userupdate="no" comments="primary key">id</field>
+<field type="text" length="##?##" userupdate="no" width="30">sequence</field>
+<field type="text" length="##?##" required="no" maindisplay="no">genbank</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference1</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference2</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference3</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference4</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed number if published">reference5</field>
+<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
+<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date last modified">datestamp</field>
+<field type="int" maindisplay="no" userupdate="no" length="4" comments="curator who entered data,link to users">curator</field>
+</peptide>
+</locus>
+
+</mlstdb>
Added: trunk/packages/mlstdbnet/trunk/debian/templates
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/templates (rev 0)
+++ trunk/packages/mlstdbnet/trunk/debian/templates 2009-01-18 14:57:43 UTC (rev 3019)
@@ -0,0 +1,132 @@
+Template: mlstdbnet/xmlname
+Type: string
+_Description: Name of the mlstdbnet database:
+ The package mlstdbnet is using a configuration file which stores the
+ name of the database. The configuration file should have the same
+ name. The database specific configuration items will be stored in
+ the file /etc/mlstdbnet/<name_you_input_here>.xml and can be adjusted
+ there.
+ .
+ It is suggested to use a characteristical lower-case character
+ name which is handy for file names for instance. A shortcut for
+ the pathogen that will be typed by mlstdbnet makes perfectly sense.
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ See the description of the attribute "longcode" for the
+ "<system>" element.
+
+Template: mlstdbnet/description
+Type: string
+_Description: Database description:
+ Each mlstdbnet database should have a description which includes
+ the pathogen name and genetic locus/loci that the database holds.
+ It is used as <h1> heading and <title> of the generated HTML pages.
+ The description will be stored in the configuration file in
+ /etc/mlstdbnet and can be changed there if needed.
+ .
+ Resonable values for such a short description are something
+ like:
+ * Campylobacter jejuni FlaA
+ * Neisseria meningitidis FetA variable region
+ * Streptococcus equi seM
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ See the description of the attribute "description" for the
+ "<system>" element.
+
+Template: mlstdbnet/locusfullname
+Type: string
+_Description: Full name of locus:
+ A locus describes a genetic locus (gene, partial gene fragment,
+ operon etc.) or a gene product (protein/peptide).
+ .
+ The preconfiguration of this Debian package has a template
+ for one <locus> element which is the minimal required number.
+ If you need more loci you have to edit the XML file manually
+ as it is described later.
+ .
+ Reasonable values might be: variable region <number>.
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ See the description of the attribute "fullname" for the
+ "<locus>" element.
+
+Template: mlstdbnet/locus
+Type: string
+_Description: Locus abbreviation:
+ Within the locus element you must have either a nucleotide or
+ a peptide element (or both if you have tables defined for both).
+ The generated XML file in /etc/mlstdbnet contains templates for
+ both and you have to edit this manually as described later.
+ .
+ The abbreviation should be short and describe only the locus -
+ for instance for "variable region 1" the abbreviation 'VR1' is
+ fine or 'flaA' for "Campylobacter jejuni FlaA". The name here
+ is used throughout the website - including the name of sequences
+ when you download in FASTA format. It should definitely be short.
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ The value here corresponds to the man attribute of the "<locus>"
+ element.
+
+Template: mlstdbnet/note
+Type: note
+_Description: Hint about configuration of the PubMed reference database
+ You are now finished with the mlstdbnet configuration. Please
+ read more about mlstdbnet configuration at
+ http://pubmlst.org/software/database/mlstdbnet/xml.shtml and
+ http://pubmlst.org/software/database/mlstdbnet/attributes.shtml
+ and review the XML file in /etc/mlstdbnet and make sure that all values
+ are reasonable. The database is not created automatically and you have
+ to follow the procedure described in /usr/share/doc/mlstdbnet/README.Debian
+ to finish the installation process.
+ .
+ The following questions concern the creation of the database for PubMed
+ references. It should be safe to use always default values (just <Enter>).
+ .
+ To enable daily updates of PubMed references you have to create
+ /etc/mlstdbnet/getrefs.conf
+ according to the template in examples. It is strongly recommended to read
+ /usr/share/doc/mlstdbnet/README.Debian
+ how to create this file.
+
+Template: mlstdbnet/curator/username
+Type: string
+_Description: Username of database curator:
+ Curators of agdbnat are people who are allowed to insert new sequences
+ into the database which can be used to compare with user provided
+ sequences in mlstdbnet. Curators should be knowledged administrators of
+ the database and need to authenticate themself before they will be able
+ to manage database information. You have to provide a username, real
+ name information and a valid e-mail address.
+ .
+ Attention: The method currently used for authentication is insecure.
+ Please read /usr/share/doc/mlstdbnet/README.Debian how to change this
+ to a secure method.
+ .
+ Please input the login username for one curator now. Others can be
+ added later.
+
+Template: mlstdbnet/curator/surname
+Type: string
+_Description: Surname of database curator:
+ Please input the surname of the person which should work as a curator
+ for mlstdbnet.
+
+Template: mlstdbnet/curator/firstname
+Type: string
+_Description: First name of database curator:
+ Please input the first name of the person which should work as a curator
+ for mlstdbnet.
+
+Template: mlstdbnet/curator/email
+Type: string
+_Description: E-mail address of database curator:
+ Please input the e-mail address of the person which should work as a
+ 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.
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