[med-svn] r3036 - in trunk/packages/mlstdbnet/trunk/debian: . patches po template
tille at alioth.debian.org
tille at alioth.debian.org
Thu Jan 22 14:20:56 UTC 2009
Author: tille
Date: 2009-01-22 14:20:55 +0000 (Thu, 22 Jan 2009)
New Revision: 3036
Modified:
trunk/packages/mlstdbnet/trunk/debian/apache.conf
trunk/packages/mlstdbnet/trunk/debian/config
trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql
trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
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/rules
trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
trunk/packages/mlstdbnet/trunk/debian/templates
Log:
Fixed several cut-n-pastos from agdbnet packaging - some might have left; database creation and connection does not yet work; just want to commit current status of packaging
Modified: trunk/packages/mlstdbnet/trunk/debian/apache.conf
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/apache.conf 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/apache.conf 2009-01-22 14:20:55 UTC (rev 3036)
@@ -1,11 +1,11 @@
# agcurate default Apache configuration
-ScriptAlias /agcurate/ /usr/share/mlstdbnet/cgi-bin/
+ScriptAlias /curate/ /usr/share/mlstdbnet/cgi-bin/
<Directory "/usr/share/mlstdbnet/cgi-bin">
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
- AuthName "Authentication for agcurator"
+ AuthName "Authentication for curator"
AuthType Basic
# This is a very simple Authentication method which in principle enables
@@ -23,7 +23,7 @@
# 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
+ # not need to remember just another password for curator but can use
# the same as for local network authentication
#
# I repeat: CHANGE THE AUTHENTICATION METHOD TO SOMETHING MORE SECURE
Modified: trunk/packages/mlstdbnet/trunk/debian/config
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/config 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/config 2009-01-22 14:20:55 UTC (rev 3036)
@@ -47,23 +47,23 @@
# 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
+ PUBLICDESCRIPTION=`grep 'description="' /etc/${pkg}/${XMLNAME}.xml | sed 's/.*description="[^"]\+">\([^<]\+\)<.*/\1/'`
+ # verify whether description is set in config file
+ if [ "$PUBLICDESCRIPTION" != "##PublicDescription##" -a "$PUBLICDESCRIPTION" != "" ] ; then
+ db_set ${pkg}/publicdescription "$PUBLICDESCRIPTION"
+ 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/'`
+ LOCUS=`grep '<locus fullname=' /etc/${pkg}/${XMLNAME}.xml | sed 's?.*<locus fullname="[^>]*>\([^<]\+\)</locus>?\1?'`
# verify whether Locus is set in config file
if [ "$LOCUS" != "##Locus##" -a "$LOCUS" != "" ] ; then
db_set ${pkg}/locus "$LOCUS"
@@ -76,39 +76,39 @@
db_input high ${pkg}/locus || true
db_input high ${pkg}/note || true
-## Now configure a curator for the agcurator.pl cgi script
+## Now configure a curator for the curator.pl cgi script
## values are stored in
-CURATORCONF=/etc/${pkg}/agcurator.conf
+CURATORCONF=/etc/${pkg}/curator.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
+#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
-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 ${pkg}/dbconfig-install "true" || true
Modified: trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/mlstdbnet_xml2sql 2009-01-22 14:20:55 UTC (rev 3036)
@@ -50,7 +50,7 @@
psql "$XMLNAME" < "$SQLDIR"/"$XMLNAME".sql
# try to set curator information
-CURATORCONF=/etc/${pkg}/agcurator.conf
+CURATORCONF=/etc/${pkg}/curator.conf
parse_config_string () {
RET=`grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"`
Modified: trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/patches/10_config_location.patch 2009-01-22 14:20:55 UTC (rev 3036)
@@ -1,16 +1,5 @@
--- mlstdbnet_v2.0.0.orig/cgi-bin/mlstdbnet.pl
+++ mlstdbnet_v2.0.0/cgi-bin/mlstdbnet.pl
-@@ -54,7 +54,7 @@
- ######################################################
-
- ###########Local configuration########################
--local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
-+local ( our $configfile = '/etc/mlstdbnet/mlstdbnet.conf' );
- #######End Local configuration########################
-
- #######Lexically-scoped variables#####################
---- mlstdbnet_v2.0.0.orig/cgi-bin/mlstdbnet.pl
-+++ mlstdbnet_v2.0.0/cgi-bin/mlstdbnet.pl
@@ -29,9 +29,11 @@
use DBI;
use strict;
@@ -26,3 +15,34 @@
use Parser;
use Utils;
use Plugins;
+@@ -54,7 +56,7 @@
+ ######################################################
+
+ ###########Local configuration########################
+-local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
++local ( our $configfile = '/etc/mlstdbnet/mlstdbnet.conf' );
+ #######End Local configuration########################
+
+ #######Lexically-scoped variables#####################
+@@ -107,7 +109,20 @@
+ #directory as the script. This prevents
+ #a public script from accessing a private database.
