bika-users

[bika-users] Making changes to the LIMS

[Lee J. <lee...@ec...>]

I have successfully installed Bika Inkosi. We are evaluating whether we 
can use it for our application.  Basically, we are a startup and hope to 
use a LIMS rather than do all our chemistry notes on paper and in random 
files. In order to make Bika fit our needs more closely I would need to 
make some small changes.  In a few cases I can do so because they are at 
the level of changing a title on a page.  However in most cases I have 
no idea how to proceed. Here are a sample of change requests.  If you 
could either point me to whichever documentation applies or tell me that 
the changes are not possible, I would appreciate it.

   1. We do not need the bika_products table and would either like to
      repurpose it, re-titling some of the columns or add a similar
      table with the columns we need.  I am not at all clear where to
      start in either of these endeavors.
   2. Under the ZMI I can access a number of bika entities (e.g.
      bika_services).  Can I use the ZMI to make changes? I seem to
      recall reading somewhere that I should stay away from the ZMI
      because I could compromise the system integrity that way.
   3. Is there a way to use the calendar to reserve blocks of time with
      any of a number of pieces of equipment?
   4. When someone request an new analysis, he is presented with a form
      containing many rows.  Each row specifies some characteristic of
      the analysis being requested.  Some of the rows are fields from
      Analysis Services. However other rows, like Client Order Id seem
      to be preordained.  How would one go about defining additional
      rows like these?
   5. Is it possible to add "alerts" or "red flags" when the input of a
      result does not have the proper number of significant figures?

I am reasonable competent with Python and have used databases in the 
past, so I feel reasonably confident that I could handle many of these 
changes once I am on the right track.

Thanks again for your assistance and patience.

Lee James

Re: [bika-users] Making changes to the LIMS

[lemoene <le...@bi...>]

Hi  Lee

I'm no techie but will try to answer to the best of my abilities. Am 
also cross posting to the dev list

> I have successfully installed Bika Inkosi. We are evaluating whether 
> we can use it for our application.  Basically, we are a startup and 
> hope to use a LIMS rather than do all our chemistry notes on paper and 
> in random files. 

Good move!-) If you need to convince somebody: Why LIMS?
<http://www.bikalabs.com/whylims>
> In order to make Bika fit our needs more closely I would need to make 
> some small changes.  In a few cases I can do so because they are at 
> the level of changing a title on a page.  However in most cases I have 
> no idea how to proceed. Here are a sample of change requests.  If you 
> could either point me to whichever documentation applies or tell me 
> that the changes are not possible, I would appreciate it.
>
> 1. We do not need the bika_products table and would either like to 
> repurpose it, re-titling some of the columns or add a similar table 
> with the columns we need.  I am not at all clear where to start in 
> either of these endeavors.

If the workflow and functionality is in order you probably only have to 
work on the upper templating level, the .pt files if i remember correctly

> 2. Under the ZMI I can access a number of bika entities (e.g. 
> bika_services).  Can I use the ZMI to make changes? I seem to recall 
> reading somewhere that I should stay away from the ZMI because I could 
> compromise the system integrity that way.

Indeed. Best to make changes in the code itself. Better for re-usability too

> 3.  Is there a way to use the calendar to reserve blocks of time with 
> any of a number of pieces of equipment?

The highly desirable analysis scheduling module... notoriously 
complicated. I suppose one could keep it simple but you'd want to tie it 
in with instrument maintenance and maybe HR too and check for instrument 
capacity in the analysis workflow. You'll need to know your way around 
Plone for this one. The technical design itself won't be simple. That 
said, it was for this exact purpose we started with the true time calendar

We normally propose for big development items that you write the 
functional specification and use cases and post it on-line to attract 
co-sponsorship for its development. Note smattering of Bika specs all 
over the Interweb. Bika Lab Systems could venture a quote too but i 
don't think this is a cheapie, my guestimate is 3 man months for 
experienced LIMS analyst, Plone programmer and testers. Then again we 
quote in pretty worthless South African Rand

> 4. When someone request a new analysis, he is presented with a form 
> containing many rows.  Each row specifies some characteristic of the 
> analysis being requested.  Some of the rows are fields from Analysis 
> Services. However other rows, like Client Order Id seem to be 
> preordained.  How would one go about defining additional rows like these?

Extra Analysis Request  (AR) and Sample attributes. Have to be added on 
those objects in the code and them templated upfront

> 5.  Is it possible to add "alerts" or "red flags" when the input of a 
> result does not have the proper number of significant figures?

Everything is possible;-) I am sure a bit of JavaScript in the AR  and 
Worksheet templates will do that quite easily

> I am reasonable competent with Python and have used databases in the 
> past, so I feel reasonably confident that I could handle many of these 
> changes once I am on the right track.

