[med-svn] r12526 - in trunk/packages/bigsdb/trunk/debian: . more_examples po template
Andreas Tille
tille at alioth.debian.org
Thu Nov 8 15:37:05 UTC 2012
Author: tille
Date: 2012-11-08 15:37:05 +0000 (Thu, 08 Nov 2012)
New Revision: 12526
Added:
trunk/packages/bigsdb/trunk/debian/template/bigsdb.xml
Removed:
trunk/packages/bigsdb/trunk/debian/template/mlstdbnet.xml
Modified:
trunk/packages/bigsdb/trunk/debian/getrefs.conf
trunk/packages/bigsdb/trunk/debian/install
trunk/packages/bigsdb/trunk/debian/modperl_startup.pl
trunk/packages/bigsdb/trunk/debian/more_examples/cdif.xml
trunk/packages/bigsdb/trunk/debian/po/templates.pot
trunk/packages/bigsdb/trunk/debian/postinst
trunk/packages/bigsdb/trunk/debian/postrm
trunk/packages/bigsdb/trunk/debian/prerm
trunk/packages/bigsdb/trunk/debian/rules
trunk/packages/bigsdb/trunk/debian/template/footer.html
trunk/packages/bigsdb/trunk/debian/template/index.html
trunk/packages/bigsdb/trunk/debian/templates
Log:
Simply do some more s/mlstdbnet/bigsdb/g without any care whether this might work properly or not - sorry, team mates no time for testing it.
Modified: trunk/packages/bigsdb/trunk/debian/getrefs.conf
===================================================================
--- trunk/packages/bigsdb/trunk/debian/getrefs.conf 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/getrefs.conf 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1 +1 @@
-mlstdb_refs
+bigsdb_refs
Modified: trunk/packages/bigsdb/trunk/debian/install
===================================================================
--- trunk/packages/bigsdb/trunk/debian/install 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/install 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,11 +1,11 @@
-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
-debian/getrefs.conf etc/mlstdbnet
-images usr/share/mlstdbnet
-debian/modperl_startup.pl etc/apache2
+cgi-bin/bigsdb.pl usr/lib/cgi-bin
+cgi-bin/curate.pl usr/share/bigsdb/cgi-bin
+cgi-bin/lib usr/share/perl5/bigsdb
+cgi-bin/Plugins usr/share/perl5/bigsdb
+debian/template usr/share/bigsdb
+scripts/*.pl usr/share/bigsdb
+css/stylesheet.css usr/share/bigsdb/template
+conf/* etc/bigsdb
+debian/getrefs.conf etc/bigsdb
+images usr/share/bigsdb
+debian/modperl_startup.pl etc/apache2
Modified: trunk/packages/bigsdb/trunk/debian/modperl_startup.pl
===================================================================
--- trunk/packages/bigsdb/trunk/debian/modperl_startup.pl 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/modperl_startup.pl 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,6 +1,6 @@
#!/usr/bin/perl
-use lib "/usr/share/perl5/mlstdbnet/lib";
-use lib "/usr/share/perl5/mlstdbnet/Plugins";
+use lib "/usr/share/perl5/bigsdb/lib";
+use lib "/usr/share/perl5/bigsdb/Plugins";
1;
Modified: trunk/packages/bigsdb/trunk/debian/more_examples/cdif.xml
===================================================================
--- trunk/packages/bigsdb/trunk/debian/more_examples/cdif.xml 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/more_examples/cdif.xml 2012-11-08 15:37:05 UTC (rev 12526)
@@ -7,16 +7,16 @@
<!-- ________________ -->
<!-- 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 -->
+<!-- Make sure you read /usr/share/doc/bigsdb/README.Debian -->
<!-- to learn what has to be done! -->
<!-- _________________________________________________________ -->
<system
longcode="cdif"
- webroot="/mlstdbnet"
+ webroot="/bigsdb"
indexpage=""
dbprof=""
- profhome="/cgi-bin/mlstdbnet/mlstdbnet.pl?file=pub-cdif.xml"
+ profhome="/cgi-bin/bigsdb/bigsdb.pl?file=pub-cdif.xml"
description="Clostridium Difficile">Test</system>
<!-- LOCI -->
Modified: trunk/packages/bigsdb/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/bigsdb/trunk/debian/po/templates.pot 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/po/templates.pot 2012-11-08 15:37:05 UTC (rev 12526)
@@ -7,7 +7,7 @@
msgid ""
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
-"Report-Msgid-Bugs-To: mlstdbnet at packages.debian.org\n"
+"Report-Msgid-Bugs-To: bigsdb at packages.debian.org\n"
"POT-Creation-Date: 2009-01-23 08:49+0100\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
@@ -19,17 +19,17 @@
#. Type: string
#. Description
#: ../templates:1001
-msgid "Name of the mlstdbnet database:"
+msgid "Name of the bigsdb database:"
msgstr ""
#. Type: string
#. Description
#: ../templates:1001
msgid ""
-"The package mlstdbnet is using a configuration file which stores the name of "
+"The package bigsdb 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."
