1.5. Installing Bika LIMS 2 Inkosi on Linux

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      Tested with Ubuntu Gutsy Gibbon 7.10 and Hardy Heron 8.04

Version 1.0,  26 May 2008

Requirements

Plone 2.5

Zope 2.9

Python 2.4

Tested with Plone 2.5.1 and Zope 2.9.5   

Installation guide

1. Download Bika LIMS from: http://sourceforge.net/project/showfiles.php?group_id=145464
   
   
2. If you want to install Bika LIMS 2 Inkosi, then download the Bika package in the archive format that suits you best
   
   There are two types of packages:
   
   Bika only
   bika-2_1.rar - This archive only contains the Bika products, but not Bika dependent products. Only download if you already have a Bika installation
   Make sure your Bika dependent products are up to date
   
   Bika Product Bundle, bika-2_1_bundle. rar - this archive contains
   Plone Products
       * ATExtensions - version 0.7.1
       * ATSchemaEditorNG - version 0.4.2
       * bika - version LIMS 2.1
       * BikaCalendar - version 1.0
       * PloneHelpCenter - version 0.9-Modified_by_Upfront
       * Portal Transport - version 1.1
       * RenderableCharts version 0.9.8
       * stripogram
       * Upfront Contacts - version 0.4
   Additional Products
       * Reportlab - version 1.19    
       * ReportlabFonts                    Adobe fonts required by Reportlab
   
   The bundle folders are structured like this:
   
   
   
   Extract the downloaded archive to a temporary folder
   
   
3. Install Reportlab
   
   NB Ubuntu Hardy Users, specify reportlab be installed on the Python 2.4 instance. On Ubuntu 8.04 onwards, Python 2.5 is used by the OS, and Plone 2.5 uses Python 2.4
   
   If you can't find the re_config.py file, it is suggested you install Reporlab from source
   

   python2.4 setup.py install

   Additional Installation Notes¹:

   There are two ways two go about dealing with the report lab dependency on Ubuntu:

   sudo apt-get install python-reportlab

   But you don't get renderPM which is a dependency for  Bika.
   
   Or installing reportlab from the package and renderPM from source via svn checkout. Make sure you check out the source with https because they are having some issue with port 80 on the repository and 443 works.

   svn co https://www.reportlab.co.uk/svn/public/reportlab/trunk
   

   1) Additional Contribution to this document by Zaki Manian
   
4. Copy the BikaFonts to a directory. e.g. /usr/local/lib/python2.4/site-packages/reportlab/fonts if Reportlab is installed here


5. In Reportlab, e.g. /var/lib/zope2.9/instance/plone-site/Products/reportlab', edit rl_config.py, adding the BikaFonts path to the T1SearchPath parameter
   
   Example, depending on your installation, in /usr/local/lib/python2.4/site-packages/reportlab
   
   

   # places to look for T1Font information
   T1SearchPath =  '/usr/local/lib/python2.4/site-packages/reportlab/fonts', #Linux, Acrobat 8?
                   '/usr/local/Acrobat4', #Linux, Acrobat 4
                   '/usr/local/Acrobat5', #Linux, Acrobat 5?
                   '/usr/local/Acrobat7/Font', #Linux, Acrobat 5?
                   '%(REPORTLAB_DIR)s/fonts' #special
   )

   
   
6. Copy the _renderPM directory to /var/lib/zope2.9/instance/plone-site/Products


7. Copy the Bika Product package or Bika Product Bundle to the Products directory of your Zope instance, assuming you have the same set-up described in the Linux Plone installation page, this would be /var/lib/zope2.9/instance/plone-site/Products


1. If you would like to create a separate instance for bika, rather then the default 'Plone Site', open your Command line editor and enter the following
   

   ~$ cd /usr/lib/zope2.9/bin/mkzopeinstance

2. You will be prompted to give the instance a name, and access details
   
   
8. ID server
   
   Before you start up your Zope instance, generally Zope starts automatically, you need to setup the ID server
   
   Copy the 'start-id-server' shell script from the BIKA products directory inside /var/lib/zope2.9/instance/plone-site/Products/bika/scripts to the root of your Zope instance, e.g. /var/lib/zope2.9/instance/plone-site
   
   
9. Modify the path to the Python binary inside the 'start-id-server' shell script and change the port if necessary
   
   
10. Edit the zope.conf file in your Zope instance /var/lib/zope2.9/instance/plone-site/etc and add an <environment> section for the ID Server:
    
    

    <environment>

    IDServerURL http://localhost:8081

    </environment>
    
    

11. Re-start Zope and browse to the management interface at http://localhost:8080/manage. Provide your login and password
    
    

    
    

    
    Assuming you have the same set-up described in the Linux Plone installation page  this would be
    
    

    Login: admin
    Password: local
    
    

12. Following successful authentication you should see the following screen, the infamous Zope Management Interface or ZMI:
    
    
    
    
    

13. Select 'Plone site' from the 'Add' drop down menu
    
    

