Author: tille Date: 2012-11-08 15:25:29 +0000 (Thu, 08 Nov 2012) New Revision: 12524
Added: trunk/packages/bigsdb/trunk/debian/bigsdb_xml2sql Removed: trunk/packages/bigsdb/trunk/debian/mlstdbnet_xml2sql Modified: trunk/packages/bigsdb/trunk/debian/README.Debian trunk/packages/bigsdb/trunk/debian/README.source trunk/packages/bigsdb/trunk/debian/apache.conf trunk/packages/bigsdb/trunk/debian/changelog trunk/packages/bigsdb/trunk/debian/compat trunk/packages/bigsdb/trunk/debian/config trunk/packages/bigsdb/trunk/debian/control trunk/packages/bigsdb/trunk/debian/copyright trunk/packages/bigsdb/trunk/debian/cron.daily trunk/packages/bigsdb/trunk/debian/dirs trunk/packages/bigsdb/trunk/debian/docs Log: Turn mlstdbnet packaging somehow roughly to bigsdb packaging Modified: trunk/packages/bigsdb/trunk/debian/README.Debian =================================================================== --- trunk/packages/bigsdb/trunk/debian/README.Debian 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/README.Debian 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,8 +1,8 @@ -mlstdbnet for Debian --------------------- +bigsdb for Debian +----------------- -Creating the database for MlstDbNet ------------------------------------ +Creating the database for BIGSdb +-------------------------------- Creating graphs using Cahrtdirector ----------------------------------- @@ -10,7 +10,7 @@ this is non-free software which can be bought at http://www.advsofteng.com/ If you have installed this software please edit the file -/etc/mlstdbnet/mlstdbnet.conf accordingly. +/etc/bigsdb/bigsdb.conf accordingly. -- Andreas Tille <[email protected]>, Wed, 24 Sep 2008 14:23:04 +0200 Modified: trunk/packages/bigsdb/trunk/debian/README.source =================================================================== --- trunk/packages/bigsdb/trunk/debian/README.source 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/README.source 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,6 +1,11 @@ -README.source for mlstdbnet -=========================== +------------------------------------------------------------------------- +Important note: This text applied for mlstdbnet. Bigsdb is the successor +of mlstdbnet - you need to check whether this text really applies +------------------------------------------------------------------------- +README.source for BIGSdb +======================== + The old and unreproducible tweaked java/Djalview.jar is removed from the upstream source because Upstream said: Modified: trunk/packages/bigsdb/trunk/debian/apache.conf =================================================================== --- trunk/packages/bigsdb/trunk/debian/apache.conf 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/apache.conf 2012-11-08 15:25:29 UTC (rev 12524) @@ -4,9 +4,9 @@ #If running under apache2 + mod_perl2 the following is needed PerlRequire "/etc/apache2/modperl_startup.pl" -# Authentication of MlstDbNet curator -ScriptAlias /mlstdbnet-curate /usr/share/mlstdbnet/cgi-bin/curate.pl -<Directory "/usr/share/mlstdbnet/cgi-bin"> +# Authentication of bigsdb curator +ScriptAlias /bigsdb-curate /usr/share/bigsdb/cgi-bin/curate.pl +<Directory "/usr/share/bigsdb/cgi-bin"> AllowOverride None Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch @@ -23,7 +23,7 @@ # http://httpd.apache.org/docs/2.2/mod/mod_authn_file.html # and could be configured like this: # AuthBasicProvider file - # AuthUserFile /etc/mlstdbnet/htpasswd + # AuthUserFile /etc/bigsdb/htpasswd # Alternatively you might have an LDAP directory for your local users # which can be used with Apache LDAP athentication which is described here # http://httpd.apache.org/docs/2.2/mod/mod_authnz_ldap.html @@ -33,7 +33,7 @@ # # I repeat: CHANGE THE AUTHENTICATION METHOD TO SOMETHING MORE SECURE # BECAUSE EVERYBODY WHO KNOWS YOUR NAME AND E_MAIL ADDRESS MIGHT CURATE - # YOUR mlstdbnet DATABASE OTHERWISE. + # YOUR bigsdb DATABASE OTHERWISE. Anonymous_NoUserID off Anonymous_MustGiveEmail on Copied: trunk/packages/bigsdb/trunk/debian/bigsdb_xml2sql (from rev 12523, trunk/packages/bigsdb/trunk/debian/mlstdbnet_xml2sql) =================================================================== --- trunk/packages/bigsdb/trunk/debian/bigsdb_xml2sql (rev 0) +++ trunk/packages/bigsdb/trunk/debian/bigsdb_xml2sql 2012-11-08 15:25:29 UTC (rev 12524) @@ -0,0 +1,75 @@ +#!