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Note: This is the print view with all the Reference Manual pages on one page. The paginated version is available here, if you prefer that.

Ubuntu and Windows installation guides for Bika LIMS · In progress: Bika Wine and Interlab, FreeBSD

2. Windows

Installing Bika on MS Windows

2.1. Installing Plone on Windows

Downloading and installing Plone 2.5. Tested with Plone 2.5.3
  • Browse to http://plone.org/products/plone/release
  • Select and download the recommended Plone Windows installer
  • Once downloaded completely, run the installer, e.g.  plone-2.5.2-zope-2.exe, double-click on it
  •  This screen appears:



  • Click 'Next' to continue the set-up


  • Accept the License Agreement and click 'Next'


  • Browse to set a different path then the default. Or leave to default. Click 'Next'


  • Enter your administrative account details and click 'Next'

    For the purpose of this manual we use:
    Login: admin
    Password: local

Plone Setup - Ready to Install

  • Click on Install, and the Plone will be installed -> this process will take na bit of time depending on your hardware spec.
  • Once finished the following screen will appear, click 'Finish'




2.2. Installing Bika LIMS

Windows Bika LIMS installation manual
  1. Download Bika LIMS from: http://sourceforge.net/project/showfiles.php?group_id=145464
  2. There are several Products listed;
    1. If you want to install Bika LIMS, then download the bika package, in whichever archive made available (rar, tar.gz, zip)
    2. There are two package types;
      1. Bika Product (stand-alone): e.g. bika-1.2.2.rar - this archive only contains the Bika product, but not Bika dependent products. Only download this package if you're upgrading Bika, but take note to make sure your Bika dependent products are up to date
      2. Bika Product Bundle; e.g.  bika-1.2.2_bundle.rar  - this archive contains the following;
        • bika - version LIMS 1.2.2
        • ATExtensions - version 0.7.1
        • ATSchemaEditorNG - version 0.4.2
        • PloneHelpCenter - version 0.9-Modified_by_Upfront
        • Portal Transport - version 1.1
        • stripogram
        • Upfront Contacts - version 0.4
  3. Extract the BIKA Product Package or Bika Product Bundle inside the Products directory of your Zope instance, assuming you have the same set-up described in the Plone installation page, this would be: C:\Program Files\Plone 2\Data\Products
  4. Copy start-id-server.bat from C:\Program Files\Plone2\Data\Products\bika\scripts to C:\Program Files\Plone2\Data
  5. Edit 'start-id-server.bat' so PYTHON and BIKA_BASE variables reflect your installation
    The Final content of the start-id-server.bat should look like this:

    @set PYTHON=C:\Program Files\Plone212\Python\python.exe
    @set BIKA_BASE=C:\Program Files\Plone212\Data
    @set COUNTER_FILE=%BIKA_BASE%\var\idserver.counter
    @set LOG_FILE=%BIKA_BASE%\var\idserver.log
    @set PID_FILE=%BIKA_BASE%\var\idserver.pid
    @set SCRIPT=%BIKA_BASE%\Products\bika\scripts\id-server.py
    @set PORT=8081
    "%PYTHON%" "%SCRIPT%" -f "%COUNTER_FILE%" -p "%PORT%" -l "%LOG_FILE%" %1 %2 %3 %4 %5 %6 %7

    The section in bold needs to be added

    ONLY for Windows users: Alternatively you can download the patched start-id-server.bat from here:

  6. Edit C:\Program Files\Plone2\Data\etc\zope.conf with <Environment> variable
    Add in 'environment' section for the ID Server (and remove all other 'environment' settings):

     <environment>
     IDServerURL http://localhost:8081
    </environment>
  7. ALSO due to a quirk between Plone & windows, edit C:\Program Files\Plone2\Data\etc\zope.conf also un-comment the following section: 'Directive: suppress-all-access-rules'
    so that you get the following line below Example;

    suppress-all-access-rules on
  8. Run 'runzope.bat' from C:\Program Files\Plone212\Data\bin or

    1. Run the Plone Control panel (which you can find from Start -> Programs -> Plone -> Plone



      Click on the Start button

      Click on the 'Zope Management Interface' button, and the ZMI should open up in a new browser window
  9. Start the IDServer from C:\Program Files\Plone 2\Data
    Test by browsing to http://localhost:8081/ - if running it will display a number, and will increment it with every reload
  10. {Skip this step if you used the Plone Controller} Open Browser, go to ZMI, typically http://localhost:8080/manage
  11. ZMI: a pop-up will appear requesting your login and password
    zope login
    assuming you have the same set-up described in the Plone installation page, this would be:

    Login: admin & Password: local

  12. Following successful authentication you should see the following screen;


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

  14. Specify the id (short name, part of site's address), Title (title of the Bika site) and Description (of your BIKA instance) and select 'bika' from the 'Extension Profiles' at the bottom of the form. And click on 'Add Plone Site' and the following screen will appear:

    e.g. Id: 'bika', Title: 'Bika LIMS Portal', Description: 'This is the demo of Bika 1.2.2'
  15. After step 14 you should be automatically redirected to the ZMI, showing your new Bika instance
  16. Click on you bika instance, and then click on the 'View' tab to see bika full screen. Or alternatively, open a new browser window or tab, and enter the following address: http://localhost:8080/bika
  17. Uploading Sample Data for bika.

