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: [email protected]\n" +"Report-Msgid-Bugs-To: [email protected]\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@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 <[email protected]>; 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. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