+ $instance = $1 if $q->param('file') =~ /^([\w\d\-_]+\.xml)$/;
+- eval { $parser->parse( Source => { SystemId => $instance } ); };
++ my $xmlinstance;
++ if ( $ENV{MOD_PERL} ) {
++ if ( $ENV{SCRIPT_FILENAME} =~ /(.*)mlstdbnet\.pl/ ) {
++ $xmlinstance = "$1/$instance";
++ }
++ } else {
++ $xmlinstance = $instance;
++ }
++ if ( !-e $xmlinstance ){
++ $xmlinstance = "/etc/mlstdbnet/$instance";
++ }
++ eval {
++ $parser->parse( Source => { SystemId => $xmlinstance } );
++ };
+ if ($@) {
+ warn $@ if $config{'debug'};
+ $invalidXML = 1;
Modified: trunk/packages/mlstdbnet/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/po/templates.pot 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/po/templates.pot 2009-01-22 14:20:55 UTC (rev 3036)
@@ -8,7 +8,7 @@
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"
+"POT-Creation-Date: 2009-01-20 14:54+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"
@@ -46,8 +46,8 @@
#: ../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."
+"mlstdbnet/xml.shtml . See the description of the attribute \"longcode\" for "
+"the \"<system>\" element."
msgstr ""
#. Type: string
@@ -61,10 +61,9 @@
#: ../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."
+"pathogen name and genetic locus/loci that the database holds. The "
+"description will be stored in the configuration file in /etc/mlstdbnet and "
+"can be changed there if needed."
msgstr ""
#. Type: string
@@ -72,14 +71,16 @@
#: ../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"
+" * Neisseria MLST\n"
+" * Neisseria meningitidis MLST\n"
+" * Clostridium Difficile"
msgstr ""
#. Type: string
#. Description
-#: ../templates:2001
+#. Type: string
+#. Description
+#: ../templates:2001 ../templates:3001
msgid ""
"More information is provided online at http://pubmlst.org/software/database/"
"mlstdbnet/attributes.shtml . See the description of the attribute "
@@ -89,20 +90,47 @@
#. Type: string
#. Description
#: ../templates:3001
-msgid "Full name of locus:"
+msgid "Brief description to appear on web pages"
msgstr ""
#. Type: string
#. Description
#: ../templates:3001
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:3001
+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:4001
+msgid "Full name of locus:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:4001
+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
+#: ../templates:4001
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 "
@@ -111,13 +139,13 @@
#. Type: string
#. Description
-#: ../templates:3001
+#: ../templates:4001
msgid "Reasonable values might be: variable region <number>."
msgstr ""
#. Type: string
#. Description
-#: ../templates:3001
+#: ../templates:4001
msgid ""
"More information is provided online at http://pubmlst.org/software/database/"
"mlstdbnet/attributes.shtml . See the description of the attribute \"fullname"
@@ -126,13 +154,13 @@
#. Type: string
#. Description
-#: ../templates:4001
+#: ../templates:5001
msgid "Locus abbreviation:"
msgstr ""
#. Type: string
#. Description
-#: ../templates:4001
+#: ../templates:5001
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 "
@@ -142,7 +170,7 @@
#. Type: string
#. Description
-#: ../templates:4001
+#: ../templates:5001
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 "
@@ -153,7 +181,7 @@
#. Type: string
#. Description
-#: ../templates:4001
+#: ../templates:5001
msgid ""
"More information is provided online at http://pubmlst.org/software/database/"
"mlstdbnet/attributes.shtml . The value here corresponds to the man attribute "
@@ -162,13 +190,13 @@
#. Type: note
#. Description
-#: ../templates:5001
+#: ../templates:6001
msgid "Hint about configuration of the PubMed reference database"
msgstr ""
#. Type: note
#. Description
-#: ../templates:5001
+#: ../templates:6001
msgid ""
"You are now finished with the mlstdbnet configuration. Please read more "
"about mlstdbnet configuration at\n"
@@ -182,7 +210,7 @@
#. Type: note
#. Description
-#: ../templates:5001
+#: ../templates:6001
msgid ""
"The following questions concern the creation of the database for PubMed "
"references. It should be safe to use always default values (just <Enter>)."
