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Commit 1c9e59e5 authored by Piotr Gawron's avatar Piotr Gawron
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Merge branch 'rpm-simplify-build' into 'master' 

remove unneeded shell scripting from RPM; adjust RPM installation instruction

See merge request !370
parents 8feedb94 c719d430
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rpm/INSTALL.rst
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− 38
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......@@ -3,15 +3,9 @@ MINERVA installation instructions using RPM Package Manager
These instructions guide you through the installation process of
`MINERVA <https://git-r3lab.uni.lu/piotr.gawron/minerva>`_ on Red Hat
Enterprise Linux 7 or CentOS 7. The server will also host the database
required for the functioning of MINERVA.
.. note::
Content visualization of MINERVA platform is supported by Google
Maps API. Users of MINERVA platform are obliged to comply with the
`Google Maps/Google Earth APIs Terms of Service
<https://www.google.com/intl/en-US_US/help/terms_maps.html>`_.
Enterprise Linux 7 or CentOS 7. In these instructions the server will
also host the database required for the functioning of MINERVA, but
using a different server is possible as well.
Overview
......@@ -32,12 +26,13 @@ Install PostgreSQL and initialise it with
.. code:: shell
yum install -y postgresql-server
postgresql-setup initdb
yum install -y https://download.postgresql.org/pub/repos/yum/9.6/redhat/rhel-7-x86_64/pgdg-centos96-9.6-3.noarch.rpm
yum install -y postgresql96-server
/usr/pgsql-9.6/bin/postgresql96-setup initdb
Ensure that the database authentication on IPv4 on ``localhost`` is
done with md5-based passwords by adding the following line to
``/var/lib/pgsql/data/pg_hba.conf``
``/var/lib/pgsql/9.6/data/pg_hba.conf``
.. code::
......@@ -48,33 +43,26 @@ Enable and start postgresql
.. code:: shell
systemctl enable postgresql
systemctl start postgresql
systemctl enable postgresql-9.6
systemctl start postgresql-9.6
Create the MINERVA database user and the database
.. code:: shell
su - postgres -c "createuser -d -r -s map_viewer"
su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD '123qweasdzxc';\"| psql"
su - postgres -c "echo \"ALTER USER map_viewer WITH PASSWORD 'yourSecretPasswordHere';\"| psql"
su - postgres -c "createdb -O map_viewer map_viewer"
.. warning::
Currently the password for the database user ``map_viewer`` is
hardcoded, therefore make sure the database cannot be accessed
from distrusted hosts.
Apache Tomcat
-------------
Install and enable (don't start yet) Apache Tomcat with
Install Apache Tomcat with
.. code:: shell
yum install -y tomcat
systemctl enable tomcat
In ``/etc/sysconfig/tomcat``, adjust the memory settings, e.g.
......@@ -91,30 +79,42 @@ connections, e.g. using ``firewalld`` this can be accomplished with
.. warning::
Currently the administrator password of MINERVA is hardcoded,
therefore make sure the MINERVA cannot be accessed from distrusted
hosts until the password was changed.
Currently the initial administrator password of MINERVA is
hardcoded, therefore make sure the MINERVA cannot be accessed from
distrusted hosts until the password was changed.
Enable and start Tomcat
.. code:: shell
systemctl enable tomcat
systemctl start tomcat
MINERVA
-------
Install MINERVA using ``yum``
Create a configuration file at ``/etc/minerva/db.properties`` so
MINERVA knows how to connect to the database:
.. code:: shell
.. code::
yum install -y minerva-X.Y.Z-1.el7.centos.noarch.rpm
database.uri=jdbc:postgresql://localhost:5432/map_viewer
database.username=map_viewer
database.password=yourSecretPasswordHere
and start tomcat
Install MINERVA with
.. code:: shell
systemctl start tomcat
Now point your browser to the newly installed service, e.g. on a local
network this could be `<http://192.168.0.42:8080/minerva/>`_.
yum install -y minerva-X.Y.Z-1.el7.noarch.rpm
.. warning::
Tomcat will automatically deploy the MINERVA web archive, and after a
short time it will have initialised the database and MINERVA will be
running. Point point your browser to the newly installed service,
e.g. on a local network this could be
`<http://192.168.0.42:8080/minerva/>`_.
