Bika LIMS Installation

Currently Maintained for historic purposes only

Please use the latest Bika Senaite code

Bika Open Source LIMS code is being re-engineered as Senaite for better maintainability and performance, under a more equitable brand and structure. The Bika Collective contributes generically acceptable code to the Senaite repos, and publishes lab discipline specific releases here as Bika Senaite add-ons.

Thanks, Lemoene

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Introduction

Before beginning this process you should read the following documentation:

Plone Installation Documentation.

If you have any issues you should read the following pages carefully:

Linux Installation Steps

The most commonly used OS for running Plone and Bika LIMS is Linux, although this process should be fairly similar for all systems on which Plone is supported.

Install the following system packages

If you are running Ubuntu 12.04 or later, or Debian Wheezy (or later), you can paste the following directly into a terminal:

sudo apt-get install build-essential gcc python-dev git-core libffi-dev
sudo apt-get install libpcre3 libpcre3-dev autoconf libtool pkg-config
sudo apt-get install zlib1g-dev libssl-dev libexpat1-dev libxslt1.1
sudo apt-get install gnuplot libcairo2 libpango1.0-0 libgdk-pixbuf2.0-0

The following package list valid for Fedora 22:

sudo dnf install make automake-1.15-1.fc22.noarch gcc gcc-c++-5.3.1-2.fc22.x86_64
sudo dnf install kernel-devel-4.3.4-200.fc22.x86_64 gdk-pixbuf2-devel-2.31.6-1.fc22.x86_64
sudo dnf install python-devel-2.7.10-8.fc22.x86_64 git-2.4.3-7.fc22.x86_64
sudo dnf install libffi-devel-3.1-7.fc22.x86_64 pcre-devel-8.38-1.fc22.x86_64
sudo dnf install autoconf-2.69-20.fc22.noarch libtool-2.4.2-35.fc22.x86_64
sudo dnf install pkgconfig-1\:0.28-8.fc22.x86_64 zlib-devel-1.2.8-7.fc22.x86_64
sudo dnf install openssl-devel-1\:1.0.1k-13.fc22.x86_64 expat-devel-2.1.0-10.fc22.x86_64
sudo dnf install libxslt-devel-1.1.28-8.fc22.x86_64 gnuplot-5.0.0-8.fc22.x86_64
sudo dnf install cairo-devel-1.14.2-1.fc22.x86_64 pango-devel-1.36.8-6.fc22.x86_64

Similar packages are available and can be installed via "yum" on CentOS and older distributions of Fedora. If you use a different distribution, you may need to find the versions of these packages which are provided with your system.

Download and Install Plone

Download the latest stable release (4.3.x series) of the Plone Unified Installer from http://plone.org/products/plone/releases and unpack the file. The following installation command will be sufficient for most purposes:

./install.sh --target=/usr/local/Plone --build-python zeo

If you receive an lxml error, you may need to include the --static-lxml flag in the above command.

If you are installing for a production system, you should run the above command as root. This will create additional users plone_buildout and plone_daemon, to add an extra layer of security to the installation. If you do this, you will need to run buildout related commands as the plone_buildout user, and you will need to run Plone as the plone_daemon user. For demo and testing instances, you can run the installation as a normal user.

Add Bika LIMS to your buildout.cfg

In your new Plone folder, you will see a folder named zeocluster. Change directory into this folder, and edit buildout.cfg. Find the section beginning with eggs=, and add bika.lims to the existing entries.

eggs =
    Plone
    Pillow
    bika.lims

In buildout.cfg, each line should have the same indentation as the one preceding it. Mixing tabs and spaces may also cause errors.

Save the file, and then run bin/buildout. Buildout will download and install all remaining dependencies.

If you created a root installation, you will need to run buildout like this:

sudo -u plone_buildout bin/buildout

Verify successful build from the output of the installer script, which should include a list of found versions like this:

*************** PICKED VERSIONS ****************
[versions]
Babel = 1.3
...
plone.jsonapi.core = 0.4
*************** /PICKED VERSIONS ***************

The "PICKED VERSIONS" block above indicates a successful buildout. If warnings appear while buildout is installing dependencies, you can safely ignore them if this message is displayed.

