Updating utility/*.sh scripts from sodar-server

Closes: #531
Related-Issue: #531
Projected-Results-Impact: none

HISTORY.rst

@@ -46,6 +46,7 @@ Full Change List
 - Switching scoring to MutationTaster 85 interface, added back MT 85 link-out alongside MT 2021 link-out (#509).
 - CADD setup fix for documentation (#520)
 - Made flag filter and flag form nomenclature consistent (#297)
+- Updating ``utility/*.sh`` scripts from "upstream" sodar-server (#531).
 
 ------
 v1.2.0

utility/install_chrome.sh

@@ -5,7 +5,7 @@ echo "Installing Chrome + Driver for UI Testing"
 echo "***********************************************"
 
 # Version
-CHROME_DRIVER_VERSION=98.0.4758.80
+CHROME_DRIVER_VERSION=$(curl http://chromedriver.storage.googleapis.com/LATEST_RELEASE)
 
 # Install dependencies
 sudo apt-get update

utility/install_chrome_gitlab.sh

@@ -5,7 +5,7 @@ echo "Installing Chrome + Driver for UI Testing"
 echo "***********************************************"
 
 # Version
-CHROME_DRIVER_VERSION=98.0.4758.80
+CHROME_DRIVER_VERSION=$(curl http://chromedriver.storage.googleapis.com/LATEST_RELEASE)
 
 # Install dependencies
 apt-get -y install unzip libgconf-2-4 xvfb gtk2-engines-pixbuf

utility/install_ldap_dependencies.sh

@@ -1,3 +1,5 @@
+#!/usr/bin/env bash
+
 echo "***********************************************"
 echo "Installing LDAP/AD dependencies"
 echo "***********************************************"

utility/install_os_dependencies.sh

@@ -1,96 +1,44 @@
-#!/bin/bash
-
-WORK_DIR="$(dirname "$0")"
-DISTRO_NAME=$(lsb_release -sc)
-OS_REQUIREMENTS_FILENAME="requirements-$DISTRO_NAME.apt"
-
-cd $WORK_DIR
-
-# Check if a requirements file exist for the current distribution.
-if [ ! -r "$OS_REQUIREMENTS_FILENAME" ]; then
-    cat <<-EOF >&2
-		There is no requirements file for your distribution.
-		You can see one of the files listed below to help search the equivalent package in your system:
-		$(find ./ -name "requirements-*.apt" -printf "  - %f\n")
-	EOF
-    exit 1;
-fi
-
-# Handle call with wrong command
-function wrong_command()
-{
-    echo "${0##*/} - unknown command: '${1}'" >&2
-    usage_message
-}
-
-# Print help / script usage
-function usage_message()
-{
-    cat <<-EOF
-		Usage: $WORK_DIR/${0##*/} <command>
-		Available commands are:
-		    list        Print a list of all packages defined on ${OS_REQUIREMENTS_FILENAME} file
-		    help        Print this help
-
-		Commands that require superuser permission:
-		    install     Install packages defined on ${OS_REQUIREMENTS_FILENAME} file. Note: This
-		                does not upgrade the packages already installed for new versions, even if
-		                new version is available in the repository.
-		    upgrade     Same that install, but upgrade the already installed packages, if new
-		                version is available.
-	EOF
-}
-
-# Read the requirements.apt file, and remove comments and blank lines
-function list_packages(){
-    grep -v "#" "${OS_REQUIREMENTS_FILENAME}" | grep -v "^$";
-}
-
-function install_packages()
-{
-    list_packages | xargs apt-get --no-upgrade install -y;
-}
-
-function upgrade_packages()
-{
-    list_packages | xargs apt-get install -y;
-}
-
-function install_or_upgrade()
-{
-    P=${1}
-    PARAN=${P:-"install"}
-
-    if [[ $EUID -ne 0 ]]; then
-        cat <<-EOF >&2
-			You must run this script with root privilege
-			Please do:
-			sudo $WORK_DIR/${0##*/} $PARAN
-		EOF
-        exit 1
-    else
-
-        apt-get update
-
-        # Install the basic compilation dependencies and other required libraries of this project
-        if [ "$PARAN" == "install" ]; then
-            install_packages;
-        else
-            upgrade_packages;
-        fi
-
-        # cleaning downloaded packages from apt-get cache
-        apt-get clean
-
-        exit 0
-    fi
-}
-
-# Handle command argument
-case "$1" in
-    install) install_or_upgrade;;
-    upgrade) install_or_upgrade "upgrade";;
-    list) list_packages;;
-    help|"") usage_message;;
-    *) wrong_command "$1";;
-esac
+#!/usr/bin/env bash
+
+echo "***********************************************"
+echo "Apt-get update"
+echo "***********************************************"
+apt-get -y update
+
+echo "***********************************************"
+echo "Installing general OS dependencies"
+echo "***********************************************"
+apt-get -y install build-essential
+apt-get -y install python3-dev
+apt-get -y install curl
+
+echo "***********************************************"
+echo "Installing Pillow and pylibmc dependencies"
+echo "***********************************************"
+apt-get -y install zlib1g-dev
+apt-get -y install libtiff5-dev
+apt-get -y install libjpeg8-dev
+apt-get -y install libfreetype6-dev
+apt-get -y install liblcms2-dev
+apt-get -y install libwebp-dev
+
+echo "***********************************************"
+echo "Installing Postgresql and psycopg2 dependencies"
+echo "***********************************************"
+apt-get -y install libpq-dev
+
+echo "***********************************************"
+echo "Installing django-extensions dependencies"
+echo "***********************************************"
+apt-get -y install graphviz-dev
+
+echo "***********************************************"
+echo "Installing SAML dependencies"
+echo "***********************************************"
+apt-get -y install xmlsec1
+
+echo "***********************************************"
+echo "Installing lxml dependencies"
+echo "***********************************************"
+apt-get -y install libxml2-dev
+apt-get -y install libxslt-dev

