[med-svn] r12524 - trunk/packages/bigsdb/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu Nov 8 15:25:29 UTC 2012
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 <tille at debian.org>, 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-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 <keith.jolley at medawar.ox.ac.uk>
-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
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