[med-svn] r2512 - in trunk/packages/agdbnet/trunk/debian: . patches po
tille at alioth.debian.org
tille at alioth.debian.org
Fri Sep 19 12:36:56 UTC 2008
Author: tille
Date: 2008-09-19 12:36:55 +0000 (Fri, 19 Sep 2008)
New Revision: 2512
Added:
trunk/packages/agdbnet/trunk/debian/TODO
trunk/packages/agdbnet/trunk/debian/mlstdbnet.conf
Removed:
trunk/packages/agdbnet/trunk/debian/docs
Modified:
trunk/packages/agdbnet/trunk/debian/README.Debian
trunk/packages/agdbnet/trunk/debian/config
trunk/packages/agdbnet/trunk/debian/cron.daily
trunk/packages/agdbnet/trunk/debian/install
trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
trunk/packages/agdbnet/trunk/debian/po/templates.pot
trunk/packages/agdbnet/trunk/debian/templates
Log:
Enhanced debconf questions (regarding sequence of asking, better descriptions with links to upstream to give better understanding, additional note); do not ship installtion.html in binary package any more, because it is more or less done and might rather lead to confusion that to better understanding; mlstdbnet.conf which is read by agcurate.pl; TODO to collect questions to upstream
Modified: trunk/packages/agdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-19 12:36:55 UTC (rev 2512)
@@ -1,10 +1,29 @@
agdbnet for Debian
------------------
-This Debian package tries to prepare your server as good as possible
-enable you to do the final steps to run agdbnet. Here are the last
-steps from installation manual that have to be done.
+Creating the database for AgdbNet
+---------------------------------
+In the installation process some debconf questions have to
+be answered to prepare a reasonable XML config file in
+/etc/agdbnet/<database name>.xml. This config file has
+to reviewed before a database is finally created. Before
+you inspect the config file it is strongly advised to read
+the introduction "Creating a XML description of an agdbnet
+database" on the AgdbNet homepage at
+
+ http://pubmlst.org/software/database/agdbnet/xml.shtml
+
+including the detailed "Database XML description" at
+
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml
+
+to understand the meaning of the fields you have to configure.
+You should also have a look at the examples directory which
+contains some example configuration files provided by the
+agdbnet authors.
+
+
PubMed references
-----------------
Added: trunk/packages/agdbnet/trunk/debian/TODO
===================================================================
--- trunk/packages/agdbnet/trunk/debian/TODO (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/TODO 2008-09-19 12:36:55 UTC (rev 2512)
@@ -0,0 +1,6 @@
+agdbnet.pl is referencing an image
+ $system{'webroot'}/images/download.gif
+which is missing in the tarball
+
+ --> ask upstream
+
Modified: trunk/packages/agdbnet/trunk/debian/config
===================================================================
--- trunk/packages/agdbnet/trunk/debian/config 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/config 2008-09-19 12:36:55 UTC (rev 2512)
@@ -9,23 +9,7 @@
. /usr/share/debconf/confmodule
db_version 2.0
-# 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} $@
-fi
-
# Check whether there is an xmlname stored in debconf database
# Yes, debconf is no registry, but the real place of the real
# information is stored in the configfile /etc/agdbnet/${xmlname}
@@ -87,13 +71,24 @@
fi
db_input high ${pkg}/pathogen || true
-db_go || true
-
db_input high ${pkg}/description || true
-db_go || true
-
db_input high ${pkg}/locusfullname || true
-db_go || true
-
db_input high ${pkg}/locus || true
+db_input high ${pkg}/note || 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
Modified: trunk/packages/agdbnet/trunk/debian/cron.daily
===================================================================
--- trunk/packages/agdbnet/trunk/debian/cron.daily 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/cron.daily 2008-09-19 12:36:55 UTC (rev 2512)
