[med-svn] r2531 - in trunk/packages/agdbnet/trunk/debian: . po
tille at alioth.debian.org
tille at alioth.debian.org
Wed Sep 24 13:14:13 UTC 2008
Author: tille
Date: 2008-09-24 13:14:12 +0000 (Wed, 24 Sep 2008)
New Revision: 2531
Added:
trunk/packages/agdbnet/trunk/debian/doc
Modified:
trunk/packages/agdbnet/trunk/debian/README.Debian
trunk/packages/agdbnet/trunk/debian/config
trunk/packages/agdbnet/trunk/debian/po/templates.pot
trunk/packages/agdbnet/trunk/debian/postinst
trunk/packages/agdbnet/trunk/debian/postrm
trunk/packages/agdbnet/trunk/debian/templates
Log:
Add debconf configuration for curator
Modified: trunk/packages/agdbnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/README.Debian 2008-09-24 13:14:12 UTC (rev 2531)
@@ -4,13 +4,12 @@
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
+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
@@ -18,26 +17,56 @@
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.
+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.
+To simplify the creation of the database you can find a script named
+agdbnet_xml2sql in this directory. This script might serve as an
+example how to intialise the agdbnet database which means - it was not
+yet thoroughly tested but it implements the hints of the installation
+manual and works for the maintainer of this package. Any hints for
+enhancing this script are welcome. In case you do not want to use
+this script you have to do the following steps:
+ /usr/share/agdbnet/xml2sql.pl -u '"www-data"' \
+ /etc/agdbnet/[your_database].xml > init.sql
+ createdb [your_database]
+ psql [your_database] < init.sql
+
+Finally you have to insert the data of the curator
+
+ psql [your_database] -c \
+ "INSERT INTO users VALUES (1, 'username', 'surname', 'firstname', 'email', '', '', now(), '') ;"
+
+These steps including some sanity checks are done by the
+agdbnet_xml2sql script and thus the manual initialisation could be
+simplified by just calling
+
+ . agdbnet_xml2sql
+
+To populate the database with the data of the curator user the file
+/etc/agdbnet/agcurator.conf is read. Once the database is initialised
+there is not much use for this file any more but you might keep it for
+later reference.
+
+In case this might fail just use the reportbug tool to report the
+problem that might have occured.
+
+
PubMed references
-----------------
According to item 6. of the original installation manual (see
-installation.html) the configuration file has to be adjusted to
-enable obtaining PubMed references. You can find the original
-getrefs.conf example file in the examples directory. The data
-in this example file correspond to the configuration file example
-poravr.xml. Please adapt this to your own needs and finally copy
-a working getrefs.conf file into the directory /etc/agdbnet.
-Once you have done this the cron job in /etc/cron.daily/agdbnet
-will fetch the references once a day. It is strongly advised
-to call /etc/cron.daily/agdbnet manually for testing proper
-operation.
+installation.html) the configuration file has to be adjusted to enable
+obtaining PubMed references. You can find the original getrefs.conf
+example file in the examples directory. The data in this example file
+correspond to the configuration file example poravr.xml. Please adapt
+this to your own needs and finally copy a working getrefs.conf file
+into the directory /etc/agdbnet. Once you have done this the cron job
+in /etc/cron.daily/agdbnet will fetch the references once a day. It
+is strongly advised to call /etc/cron.daily/agdbnet manually for
+testing proper operation.