+"bigsdb/<name_you_input_here>.xml and can be adjusted there."
msgstr ""
#. Type: string
@@ -38,7 +38,7 @@
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."
+"typed by bigsdb makes perfectly sense."
msgstr ""
#. Type: string
@@ -46,7 +46,7 @@
#: ../templates:1001
msgid ""
"More information is provided online at http://pubmlst.org/software/database/"
-"mlstdbnet/xml.shtml . See the description of the attribute \"longcode\" for "
+"bigsdb/xml.shtml . See the description of the attribute \"longcode\" for "
"the \"<system>\" element."
msgstr ""
@@ -60,9 +60,9 @@
#. Description
#: ../templates:2001
msgid ""
-"Each mlstdbnet database should have a description which includes the "
+"Each bigsdb 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 "
+"description will be stored in the configuration file in /etc/bigsdb and "
"can be changed there if needed."
msgstr ""
@@ -83,7 +83,7 @@
#: ../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 "
+"bigsdb/attributes.shtml . See the description of the attribute "
"\"description\" for the \"<system>\" element."
msgstr ""
@@ -97,10 +97,10 @@
#. Description
#: ../templates:3001
msgid ""
-"Each mlstdbnet database should have a description which includes the "
+"Each bigsdb 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 "
+"be stored in the configuration file in /etc/bigsdb and can be changed "
"there if needed."
msgstr ""
@@ -148,7 +148,7 @@
#: ../templates:4001
msgid ""
"More information is provided online at http://pubmlst.org/software/database/"
-"mlstdbnet/attributes.shtml . See the description of the attribute \"fullname"
+"bigsdb/attributes.shtml . See the description of the attribute \"fullname"
"\" for the \"<locus>\" element."
msgstr ""
@@ -164,7 +164,7 @@
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 "
+"file in /etc/bigsdb contains templates for both and you have to edit this "
"manually as described later."
msgstr ""
@@ -184,7 +184,7 @@
#: ../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 "
+"bigsdb/attributes.shtml . The value here corresponds to the man attribute "
"of the \"<locus>\" element."
msgstr ""
@@ -198,13 +198,13 @@
#. Description
#: ../templates:6001
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 "
+"You are now finished with the bigsdb configuration. Please read more "
+"about bigsdb configuration at\n"
+" http://pubmlst.org/software/database/bigsdb/xml.shtml and\n"
+" http://pubmlst.org/software/database/bigsdb/attributes.shtml\n"
+"and review the XML file in /etc/bigsdb 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 "
+"follow the procedure described in /usr/share/doc/bigsdb/README.Debian to "
"finish the installation process."
msgstr ""
@@ -221,9 +221,9 @@
#: ../templates:6001
msgid ""
"To enable daily updates of PubMed references you have to create\n"
-" /etc/mlstdbnet/getrefs.conf\n"
+" /etc/bigsdb/getrefs.conf\n"
"according to the template in examples. It is strongly recommended to read\n"
-" /usr/share/doc/mlstdbnet/README.Debian\n"
+" /usr/share/doc/bigsdb/README.Debian\n"
"how to create this file."
msgstr ""
@@ -239,7 +239,7 @@
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 "
+"bigsdb. 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."