    
14. Specify the id - its short name, part of site's address, e.g. 'bika', Title, say 'Bika LIMS Portal' and Description of your choice
    
    Select 'bika' from the 'Extension Profiles' at the bottom of the form
    
    Click the [Add Plone Site] button
    
    

    
    

    
    
    
15. After this step you should be automatically redirected to the ZMI, listing your new Bika instance
    
    
16. Click on your bika instance, and then click on the 'View' tab to see bika full screen
    
    Alternatively, browse to http://localhost:8080/bika
    
    

17. Test. Once your Bika installation is complete, navigate to 
     http://localhost:8080/bika/test_install
    
    It should display:
    
    
    
    
    
    
    http://www.reportlab.org/
    

18. Uploading Sample Data for bika
    
    

    If you want to populate your Bika LIMS with demonstration data, login into bika as administrator, and run a set-up script by navigating too http://localhost:8080/bika/load_sample_data
    

    The script will run for several seconds, and then load a  white screen with reading 'Ok' at top left

    NB. Make sure your IDServer is running!
    
    To run the IDServer on Ubuntu open your command line terminal and type
    

    ~$ su zope
    ~$ cd /var/lib/zope2.9/instance/plone-site
    ~$ ./start-id-server
    

19. Use the browser's back button to return to the Bika LIMS
    
    
    

Important ID Server Notes²:

The IDServer, once run, is supposed to create the following files;

• /var/lib/zope2.9/instance/plone-site/log/id.counter

• /var/lib/zope2.9/instance/plone-site/log/idserver.log

• /var/lib/zope2.9/instance/plone-site/log/idserver.pid

If these files are NOT created when running the IDServer, it's most probably due to the access rights on the Zope's log folder /var/lib/zope2.9/instance/plone-site/log

Either change the rights to the log folder so that the files can be created

or

Create the files manually, but make sure they've got 'write' permissions

If you have any trouble with the above installation procedure, please join the Bika users mailing list and report any problems you might have

http://lists.sourceforge.net/lists/listinfo/bika-users

Additional Contribution to this document by

2) Sébastien DOVILLEZ - Magikal

Additional ReportLab installation notes

From the ReportLab README - additional information in the ReportLab installation package

Either unpack reportlab.zip or reportlab.tgz to some directory say d:\ReportLab. If you can, ensure that the line terminator style is correct for your OS (man zip programs have a text mode option eg -a)

Create a .pth file, say reportlab.pth in your Python home directory. It should have one line: e.g. /home/zope/plone/Products/ReportLab

Alternatively unpack the archive into a directory which is already on your python path

The Font Problem (Linux)
------------------------

On Linux, renderPM needs to know the locations of the following
fonts:

AdobeSansMM.MMM.pfb
AdobeSansMM.pfb
AdobeSerifMM.MMM.pfb
AdobeSerifMM.pfb
Arial-BoldItalic.pfb
Arial-Bold.pfb
Arial-Italic.pfb
Arial.pfb
Courier-BoldOblique.pfb
Courier-Bold.pfb
Courier-Oblique.pfb
Courier.pfb
Symbol.pfb
TimesNewRoman-BoldItalic.pfb
TimesNewRoman-Bold.pfb
TimesNewRoman-Italic.pfb
TimesNewRoman.pfb
ZapfDingbats.pfb

These fonts may be downloaded from:

http://bioinf.scri.ac.uk/lp/downloads/programs/genomediagram/linfonts.zip

The locations that ReportLab will look for these fonts are defined in
the file rl_config.py.  The relevant part of this file, at the time of
writing, looks like this: 

# places to look for T1Font information
T1SearchPath =  (
                'c:/Program Files/Adobe/Acrobat 6.0/Resource/Font', #Win32, Acrobat 6
                'c:/Program Files/Adobe/Acrobat 5.0/Resource/Font',     #Win32, Acrobat 5
                'c:/Program Files/Adobe/Acrobat 4.0/Resource/Font', #Win32, Acrobat 4
                '%(disk)s/Applications/Python %(sys_version)s/reportlab/fonts', #Mac?
                '/usr/lib/Acrobat5/Resource/Font',      #Linux, Acrobat 5?
                '/usr/lib/Acrobat4/Resource/Font',      #Linux, Acrobat 4
                '/usr/local/Acrobat6/Resource/Font',    #Linux, Acrobat 5?
                '/usr/local/Acrobat5/Resource/Font',    #Linux, Acrobat 5?
                '/usr/local/Acrobat4/Resource/Font',    #Linux, Acrobat 4
                '%(REPORTLAB_DIR)s/fonts',              #special
                '%(REPORTLAB_DIR)s/../fonts',           #special
                '%(REPORTLAB_DIR)s/../../fonts',        #special
                '%(HOME)s/fonts',                       #special
                 )

Placing the font files in any of these locations should be enough to
solve the problem.  Otherwise, you may need to edit the rl_config.py
file yourself to specify the appropriate location.

Next: Windows Previous: Installing Bika Interlab