If the downloads are interrupted, simply run bin/buildout again. The process will be resumed.

If the buildout finished successfully, an 'adminPassword.txt' will be created automatically inside the Plone instance folder. It contains the super-user credentials you'll need to login with.

Test run

First, you will need to start the zeoserver (this is the database process).

bin/zeoserver start

To start a Plone client debug mode, run this command:

bin/client1 fg

If you installed Plone using a root installation, you will need to use the following commands instead:

sudo -u plone_daemon bin/zeoserver start
sudo -u plone_daemon bin/client1 fg

Note any error messages, and take corrective action if required. If no errors are encountered, you can press Control+C to exit.

Add a new Plone site

Open a browser and go to http://localhost:8080/. Select "Add Plone Site", ensure that the Bika LIMS option is checked, then submit the form.

Start working with Bika LIMS

Open a browser and go to your Bika LIMS instance: http://localhost:8080/Plone

Upgrading Bika LIMS

If a new release of the LIMS is made available, the following procedure will upgrade your existing installation to use the new packages.

Please read Releases life-cycle documentation before upgrading your Bika LIMS instance.

Backup

Make a full backup of your instance before continuing:

bin/snapshotbackup

Buildout

Run buildout with the "-n" option, to retreive the latest version of Bika LIMS and it's dependencies.

bin/buildout -n

Restart Plone

bin/plonectl restart

Migrate

Start Plone and login to your site as admin. Go to site-setup, and click Add-ons. Find Bika LIMS in the list of activated addons, and click the "bika.lims" upgrade button.

Windows Installation Steps

Please reconsider, and use Linux

Plone recently stopped building the Unified Installer for Windows in favour of a VirtualBox/Vagrant setup. Unless someone is really interested in integrating Bika into the Windows ways of doing things (i.e. server roles, IIS config, whatever), Bika LIMS can be installed in a single well-maintained Virtual Machine.

Getting help on users/developer lists for Windows-specific questions could be harder because most of the developers behind the scenes use GNU/Linux instead of Windows.

Bika Windows users are participating bika-win@googlegroups.com. Post to bika-win@googlegroups.com. Please also Google using the error messages you get, many have been dealt with before.

Please do not post to any of our team directly, or the Bika User list, with Windows questions.

Save yourself a lot of pain by using industry standard, robust and secure Linux.

1. Download and Install Plone

Download the latest version of the Plone 4.3 Unified Installer from http://plone.org/products/plone/releases. Execute the installer and follow through the steps.

For this guide we will assume the default location of C:\Plone43

2. Add Bika LIMS to your buildout.cfg

Open C:\Plone43\buildout.cfg in a text editor

Add bika.lims to the eggs section

eggs =
    Plone
    Pillow
    Products.PloneHotfix20130618
    bika.lims

3. Run buildout

Save and close the file, start cmd as Administrator (Click start, type "cmd", and press CTRL+SHIFT+ENTER), and then run bin/buildout. Buildout will download and install all remaining dependencies.

cd C:\Plone43
bin\buildout

Verify successful build from the output of the installer script, which should include a list of found versions like this:

*************** PICKED VERSIONS ****************
[versions]
bika.lims = 3.0
...
pyphen = 0.9.1
*************** /PICKED VERSIONS ***************

The "PICKED VERSIONS" block above indicates a successful buildout. If errors appear while buildout is installing dependencies, you can safely ignore them if this message is displayed.

If the download is interrupted, simply run bin/buildout again. The process will be resumed.

If you see the following error: Error: Couldn't install: cffi 0.8.2 Refer to: Troubleshooting: A) Dependencies

If you see the following error: Error 5: Access is denied Refer to: Troubleshooting: B) Privileges

4. Setting up Plone Services

Navigate to the Plone root directory

cd C:\Plone43

Plone and Windows do not always play well together. Install, Start and bring your newly created instance to the Foreground (this should stop the default Plone 4.3 Service)

bin\instance.exe install
bin\instance.exe start
bin\instance.exe fg

If you see the following error: OSError: cannot load library libcairo.so.2 Refer to: Troubleshooting: A) Dependencies

When you see INFO Zope Ready to handle requests the server is ready.