/bin/sh -e +pkg=mlstdbnet +SQLDIR="/var/lib/${pkg}" + +if [ "$1" != "" ] ; then + XML="/etc/${pkg}/$1" + if [ ! -s "$XML" ] ; then + XML="/etc/${pkg}/$1.xml" + if [ ! -s "$XML" ] ; then + echo "$0: File /etc/${pkg}/$1 or $XML not found." + exit 66 # EX_NOINPUT + fi + fi +else + if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 1 ] ; then + XML=`grep -l "<mlstdb>" /etc/${pkg}/*.xml` + else + if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 0 ] ; then + echo "$0: There are no valid XML configuration files for ${pkg} available in /etc/${pkg}" + exit 66 # EX_NOINPUT + else + cat <<EOT +Usage: $0 [${pkg}.xml] + There are more than one XML files available. + You need to specify the one which should be used to create the database. +EOT + grep -l "<mlstdb>" /etc/${pkg}/*.xml + exit 64 # EX_USAGE + fi + fi +fi + +XMLNAME=`basename $XML .xml` + +if [ -e "$SQLDIR"/"$XMLNAME".sql ] ; then + mv "$SQLDIR"/"$XMLNAME".sql "$SQLDIR"/"$XMLNAME".sql~ +fi +/usr/share/${pkg}/xml2sql.pl -u 'www-data' "$XML" > "$SQLDIR"/"$XMLNAME".sql + +if psql -l | grep -wq "$XMLNAME" ; then + cat <<EOT +$0: The database $XMLNAME just exists. + You might like to manually drop this database and populate a newly created + one with the data in "$SQLDIR"/"$XMLNAME".sql. +EOT + exit 0 +fi + +createdb "$XMLNAME" +psql "$XMLNAME" < "$SQLDIR"/"$XMLNAME".sql + +# try to set curator information +CURATORCONF=/etc/${pkg}/curator.conf + +parse_config_string () { + RET=`grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"` + if [ "$RET" = "" ] ; then + echo "Unable to find value $1 in $CURATORCONF. Curator information can not be set." + return -1 + fi + echo "$RET" + return 0 +} + +if [ -s "$CURATORCONF" ] ; then + USERNAME=`parse_config_string USERNAME` + SURNAME=`parse_config_string SURNAME` + FIRSTNAME=`parse_config_string FIRSTNAME` + EMAIL=`parse_config_string EMAIL` +fi + +set -x +psql "$XMLNAME" <<EOT + INSERT INTO users VALUES (1, '$USERNAME', '$SURNAME', '$FIRSTNAME', '$EMAIL', '', 'curator', now(), '') ; +EOT Modified: trunk/packages/bigsdb/trunk/debian/changelog =================================================================== --- trunk/packages/bigsdb/trunk/debian/changelog 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/changelog 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,5 +1,5 @@ -mlstdbnet (2.0.2-1) UNRELEASED; urgency=low +bigsdb (1.5.0-1) UNRELEASED; urgency=low - * Initial release (Closes: #??????) + * Initial release (Closes: #500106) -- Andreas Tille <[email protected]> Tue, 13 Jan 2009 11:48:08 +0100 Modified: trunk/packages/bigsdb/trunk/debian/compat =================================================================== --- trunk/packages/bigsdb/trunk/debian/compat 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/compat 2012-11-08 15:25:29 UTC (rev 12524) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/bigsdb/trunk/debian/config =================================================================== --- trunk/packages/bigsdb/trunk/debian/config 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/config 2012-11-08 15:25:29 UTC (rev 12524) @@ -2,7 +2,7 @@ # set -ex # export should ensure that pkg is available in the template -export pkg=mlstdbnet +export pkg=bigsdb DEBCONF_DEBUG=developer @@ -11,7 +11,7 @@ # 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/mlstdbnet/${xmlname} +# information is stored in the configfile /etc/bigsdb/${xmlname} # and thus we have to look first, where the config items are stored. # Then