@@ -8,7 +8,7 @@
# be accomplished. So this cron job does not do anything until a valid
# $CONFFILE exists.
#
-# See /usr/share/agdbnet/README.Debian for more detailed information
+# See /usr/share/doc/agdbnet/README.Debian for more detailed information
PROG=/usr/share/agdbnet/getrefs.pl
Deleted: trunk/packages/agdbnet/trunk/debian/docs
===================================================================
--- trunk/packages/agdbnet/trunk/debian/docs 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/docs 2008-09-19 12:36:55 UTC (rev 2512)
@@ -1 +0,0 @@
-installation.html
Modified: trunk/packages/agdbnet/trunk/debian/install
===================================================================
--- trunk/packages/agdbnet/trunk/debian/install 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/install 2008-09-19 12:36:55 UTC (rev 2512)
@@ -2,3 +2,4 @@
debian/template usr/share/agdbnet
scripts/*.pl usr/share/agdbnet
stylesheets/stylesheet.css usr/share/agdbnet/template
+debian/mlstdbnet.conf etc/agdbnet
Added: trunk/packages/agdbnet/trunk/debian/mlstdbnet.conf
===================================================================
--- trunk/packages/agdbnet/trunk/debian/mlstdbnet.conf (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/mlstdbnet.conf 2008-09-19 12:36:55 UTC (rev 2512)
@@ -0,0 +1,84 @@
+## This is an adapted copy of the file conf/mlstdbnet.conf from the
+## mlstdbnet contribution available at
+## http://pubmlst.org/software/database/mlstdbnet/download/mlstdbnet_v2.0.0.tar.gz
+
+###GENERAL####
+tmp_dir=/var/www/agdbnet/tmp
+
+####EMBOSS####
+#used for sequence alignment in allele query
+#set 'emboss=0' to remove functionality
+emboss=1
+emboss_path=/usr/lib/emboss
+
+####JALVIEW####
+#used for global sequence alignment in allele query
+#and tree-drawing
+jalview=1
+
+####BIOPERL####
+#Used for creating sequences in multiple formats.
+#Set to 1 if BioPerl is installed
+bioperl=1
+
+####BLAST######
+#Used for databases where sequences are of unequal
+#length
+blast=1
+blast_path=/usr/bin
+
+##REFERENCE DB#
+#Set to 1 if you have set up a local reference database.
+#You will need to run the accompaning getrefs.pl script regularly to
+#keep this updated (unless you're mirroring another system)
+reference=1
+refdb=refs
+
+###PRIVACY#####
+#Set to 1 to hide the sender's E-mail address when displaying
+#information on a strain.
+privacy=1
+
+###EXPORT######
+#Set to 'export=1' to enable E-mail export of datasets. Ensure that you have
+#a valid SMTP server set (depending on your network, the server running
+#this script may act as an SMTP server and the IP address 127.0.0.1 may
+#work fine. Set the export_sender address to include a valid domain
+#or your mail server (or the recipient's) may reject it.
+#To log exports to a database, set 'exportlog=1' - make sure
+#you have created a log database calleld 'export_log' using the provided
+#SQL script.
+export=1
+##FIXME## smtp_server=127.0.0.1
+##FIXME## export_sender=mlstdbNet at yourdomain.com
+exportlog=1
+
+#SEQ DOWNLOAD##
+trace_dl=1
+
+#BCM TRACE VIEWER#
+traceviewer=1
+
+#CHARTDIRECTOR####
+#Set chartdirector=1 if chartdirector library installed
+#Set other values to 1 if functionality is available in
+#the version of CD installed (some are only available in later
+#versions)
+chartdirector=1
+doughnut=1
+transparent=1
+mintick=0
+
+#MOGRIFY#################
+#Set the path to mogrify if installed. Mogrify is part of
+#the ImageMagick library. Set to 0 if not installed.
+mogrify=/usr/bin/mogrify
+
+####DEBUG####
+#Set to 0 to reduce messages in apache error log. You should do
+#this in production environments. With this set to 0, the only log messages
+#you should see are malicious SQL injection attempts. Any other errors
+#suggest a bug and should be reported.
+debug=0
+#BENCHMARKING#
+debug_timing=0
Modified: trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_config_location.patch 2008-09-19 12:36:55 UTC (rev 2512)
@@ -20,6 +20,15 @@
if ($@) {
--- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
+++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
+@@ -30,7 +30,7 @@
+ use strict;
+
+ ###########Local configuration########################
+-local ( our $configfile = '/usr/local/mlstdbnet/mlstdbnet.conf' );
++local ( our $configfile = '/etc/agdbnet/mlstdbnet.conf' );
+ #######End Local configuration########################
+
+ local (our (
@@ -64,7 +64,7 @@
if ( $q->param('file') =~ /^([\w\d\-_]+\.xml)$/ ) {
$instance = $1;
Modified: trunk/packages/agdbnet/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/agdbnet/trunk/debian/po/templates.pot 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/po/templates.pot 2008-09-19 12:36:55 UTC (rev 2512)
@@ -8,7 +8,7 @@
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: agdbnet at packages.debian.org\n"
-"POT-Creation-Date: 2008-09-17 11:40+0200\n"
+"POT-Creation-Date: 2008-09-19 14:10+0200\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"
@@ -43,6 +43,15 @@
#. Type: string
#. Description
+#: ../templates:1001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"agdbnet/attributes.shtml . See the description of the attribute \"longcode\" "
+"for the \"<system>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../templates:2001
msgid "Systematic name of pathogen:"
msgstr ""
@@ -63,8 +72,17 @@
#. Type: string
#. Description
+#: ../templates:2001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"agdbnet/attributes.shtml . The value here corresponds to the man attribute "
+"of the \"<system>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../templates:3001
-msgid "Short description of the pathogen:"
+msgid "Database description:"
msgstr ""
#. Type: string
@@ -88,16 +106,26 @@
#. Type: string
#. Description
+#: ../templates:3001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"agdbnet/attributes.shtml . See the description of the attribute \"description"
+"\" for the \"<system>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../templates:4001
-msgid "Locus full name of pathogen:"
+msgid "Full name of locus:"
msgstr ""
#. Type: string
#. Description
#: ../templates:4001
msgid ""
-"The full name of the locus specifies the region which will be used for "
-"typing."
