Merge in original drupal image stuff

Dockerfile

-FROM samos123/drupal:latest
+FROM php:apache
+MAINTAINER Eric Rasche <esr@tamu.edu>
 
-RUN a2enmod proxy && a2enmod proxy_http
+ENTRYPOINT ["/entrypoint.sh"]
 
-#TODO: gpg verify
+# Provide compatibility for images depending on previous versions
+RUN ln -s /var/www/html /app
+# Update apache2 configuration for drupal
+RUN a2enmod rewrite && a2enmod proxy && a2enmod proxy_http
+
+# Install packages and PHP-extensions
 RUN apt-get -q update && \
-    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install wget patch && \
-    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install \
+    file libfreetype6 libjpeg62 libpng12-0 libpq-dev libx11-6 libxpm4 \
+    postgresql-client wget patch && \
+    BUILD_DEPS="libfreetype6-dev libjpeg62-turbo-dev libmcrypt-dev libpng12-dev libxpm-dev re2c zlib1g-dev"; \
+    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install $BUILD_DEPS \
+ && docker-php-ext-configure gd \
+        --with-jpeg-dir=/usr/lib/x86_64-linux-gnu --with-png-dir=/usr/lib/x86_64-linux-gnu \
+        --with-xpm-dir=/usr/lib/x86_64-linux-gnu --with-freetype-dir=/usr/lib/x86_64-linux-gnu \
+ && docker-php-ext-install gd mbstring pdo_pgsql zip \
+ && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false -o APT::AutoRemove::SuggestsImportant=false $BUILD_DEPS \
+ && rm -rf /var/lib/apt/lists/* \
+ && pecl install uploadprogress
+
+# Download Drupal from ftp.drupal.org
+ENV DRUPAL_VERSION=7.50
+ENV DRUPAL_TARBALL_MD5=f23905b0248d76f0fc8316692cd64753
+WORKDIR /var/www
+RUN rm -R html \
+ && curl -OsS https://ftp.drupal.org/files/projects/drupal-${DRUPAL_VERSION}.tar.gz \
+ && echo "${DRUPAL_TARBALL_MD5}  drupal-${DRUPAL_VERSION}.tar.gz" | md5sum -c \
+ && tar -xf drupal-${DRUPAL_VERSION}.tar.gz && rm drupal-${DRUPAL_VERSION}.tar.gz \
+ && mv drupal-${DRUPAL_VERSION} html \
+ && cd html \
+ && rm [A-Z]*.txt install.php web.config sites/default/default.settings.php
+
+# Install composer and drush by using composer
+ENV COMPOSER_BIN_DIR=/usr/local/bin
+RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local/bin --filename=composer \
+ && composer global require drush/drush:7.* \
+ && drush cc drush \
+ && mkdir /etc/drush && echo "<?php\n\$options['yes'] = TRUE;\n\$options['v'] = TRUE;\n" > /etc/drush/drushrc.php
+
+# Add PHP-settings
+ADD php-conf.d/ $PHP_INI_DIR/conf.d/
+
+# copy sites/default's defaults
+WORKDIR html
+ADD sites/ sites/
+
+# Add README.md, entrypoint-script and scripts-folder
+ADD entrypoint.sh README.md  /
+ADD /scripts/ /scripts/
 
 RUN wget https://cpt.tamu.edu/jenkins/job/Chado-Prebuilt-Schemas/19/artifact/compile-chado-schema/chado/default/chado-master-tripal.sql.gz -O /chado-master-tripal.sql.gz
 