we can read out the remaining config items from the apropriate # config file @@ -26,9 +26,9 @@ confavail="false" # Verify whether there are other potential XML conffiles if [ -d /etc/${pkg} ] ; then - if grep -q "<mlstdb>" /etc/${pkg}/*.xml 2> /dev/null ; then + if grep -q "<bigsdb>" /etc/${pkg}/*.xml 2> /dev/null ; then # use first potential conffile - confxml=`grep -l "<mlstdb>" /etc/${pkg}/*.xml | head -1` + confxml=`grep -l "<bigsdb>" /etc/${pkg}/*.xml | head -1` confxml=`basename ${confxml} .xml` fi fi @@ -140,7 +140,7 @@ # prevents dbconfig-common from asking about these values again :-(( dbc_dbuser='www-data' -dbc_dbname='mlstdb_refs' +dbc_dbname='bigsdb_refs' dbc_authmethod_user="ident" # source dbconfig-common shell library, and call the hook function Modified: trunk/packages/bigsdb/trunk/debian/control =================================================================== --- trunk/packages/bigsdb/trunk/debian/control 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/control 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,23 +1,27 @@ -Source: mlstdbnet +Source: bigsdb Section: science Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7), quilt, cdbs -Standards-Version: 3.8.0 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mlstdbnet/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mlstdbnet/trunk/ -Homepage: http://pubmlst.org/software/database/mlstdbnet/ +Build-Depends: debhelper (>= 9), cdbs +Standards-Version: 3.9.4 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bigsdb/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bigsdb/trunk/ +Homepage: http://pubmlst.org/software/database/bigsdb/ -Package: mlstdbnet +Package: bigsdb Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, blast2, postgresql-8.3, +Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, blast2, libcgi-pm-perl, libdbd-pg-perl, libxml-perl, dbconfig-common, apache2, imagemagick | graphicsmagick, bioperl, libmail-sender-perl, libapache2-mod-perl2 -Description: mlst typing database - mlstdbNet is the software that drives the majority of publicly available - MLST databases, including those for Neisseria, the largest scheme available. - The software is derived from the original mlstdb package written by Man-Suen - Chan (Chan et al, 2001, Bioinformatics, 17, 1077-1083). This implementation - introduces significant improvements, allowing a distributed database structure. +Description: Bacterial Isolate Genome Sequence Database + The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, + web-accessible database system designed to store and analyse linked + phenotypic and genotypic information in a computationally efficient + manner. Sequence data can range from single sequence reads to multiple + contigs generated by whole genome sequencing technologies. The system + incorporates the capacity to define and identify any number of loci and + genetic variants at those loci within the stored nucleotide sequences. + These loci can be further organised into schemes for isolate + characterisation or for evolutionary or functional analyses. Modified: trunk/packages/bigsdb/trunk/debian/copyright =================================================================== --- trunk/packages/bigsdb/trunk/debian/copyright 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/copyright 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,7 +1,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: mlstdbnet +Upstream-Name: BIGSdb Upstream-Contact: Keith Jolley <[email protected]> -Source: http://pubmlst.org/software/database/mlstdbnet/download +Source: http://sourceforge.net/projects/bigsdb/files/ Files-Excluded: java/ Files-Excluded-Comment: Modified: trunk/packages/bigsdb/trunk/debian/cron.daily =================================================================== --- trunk/packages/bigsdb/trunk/debian/cron.daily 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/cron.daily 