+"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 eddit the XML file manually as it is described later."
msgstr ""
#. Type: string
@@ -108,14 +136,27 @@
#. Type: string
#. Description
+#: ../templates:4001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"agdbnet/attributes.shtml . See the description of the attribute \"fullname\" "
+"for the \"<locus>\" element."
+msgstr ""
+
+#. Type: string
+#. Description
#: ../templates:5001
-msgid "Short name of locus:"
+msgid "Locus abbreviation:"
msgstr ""
#. Type: string
#. Description
#: ../templates:5001
-msgid "A shortcut for the locus which will be used in the web interface."
+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/agdbnet contains templates for both and you have to edit this "
+"manually as described later."
msgstr ""
#. Type: string
@@ -125,3 +166,12 @@
"Reasonable values might be: VR1 for \"variable region 1\" or also "
"Campylobacter jejuni flaA for \"Campylobacter jejuni FlaA\"."
msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:5001
+msgid ""
+"More information is provided online at http://pubmlst.org/software/database/"
+"agdbnet/attributes.shtml . The value here corresponds to the man attribute "
+"of the \"<locus>\" element."
+msgstr ""
Modified: trunk/packages/agdbnet/trunk/debian/templates
===================================================================
--- trunk/packages/agdbnet/trunk/debian/templates 2008-09-19 09:06:39 UTC (rev 2511)
+++ trunk/packages/agdbnet/trunk/debian/templates 2008-09-19 12:36:55 UTC (rev 2512)
@@ -10,6 +10,11 @@
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 agdbnet makes perfectly sense.
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml .
+ See the description of the attribute "longcode" for the
+ "<system>" element.
Template: agdbnet/pathogen
Type: string
@@ -18,10 +23,15 @@
.
Reasonable values for pathogen are things like: Campylobacter,
Neisseria, Streptococcus, etc.
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml .
+ The value here corresponds to the man attribute of the "<system>"
+ element.
Template: agdbnet/description
Type: string
-_Description: Short description of the pathogen:
+_Description: Database description:
Each agdbnet database should have a description of the pathogen
that will be analysed. The description will be stored in the
configuration file in /etc/agdbnet and can be changed there if
@@ -32,20 +42,60 @@
* Campylobacter jejuni FlaA
* Neisseria meningitidis FetA variable region
* Streptococcus equi seM
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml .
+ See the description of the attribute "description" for the
+ "<system>" element.
Template: agdbnet/locusfullname
Type: string
-_Description: Locus full name of pathogen:
- The full name of the locus specifies the region which will
- be used for typing.
+_Description: Full name of locus:
+ 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 eddit 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/agdbnet/attributes.shtml .
+ See the description of the attribute "fullname" for the
+ "<locus>" element.
Template: agdbnet/locus
Type: string
-_Description: Short name of locus:
- A shortcut for the locus which will be used in the web
- interface.
+_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/agdbnet contains templates for
+ both and you have to edit this manually as described later.
.
Reasonable values might be: VR1 for "variable region 1" or
also Campylobacter jejuni flaA for "Campylobacter jejuni FlaA".
+ .
+ More information is provided online at
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml .
+ The value here corresponds to the man attribute of the "<locus>"
+ element.
+
+Template: agdbnet/note
+Type: note
+Description: Hint about configuration of the PubMed reference database
+ You are now finished with the AgdbNet configuration. Please
+ read more about AgdbNet configuration at
+ http://pubmlst.org/software/database/agdbnet/xml.shtml and
+ http://pubmlst.org/software/database/agdbnet/attributes.shtml
+ and review the XML file in /etc/agdbnet 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/agdbnet/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/agdbnet/getrefs.conf
+ according to the template in examples. It is strongly recommended to read
+ /usr/share/doc/agdbnet/README.Debian
+ how to create this file.
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