- -- Andreas Tille <tille at debian.org> Fri, 05 Sep 2008 11:07:50 +0200
+ -- Andreas Tille <tillea at rki.de>, Wed, 24 Sep 2008 14:23:04 +0200
Modified: trunk/packages/agdbnet/trunk/debian/config
===================================================================
--- trunk/packages/agdbnet/trunk/debian/config 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/config 2008-09-24 13:14:12 UTC (rev 2531)
@@ -9,7 +9,6 @@
. /usr/share/debconf/confmodule
db_version 2.0
-
# 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}
@@ -76,6 +75,39 @@
db_input high ${pkg}/locus || true
db_input high ${pkg}/note || true
+## Now configure a curator for the agcurator.pl cgi script
+## values are stored in
+CURATORCONF=/etc/${pkg}/agcurator.conf
+
+parse_config_string () {
+ grep "^[[:space:]]*$1[[:space:]]*=[[:space:]]*[^#]\+" "$CURATORCONF" | head -1 | sed "s/^[[:space:]]*$1[[:space:]]*=[[:space:]]*\([^#]\+\).*/\1/"
+ return 0
+}
+
+if [ -s "$CURATORCONF" ] ; then
+ USERNAME=`parse_config_string USERNAME`
+ if [ "$USERNAME" != "" ] ; then
+ db_set ${pkg}/curator/username "$USERNAME"
+ fi
+ SURNAME=`parse_config_string SURNAME`
+ if [ "$SURNAME" != "" ] ; then
+ db_set ${pkg}/curator/surname "$SURNAME"
+ fi
+ FIRSTNAME=`parse_config_string FIRSTNAME`
+ if [ "$FIRSTNAME" != "" ] ; then
+ db_set ${pkg}/curator/firstname "$FIRSTNAME"
+ fi
+ EMAIL=`parse_config_string EMAIL`
+ if [ "$EMAIL" != "" ] ; then
+ db_set ${pkg}/curator/email "$EMAIL"
+ fi
+fi
+
+db_input high ${pkg}/curator/username || true
+db_input high ${pkg}/curator/surname || true
+db_input high ${pkg}/curator/firstname || true
+db_input high ${pkg}/curator/email || 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
Added: trunk/packages/agdbnet/trunk/debian/doc
===================================================================
--- trunk/packages/agdbnet/trunk/debian/doc (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/doc 2008-09-24 13:14:12 UTC (rev 2531)
@@ -0,0 +1,2 @@
+agdbnet_xml2sql
+
Modified: trunk/packages/agdbnet/trunk/debian/po/templates.pot
===================================================================
--- trunk/packages/agdbnet/trunk/debian/po/templates.pot 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/po/templates.pot 2008-09-24 13:14:12 UTC (rev 2531)
@@ -8,7 +8,7 @@
msgstr ""
"Project-Id-Version: PACKAGE VERSION\n"
"Report-Msgid-Bugs-To: agdbnet at packages.debian.org\n"
-"POT-Creation-Date: 2008-09-19 14:10+0200\n"
+"POT-Creation-Date: 2008-09-24 14:39+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"
@@ -175,3 +175,121 @@
"agdbnet/attributes.shtml . The value here corresponds to the man attribute "
"of the \"<locus>\" element."
msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:6001
+msgid "Hint about configuration of the PubMed reference database"
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:6001
+msgid ""
+"You are now finished with the AgdbNet configuration. Please read more about "
+"AgdbNet configuration at\n"
+" http://pubmlst.org/software/database/agdbnet/xml.shtml and\n"
+" http://pubmlst.org/software/database/agdbnet/attributes.shtml\n"
+"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."
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:6001
+msgid ""
+"The following questions concern the creation of the database for PubMed "
+"references. It should be safe to use always default values (just <Enter>)."
+msgstr ""
+
+#. Type: note
+#. Description
+#: ../templates:6001
+msgid ""
+"To enable daily updates of PubMed references you have to create\n"
+" /etc/agdbnet/getrefs.conf\n"
+"according to the template in examples. It is strongly recommended to read\n"
+" /usr/share/doc/agdbnet/README.Debian\n"
+"how to create this file."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid "Username of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid ""
+"Curators of agdbnat are people who are allowed to insert new strains into "
+"the database which can be used to compare with user provided strains in "
+"agdbnet. 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."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid ""
+"Attention: The method currently used for authentication is insecure. Please "
+"read /usr/share/doc/agdbnet/README.Debian how to change this to a secure "
+"method."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:7001
+msgid ""
+"Please input the login username for one curator now. Others can be added "
+"later."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:8001
+msgid "Surname of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:8001
+msgid ""
+"Please input the surname of the person which should work as a curator for "
+"agdbnet."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:9001
+msgid "First name of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:9001
+msgid ""
+"Please input the first name of the person which should work as a curator for "
+"agdbnet."