@@ -250,7 +250,7 @@
#: ../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 "
+"read /usr/share/doc/bigsdb/README.Debian how to change this to a secure "
"method."
msgstr ""
@@ -273,7 +273,7 @@
#: ../templates:8001
msgid ""
"Please input the surname of the person which should work as a curator for "
-"mlstdbnet."
+"bigsdb."
msgstr ""
#. Type: string
@@ -287,7 +287,7 @@
#: ../templates:9001
msgid ""
"Please input the first name of the person which should work as a curator for "
-"mlstdbnet."
+"bigsdb."
msgstr ""
#. Type: string
@@ -301,7 +301,7 @@
#: ../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-"
+"for bigsdb. 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 ""
@@ -316,7 +316,7 @@
#. Description
#: ../templates:11001
msgid ""
-"Please input the directory where the mlstdbnet CGI script should be "
+"Please input the directory where the bigsdb CGI script should be "
"located. By default this is the same as the database name."
msgstr ""
@@ -330,7 +330,7 @@
#. Description
#: ../templates:12001
msgid ""
-"MlstDBNet accepts a profiles database. By default this is the same as the "
+"bigsdb accepts a profiles database. By default this is the same as the "
"database name. But you might like to use a different name which can be "
"given here."
msgstr ""
Modified: trunk/packages/bigsdb/trunk/debian/postinst
===================================================================
--- trunk/packages/bigsdb/trunk/debian/postinst 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/postinst 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,8 +1,8 @@
#!/bin/sh -e
-# postinst script for agdbnet/mlstdbnet
+# postinst script for bigsdb
# set -ex
-pkg=mlstdbnet
+pkg=bigsdb
DEBCONF_DEBUG=developer
. /usr/share/debconf/confmodule
@@ -87,7 +87,7 @@
fi
done
-# Finally a link is put into place to enable agdbdnnet/mlstdbnet to find these files.
+# Finally a link is put into place to enable agdbdnnet/bigsdb 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"
@@ -115,7 +115,7 @@
CURATORCONF=/etc/${pkg}/curator.conf
if [ ! -s "$CURATORCONF" ] ; then
cat > "$CURATORCONF" <<EOT
-# This file is used when creating the agdbdnnet/mlstdbnet database to add an initial curator
+# This file is used when creating the agdbdnnet/bigsdb database to add an initial curator
# Please read /usr/share/${pkg}/README.Debian for further information.
USERNAME=${USERNAME}
SURNAME=${SURNAME}
@@ -141,7 +141,7 @@
if [ -x /usr/share/${pkg}/xml2sql.pl ] ; then
# agdbnet came with a script which generated the SQL code to
- # bootstrap the database which is not contained in mlstdbnet.
+ # bootstrap the database which is not contained in bigsdb.
# Just verifying the existence of the script enables using
# nearly the same postinst script (module package name) for
# both projects.
Modified: trunk/packages/bigsdb/trunk/debian/postrm
===================================================================
--- trunk/packages/bigsdb/trunk/debian/postrm 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/postrm 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,8 +1,8 @@
#!/bin/sh -e
-# postrm script for mlstdbnet
+# postrm script for bigsdb
# set -ex
-pkg=mlstdbnet
+pkg=bigsdb
. /usr/share/debconf/confmodule
db_version 2.0
@@ -17,7 +17,7 @@
purge)
# remove all potential config files and dirs in /var/www
if ls /etc/${pkg}/*.xml 1>/dev/null 2>/dev/null ; then
- for confxml in `grep -l "<mlstdb>" /etc/${pkg}/*.xml` ; do
+ for confxml in `grep -l "<bigsdb>" /etc/${pkg}/*.xml` ; do
XMLNAME=`basename ${confxml} .xml`
rm -f /etc/${pkg}/"$XMLNAME".xml
Modified: trunk/packages/bigsdb/trunk/debian/prerm
===================================================================
--- trunk/packages/bigsdb/trunk/debian/prerm 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/prerm 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,8 +1,8 @@
#!/bin/sh -e
-# prerm script for mlstdbnet
+# prerm script for bigsdb
# set -ex
-pkg=mlstdbnet
+pkg=bigsdb
. /usr/share/debconf/confmodule
db_version 2.0
Modified: trunk/packages/bigsdb/trunk/debian/rules
===================================================================
--- trunk/packages/bigsdb/trunk/debian/rules 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/rules 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,11 +1,11 @@
#!/usr/bin/make -f
-# debian/rules for mlstdbnet