@@ -190,7 +218,7 @@
#. Type: note
#. Description
-#: ../templates:5001
+#: ../templates:6001
msgid ""
"To enable daily updates of PubMed references you have to create\n"
" /etc/mlstdbnet/getrefs.conf\n"
@@ -201,13 +229,13 @@
#. Type: string
#. Description
-#: ../templates:6001
+#: ../templates:7001
msgid "Username of database curator:"
msgstr ""
#. Type: string
#. Description
-#: ../templates:6001
+#: ../templates:7001
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 "
@@ -219,7 +247,7 @@
#. Type: string
#. Description
-#: ../templates:6001
+#: ../templates:7001
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 "
@@ -228,7 +256,7 @@
#. Type: string
#. Description
-#: ../templates:6001
+#: ../templates:7001
msgid ""
"Please input the login username for one curator now. Others can be added "
"later."
@@ -236,13 +264,13 @@
#. Type: string
#. Description
-#: ../templates:7001
+#: ../templates:8001
msgid "Surname of database curator:"
msgstr ""
#. Type: string
#. Description
-#: ../templates:7001
+#: ../templates:8001
msgid ""
"Please input the surname of the person which should work as a curator for "
"mlstdbnet."
@@ -250,13 +278,13 @@
#. Type: string
#. Description
-#: ../templates:8001
+#: ../templates:9001
msgid "First name of database curator:"
msgstr ""
#. Type: string
#. Description
-#: ../templates:8001
+#: ../templates:9001
msgid ""
"Please input the first name of the person which should work as a curator for "
"mlstdbnet."
@@ -264,13 +292,13 @@
#. Type: string
#. Description
-#: ../templates:9001
+#: ../templates:10001
msgid "E-mail address of database curator:"
msgstr ""
#. Type: string
#. Description
-#: ../templates:9001
+#: ../templates:10001
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-"
Modified: trunk/packages/mlstdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/postinst 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/postinst 2009-01-22 14:20:55 UTC (rev 3036)
@@ -21,6 +21,9 @@
db_get ${pkg}/description
DESCRIPTION=${RET}
+db_get ${pkg}/publicdescription
+PUBLICDESCRIPTION=${RET}
+
## According to upstream pathogen is not used any more
## db_get ${pkg}/pathogen
## PATHOGEN=${RET}
@@ -39,6 +42,7 @@
if [ ! -e "$XMLOUT" ] ; then
sed -e "s/##database##/${XMLNAME}/g" \
-e "s/##Description##/${DESCRIPTION}/g" \
+ -e "s/##PublicDescription##/${PUBLICDESCRIPTION}/g" \
-e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
-e "s/##Locus##/${LOCUS}/g" \
/usr/share/${pkg}/template/${pkg}.xml > \
@@ -48,6 +52,7 @@
sed -i \
-e "s/longcode=\"[^\"]\+\"/longcode=\"${XMLNAME}\"/g" \
-e "s/description=\"[^\"]\+\"/description=\"${DESCRIPTION}\"/g" \
+ -e "s/\(description=\"[^\"]\+\">\)[^<]\+/\1${PUBLICDESCRIPTION}/g" \
-e "s/<locus fullname=\"[^\"]*\">[^<]\+/<locus fullname=\"${LOCUSFULLNAME}\">${LOCUS}/" \
"$XMLOUT"
fi
@@ -64,6 +69,7 @@
if [ "$confstyle" = "index.html" ] ; then
sed -e "s/##database##/${XMLNAME}/g" \
-e "s/##Description##/${DESCRIPTION}/g" \
+ -e "s/##PublicDescription##/${PUBLICDESCRIPTION}/g" \
-e "s/##LocusFullName##/${LOCUSFULLNAME}/g" \
-e "s/##Locus##/${LOCUS}/g" \
"$style" > "$STYLEDIR/$confstyle"
@@ -84,7 +90,7 @@
ln -s "/usr/share/${pkg}/images" "/var/www/${pkg}"
fi
-# Obtaining user information for agcurator and write this to the config file
+# Obtaining user information for curator and write this to the config file
db_get ${pkg}/curator/username
USERNAME=${RET}
@@ -97,7 +103,7 @@
db_get ${pkg}/curator/email
EMAIL=${RET}
-CURATORCONF=/etc/${pkg}/agcurator.conf
+CURATORCONF=/etc/${pkg}/curator.conf
if [ ! -s "$CURATORCONF" ] ; then
cat > "$CURATORCONF" <<EOT
# This file is used when creating the agdbdnnet/mlstdbnet database to add an initial curator
@@ -142,7 +148,7 @@
chmod 666 "$SQLDIR"/"$XMLNAME".sql
fi
- # Enable Apache anonymous authentication for agcurate.pl
+ # Enable Apache anonymous authentication for curate.pl
# script
# apache-modconf apache enable authn_anon
# I have no idea for what purpose apache-modconf exists -
@@ -151,7 +157,7 @@
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