This way of installing MINERVA does **not** ensure that security
updates are installed with ``yum update``, therefore you have to
establish a process to install such updates manually.
Login with the username ``admin`` and the password ``admin``. Click on
the ``INFO`` tab in the left panel, and click on ``MANUAL`` to get
more information about administrating and using MINERVA.
rpm/buildrpm.sh
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......@@ -4,6 +4,27 @@ set -e
MINERVA_SRC_DIR="$(dirname "$(dirname "$0")")"
# file that should be deployed on tomcat; if an argument is given to this script, use it as war-file
TOMCAT_FILE="${1:-$MINERVA_SRC_DIR/web/target/web-1.0.war}"
endswith() { case $2 in *"$1") true;; *) false;; esac; }
if ! endswith ".war" "$TOMCAT_FILE"; then
echo "first argument should be a file ending in '.war'"
exit -1
fi
if [ ! -f "$TOMCAT_FILE" ]; then
echo "file does not exist: $TOMCAT_FILE"
exit -1
fi
# get the version number from the changelog in war file
current_version=$(unzip -p $TOMCAT_FILE CHANGELOG | head -1 | sed 's/^minerva (\(.*\)).*/\1/')
if [ -z "$current_version" ]; then
echo "could not extract version number from CHANGELOG in $TOMCAT_FILE"
exit -1
fi
# where generated files will be written
RPMBUILD_TEMP="${RPMBUILD_TEMP:-$MINERVA_SRC_DIR/rpm/rpmbuildtemp}"
......@@ -17,18 +38,6 @@ fi
# current date (for automatic changelog)
CURDATE=$(date +"%a %b %d %Y")
# file that should be deployed on tomcat
TOMCAT_FILE="$MINERVA_SRC_DIR/web/target/web-1.0.war"
# file with bash code generating DB schema diffs for different versions
dbschemadiff="$MINERVA_SRC_DIR/management_scripts/db_schema_and_diff.sh"
# directory with database schema
DB_SCHEMA_DIR="$MINERVA_SRC_DIR/persist/src/db"
# destination directory for database upgrade scripts
DBSCRIPT_DEST_DIR="$RPMBUILD_TEMP/BUILD/sql"
# clean build directories
rm -rf "$RPMBUILD_TEMP"
......@@ -39,13 +48,6 @@ mkdir -p "$RPMBUILD_TEMP/"{BUILD,SPECS}
cp "$TOMCAT_FILE" "$RPMBUILD_TEMP/BUILD/minerva.war"
cp "$MINERVA_SRC_DIR/README.md" "$MINERVA_SRC_DIR/CHANGELOG" "$MINERVA_SRC_DIR/rpm/INSTALL.rst" "$MINERVA_SRC_DIR/rpm/logrotate_minerva" "$RPMBUILD_TEMP/BUILD"
mkdir -p "$DBSCRIPT_DEST_DIR"
# copy base sql schema
cp "$DB_SCHEMA_DIR/base.sql" "$DBSCRIPT_DEST_DIR/db_0.sql"
# set $versions and $current_version; generate upgrade scripts in DBSCRIPT_DEST_DIR
source "$dbschemadiff"
# create RPM spec file
cp "$MINERVA_SRC_DIR/rpm/minerva.spec.in" "$RPMBUILD_TEMP/SPECS/minerva.spec"
sed -i "s/__CURRENT_VERSION__/$current_version/g" "$RPMBUILD_TEMP/SPECS/minerva.spec"
......
rpm/minerva.spec.in
+ 1
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View file @ 1c9e59e5
......@@ -15,69 +15,15 @@ Web application for visualization, exploration and management of
molecular networks encoded in SBGN-compliant format. The resource is
used and managed via a webbrowser.