 ADD tripal_chado_install /scripts/setup.d/50tripal_chado_install
-
 ADD tripal_apache.conf /etc/apache2/conf-enabled/tripal_apache.conf

entrypoint.sh

+#!/bin/bash
+set -e
+
+function run_scripts () {
+	SCRIPTS_DIR="/scripts/$1.d"
+	SCRIPT_FILES_PATTERN="^${SCRIPTS_DIR}/[0-9][0-9][a-zA-Z0-9_-]+$"
+	SCRIPTS=$(find "$SCRIPTS_DIR" -type f -uid 0 -executable -regex "$SCRIPT_FILES_PATTERN" | sort)
+	if [ -n "$SCRIPTS" ] ; then
+		echo "=>> $1-scripts:"
+	    for script in $SCRIPTS ; do
+	        echo "=> $script"
+			. "$script"
+	    done
+	fi
+}
+
+### auto-configure database from environment-variables
+
+DB_DRIVER=pgsql
+DB_HOST=postgres
+: ${DB_PORT:='5432'}
+: ${DB_NAME:='postgres'}
+: ${DB_USER:='postgres'}
+: ${DB_PASS:='postgres'}
+
+: ${ADMIN_USER:='admin'}  # DO NOT export!
+: ${ADMIN_PASSWORD:='changeme'}  # DO NOT export!
+
+export DB_DRIVER DB_HOST DB_PORT DB_NAME DB_USER DB_PASS
+echo -e "# Drupals's database configuration, parsed in /var/www/sites/default/settings.php\n
+export DB_DRIVER=${DB_DRIVER} DB_HOST=${DB_HOST} DB_PORT=${DB_PORT} DB_NAME=${DB_NAME} DB_USER=${DB_USER} DB_PASS=${DB_PASS}" >> /etc/bash.bashrc
+
+
+###  connect to database
+
+echo
+echo "=> Trying to connect to a database using:"
+echo "      Database Driver:   $DB_DRIVER"
+echo "      Database Host:     $DB_HOST"
+echo "      Database Port:     $DB_PORT"
+echo "      Database Username: $DB_USER"
+echo "      Database Password: $DB_PASS"
+echo "      Database Name:     $DB_NAME"
+echo
+
+for ((i=0;i<20;i++))
+do
+    DB_CONNECTABLE=$(PGPASSWORD=$DB_PASS psql -U "$DB_USER" -h "$DB_HOST" -p "$DB_PORT" -l >/dev/null 2>&1; echo "$?")
+	if [[ $DB_CONNECTABLE -eq 0 ]]; then
+		break
+	fi
+    sleep 3
+done
+
+if ! [[ $DB_CONNECTABLE -eq 0 ]]; then
+	echo "Cannot connect to database"
+    exit "${DB_CONNECTABLE}"
+fi
+
+
+### Initial setup if database doesn't exist
+
+if ! drush pm-list > /dev/null 2>&1; then
+	run_scripts setup
+	echo "=> Done installing site!"
+	if [ $EXTRA_SETUP_SCRIPT ]; then
+		echo "=> WARNING: The usage of EXTRA_SETUP_SCRIPT is deprectated. Put your script into /scripts/post-setup.d/"
+		. $EXTRA_SETUP_SCRIPT
+		echo "=> Successfully ran extra setup script ${EXTRA_SETUP_SCRIPT}."
+	fi
+	else
+	echo "=> Skipped setup - database ${DB_NAME} already exists."
+fi
+
+
+###
+
+run_scripts pre-launch
+
+unset ADMIN_USER
+unset ADMIN_PASSWORD
+
+exec apache2-foreground
+
+exit 1

php-conf.d/drupal-recommends.ini

+allow_url_fopen = off
+display_errors = off
+expose_php = off
+extension = uploadprogress.so
+session.auto_start = 0
+session.cache_limiter = nocache

scripts/pre-launch.d/00conf_php

+: ${UPLOAD_LIMIT:='10M'}
+echo -e "upload_max_filesize = ${UPLOAD_LIMIT}\npost_max_size = ${UPLOAD_LIMIT}" \
+	> $PHP_INI_DIR'/conf.d/upload-limit.ini'
+: ${MEMORY_LIMIT:='64M'}
+echo "memory_limt = ${MEMORY_LIMIT}" > $PHP_INI_DIR'/conf.d/memory-limit.ini'

