Added docker container for 1.3.4

1.3.4/Dockerfile

@@ -0,0 +1,70 @@
+# Use an official Python runtime as a parent image
+FROM python:2.7-stretch
+
+# Set one or more individual labels
+LABEL maintainer="Ramon Bartl"
+LABEL email="rb@ridingbytes.com"
+LABEL senaite.core.version="1.3.4"
+
+# Set environment variables
+ENV PLONE_MAJOR=4.3 \
+    PLONE_VERSION=4.3.19 \
+    PLONE_MD5=04ed5beac7fb8504f06a36d44e407b06 \
+    SENAITE_HOME=/home/senaite \
+    SENAITE_USER=senaite \
+    SENAITE_INSTANCE_HOME=/home/senaite/senaitelims \
+    SENAITE_DATA=/data \
+    SENAITE_FILESTORAGE=/data/filestorage \
+    SENAITE_BLOBSTORAGE=/data/blobstorage
+
+# Create the senaite user
+RUN useradd --system -m -d $SENAITE_HOME -U -u 500 $SENAITE_USER
+
+# Create direcotries
+RUN mkdir -p $SENAITE_INSTANCE_HOME $SENAITE_FILESTORAGE $SENAITE_BLOBSTORAGE
+
+# Copy the package config
+COPY packages.txt /
+
+# Install package dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends $(grep -vE "^\s*#" /packages.txt  | tr "\n" " ")
+
+# Fetch unified installer
+RUN wget -O Plone.tgz https://launchpad.net/plone/$PLONE_MAJOR/$PLONE_VERSION/+download/Plone-$PLONE_VERSION-UnifiedInstaller.tgz \
+    && echo "$PLONE_MD5 Plone.tgz" | md5sum -c - \
+    && tar -xzf Plone.tgz \
+    && cp -rv /Plone-$PLONE_VERSION-UnifiedInstaller/base_skeleton/* $SENAITE_INSTANCE_HOME \
+    && cp -v /Plone-$PLONE_VERSION-UnifiedInstaller/buildout_templates/buildout.cfg $SENAITE_INSTANCE_HOME/buildout-base.cfg \
+    && cd $SENAITE_HOME \
+    && tar -xjf /Plone-$PLONE_VERSION-UnifiedInstaller/packages/buildout-cache.tar.bz2 \
+    && rm -rf /Plone-$PLONE_VERSION-UnifiedInstaller /Plone.tgz
+
+# Change working directory
+WORKDIR $SENAITE_INSTANCE_HOME
+
+# Copy Buildout
+COPY bootstrap.py buildout.cfg ./
+
+# Bootstrap and buildout
+RUN python bootstrap.py \
+    && bin/buildout \
+    && ln -s $SENAITE_FILESTORAGE/ var/filestorage \
+    && ln -s $SENAITE_BLOBSTORAGE/ var/blobstorage \
+    && chown -R senaite:senaite $SENAITE_HOME $SENAITE_DATA \
+    && rm -rf $SENAITE_HOME/buildout-cache/downloads/dist
+
+# Mount external volume
+VOLUME /data
+
+# Copy startup scripts
+COPY docker-initialize.py docker-entrypoint.sh /
+
+# Expose instance port
+EXPOSE 8080
+
+# Add instance healthcheck
+HEALTHCHECK --interval=1m --timeout=5s --start-period=1m \
+  CMD nc -z -w5 127.0.0.1 8080 || exit 1
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
+CMD ["start"]