2012-11-08 15:25:29 UTC (rev 12524) @@ -2,15 +2,15 @@ # populate the refs database once isolate databases have been set up # # The config file -CONFFILE=/etc/mlstdbnet/getrefs.conf +CONFFILE=/etc/bigsdb/getrefs.conf # is not installed at package installation time because the information # in this file has to be edited manually before reasonable operation can # be accomplished. So this cron job does not do anything until a valid # $CONFFILE exists. # -# See /usr/share/doc/mlstdbnet/README.Debian for more detailed information +# See /usr/share/doc/bigsdb/README.Debian for more detailed information -PROG=/usr/share/mlstdbnet/getrefs.pl +PROG=/usr/share/bigsdb/getrefs.pl if [ -x $PROG -a -s $CONFFILE ] ; then su --command "$PROG $CONFFILE" www-data Modified: trunk/packages/bigsdb/trunk/debian/dirs =================================================================== --- trunk/packages/bigsdb/trunk/debian/dirs 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/dirs 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,3 +1,3 @@ -etc/mlstdbnet +etc/bigsdb etc/apache2/conf.d -usr/share/dbconfig-common/data/mlstdbnet/install +usr/share/dbconfig-common/data/bigsdb/install Modified: trunk/packages/bigsdb/trunk/debian/docs =================================================================== --- trunk/packages/bigsdb/trunk/debian/docs 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/docs 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,2 +1,2 @@ -debian/mlstdbnet_xml2sql +debian/bigsdb_xml2sql Deleted: trunk/packages/bigsdb/trunk/debian/mlstdbnet_xml2sql =================================================================== --- trunk/packages/bigsdb/trunk/debian/mlstdbnet_xml2sql 2012-11-08 15:07:24 UTC (rev 12523) +++ trunk/packages/bigsdb/trunk/debian/mlstdbnet_xml2sql 2012-11-08 15:25:29 UTC (rev 12524) @@ -1,75 +0,0 @@ -#!/bin/sh -e -pkg=mlstdbnet -SQLDIR="/var/lib/${pkg}" - -if [ "$1" != "" ] ; then - XML="/etc/${pkg}/$1" - if [ ! -s "$XML" ] ; then - XML="/etc/${pkg}/$1.xml" - if [ ! -s "$XML" ] ; then - echo "$0: File /etc/${pkg}/$1 or $XML not found." - exit 66 # EX_NOINPUT - fi - fi -else - if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 1 ] ; then - XML=`grep -l "<mlstdb>" /etc/${pkg}/*.xml` - else - if [ `grep -c "<mlstdb>" /etc/${pkg}/*.xml` -eq 0 ] ; then - echo "$0: There are no valid XML configuration files for ${pkg} available in /etc/${pkg}" - exit 66 # EX_NOINPUT - else - cat <<EOT -Usage: $0 [${pkg}.xml] - There are more than one XML files available. - You need to specify the one which should be used to create the database. -EOT - grep -l "<mlstdb>" /etc/${pkg}/*.xml - exit 64 # EX_USAGE - fi - fi -fi - -XMLNAME=`basename $XML .xml` - -if [ -e "$SQLDIR"/"$XMLNAME".sql ] ; then - mv "$SQLDIR"/"$XMLNAME".sql "$SQLDIR"/"$XMLNAME".sql~ -fi -/usr/share/${pkg}/xml2sql.pl -u 'www-data' "$XML" > "$SQLDIR"/"$XMLNAME".sql - -if psql -l | grep -wq "$XMLNAME" ; then - cat <<EOT -$0: The database $XMLNAME just exists. - You might like to manually drop this database and populate a newly created - one with the data in "$SQLDIR"/"$XMLNAME".sql. -EOT - exit 0 -fi - -createdb "$XMLNAME" -psql "$XMLNAME" < "$SQLDIR"/"$XMLNAME".sql - -# try to set curator information -CURATORCONF=/etc/${pkg}/curator.conf - -parse_config_string () { - RET=`grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"` - if [ "$RET" = "" ] ; then - echo "Unable to find value $1 in $CURATORCONF. Curator information can not be set." - return -1 - fi - echo "$RET" - return 0 -} - -if [ -s "$CURATORCONF" ] ; then - USERNAME=`parse_config_string USERNAME` - SURNAME=`parse_config_string SURNAME` - FIRSTNAME=`parse_config_string FIRSTNAME` - EMAIL=`parse_config_string EMAIL` -fi - -set -x -psql "$XMLNAME" <<EOT - INSERT INTO users VALUES (1, '$USERNAME', '$SURNAME', '$FIRSTNAME', '$EMAIL', '', 'curator', now(), '') ; -EOT _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