scripts/pre-launch.d/05servername_baseurl

+: "${BASE_URL_PROTO:='https://'}"
+
+if [ -n "$VIRTUAL_HOST" ]; then
+	if [ -z "$SERVERNAME" ]; then
+		SERVERNAME=$(echo "$VIRTUAL_HOST" | cut -f 1 -d ,)
+	fi
+	if [ -z "$BASE_URL" ]; then
+		BASE_URL="${BASE_URL_PROTO}"$(echo "$VIRTUAL_HOST" | cut -f 1 -d ,)
+	fi
+fi
+
+: "${SERVERNAME:=$(cat /etc/hostname)}"
+echo ServerName "${SERVERNAME}" >> /etc/apache2/apache2.conf
+
+if [ -n "$BASE_URL" ]; then
+	export BASE_URL
+	echo -e "# Drupal's base_url-variable\nexport BASE_URL=${BASE_URL}" >> /etc/bash.bashrc
+fi

scripts/pre-launch.d/99file_perm

+prev_dir=$(pwd)
+
+cd /var/www
+chown -R www-data.www-data .
+find . -type d -exec chmod ug=rx,o= '{}' \;
+find . -type f -exec chmod ug=r,o= '{}' \;
+
+chmod ug=rwx,o= private
+find private -type d -exec chmod ug=rwx,o= '{}' \;
+find private -type f -exec chmod ug=rw,o= '{}' \;
+
+cd html/sites
+find . -type d -exec chmod ug=rwx,o= '{}' \;
+for x in ./*/files; do
+    find ${x} -type d -exec chmod ug=rwx,o= '{}' \;
+    find ${x} -type f -exec chmod ug=rw,o= '{}' \;
+done
+
+cd "${prev_dir}"

scripts/pre-launch.d/README.txt

+This folder contains scripts that will be executed before the launch of a Drupal-instance.
+See /README.md for details.

scripts/setup.d/40site-install

+/usr/bin/env PHP_OPTIONS="-d sendmail_path=$(which true)" drush site-install --site-name=default --account-name="${ADMIN_USER}" --account-pass="${ADMIN_PASSWORD}"

scripts/setup.d/README.txt

+This folder contains scripts that will be executed as installation-process of a
+Drupal-instance. See /README.md for details.