utility/install_os_gitlab.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
-# Install OS dependencies for Docker image python:3.4 used in Gitlab CI
-# TODO: Some of these are up-to-date on image, remove or keep just in case?
+# Install OS dependencies for Docker image python:3.6 used in Gitlab CI
 
 echo "***********************************************"
 echo "Apt-get update"
@@ -10,41 +9,20 @@ apt-get -y update
 echo "***********************************************"
 echo "Installing OS dependencies"
 echo "***********************************************"
+apt-get -y install apt-utils
 apt-get -y install build-essential
-apt-get -y install python3-dev python3-setuptools
-apt-get -y install git
 apt-get -y install supervisor
 
 echo "***********************************************"
 echo "Installing translation requirements"
 echo "***********************************************"
 apt-get -y install gettext
 
-echo "***********************************************"
-echo "Installing shared Pillow/pylibmc dependencies"
-echo "***********************************************"
-apt-get -y install zlib1g-dev
-
-echo "***********************************************"
-echo "Installing Posgresql and psycopg2 dependencies"
-echo "***********************************************"
-apt-get -y install libpq-dev
-
-echo "***********************************************"
-echo "Installing Pillow dependencies"
-echo "***********************************************"
-apt-get -y install libtiff5-dev
-apt-get -y install libjpeg62-turbo-dev
-apt-get -y install libfreetype6-dev
-apt-get -y install liblcms2-dev
-apt-get -y install libwebp-dev
-
 echo "***********************************************"
 echo "Installing django-extensions dependencies"
 echo "***********************************************"
 apt-get -y install graphviz-dev
 
-
 echo "***********************************************"
 echo "Installing LDAP/AD dependencies"
 echo "***********************************************"
@@ -54,5 +32,5 @@ apt-get -y install libldap2-dev
 echo "***********************************************"
 echo "Installing Node.js"
 echo "***********************************************"
-curl -sL https://deb.nodesource.com/setup_10.x | bash -
+curl -sL https://deb.nodesource.com/setup_12.x | bash -
 apt-get install -y nodejs

utility/install_python_dependencies.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 WORK_DIR="$(dirname "$0")"
 PROJECT_DIR="$(dirname "$WORK_DIR")"
@@ -12,15 +12,6 @@ pip --version >/dev/null 2>&1 || {
     exit 1;
 }
 
-virtualenv --version >/dev/null 2>&1 || {
-    echo >&2 -e "\nvirtualenv is required but it's not installed."
-    echo >&2 -e "You can install it by running the following command:\n"
-    echo >&2 "sudo -H pip3 install virtualenv"
-    echo >&2 -e "\n"
-    echo >&2 -e "\nFor more information, see virtualenv documentation: https://virtualenv.pypa.io/en/latest/"
-    exit 1;
-}
-
 if [ -z "$VIRTUAL_ENV" ]; then
     echo >&2 -e "\nYou need activate a virtualenv first"
     echo >&2 -e 'If you do not have a virtualenv created, run the following command to create and automatically activate a new virtualenv named "venv" on current folder:\n'
@@ -34,7 +25,8 @@ if [ -z "$VIRTUAL_ENV" ]; then
     exit 1;
 else
 
+    pip install wheel==0.37.1
     pip install -r $PROJECT_DIR/requirements/local.txt
     pip install -r $PROJECT_DIR/requirements/test.txt
-#pip install -r $PROJECT_DIR/requirements.txt
+    pip install -r $PROJECT_DIR/requirements.txt
 fi

utility/install_vue_dev.sh

@@ -3,7 +3,7 @@ echo "***********************************************"
 echo "Installing Node.js"
 echo "***********************************************"
 curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
-sudo apt-get install -y nodejs
+apt-get install -y nodejs
 
 echo "***********************************************"
 echo "Installing Vue CLI and Init"