+# debian/rules for bigsdb
# 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
+pkg=bigsdb
DEB_COMPRESS_EXCLUDE := .xml
@@ -25,6 +25,3 @@
# To update po files as recommended in po-debconf(7)
clean::
@debconf-updatepo
-
-get-orig-source:
- sh debian/get-orig-source
Copied: trunk/packages/bigsdb/trunk/debian/template/bigsdb.xml (from rev 12523, trunk/packages/bigsdb/trunk/debian/template/mlstdbnet.xml)
===================================================================
--- trunk/packages/bigsdb/trunk/debian/template/bigsdb.xml (rev 0)
+++ trunk/packages/bigsdb/trunk/debian/template/bigsdb.xml 2012-11-08 15:37:05 UTC (rev 12526)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!DOCTYPE mlst SYSTEM "mlst.dtd">
+<mlst>
+
+<!-- _________________________________________________________ -->
+<!-- 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/bigsdb/README.Debian -->
+<!-- to learn what has to be done! -->
+<!-- _________________________________________________________ -->
+
+<system
+ longcode="##database##"
+ webroot="##webroot##"
+ indexpage=""
+ dbprof="##dbprofiles##"
+ profhome="/cgi-bin/bigsdb.pl?file=##dbprofiles##.xml"
+ description="##Description##">##PublicDescription##</system>
+
+<!-- LOCI -->
+<locus fullname="##LocusFullName##" length="0">##Locus##</locus>
+
+<!-- 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>
+<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
+</mlst>
Modified: trunk/packages/bigsdb/trunk/debian/template/footer.html
===================================================================
--- trunk/packages/bigsdb/trunk/debian/template/footer.html 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/template/footer.html 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,3 +1,3 @@
-<!-- This html snippet will be included after the output of the mlstdbnet --
- -- cgi script -->
+<!-- This html snippet will be included after the output of the bigsdb --
+ -- cgi script -->
<p>This is the footer.html file.</p>
Modified: trunk/packages/bigsdb/trunk/debian/template/index.html
===================================================================
--- trunk/packages/bigsdb/trunk/debian/template/index.html 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/template/index.html 2012-11-08 15:37:05 UTC (rev 12526)
@@ -5,13 +5,13 @@
<title>##Description##</title>
<meta name="description" content="##Description##" />
- <meta name="keywords" content="mlstdbnet" />
+ <meta name="keywords" content="bigsdb" />
<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 />
+##Description##: <a href="http://localhost/cgi-bin/bigsdb.pl?file=##database##.xml">##database##</a><br />
##LocusFullName##
</body>
Deleted: trunk/packages/bigsdb/trunk/debian/template/mlstdbnet.xml
===================================================================
--- trunk/packages/bigsdb/trunk/debian/template/mlstdbnet.xml 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/template/mlstdbnet.xml 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,33 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!DOCTYPE mlst SYSTEM "mlst.dtd">
-<mlst>
-
-<!-- _________________________________________________________ -->
-<!-- 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="##webroot##"
- indexpage=""
- dbprof="##dbprofiles##"
- profhome="/cgi-bin/mlstdbnet.pl?file=##dbprofiles##.xml"
- description="##Description##">##PublicDescription##</system>
-
-<!-- LOCI -->
-<locus fullname="##LocusFullName##" length="0">##Locus##</locus>
-
-<!-- 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>
-<field type="int" maindisplay="no" length="4" comments="sender unique name, link to users">sender</field>
-</mlst>
Modified: trunk/packages/bigsdb/trunk/debian/templates
===================================================================
--- trunk/packages/bigsdb/trunk/debian/templates 2012-11-08 15:29:37 UTC (rev 12525)
+++ trunk/packages/bigsdb/trunk/debian/templates 2012-11-08 15:37:05 UTC (rev 12526)
@@ -1,28 +1,28 @@
-Template: mlstdbnet/xmlname
+Template: bigsdb/xmlname
Type: string
-_Description: Name of the mlstdbnet database:
- The package mlstdbnet is using a configuration file which stores the
+_Description: Name of the bigsdb database:
+ The package bigsdb 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
+ the file /etc/bigsdb/<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.