Open a browser and go to http://localhost:8080/. Select "Add Plone Site", ensure that the Bika LIMS option is checked, then submit the form.

Congratulations!! you have a successful build of Bika LIMS on Windows.

5. Notes

If you are having trouble starting bin\instance.exe fg as follows:

The program seems already to be running. If you believe not,
check for dangling .pid and .lock files in var/.

You can try the following steps:

-Find the running process id by opening the .pid file within your instance's var/ directory.
-Open the Windows Task Manager and stop the running process with the above identifier.
-Delete all .pid and .lock files in your instance's var/ directory.
-Start your instance.

__OR__

-Run services.msc
-Search for Plone 4.3
-Try Starting or Stopping it along with your instance

6. Troubleshooting

A) Dependencies You need to install some dependencies manually Download and install bika_dependencies(Plone 4.3.1).exe from https://github.com/zylinx/bika.dependencies This fixes the fact that Plone's buildout cannot compile the libraries required by weasyprint. It installs the pre-compiled binaries into System32 and Plone's installation folder instead.

B) Privileges Open Explorer >> Navigate to C:\ >> Right-Click on the Plone43 directory >> select Properties Select the Security Tab >> Click Edit >> Check Full Control Allow for necessary User / Group Click Apply

OS X Yosemite Installation Steps

We need homebrew for install some dependencies, open a terminal and install brew with this command:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

After the installation of brew we need to install some packages, so:

brew install Caskroom/cask/xquartz
brew install cairo pango gdk-pixbuf libxml2 libffi

Download and install Plone 4.3.3 OSX installer from official Plone repository (https://launchpad.net/plone/4.3/4.3.3/+download/Plone-4.3.3-64.dmg) because the 4.3.4 doesn’t have the OsX package, compiling from source give lot of error during compilation and i want to keep the system as clean as possible. Install Plone with zeocluster option, then open a terminal and

cd /Applications/Plone/zeocluster
nano buildout.cfg

replace

extends =
    base.cfg
    versions.cfg
#    http://dist.plone.org/release/4.3.3-xxxxxxx/versions.cfg


# If you change your Plone version, you'll also need to update
# the repository link below.
find-links +=
    http://dist.plone.org/release/4.3.3-xxxxx

with

extends =
    base.cfg
#    versions.cfg
    http://dist.plone.org/release/4.3.4/versions.cfg


# If you change your Plone version, you'll also need to update
# the repository link below.
find-links +=
    http://dist.plone.org/release/4.3.4

then

./bin/buildout

This will upgrade your Plone to the last stable version, it take some time depending on your connection and system.

Edit again buildout.cfg

nano buildout.cfg

and replace

eggs =
    Plone
    Pillow

with

eggs =
    Plone
    Pillow
    bika.health (or bika.lims it depend on your choice)

then

./bin/buildout

If no errors are shown simply start the zeocluster server and clients

./bin/plonectl start

Point your browser to http://localhost:8080 and install your Bika site.

Enable error reporting

If you have problems that are hard to diagnose or reproduce, or if you just want to help us find and fix errors faster, please consider adding the following lines to your buildout's eggs= section. It's the easiest way to contribute!

eggs =
    ...
    raven

Then, in all [client] or [instance] sections, insert this:

event-log-custom =
    %import raven.contrib.zope
    <logfile>
      path ${buildout:directory}/var/client1/event.log
      level INFO
      max-size 5 MB
      old-files 5
    </logfile>
    <sentry>
      dsn http://ffa1dbda4858459a99a80065947bc666:8989999123e54cf0acdd8dca79899872@sentry.bikalabs.com/2
      level ERROR
    </sentry>

Finally, add raven 4.0.4 into [versions] section

[versions]
    ...
    raven = 4.0.4

Run bin/buildout, and restart Plone.

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