sites/default/files/.dockerignore

+*

sites/default/settings.php

+<?php
+
+/**
+ * Docker-image specifics
+ */
+$databases = array();
+$databases['default']['default'] = array(
+  'driver' => getenv('DB_DRIVER'),
+  'database' => getenv('DB_NAME'),
+  'username' => getenv('DB_USER'),
+  'password' => getenv('DB_PASS'),
+  'host' => getenv('DB_HOST'),
+  'prefix' => '',
+);
+
+if (getenv('BASE_URL'))
+  $base_url = getenv('BASE_URL');
+
+$update_free_access = FALSE;
+
+$conf['drupal_http_request_fails'] = FALSE;
+$conf['file_private_path'] = '/var/www/private';
+
+/**
+ * Salt for one-time login links and cancel links, form tokens, etc.
+ *
+ * This variable will be set to a random value by the installer. All one-time
+ * login links will be invalidated if the value is changed. Note that if your
+ * site is deployed on a cluster of web servers, you must ensure that this
+ * variable has the same value on each server. If this variable is empty, a hash
+ * of the serialized database credentials will be used as a fallback salt.
+ *
+ * For enhanced security, you may set this variable to a value using the
+ * contents of a file outside your docroot that is never saved together
+ * with any backups of your Drupal files and database.
+ *
+ * Example:
+ *   $drupal_hash_salt = file_get_contents('/home/example/salt.txt');
+ *
+ */
+# TODO  think of something clever here
+$drupal_hash_salt = '';
+
+/**
+ * PHP settings:
+ *
+ * To see what PHP settings are possible, including whether they can be set at
+ * runtime (by using ini_set()), read the PHP documentation:
+ * http://www.php.net/manual/ini.list.php
+ * See drupal_environment_initialize() in includes/bootstrap.inc for required
+ * runtime settings and the .htaccess file for non-runtime settings. Settings
+ * defined there should not be duplicated here so as to avoid conflict issues.
+ */
+
+/**
+ * Some distributions of Linux (most notably Debian) ship their PHP
+ * installations with garbage collection (gc) disabled. Since Drupal depends on
+ * PHP's garbage collection for clearing sessions, ensure that garbage
+ * collection occurs by using the most common settings.
+ */
+ini_set('session.gc_probability', 1);
+ini_set('session.gc_divisor', 100);
+
+/**
+ * Set session lifetime (in seconds), i.e. the time from the user's last visit
+ * to the active session may be deleted by the session garbage collector. When
+ * a session is deleted, authenticated users are logged out, and the contents
+ * of the user's $_SESSION variable is discarded.
+ */
+ini_set('session.gc_maxlifetime', 200000);
+
+/**
+ * Set session cookie lifetime (in seconds), i.e. the time from the session is
+ * created to the cookie expires, i.e. when the browser is expected to discard
+ * the cookie. The value 0 means "until the browser is closed".
+ */
+ini_set('session.cookie_lifetime', 2000000);
+
+/**
+ * If you encounter a situation where users post a large amount of text, and
+ * the result is stripped out upon viewing but can still be edited, Drupal's
+ * output filter may not have sufficient memory to process it.  If you
+ * experience this issue, you may wish to uncomment the following two lines
+ * and increase the limits of these variables.  For more information, see
+ * http://php.net/manual/pcre.configuration.php.
+ */
+# ini_set('pcre.backtrack_limit', 200000);
+# ini_set('pcre.recursion_limit', 200000);
+
+/**
+ * Drupal automatically generates a unique session cookie name for each site
+ * based on its full domain name. If you have multiple domains pointing at the
+ * same Drupal site, you can either redirect them all to a single domain (see
+ * comment in .htaccess), or uncomment the line below and specify their shared
+ * base domain. Doing so assures that users remain logged in as they cross
+ * between your various domains. Make sure to always start the $cookie_domain
+ * with a leading dot, as per RFC 2109.
+ */
+# $cookie_domain = '.example.com';
+
+/**
+ * Variable overrides:
+ *
+ * To override specific entries in the 'variable' table for this site,
+ * set them here. You usually don't need to use this feature. This is
+ * useful in a configuration file for a vhost or directory, rather than
+ * the default settings.php. Any configuration setting from the 'variable'
+ * table can be given a new value. Note that any values you provide in
+ * these variable overrides will not be modifiable from the Drupal
+ * administration interface.
+ *
+ * The following overrides are examples:
+ * - site_name: Defines the site's name.
+ * - theme_default: Defines the default theme for this site.
+ * - anonymous: Defines the human-readable name of anonymous users.
+ * Remove the leading hash signs to enable.
+ */
+# $conf['site_name'] = 'My Drupal site';
+# $conf['theme_default'] = 'garland';
+# $conf['anonymous'] = 'Visitor';
+
+/**
+ * A custom theme can be set for the offline page. This applies when the site
+ * is explicitly set to maintenance mode through the administration page or when
