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## [EMAIL PROTECTED] +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: [EMAIL PROTECTED]" -"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 PROTECTED]>\n" "Language-Team: LANGUAGE <[EMAIL PROTECTED]>\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. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