+ # Restart Apache to register configuration for curator
if apache2ctl configtest 2>/dev/null; then
if [ -x /usr/sbin/invoke-rc.d ]; then
invoke-rc.d apache2 reload 3>/dev/null || true
Modified: trunk/packages/mlstdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/postrm 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/postrm 2009-01-22 14:20:55 UTC (rev 3036)
@@ -46,7 +46,7 @@
fi
# Remove configuration for curator
- rm -f /etc/${pkg}/agcurator.conf
+ rm -f /etc/${pkg}/curator.conf
;;
remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
Modified: trunk/packages/mlstdbnet/trunk/debian/rules
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/rules 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/rules 2009-01-22 14:20:55 UTC (rev 3036)
@@ -19,7 +19,7 @@
# keep lintian silent ...
chmod 644 debian/$(pkg)/usr/share/dbconfig-common/data/${pkg}/install/pgsql
- # Apache configuration for agcurator.pl
+ # Apache configuration for curator.pl
cp -a debian/apache.conf debian/$(pkg)/etc/apache2/conf.d/$(pkg)
# To update po files as recommended in po-debconf(7)
Modified: trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/template/mlstdbnet.xml 2009-01-22 14:20:55 UTC (rev 3036)
@@ -1,52 +1,35 @@
<?xml version="1.0" encoding="ISO-8859-1" ?>
-<mlstdb>
+<!DOCTYPE mlst SYSTEM "mlst.dtd">
+<mlst>
-<!-- _______________________________________________________ -->
-<!-- Before you start -->
-<!-- ________________ -->
-<!-- As long as there are values marked like ##this## the -->
-<!-- XML file is not usable -->
+<!-- _________________________________________________________ -->
+<!-- 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! -->
-<!-- _______________________________________________________ -->
+<!-- to learn what has to be done! -->
+<!-- _________________________________________________________ -->
<system
- longcode="##database##" webroot="/mlstdbnet" indexpage=""
- description="##Description##"
- downloadFASTAonly="yes"
->
-</system>
+ longcode="##database##"
+ webroot="##webroot##"
+ indexpage=""
+ dbprof="##dbprofiles##"
+ profhome="/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-##dbprofiles##.xml"
+ noshow="other_name,Z_number,region"
+ view="isolates" dbtype="st"
+ description="##Description##">##PublicDescription##</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>
+<locus fullname="##LocusFullName##" length="0">##Locus##</locus>
-<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>
+<!-- PROFILES FIELDS -->
+<field type="int" length="5" userupdate="no" comments="primary key">id</field>
+<!-- ATTENTION: The following lines need menual configuration and are just examples -->
+<field type="text" length="20" comments="Original strain name as supplied by sender">strain</field>
+<field type="text" required="no" length="50" comments="clonal complex">clonal_complex</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>
+<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
+</mlst>
Modified: trunk/packages/mlstdbnet/trunk/debian/templates
===================================================================
--- trunk/packages/mlstdbnet/trunk/debian/templates 2009-01-22 07:37:00 UTC (rev 3035)
+++ trunk/packages/mlstdbnet/trunk/debian/templates 2009-01-22 14:20:55 UTC (rev 3036)
@@ -12,7 +12,7 @@
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 .
+ http://pubmlst.org/software/database/mlstdbnet/xml.shtml .
See the description of the attribute "longcode" for the
"<system>" element.
@@ -21,6 +21,25 @@
_Description: Database description:
Each mlstdbnet database should have a description which includes
the pathogen name and genetic locus/loci that the database holds.
+ 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:
+ * Neisseria MLST
+ * Neisseria meningitidis MLST
+ * Clostridium Difficile
+ .
+ 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/publicdescription
+Type: string
+_Description: Brief description to appear on web pages
+ 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.
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