1.3.4/bootstrap.py

@@ -0,0 +1,210 @@
+##############################################################################
+#
+# Copyright (c) 2006 Zope Foundation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+"""
+
+import os
+import shutil
+import sys
+import tempfile
+
+from optparse import OptionParser
+
+__version__ = '2015-07-01'
+# See zc.buildout's changelog if this version is up to date.
+
+tmpeggs = tempfile.mkdtemp(prefix='bootstrap-')
+
+usage = '''\
+[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
+
+Bootstraps a buildout-based project.
+
+Simply run this script in a directory containing a buildout.cfg, using the
+Python that you want bin/buildout to use.
+
+Note that by using --find-links to point to local resources, you can keep
+this script from going over the network.
+'''
+
+parser = OptionParser(usage=usage)
+parser.add_option("--version",
+                  action="store_true", default=False,
+                  help=("Return bootstrap.py version."))
+parser.add_option("-t", "--accept-buildout-test-releases",
+                  dest='accept_buildout_test_releases',
+                  action="store_true", default=False,
+                  help=("Normally, if you do not specify a --version, the "
+                        "bootstrap script and buildout gets the newest "
+                        "*final* versions of zc.buildout and its recipes and "
+                        "extensions for you.  If you use this flag, "
+                        "bootstrap and buildout will get the newest releases "
+                        "even if they are alphas or betas."))
+parser.add_option("-c", "--config-file",
+                  help=("Specify the path to the buildout configuration "
+                        "file to be used."))
+parser.add_option("-f", "--find-links",
+                  help=("Specify a URL to search for buildout releases"))
+parser.add_option("--allow-site-packages",
+                  action="store_true", default=False,
+                  help=("Let bootstrap.py use existing site packages"))
+parser.add_option("--buildout-version",
+                  help="Use a specific zc.buildout version")
+parser.add_option("--setuptools-version",
+                  help="Use a specific setuptools version")
+parser.add_option("--setuptools-to-dir",
+                  help=("Allow for re-use of existing directory of "
+                        "setuptools versions"))
+
+options, args = parser.parse_args()
+if options.version:
+    print("bootstrap.py version %s" % __version__)
+    sys.exit(0)
+
+
+######################################################################
+# load/install setuptools
+
+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+ez = {}
+if os.path.exists('ez_setup.py'):
+    exec(open('ez_setup.py').read(), ez)
+else:
+    exec(urlopen('https://bootstrap.pypa.io/ez_setup.py').read(), ez)
+
+if not options.allow_site_packages:
+    # ez_setup imports site, which adds site packages
+    # this will remove them from the path to ensure that incompatible versions
+    # of setuptools are not in the path
+    import site
+    # inside a virtualenv, there is no 'getsitepackages'.
+    # We can't remove these reliably
+    if hasattr(site, 'getsitepackages'):
+        for sitepackage_path in site.getsitepackages():
+            # Strip all site-packages directories from sys.path that
+            # are not sys.prefix; this is because on Windows
+            # sys.prefix is a site-package directory.
+            if sitepackage_path != sys.prefix:
+                sys.path[:] = [x for x in sys.path
+                               if sitepackage_path not in x]
+
+setup_args = dict(to_dir=tmpeggs, download_delay=0)
+
+if options.setuptools_version is not None:
+    setup_args['version'] = options.setuptools_version
+if options.setuptools_to_dir is not None:
+    setup_args['to_dir'] = options.setuptools_to_dir
+
+ez['use_setuptools'](**setup_args)
+import setuptools
+import pkg_resources
+
+# This does not (always?) update the default working set.  We will
+# do it.
+for path in sys.path:
+    if path not in pkg_resources.working_set.entries:
+        pkg_resources.working_set.add_entry(path)
+
+######################################################################
+# Install buildout
+
+ws = pkg_resources.working_set
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+# Fix sys.path here as easy_install.pth added before PYTHONPATH
+cmd = [sys.executable, '-c',
+       'import sys; sys.path[0:0] = [%r]; ' % setuptools_path +
+       'from setuptools.command.easy_install import main; main()',
+       '-mZqNxd', tmpeggs]
+
+find_links = os.environ.get(
+    'bootstrap-testing-find-links',
+    options.find_links or
+    ('http://downloads.buildout.org/'
+     if options.accept_buildout_test_releases else None)
+    )
+if find_links:
+    cmd.extend(['-f', find_links])
+
+requirement = 'zc.buildout'
+version = options.buildout_version
+if version is None and not options.accept_buildout_test_releases:
+    # Figure out the most recent final version of zc.buildout.
+    import setuptools.package_index
+    _final_parts = '*final-', '*final'
+
+    def _final_version(parsed_version):
+        try:
+            return not parsed_version.is_prerelease
+        except AttributeError:
+            # Older setuptools
+            for part in parsed_version:
+                if (part[:1] == '*') and (part not in _final_parts):
+                    return False
+            return True
+
+    index = setuptools.package_index.PackageIndex(
+        search_path=[setuptools_path])
+    if find_links:
+        index.add_find_links((find_links,))
+    req = pkg_resources.Requirement.parse(requirement)
+    if index.obtain(req) is not None:
+        best = []
+        bestv = None
+        for dist in index[req.project_name]:
+            distv = dist.parsed_version
+            if _final_version(distv):
+                if bestv is None or distv > bestv:
+                    best = [dist]
+                    bestv = distv
+                elif distv == bestv:
+                    best.append(dist)
+        if best:
+            best.sort()
+            version = best[-1].version
+if version:
+    requirement = '=='.join((requirement, version))
+cmd.append(requirement)
+
+import subprocess
+if subprocess.call(cmd) != 0:
+    raise Exception(
+        "Failed to execute command:\n%s" % repr(cmd)[1:-1])
+
+######################################################################
+# Import and run buildout
+
+ws.add_entry(tmpeggs)
+ws.require(requirement)
+import zc.buildout.buildout
+
+if not [a for a in args if '=' not in a]:
+    args.append('bootstrap')
+
+# if -c was provided, we push it back into args for buildout' main function
+if options.config_file is not None:
+    args[0:0] = ['-c', options.config_file]
+
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)