+ * the database is inactive due to an error. It can be set through the
+ * 'maintenance_theme' key. The template file should also be copied into the
+ * theme. It is located inside 'modules/system/maintenance-page.tpl.php'.
+ * Note: This setting does not apply to installation and update pages.
+ */
+# $conf['maintenance_theme'] = 'bartik';
+
+/**
+ * Reverse Proxy Configuration:
+ *
+ * Reverse proxy servers are often used to enhance the performance
+ * of heavily visited sites and may also provide other site caching,
+ * security, or encryption benefits. In an environment where Drupal
+ * is behind a reverse proxy, the real IP address of the client should
+ * be determined such that the correct client IP address is available
+ * to Drupal's logging, statistics, and access management systems. In
+ * the most simple scenario, the proxy server will add an
+ * X-Forwarded-For header to the request that contains the client IP
+ * address. However, HTTP headers are vulnerable to spoofing, where a
+ * malicious client could bypass restrictions by setting the
+ * X-Forwarded-For header directly. Therefore, Drupal's proxy
+ * configuration requires the IP addresses of all remote proxies to be
+ * specified in $conf['reverse_proxy_addresses'] to work correctly.
+ *
+ * Enable this setting to get Drupal to determine the client IP from
+ * the X-Forwarded-For header (or $conf['reverse_proxy_header'] if set).
+ * If you are unsure about this setting, do not have a reverse proxy,
+ * or Drupal operates in a shared hosting environment, this setting
+ * should remain commented out.
+ *
+ * In order for this setting to be used you must specify every possible
+ * reverse proxy IP address in $conf['reverse_proxy_addresses'].
+ * If a complete list of reverse proxies is not available in your
+ * environment (for example, if you use a CDN) you may set the
+ * $_SERVER['REMOTE_ADDR'] variable directly in settings.php.
+ * Be aware, however, that it is likely that this would allow IP
+ * address spoofing unless more advanced precautions are taken.
+ */
+# $conf['reverse_proxy'] = TRUE;
+
+/**
+ * Specify every reverse proxy IP address in your environment.
+ * This setting is required if $conf['reverse_proxy'] is TRUE.
+ */
+# $conf['reverse_proxy_addresses'] = array('a.b.c.d', ...);
+
+/**
+ * Set this value if your proxy server sends the client IP in a header
+ * other than X-Forwarded-For.
+ */
+# $conf['reverse_proxy_header'] = 'HTTP_X_CLUSTER_CLIENT_IP';
+
+/**
+ * Page caching:
+ *
+ * By default, Drupal sends a "Vary: Cookie" HTTP header for anonymous page
+ * views. This tells a HTTP proxy that it may return a page from its local
+ * cache without contacting the web server, if the user sends the same Cookie
+ * header as the user who originally requested the cached page. Without "Vary:
+ * Cookie", authenticated users would also be served the anonymous page from
+ * the cache. If the site has mostly anonymous users except a few known
+ * editors/administrators, the Vary header can be omitted. This allows for
+ * better caching in HTTP proxies (including reverse proxies), i.e. even if
+ * clients send different cookies, they still get content served from the cache.
+ * However, authenticated users should access the site directly (i.e. not use an
+ * HTTP proxy, and bypass the reverse proxy if one is used) in order to avoid
+ * getting cached pages from the proxy.
+ */
+# $conf['omit_vary_cookie'] = TRUE;
+
+/**
+ * CSS/JS aggregated file gzip compression:
+ *
+ * By default, when CSS or JS aggregation and clean URLs are enabled Drupal will
+ * store a gzip compressed (.gz) copy of the aggregated files. If this file is
+ * available then rewrite rules in the default .htaccess file will serve these
+ * files to browsers that accept gzip encoded content. This allows pages to load
+ * faster for these users and has minimal impact on server load. If you are
+ * using a webserver other than Apache httpd, or a caching reverse proxy that is
+ * configured to cache and compress these files itself you may want to uncomment
+ * one or both of the below lines, which will prevent gzip files being stored.
+ */
+# $conf['css_gzip_compression'] = FALSE;
+# $conf['js_gzip_compression'] = FALSE;
+
+/**
+ * String overrides:
+ *
+ * To override specific strings on your site with or without enabling the Locale
+ * module, add an entry to this list. This functionality allows you to change
+ * a small number of your site's default English language interface strings.
+ *
+ * Remove the leading hash signs to enable.
+ */
+# $conf['locale_custom_strings_en'][''] = array(
+#   'forum'      => 'Discussion board',
+#   '@count min' => '@count minutes',
+# );
+
+/**
+ *
+ * IP blocking:
+ *
+ * To bypass database queries for denied IP addresses, use this setting.
+ * Drupal queries the {blocked_ips} table by default on every page request
+ * for both authenticated and anonymous users. This allows the system to
+ * block IP addresses from within the administrative interface and before any