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:10001
+msgid "E-mail address of database curator:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../templates:10001
+msgid ""
+"Please input the e-mail address of the person which should work as a curator "
+"for agdbnet. 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 ""
Modified: trunk/packages/agdbnet/trunk/debian/postinst
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postinst 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/postinst 2008-09-24 13:14:12 UTC (rev 2531)
@@ -30,6 +30,7 @@
db_get ${pkg}/locus
LOCUS=${RET}
+
# Substitute the value ##variables## in the templates and move them
# right into place
XMLOUT=/etc/${pkg}/"$XMLNAME".xml
@@ -80,6 +81,37 @@
ln -s "$STYLEDIR" "/var/www/${pkg}/$XMLNAME"
fi
+# Obtaining user information for agcurator and write this to the config file
+db_get ${pkg}/curator/username
+USERNAME=${RET}
+
+db_get ${pkg}/curator/surname
+SURNAME=${RET}
+
+db_get ${pkg}/curator/firstname
+FIRSTNAME=${RET}
+
+db_get ${pkg}/curator/email
+EMAIL=${RET}
+
+CURATORCONF=/etc/${pkg}/agcurator.conf
+if [ ! -s "$CURATORCONF" ] ; then
+ cat > "$CURATORCONF" <<EOT
+# This file is used when creating the agdbnet database to add an initial curator
+# Please read /usr/share/${pkg}/README.Debian for further information.
+USERNAME=${USERNAME}
+SURNAME=${SURNAME}
+FIRSTNAME=${FIRSTNAME}
+EMAIL=${EMAIL}
+EOT
+else
+ sed -i~ -e "s/^\([[:space:]]*USERNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${USERNAME}/" \
+ -e "s/^\([[:space:]]*SURNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${SURNAME}/" \
+ -e "s/^\([[:space:]]*FIRSTNAME[[:space:]]*=[[:space:]]*\)[^#]\+/\1${FIRSTNAME}/" \
+ -e "s/^\([[:space:]]*EMAIL[[:space:]]*=[[:space:]]*\)[^#]\+/\1${EMAIL}/" \
+ "$CURATORCONF"
+fi
+
TMPDIR="/var/www/${pkg}/tmp"
SQLDIR="/var/lib/${pkg}"
Modified: trunk/packages/agdbnet/trunk/debian/postrm
===================================================================
--- trunk/packages/agdbnet/trunk/debian/postrm 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/postrm 2008-09-24 13:14:12 UTC (rev 2531)
@@ -43,8 +43,11 @@
rm -f /var/lib/${pkg}/"$XMLNAME".sql
rmdir --ignore-fail-on-non-empty /var/lib/${pkg}
fi
+
+ # Remove configuration for curator
+ rm -f /etc/${pkg}/agcurator.conf
;;
-
+
remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
;;
Modified: trunk/packages/agdbnet/trunk/debian/templates
===================================================================
--- trunk/packages/agdbnet/trunk/debian/templates 2008-09-24 12:43:32 UTC (rev 2530)
+++ trunk/packages/agdbnet/trunk/debian/templates 2008-09-24 13:14:12 UTC (rev 2531)
@@ -81,7 +81,7 @@
Template: agdbnet/note
Type: note
-Description: Hint about configuration of the PubMed reference database
+_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
@@ -99,3 +99,40 @@
according to the template in examples. It is strongly recommended to read
/usr/share/doc/agdbnet/README.Debian
how to create this file.
+
+Template: agdbnet/curator/username
+Type: string
+_Description: Username of database curator:
+ Curators of agdbnat are people who are allowed to insert new strains
+ into the database which can be used to compare with user provided strains
+ in agdbnet. 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/agdbnet/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: agdbnet/curator/surname
+Type: string
+_Description: Surname of database curator:
+ Please input the surname of the person which should work as a curator
+ for agdbnet.
+
+Template: agdbnet/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 agdbnet.
+
+Template: agdbnet/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 agdbnet. 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.
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