1.3.4/buildout.cfg

@@ -0,0 +1,111 @@
+[buildout]
+extends =
+  buildout-base.cfg
+
+extensions =
+
+index = https://pypi.python.org/simple/
+
+var-dir=/data
+user=admin:admin
+
+effective-user = senaite
+buildout-user = senaite
+
+eggs-directory=../buildout-cache/eggs
+download-cache=../buildout-cache/downloads
+
+parts +=
+  zeo
+
+eggs +=
+    senaite.lims
+
+[client1]
+recipe =
+
+[zeo]
+<= zeoserver_base
+recipe = plone.recipe.zeoserver
+zeo-address = 8080
+
+[versions]
+setuptools=
+zc.buildout=
+senaite.lims=1.3.4
+soupsieve = 1.9.4
+
+# The following part definition lists the versions picked:
+Chameleon = 3.6.2
+Products.ATExtensions = 1.1
+Pyphen = 0.9.5
+Werkzeug = 1.0.0
+backports.functools-lru-cache = 1.6.1
+cairocffi = 0.9.0
+cffi = 1.14.0
+cssselect2 = 0.2.2
+html5lib = 1.0.1
+more-itertools = 5.0.0
+pdfrw = 0.4
+plone.recipe.command = 1.1
+plone.recipe.precompiler = 0.6
+senaite.core.supermodel = 1.2.3
+sourcecodegen = 0.6.14
+tinycss2 = 0.6.1
+webencodings = 0.5.1
+z3c.pt = 3.2.0
+
+# Required by:
+# senaite.core==1.3.3
+Products.DataGridField = 1.9.6
+
+# Required by:
+# senaite.core==1.3.3
+Products.TextIndexNG3 = 3.4.14
+
+# Required by:
+# senaite.impress==1.2.3
+beautifulsoup4 = 4.8.2
+
+# Required by:
+# senaite.core==1.3.3
+collective.indexing = 2.1
+
+# Required by:
+# senaite.core==1.3.3
+collective.progressbar = 0.5
+
+# Required by:
+# plone.jsonapi.core==0.6
+dicttoxml = 1.7.4
+
+# Required by:
+# senaite.core==1.3.3
+jarn.jsi18n = 1.1
+
+# Required by:
+# senaite.core==1.3.3
+magnitude = 0.9.4
+
+# Required by:
+# senaite.core==1.3.3
+plone.jsonapi.core = 0.6
+
+# Required by:
+# cffi==1.14.0
+pycparser = 2.19
+
+# Required by:
+# senaite.core==1.3.3
+z3c.jbot = 0.8
+
+# Required by:
+# plone.recipe.unifiedinstaller==4.3.2
+# plone.recipe.zeoserver==1.3.1
+# plone.recipe.zope2instance==4.4.1
+# z3c.autoinclude==0.3.9
+zc.buildout = 2.13.3
+
+# Required by:
+# Products.TextIndexNG3==3.4.14
+zopyx.txng3.core = 3.6.2

1.3.4/docker-compose.yml

@@ -0,0 +1,11 @@
+version: "2"
+services:
+  senaite:
+    image: senaite
+    volumes:
+    - data:/data
+    ports:
+    - "8080:8080"
+
+volumes:
+  data:

1.3.4/docker-entrypoint.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+set -e
+
+COMMANDS="debug help logtail show stop adduser fg kill quit run wait console foreground logreopen reload shell status"
+START="start restart zeoserver"
+CMD="bin/instance"
+
+gosu senaite python /docker-initialize.py
+
+if [ -e "custom.cfg" ]; then
+  if [ ! -e "bin/develop" ]; then
+    gosu senaite /home/senaite/senaitelims/bin/buildout -c custom.cfg
+    gosu senaite python /docker-initialize.py
+  fi
+fi
+
+if [[ "$1" == "zeo"* ]]; then
+  CMD="bin/$1"
+fi
+
+if [ -z "$HEALTH_CHECK_TIMEOUT" ]; then
+  HEALTH_CHECK_TIMEOUT=1
+fi
+
+if [ -z "$HEALTH_CHECK_INTERVAL" ]; then
+  HEALTH_CHECK_INTERVAL=1
+fi
+
+if [[ $START == *"$1"* ]]; then
+  _stop() {
+    gosu senaite $CMD stop
+    kill -TERM $child 2>/dev/null
+  }
+
+  trap _stop SIGTERM SIGINT
+  gosu senaite $CMD start
+  gosu senaite $CMD logtail &
+  child=$!
+
+  pid=`$CMD status | sed 's/[^0-9]*//g'`
+  if [ ! -z "$pid" ]; then
+    echo "Application running on pid=$pid"
+    sleep "$HEALTH_CHECK_TIMEOUT"
+    while kill -0 "$pid" 2> /dev/null; do
+      sleep "$HEALTH_CHECK_INTERVAL"
+    done
+  else
+    echo "Application didn't start normally. Shutting down!"
+    _stop
+  fi
+else
+  if [[ $COMMANDS == *"$1"* ]]; then
+    exec gosu senaite bin/instance "$@"
+  fi
+  exec "$@"
+fi