+ * modules are loaded. However on high traffic websites you may want to avoid
+ * this query, allowing you to bypass database access altogether for anonymous
+ * users under certain caching configurations.
+ *
+ * If using this setting, you will need to add back any IP addresses which
+ * you may have blocked via the administrative interface. Each element of this
+ * array represents a blocked IP address. Uncommenting the array and leaving it
+ * empty will have the effect of disabling IP blocking on your site.
+ *
+ * Remove the leading hash signs to enable.
+ */
+# $conf['blocked_ips'] = array(
+#   'a.b.c.d',
+# );
+
+/**
+ * Fast 404 pages:
+ *
+ * Drupal can generate fully themed 404 pages. However, some of these responses
+ * are for images or other resource files that are not displayed to the user.
+ * This can waste bandwidth, and also generate server load.
+ *
+ * The options below return a simple, fast 404 page for URLs matching a
+ * specific pattern:
+ * - 404_fast_paths_exclude: A regular expression to match paths to exclude,
+ *   such as images generated by image styles, or dynamically-resized images.
+ *   If you need to add more paths, you can add '|path' to the expression.
+ * - 404_fast_paths: A regular expression to match paths that should return a
+ *   simple 404 page, rather than the fully themed 404 page. If you don't have
+ *   any aliases ending in htm or html you can add '|s?html?' to the expression.
+ * - 404_fast_html: The html to return for simple 404 pages.
+ *
+ * Add leading hash signs if you would like to disable this functionality.
+ */
+$conf['404_fast_paths_exclude'] = '/\/(?:styles)\//';
+$conf['404_fast_paths'] = '/\.(?:txt|png|gif|jpe?g|css|js|ico|swf|flv|cgi|bat|pl|dll|exe|asp)$/i';
+$conf['404_fast_html'] = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML+RDFa 1.0//EN" "http://www.w3.org/MarkUp/DTD/xhtml-rdfa-1.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>404 Not Found</title></head><body><h1>Not Found</h1><p>The requested URL "@path" was not found on this server.</p></body></html>';
+
+/**
+ * By default the page request process will return a fast 404 page for missing
+ * files if they match the regular expression set in '404_fast_paths' and not
+ * '404_fast_paths_exclude' above. 404 errors will simultaneously be logged in
+ * the Drupal system log.
+ *
+ * You can choose to return a fast 404 page earlier for missing pages (as soon
+ * as settings.php is loaded) by uncommenting the line below. This speeds up
+ * server response time when loading 404 error pages and prevents the 404 error
+ * from being logged in the Drupal system log. In order to prevent valid pages
+ * such as image styles and other generated content that may match the
+ * '404_fast_html' regular expression from returning 404 errors, it is necessary
+ * to add them to the '404_fast_paths_exclude' regular expression above. Make
+ * sure that you understand the effects of this feature before uncommenting the
+ * line below.
+ */
+# drupal_fast_404();
+
+/**
+ * External access proxy settings:
+ *
+ * If your site must access the Internet via a web proxy then you can enter
+ * the proxy settings here. Currently only basic authentication is supported
+ * by using the username and password variables. The proxy_user_agent variable
+ * can be set to NULL for proxies that require no User-Agent header or to a
+ * non-empty string for proxies that limit requests to a specific agent. The
+ * proxy_exceptions variable is an array of host names to be accessed directly,
+ * not via proxy.
+ */
+# $conf['proxy_server'] = '';
+# $conf['proxy_port'] = 8080;
+# $conf['proxy_username'] = '';
+# $conf['proxy_password'] = '';
+# $conf['proxy_user_agent'] = '';
+# $conf['proxy_exceptions'] = array('127.0.0.1', 'localhost');
+
+/**
+ * Authorized file system operations:
+ *
+ * The Update manager module included with Drupal provides a mechanism for
+ * site administrators to securely install missing updates for the site
+ * directly through the web user interface. On securely-configured servers,
+ * the Update manager will require the administrator to provide SSH or FTP
+ * credentials before allowing the installation to proceed; this allows the
+ * site to update the new files as the user who owns all the Drupal files,
+ * instead of as the user the webserver is running as. On servers where the
+ * webserver user is itself the owner of the Drupal files, the administrator
+ * will not be prompted for SSH or FTP credentials (note that these server
+ * setups are common on shared hosting, but are inherently insecure).
+ *
+ * Some sites might wish to disable the above functionality, and only update
+ * the code directly via SSH or FTP themselves. This setting completely
+ * disables all functionality related to these authorized file operations.
+ *
+ * @see http://drupal.org/node/244924
+ *
+ * Remove the leading hash signs to disable.
+ */
+# $conf['allow_authorize_operations'] = FALSE;