    NOTE: if you want to install Bika Wine or Bika Interlab, please only upload sample data at the end of the 'Wine' or 'Interlab' installation process.

    If you want to populate your Bika LIMS with sample data, login into bika as administrator, and enter the following address in your browser:
    http://localhost:8080/bika/load_sample_data

    NOTE: Make sure your IDServer is running!

  18. This will take several seconds, and will be followed by an blank screen with 'Ok' in the top left. 

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


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

2.3. Installing Bika LIMS 2 Inkosi on Windows

Bika LIMS 2 installation guide for Windows. Tested with XP Pro 5.1

Windows Icon    Windows XP Pro 5.1


Version 1.0 of 26 May 2008


Requirements

Plone 2.5

Zope 2.9

Python 2.4

Tested with Plone 2.5.3 and Zope 2.9.7


Installation guide


At this stage Plone must be installed already, see the Win Plone installation page

There are several Bika Products listed at http://sourceforge.net/project/showfiles.php?group_id=145464


    1. If you want to install Bika LIMS 2 Inkosi, then download the Bika package in the archive format that suits you best
    2. There are two types of packages:

      Bika only

      E.g. 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
      • _renderPM 0.99                   Win32dlls-py24
      • Reportlab - version 1.19     
      • ReportlabFonts                    Adobe fonts required by Reportlab

      It comes bundled in this folder structure:

      Inkosi Bundle Layout

    3. Extract the Bika bundle to a temporary folder

      Copy the folder in the Plone Products directory to the Products folder of your Zope instance

      Assuming you have the same set-up described in the Plone installation page, this would be C:\Program Files\Plone 2\Data\Products

    4. ID server

      Nemesis, take special care

      Copy start-id-server.bat
      from   C:\Program Files\Plone 2\Data\Products\bika\scripts
      to       C:\Program Files\Plone 2\Data

      If necessary, edit start-id-server.bat for the PYTHON and BIKA_BASE variables to reflect your installation. If you kept to the recommended folder paths and names, everything should be fine:

      @set PYTHON=C:\Program Files\Plone 2\Python\python.exe
      @set BIKA_BASE=C:\Program Files\Plone 2\Data
      @set COUNTER_FILE=%BIKA_BASE%\var\idserver.counter
      @set LOG_FILE=%BIKA_BASE%\var\idserver.log
      @set PID_FILE=%BIKA_BASE%\var\idserver.pid
      @set SCRIPT=%BIKA_BASE%\Products\bika\scripts\id-server.py
      @set PORT=8081

      "%PYTHON%" "%SCRIPT%" -f "%COUNTER_FILE%" -p "%PORT%" -l "%LOG_FILE%" %1 %2 %3 %4 %5 %6 %7

    5. Edit zope.conf, in C:\Program Files\Plone 2\Data\etc\zope.conf

      Edit the <Environment> paragraph in the Environment directive, to include the ID Server address

      Maintain the HTTP_MANAGE $ZOPE_MANAGEZODB_PORT setting
      <environment>
      HTTP_MANAGE $ZOPE_MANAGEZODB_PORT
      IDServerURL http://localhost:8081
      </environment>
    6. Graphics

      Bika 2 QC graphs require Reportlab

      If you installed the Bika Bundle, RenderableCharts will be in
      your Product directory c:\Program Files\Plone 2\Data\Products

      i) Copy the extracted reportlab folder to Python, into a reportlab - all lower case -
      folder e.g. C:\Program Files\Plone 2\Python\Lib\reportlab.
      MANIFEST.txt should be in c:\Program Files\Plone 2\Python\Lib and
      rl_config.py should be inside
      c:\Program Files\Plone 2\Python\Lib\reportlab

      ii) Copy the ReportlabFonts to a directory of your choice, e.g. C:\ReportlabFonts

      iii) In the reportlab folder, edit rl_config.py and add the
      ReportlabFonts path to the T1SearchPath parameter, e.g.
      # places to look for T1Font information
      T1SearchPath =  ('C:/ReportlabFonts',
              'c:/Program Files/Adobe/Acrobat 6.0/....

      iv) Copy _renderPM dlls from renderPM_Win32dlls-py24 to python,
      to C:\Program Files\Plone 2\Python\DLLs

      v) Test. Once your Bika installation is complete, navigate to
       http://localhost:8080/bika/test_install

      It should display:

      Reportlab test image


      Report lab logo small manual

      http://www.reportlab.org/

    7. Run 'runzope.bat' from C:\Program Files\Plone 2\Data\bin

      or

      Run the Plone Control panel which you can find from Start -> Programs -> Plone -> Plone




      Click on the Start button



      Click on the 'Zope Management Interface' button, and the ZMI should open up in a new browser window

