File Release Notes and Changelog
Release Name: 2.1.0
Notes:
BIKA is a LIMS, which is short for Laboratory Information Management
System. It is developed using Archetypes schemas and classes.
It is a complete customisation of a Plone instance and is not really
meant to be installed as a single product inside an existing
Plone instance.
Installing Bika LIMS 2 Inkosi on Linux
Tested with Ubuntu Gutsy Gibbon 7.10 and Hardy Heron 8.04
---------------------------------------------------------
Document Version 1.0, 26 May 2008
Updated versions, including screen shots,
at http://www.bikalabs.com/helpcentre/manual/bika-installation-guides/bika-on-ubuntu-linux/installing-bika-lims-2-0
Requirements
------------
Plone 2.5
Zope 2.9
Python 2.4
Tested with Plone 2.5.1 and Zope 2.9.5
Installation guide
------------------
At this stage Plone must be installed already, see the Linux Plone installation page
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
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
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 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 a test image of a bell curve and texts
See the test image at http://www.bikalabs.com/testinstall
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 Notes
-------------------------
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
1) 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
----------------
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.
Changes:
Bika LIMS core.
2.1
---
Changes:
--------
Sample object and workflow introduced
Results specifications, lab and per client
Analysis profiles
Worksheet template engine
Interface to Bika Calendar
Import of analysisrequests from csv file
Export of results to csv file
Print as publication option
Lab Departments, lab contacts, and department manager introduced
Quality Control calculations. Control, blank and duplicate analyses.
QC graphs, normal distribution, trends and duplicate variation
Various analysis calculations allowed. Described by Calculation Type
Dependant Calcs introduced. Where an analysis result is calculated from
other analyses: e.g. AnalysisX = AnalysisY * Analysis Z
Dry matter result reporting. Results are reported on sample as received,
and also as dry matter result on dried sample
Re-publication, Pre publication of individual results and per Client
Many reports including Turn around, analyses repeated and out of spec
More details on LIMS 2.0 and 2.1 Projectpages
http://www.bikalabs.com/softwarecenter/bika/releases/2.0
http://www.bikalabs.com/softwarecenter/bika/releases/2.1
Bugs fixed:
-----------
1.2.1
-----
Bugs fixed:
-----------
Removed invoice line item descriptions from core code to allow skin
integration
Create dummy titration values for analyses imported from instrument
More language translations
1.2.0
-----
Bugs fixed:
-----------
Statements renamed to Invoices
Jobcards renamed to Worksheets
New identification fields added to analysis request
Client Reference, Sample Type and Sample Point
Welcome page introduced
Late analyses list linked from late analyses portlet
Icon changes
Accreditation body logo and details added to laboratory info
Accreditation logo, disclaimers added throughout web site
Laboratory confidence level value data driven from laboratory info
Analyses methods provided as pop-up where analyses are listed
Titration factors and titration volumes added to analyses and worksheets
Measure of uncertainties introduced per analysis and intercept
Two new specialist roles created - verifier and publisher
Sample test data load script - load_sample_data.py
Implement generic instrument data import tool
Login portlet added
Modifications required to support interlab
Permit analysis parent (sample) to be in 'released' state.
Reference SampleID on AnalysisRequest
Bugs fixed:
-----------
- 1566324: Logged in page redirected to welcome page.
- 1573299: LiveSearch - Added permissions to InvoiceLineItem.
- 1573083: Status Drop Down - Invoicing
- 1551957: Contacts not visible to other contacts. Correct local owner role
- 1566334: position of 'add new ar' button changed to conform to other forms
- 1532008: query results sort order most recent first
- 1532770: Order default listing correction
- 1558458: Member discount data driven in messages on AR forms
- 1538354: SubTotal and VAT calculation on edit AR
- 1532796: AR edit - allow change of contact
1.1.3
-----
This is a bug fix release. Migration from older versions has also
been improved greatly.
Please note that AnalysisRequest now has a custom mutator that
expects the title of the Cultivar, not the UID. This will impact
anybode that customised the *analysisrequed_add.cpy* controller
script and the *validate_analysisrequest_add_form.vpy* validation
script.
Bugs fixed:
-----------
- 1423182: IndexError on surfing to LIMS pages without being logged on
- 1423238: Orders - Dispatch date
- 1429992: AR edit tab - Cultivar uneditable
- 1429996: Cultivar names to allow numbers
- 1429999: Late analysis alert - 'More...' URL
- 1430002: Sample due alerts - 'More...' URL
- 1433787: Security - Clients
- 1434100: Search - Index & Attribute errors
Patches applied:
----------------
- 1418473: Updated start-id-server.bat for Win2K & Win XP
1.1.2
-----
Features added:
---------------
- 1423205: Show logs to labmanager set-up
- 1291750: Added default ID prefixes for Order and Statement
Bugs fixed:
-----------
- 1424589: Late analysis alert to be calulated on date received
1.1.1
-----
- Updated portlets with Plone 2.1 style definition list markup
Bugs fixed:
-----------
- 1423179: Clients must not see JobCard links on Analysis Requests
- 1423182: IndexError on surfing to LIMS pages without being logged on
- 1423188: Site map - Clients should not have access to ...
- 1423191: Link rot - 'logged in' page
- 1423193: Groups folder should not be shown
- 1423194: No 'More...' if there are less than 5
- 1423204: AR view - Missing tabs and status drop down
- 1423209: Schema Editor - Drop Down List Issue (Select)
- 1423234: Late Analysis alert shows for anonymous visitors
- 1423363: Report Analysis Totals
- 1423386: Email publication error
1.1.0
-----
- Made Bika compatibable with Plone 2.1
- Added Spanish translation contributed by Luis Espinoza
- Added Italian translation contributed by Pierpaolo Baldan
- Added Dutch translation contributed by Joris Goudriaan
- Added Portugese translation contributed by Nuno R. Pinhão
- The schemas of Client, Contact, AnalysisRequest and Order can be
edited in the through-the-web schema editor, ATSchemaEditorNG.
- The maximum time allowed for the publication of results can now be
set per analysis service. The portlet
'skins/bika/portlet_late_analysis.pt' has been added to alert lab
users when analyses are late.
- Analyses on an AnalysisRequest have a reference to a Jobcard,
rendered as a hyperlink on the AnalysisRequest view.
- A bug has been fixed where 'not_requested' analyses were checked
on the AnalysisRequest edit form.
- Enabled 'changed_state' folder button globally and disabled on
AnalysisRequest and Jobcard.
1.0.1
-----
- Updated 'skins/bika/date_components_support.py' with latest
version of script in Plone 2.0.5
- Modified access to transitions in workflow scripts, normal
attribute access seems to guarded since Zope 2.7.5.
- Added CHANGES.txt and README.txt
- Added windows batch script for ID server
(scripts/start-id-server.bat)
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