bika.lims 3.1.5

Bika LIMS

Bika LIMS

The meaning of Gaob

In the tradition of Chief Inkosi Bika LIMS 2 using a title for a release, this edition is code-named Gaob Bika LIMS 3. Gaob, King, is taken from Khoi San Nama, language of the world’s first people.

Installation

• Installing Bika LIMS

Documentation

• User Manual

• GitHub Wiki

Feedback and support

• Bika Users List: bika-users

• Bika Developers List: bika-developers

• LIMS design List: lims-design

• Issue Tracker: http://jira.bikalabs.com/

• IRC: irc://freenode.net/#bika

Installing Bika LIMS

The process should be similar for all systems on which Plone is supported.

Linux Installation Steps

1. Plone and Bika LIMS have some system dependencies

   The following list of packages need to be installed. The package list is valid for Ubuntu 14.04. If you use a different distribution, you may need to find the versions of these packages which are provided with your system.

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

2. Install Plone

   Download the latest stable version of the Plone Unified Installer. You should also read the Plone Installation Documentation.

   A basic command for installing a development environment in Linux:

   ./install.sh --target=/path/to/Plone --build-python --static-lxml zeo

3. Add Bika LIMS to your buildout.cfg

   Change directory to Plone/zeocluster, and edit buildout.cfg.

   Find the section beginning with eggs =, and add bika.lims to the existing entries:

   eggs =
       Plone
       Pillow
       bika.lims

   Indentation in buildout.cfg is important, and should be kept uniform for all lines.

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

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

   Spurious errors may occur while running buildout, and may be safely ignored. Verify successful build from the output of the buildout script, which should include a list of found versions like this:

   *************** PICKED VERSIONS ****************
   [versions]
   Babel = 1.3
   CairoSVG = 1.0.7
   Products.ATExtensions = 1.1
   Products.AdvancedQuery = 3.0.3
   PyYAML = 3.11
   Pygments = 1.6
   Pyphen = 0.9.1
   Werkzeug = 0.9.4
   argh = 0.24.1
   bpython = 0.13
   cairocffi = 0.5.3
   cffi = 0.8.2
   collective.progressbar = 0.5
   collective.wtf = 1.0b9
   cssselect = 0.9.1
   gpw = 0.2
   i18ndude = 3.3.3
   magnitude = 0.9.3
   pathtools = 0.1.2
   plone.api = 1.1.0
   plone.jsonapi.core = 0.4
   *************** /PICKED VERSIONS ***************

   If the buildout finished successfully, an ‘adminPassword.txt’ will have been created automatically inside the Plone instance folder. It contains the super-user credentials you’ll need to create the Bika site.

4. Test your setup

   First, start the ZEO Server:

   bin/plonectl zeoserver start

   Then you must start one ZEO Client in the foreground, noting error messages if any and taking corrective action if so:

   bin/plonectl client1 fg

   If you see INFO Zope Ready to handle requests then the server is running. Press Control+C to stop the foreground client.

   To start the Plone server normally, use the following command:

   bin/plonectl start

5. Add a new Plone/Bika instance.

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

Windows Installation Steps

1. Download and Install Plone

   Currently Bika LIMS for Windows requires a Plone 4.3.1 installation.

   • Download the Windows Installer

   • Execute the installer and follow through the steps

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

   For more information visit: http://docs.plone.org/manage/installing/index.html

2. Installing Bika LIMS

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

   2. Find the section beginning with eggs =, and add bika.lims to the existing entries:

      eggs =
          Plone
          Pillow
          bika.lims

   3. Run buildout from cmd (press ⊞ Win, type cmd, press ↵ Enter):

      C:> cd C:\Plone43
      C:\Plone43> bin\buildout.exe

   4. A successful buildout should output:

      Updating run-instance.
      Updating service.
      *************** PICKED VERSIONS ****************
      [versions]
      bika.lims = 3.0
      cairocffi = 0.5.4
      cairosvg = 1.0.7
      cssselect = 0.9.1
      gpw = 0.2
      magnitude = 0.9.3
      products.advancedquery = 3.0.3
      products.atextensions = 1.1
      pycparser = 2.10
      pyphen = 0.9.1
      *************** /PICKED VERSIONS ***************

   If you see the following errors: Error: Couldn't install: cffi 0.8.2 or Error 5: Access is denied refer to Troubleshooting below.

3. Setting up Plone Services

   1. Run cmd as Administrator (press ⊞ Win, type: cmd, press CTRL``+``⇧ Shift``+``↵ Enter)

   2. Navigate to the Plone root directory:

      C:\> cd C:\Plone43

   3. Install, Start and bring your newly created instance to the Foreground This should stop the default Plone 4.3 Service:

      C:\Plone43> bin\instance.exe install
      C:\Plone43> bin\instance.exe start
      C:\Plone43> bin\instance.exe fg

      If you see INFO Zope Ready to handle requests then the server is running

4. Add a new Plone/Bika instance.

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

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.

1. Backup

   Stop Plone, and make a full backup of your instance before continuing:

   bin/plonectl stop
   bin/fullbackup

2. Buildout

   Run buildout with the “-n” option, to retreive the latest version of Bika LIMS and it’s dependencies:

   bin/buildout -n

3. Restart Plone

   Just as during the installation, it’s useful to start a single zeo client in the foreground to check for errors:

   bin/plonectl client1 stop bin/plonectl client1 fg

   To restart Plone issue a command like this:

   bin/plonectl restart

4. Migrate

   Go to site-setup, and click Add-ons. Find Bika LIMS in the list of activated addons, and click the bika.lims upgrade button.

Installing Bika-LIMS source

You should already have Plone and Bika LIMS installed. The paths and commands below are for Linux, but following along in windows is simple.

1. Download source:

   cd Plone/zeocluster/src
   git clone https://github.com/bikalabs/Bika-LIMS.git bika.lims

2. Select a git branch:

   We use git-flow to manage the git repository, with some quirks.  The ``next``
   branch contains code for the next hotfix or release, and ``develop`` contains
   unreleased code merged from ``feature/*`` branches. ::
   
       git checkout develop

3. Edit buildout.cfg:

   develop =
       src/bika.lims

4. Restart Plone

   bin/plonectl restart all

The Bika LIMS distribution in Plone/buildout-cache/eggs/bika.lims* will now be ignored by Plone, and the copy in src/bika.lims is used instead.

Troubleshooting

(Windows) 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.

(Windows) Privileges

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

(Windows) 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

To empty/reset the database, run the following:

rm -rf var/filestorage
bin/buildout

If your admin user does not exist or you forget the password:

bin/plonectl adduser admin admin

AttributeError: type object ‘IIdServer’ has no attribute ‘__iro__’

* The code for "bika.lims" not installed or not included
* Running buildout again usually fixes this

Log errors to sentry.bikalabs.com

Add raven to your buildout.cfg in the eggs = section:

eggs =
    ...
    raven

Then add the following snippet to your [instance] section. If you are using a ZEO configuration, add this to all [clientX] sections:

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://90723864025d4520b084acee225ddb8a:[e-mail]/2
      level ERROR
    </sentry>

Add raven 4.0.4 into [versions] section:

[versions]
    ...
    raven = 4.0.4

Run bin/buildout, and restart Plone.

Bika Lab Systems [e-mail] http://www.bikalabs.com