We have an ongoing argument in-house about Plone's steep learning 
curve...  for technical questions post to the bika dev list

>
> Thanks again for your assistance and patience.

Wish I could be more positive and of more help
Bests
l


>
> Lee James

Re: [bika-users] Making changes to the LIMS

[Campbell <alm...@gm...>]

I'm also not sure I'm the very best person to reply to this, but I heard 
you teach best that which you most need to learn.  Most of it requires 
some level of plone knowledge, and Plone is not a joke (it's Infinitely 
Flexible), so the learning curve sometimes feels like the flat side of a 
planet. Plone 2 docs are scarce, but a lot Plone 3 documentation is 
still very useful to point you in the right direction.


On 06/08/2010 16:13, Lee James wrote:
>    1. We do not need the bika_products table and would either like to
>       repurpose it, re-titling some of the columns or add a similar
>       table with the columns we need. I am not at all clear where to
>       start in either of these endeavors.

It's a fairly common precedure to create and restructure these tables. 
it works a bit manually...  You can pick some object as a reasonable 
starting point and copy it's definition python file (bika/Object.py) to 
a new file, and edit it.  there are plenty of good docs for this part, 
its quite simple.

Then just search through the system and add equivalent sections 
everywhere in the templates where you see the original field or object 
name, and ask when you get stuck - everyone here is sneaky with the Plone.

(you should be able to alter the translation files in bika/i18n to 
change the text in the templates, and edit the existing object, but I've 
never done it like this).

If you want to install from the modified bika product, you need to read 
about GenericSetup and look in profiles/default, profiles/default is 
also a good all round reference.

>    2. Under the ZMI I can access a number of bika entities (e.g.
>       bika_services). Can I use the ZMI to make changes? I seem to
>       recall reading somewhere that I should stay away from the ZMI
>       because I could compromise the system integrity that way.

The ZMI is the only way to do some plone/zope things. Exploring it can't 
hurt, and it has an undo.  If the option you want is not in Bika or the 
site seup, then exploring the ZMI is maybe the next step.

>    3. Is there a way to use the calendar to reserve blocks of time with
>       any of a number of pieces of equipment?

first reaction would be to say "not really, no", but it would be quite 
simple i think, depending on the depth of what you want.  Check out 
RecordsField and RecordsWidget in Products/ATExtensions.  If that will 
hold the kind of data you need, then add one to bika/Instrument.py - you 
will initially be able to access it directly as a list of text fields in 
the Instrument page, or you'll need to edit templates until they match 
your expectations..

otherwise... create new object type for instrument_schedule, read about 
HoldingReference and reference_catalog...  and portal_catalog and... 
anything's possible.


>    4. When someone request an new analysis, he is presented with a form
>       containing many rows. Each row specifies some characteristic of
>       the analysis being requested. Some of the rows are fields from
>       Analysis Services. However other rows, like Client Order Id seem
>       to be preordained. How would one go about defining additional rows
>       like these?

Look in bika/AnalysisRequest.py...

You'll need to edit the templates, and also some python.  Search and 
replace through skins/bika/ and edit relevant .pt, .py, .cpy, .vpy 
files, and anything else suspect.

If we ever fix this cleverly enough, we will never have to say 'fork'.

>    5. Is it possible to add "alerts" or "red flags" when the input of a
>       result does not have the proper number of significant figures?

You could duplicate/modify the "uncertainties" attribute of the 
AnalysisService.  I know this flags items which are outside of the 
acceptable limits, but making it perfect should be trivial.


If you have specific questions, ping.

Re: [bika-users] [bika-dev] Making changes to the LIMS

[lemoene <le...@bi...>]

>>> 5. Is it possible to add "alerts" or "red flags" when the input of a
>>> result does not have the proper number of significant figures?
>>>        
> Actually you might go to analysis specifications in the site setup, and
> use (for 5 digits) a minimum value of 10000 and a max of ... a lot?
>    

Lee to correct me, but I think he wants to be warned during data 
capturing that more digits are required. JavaScript?

Re: [bika-users] [bika-dev] Making changes to the LIMS

[Lee J. <lee...@ec...>]

Yes, that is right.  We need to catch, at input time,  instances where 
the data is being implemented too approximately.  Apparently there are 
instances in the past where data got rounded during the reporting and a 
flag is being contemplated to remind people that they need to chase down 
the more exact numbers.

Lee


lemoene wrote:
>>>> 5. Is it possible to add "alerts" or "red flags" when the input of a
>>>> result does not have the proper number of significant figures?
>>>>        
>>>>         
>> Actually you might go to analysis specifications in the site setup, and
>> use (for 5 digits) a minimum value of 10000 and a max of ... a lot?
>>    
>>     
>
> Lee to correct me, but I think he wants to be warned during data 
> capturing that more digits are required. JavaScript?
>
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