1.3.4/docker-initialize.py

@@ -0,0 +1,184 @@
+#!/usr/local/bin/python
+
+import re
+import os
+import warnings
+warnings.simplefilter('always', DeprecationWarning)
+
+
+class Environment(object):
+    """ Configure container via environment variables
+    """
+    def __init__(
+            self,
+            env=os.environ,
+            zope_conf="/home/senaite/senaitelims/parts/instance/etc/zope.conf",
+            custom_conf="/home/senaite/senaitelims/custom.cfg",
+            zeopack_conf="/home/senaite/senaitelims/bin/zeopack",
+            zeoserver_conf="/home/senaite/senaitelims/parts/zeoserver/etc/zeo.conf"):
+        self.env = env
+        self.zope_conf = zope_conf
+        self.custom_conf = custom_conf
+        self.zeopack_conf = zeopack_conf
+        self.zeoserver_conf = zeoserver_conf
+
+    def zeoclient(self):
+        """ ZEO Client
+        """
+        server = self.env.get("ZEO_ADDRESS", None)
+        if not server:
+            return
+
+        config = ""
+        with open(self.zope_conf, "r") as cfile:
+            config = cfile.read()
+
+        # Already initialized
+        if "<blobstorage>" not in config:
+            return
+
+        read_only = self.env.get("ZEO_READ_ONLY", "false")
+        zeo_ro_fallback = self.env.get("ZEO_CLIENT_READ_ONLY_FALLBACK", "false")
+        shared_blob_dir = self.env.get("ZEO_SHARED_BLOB_DIR", "off")
+        zeo_storage = self.env.get("ZEO_STORAGE", "1")
+        zeo_client_cache_size = self.env.get("ZEO_CLIENT_CACHE_SIZE", "128MB")
+        zeo_conf = ZEO_TEMPLATE.format(
+            zeo_address=server,
+            read_only=read_only,
+            zeo_client_read_only_fallback=zeo_ro_fallback,
+            shared_blob_dir=shared_blob_dir,
+            zeo_storage=zeo_storage,
+            zeo_client_cache_size=zeo_client_cache_size
+        )
+
+        pattern = re.compile(r"<blobstorage>.+</blobstorage>", re.DOTALL)
+        config = re.sub(pattern, zeo_conf, config)
+
+        with open(self.zope_conf, "w") as cfile:
+            cfile.write(config)
+
+    def zeopack(self):
+        """ ZEO Pack
+        """
+        server = self.env.get("ZEO_ADDRESS", None)
+        if not server:
+            return
+
+        if ":" in server:
+            host, port = server.split(":")
+        else:
+            host, port = (server, "8100")
+
+        with open(self.zeopack_conf, 'r') as cfile:
+            text = cfile.read()
+            text = text.replace('address = "8100"', 'address = "%s"' % server)
+            text = text.replace('host = "127.0.0.1"', 'host = "%s"' % host)
+            text = text.replace('port = "8100"', 'port = "%s"' % port)
+
+        with open(self.zeopack_conf, 'w') as cfile:
+            cfile.write(text)
+
+    def zeoserver(self):
+        """ ZEO Server
+        """
+        pack_keep_old = self.env.get("ZEO_PACK_KEEP_OLD", '')
+        if pack_keep_old.lower() in ("false", "no", "0", "n", "f"):
+            with open(self.zeoserver_conf, 'r') as cfile:
+                text = cfile.read()
+                if 'pack-keep-old' not in text:
+                    text = text.replace(
+                        '</filestorage>',
+                        '  pack-keep-old false\n</filestorage>'
+                    )
+
+            with open(self.zeoserver_conf, 'w') as cfile:
+                cfile.write(text)
+
+    def buildout(self):
+        """ Buildout from environment variables
+        """
+        # Already configured
+        if os.path.exists(self.custom_conf):
+            return
+
+        eggs = self.env.get("PLONE_ADDONS",
+                            self.env.get("ADDONS", "")).strip().split()
+        if not eggs:
+            eggs = self.env.get("BUILDOUT_EGGS", "").strip().split()
+            if eggs:
+                warnings.warn(
+                    "BUILDOUT_EGGS is deprecated. Please use "
+                    "PLONE_ADDONS instead !!!", DeprecationWarning)
+
+        zcml = self.env.get("PLONE_ZCML",
+                            self.env.get("ZCML", "")).strip().split()
+        if not zcml:
+            zcml = self.env.get("BUILDOUT_ZCML", "").strip().split()
+            if zcml:
+                warnings.warn(
+                    "BUILDOUT_ZCML is deprecated. Please use "
+                    "PLONE_ZCML instead !!!", DeprecationWarning)
+
+        develop = self.env.get("PLONE_DEVELOP",
+                               self.env.get("DEVELOP", "")).strip().split()
+        if not develop:
+            develop = self.env.get("BUILDOUT_DEVELOP", "").strip().split()
+            if develop:
+                warnings.warn(
+                    "BUILDOUT_DEVELOP is deprecated. Please use "
+                    "PLONE_DEVELOP instead !!!", DeprecationWarning)
+
+        if not (eggs or zcml or develop):
+            return
+
+        buildout = BUILDOUT_TEMPLATE.format(
+            eggs="\n\t".join(eggs),
+            zcml="\n\t".join(zcml),
+            develop="\n\t".join(develop)
+        )
+
+        with open(self.custom_conf, 'w') as cfile:
+            cfile.write(buildout)
+
+    def setup(self, **kwargs):
+        self.buildout()
+        self.zeoclient()
+        self.zeopack()
+        self.zeoserver()
+
+    __call__ = setup
+
+
+ZEO_TEMPLATE = """
+    <zeoclient>
+      read-only {read_only}
+      read-only-fallback {zeo_client_read_only_fallback}
+      blob-dir /data/blobstorage
+      shared-blob-dir {shared_blob_dir}
+      server {zeo_address}
+      storage {zeo_storage}
+      name zeostorage
+      var /home/senaite/senaitelims/parts/instance/var
+      cache-size {zeo_client_cache_size}
+    </zeoclient>
+""".strip()
+
+
+BUILDOUT_TEMPLATE = """
+[buildout]
+extends = develop.cfg
+develop += {develop}
+eggs += {eggs}
+zcml += {zcml}
+"""
+
+
+def initialize():
+    """ Configure Plone instance as ZEO Client
+    """
+    environment = Environment()
+    environment.setup()
+
+
+if __name__ == "__main__":
+    initialize()

1.3.4/packages.txt

@@ -0,0 +1,28 @@
+dpkg-dev
+gcc
+gosu
+libbz2-dev
+libc6-dev
+libcairo2
+libffi-dev
+libgdk-pixbuf2.0-0
+libjpeg62
+libjpeg62-turbo-dev
+libopenjp2-7
+libopenjp2-7-dev
+libpango-1.0-0
+libpangocairo-1.0-0
+libpcre3-dev
+libssl-dev
+libtiff5
+libtiff5-dev
+libxml2
+libxml2-dev
+libxslt1-dev
+libxslt1.1
+lynx
+netcat
+rsync
+wget
+wv
+zlib1g-dev