    8. Start the IDServer from C:\Program Files\Plone 2\Data
      Test by browsing to http://localhost:8081/ - if running it will display a number, and will increment it with every reload

    9. [Skip this step if you used the Plone Controller]
      Open Browser, go to ZMI, typically http://localhost:8080/manage

    10. ZMI: a pop-up will appear requesting your login and password


      zope login

    11. assuming you have the same set-up described in the 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. This screen will appears:



      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. You should be automatically redirected to the Zope Management Interface (ZMI), listing your new Bika instance

    16. Click on you bika instance, and then click on the 'View' tab to see bika full screen. Or alternatively, open a new browser window or tab, and enter the following address: http://localhost:8080/bika

    17. Uploading demonstration data

      If you want to populate your Bika LIMS with sample data, login into bika as administrator, and enter the following address in your browser:
      http://localhost:8080/bika/load_sample_data

      NOTE: Make sure your IDServer is running!

    18. This will take several seconds, and will be followed by a blank screen with 'Ok' in the top left

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

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



2.4. Installing Bika Interlab

Bika Interlab installation guide
BIKA Interlab: add-on for proficiency testing and Inter-Laboratory Comparison.


BIKA is a LIMS, which is short for Laboratory Information Management
System.
Please refer to the README.txt in the bika directory

Pre-requisites:

  • BikaLims 1.2.5
  • RenderableCharts (which requires ReportLab - see below)


Tested with:

  • Zope 2.9.5
  • Plone 2.5.1
  • BikaLIMS 1.2.5

   

Installation:

NOTE: To install BIKA, you need to be familiar with the Zope or Plone installation procedure. We hope to have graphical installers soon to simplify installation.

  1. Copy BikaInterlab folder to your Plone Products folder.
  2. Install BikaLIMS as per instructions in the BikaLIMS Installation Guide
    Do not load the BikaLIMS sample data, or create any other data.
  3. Log on to your newly created bika site as administrator, and navigate to:

    1.  [site setup]

    2. [Add/Remove Products]

  4. Select BikaInterlab from the Products available for install


    and click on install. BikaInterlab will now appear in the Installed products list. 
  5. Test the graphing software installation with a page which graphs a set of dummy data. A smooth bell curve rendered with colours should be visible. If it is not, the graphing software has not been correctly installed. e.g. http://localhost:8080/instanceid/test_install

    You should see the following; (click on image to enlarge): Test Install

  6. Sample data has been provided in  ../bikainterlab/skins/bikainterlab/load_testdata.py and a subset in ../bikainterlab/skins/bikainterlab/load_smalltestdata.py
    This can be loaded by being logged in to your BIKA instance as the administrator, and executing the script in the browser: e.g. http://localhost:8080/instanceid/load_testdata

    If successful you should see an empty browser page with: 'OK' in the top left corner.


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


For latest Manuals, Tutorials, How-To's, Instruction Movies and other Help resources, please visit Bika Lab System's Help Centre at http://www.bikalabs.com/helpcentre

RenderableCharts Installation:

(included here from RenderableCharts README)

It is recommended that the RenderableCharts installation be tested with the example below before continuing with the BikaInterlab installation

ReportLab 1.19 is needed. See below

Works with ReportLab 1.20, _renderPM 1.0, _rl_accel 0.52 !

=====================================================================

Step-by-Step Installation How-To:

  1. Install ReportLab 1.19 from http://reportlab.org/downloads.html
  2. Install _renderPM 0.99 from http://reportlab.org/downloads.html
  3. Install PIL 1.1.4 from http://www.pythonware.com/products/pil/
  4. Install Adobe Acrobat Reader for the T1-Fonts
  5. Adapt the rl_config.py T1SearchPath to fit your system path to the Acrobat*/Resource/Font directory (see below)
  6. Unpack RenderableCharts-*.tar.gz in the Zope-Products folder
  7. Restart Zope


=====================================================================

Step-by-Step Example How-To:


  1. Add a ChartObject (name: my_chart):
    Id:                                   my_chart
    Title:                                My First simple ChartObject
    Name of ChartTemplate:   my_template
    List of DataObjects:          chart:get_chart_data  

    -> Add and Edit
  2. Add a ChartTemplate (name: my_template):
    Id:                       my_template
    Title:                    My First simple ChartTemplate
    Sample:               ClusteredBar

    -> Add and Edit
  3. Goto ZMI function Test, a nice horizontal bar chart should be visible now.
  4. Goto the folder where my_chart was added.
  5. Add a Database Connection for your favorite Database
    (name: database_connection)
  6. Add a ZSQLMethod (name: get_chart_data):
    Id:                        get_chart_data
    Title:                    My First simple ChartData
    Connection Id:            database_connection
    Arguments:                (enter nothing)
    Query Template:            (put here your SQL-Query, which should return row-by-row in the first column a categoryName andin the other columns values)

    -> Add
  7. Goto ChartObject my_chart -> ZMS function Test -> the horizontal bar chart with values from database should be visible now.


=====================================================================

Additional information in the RenderableCharts README, and from the product
web sites

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: d:/ReportLab.

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

 

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