+ the pathogen that will be typed by bigsdb makes perfectly sense.
.
More information is provided online at
- http://pubmlst.org/software/database/mlstdbnet/xml.shtml .
+ http://pubmlst.org/software/database/bigsdb/ .
See the description of the attribute "longcode" for the
"<system>" element.
-Template: mlstdbnet/description
+Template: bigsdb/description
Type: string
_Description: Database description:
- Each mlstdbnet database should have a description which includes
+ Each bigsdb 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.
+ /etc/bigsdb and can be changed there if needed.
.
Resonable values for such a short description are something
like:
@@ -31,18 +31,18 @@
* Clostridium Difficile
.
More information is provided online at
- http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ http://pubmlst.org/software/database/bigsdb/ .
See the description of the attribute "description" for the
"<system>" element.
-Template: mlstdbnet/publicdescription
+Template: bigsdb/publicdescription
Type: string
_Description: Brief description to appear on web pages
- Each mlstdbnet database should have a description which includes
+ Each bigsdb 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.
+ /etc/bigsdb and can be changed there if needed.
.
Resonable values for such a short description are something
like:
@@ -51,11 +51,11 @@
* Streptococcus equi seM
.
More information is provided online at
- http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ http://pubmlst.org/software/database/bigsdb/ .
See the description of the attribute "description" for the
"<system>" element.
-Template: mlstdbnet/locusfullname
+Template: bigsdb/locusfullname
Type: string
_Description: Full name of locus:
A locus describes a genetic locus (gene, partial gene fragment,
@@ -69,16 +69,16 @@
Reasonable values might be: variable region <number>.
.
More information is provided online at
- http://pubmlst.org/software/database/mlstdbnet/attributes.shtml .
+ http://pubmlst.org/software/database/bigsdb/ .
See the description of the attribute "fullname" for the
"<locus>" element.
-Template: mlstdbnet/locus
+Template: bigsdb/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
+ The generated XML file in /etc/bigsdb contains templates for
both and you have to edit this manually as described later.
.
The abbreviation should be short and describe only the locus -
@@ -88,77 +88,76 @@
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 .
+ http://pubmlst.org/software/database/bigsdb/ .
The value here corresponds to the man attribute of the "<locus>"
element.
-Template: mlstdbnet/note
+Template: bigsdb/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
+ You are now finished with the bigsdb configuration. Please
+ read more about bigsdb configuration at
+ http://pubmlst.org/software/database/bigsdb/
+ and review the XML file in /etc/bigsdb 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 follow the procedure described in /usr/share/doc/bigsdb/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
+ /etc/bigsdb/getrefs.conf
according to the template in examples. It is strongly recommended to read
- /usr/share/doc/mlstdbnet/README.Debian
+ /usr/share/doc/bigsdb/README.Debian
how to create this file.
-Template: mlstdbnet/curator/username
+Template: bigsdb/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
+ sequences in bigsdb. 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
+ Please read /usr/share/doc/bigsdb/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
+Template: bigsdb/curator/surname
Type: string
_Description: Surname of database curator:
Please input the surname of the person which should work as a curator
- for mlstdbnet.
+ for bigsdb.
-Template: mlstdbnet/curator/firstname
+Template: bigsdb/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.
+ for bigsdb.
-Template: mlstdbnet/curator/email
+Template: bigsdb/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
+ curator for bigsdb. 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
+Template: bigsdb/webroot
Type: string
_Description: Root directory on webserver
- Please input the directory where the mlstdbnet CGI script should
+ Please input the directory where the bigsdb CGI script should
be located. By default this is the same as the database name.
-Template: mlstdbnet/dbprof
+Template: bigsdb/dbprof
Type: string
_Description: name of profiles database
- MlstDBNet accepts a profiles database. By default this is the same
+ bigsdb accepts a profiles database. By default this is the same
as the database name. But you might like to use a different name
which can be given here.
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