%pre -p /bin/bash
# check that postgres is started and tomcat is stopped, otherwise abort installation/upgrade
if ! $(systemctl -q is-active postgresql); then
echo "postgresql not running, aborting installation/upgrade of minerva" >&2
exit -1
fi
if $(systemctl -q is-active tomcat); then
echo "tomcat is running, aborting installation/upgrade of minerva" >&2
exit -1
fi
# make sure the user `map_viewer` has the required permissions
attributes_map_viewer=$(su - postgres -c "psql -F $'\t' --no-align -t -c '\du map_viewer'" | cut -f 2)
if ! [[ $attributes_map_viewer == *"Superuser"* ]] || ! [[ $attributes_map_viewer == *"Create role"* ]] || ! [[ $attributes_map_viewer == *"Create DB"* ]]; then
echo "Postgres user map_viewer does not exist or does not have the required attributes." >&2
echo "Make sure to create map_viewer with the permission 'Superuser, Create role, Create DB'." >&2
echo "Attributes are: '$attributes_map_viewer'" >&2
echo "Aborting installation/upgrade of minerva." >&2
exit -1
fi
# make sure the database map_viewer exists
if ! su - postgres -c "psql --dbname map_viewer -q -c '\q'" 2> /dev/null; then
echo "Database map_viewer does not exist, aborting installation/upgrade of minerva." >&2
exit -1
fi
%preun -p /bin/bash
if [ $1 == 1 ]; then
# save version information of the old package to make sure we run the correct DB-update script after installation
mkdir -p %{_sharedstatedir}/rpm-state/%{name}
echo -n %{version} > %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION
# remove old unpacked ("exploded") directory of war file
rm -rf %{_sharedstatedir}/tomcat/webapps/%{name}
fi
%posttrans -p /bin/bash
LOGFILE=%{_localstatedir}/log/minerva-install.log
if [ -e %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION ]; then
OLD_VERSION=$(cat %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION)
echo $(date) "Upgrading minerva from $OLD_VERSION to %{version}" >> $LOGFILE
if [ ! -e %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql ]; then
echo "ERROR: missing DB-update script %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql" >&2
exit -1
fi
su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_${OLD_VERSION}_to_%{version}.sql" >> $LOGFILE 2>&1
rm -f %{_sharedstatedir}/rpm-state/%{name}/OLD_VERSION
rmdir %{_sharedstatedir}/rpm-state/%{name}
else
echo $(date) "Installing minerva %{version}" >> $LOGFILE
if [ $(su - postgres -c "psql --dbname map_viewer -F $'\t' --no-align -t -c '\dt'" | wc -l) -gt 51 ]; then
echo "The database map_viewer is not empty, aborting initialisation of database." >&2
echo "The database map_viewer is not empty, aborting initialisation of database." >> $LOGFILE
exit -1
fi
# install base version of the framework
su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_0.sql" >> $LOGFILE 2>&1
# install patch to current version
su - postgres -c "psql map_viewer -f %{_datadir}/%{name}/schema/db_0_to_%{version}.sql" >> $LOGFILE 2>&1
fi
%install
rm -rf %{buildroot}
mkdir -p %{buildroot}/%{_datadir}/%{name}/schema
install -m 0644 sql/*.sql %{buildroot}/%{_datadir}/%{name}/schema
mkdir -p %{buildroot}/%{_datadir}/%{name}
install -m 0644 %{name}.war %{buildroot}/%{_datadir}/%{name}/%{name}.war
mkdir -p %{buildroot}/%{_sysconfdir}/logrotate.d
install -m 0644 logrotate_minerva %{buildroot}/%{_sysconfdir}/logrotate.d/minerva
......@@ -88,7 +34,6 @@ ln -s %{_datadir}/%{name}/%{name}.war %{buildroot}/%{_sharedstatedir}/tomcat/web
%defattr(-,root,root,-)
%doc README.md CHANGELOG INSTALL.rst
%{_datadir}/%{name}/%{name}.war
%{_datadir}/%{name}/schema/*
%config(noreplace) %{_sysconfdir}/logrotate.d/minerva
%attr(-,tomcat,tomcat) %{_sharedstatedir}/tomcat/webapps/%{name}.war
......
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