From c719d43009264c6ded0dd47331a54bd355210249 Mon Sep 17 00:00:00 2001
From: Nils Christian <nils.christian@ittm-solutions.com>
Date: Wed, 1 Aug 2018 15:53:39 +0200
Subject: [PATCH] remove unneeded shell scripting from RPM; adjust RPM
installation instruction
---
rpm/INSTALL.rst | 76 ++++++++++++++++++++++-----------------------
rpm/buildrpm.sh | 40 ++++++++++++------------
rpm/minerva.spec.in | 57 +---------------------------------
3 files changed, 60 insertions(+), 113 deletions(-)
diff --git a/rpm/INSTALL.rst b/rpm/INSTALL.rst
index 11116e0551..c42029bb26 100644
--- a/rpm/INSTALL.rst
+++ b/rpm/INSTALL.rst
@@ -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.
diff --git a/rpm/buildrpm.sh b/rpm/buildrpm.sh
index eb3166272a..e425be4ede 100755
--- a/rpm/buildrpm.sh
+++ b/rpm/buildrpm.sh
@@ -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"
diff --git a/rpm/minerva.spec.in b/rpm/minerva.spec.in
index 99556fd49b..555ba6d81f 100644
--- a/rpm/minerva.spec.in
+++ b/rpm/minerva.spec.in
@@ -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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