How to add a sample? (Missing "Add" button for ”Samples")


#1

Dear colleagues,

I am new to Senaite/Bika LIMS community. I just installed Plone-4.3.15 using UnifiedInstaller on CentOS Linux release 7.5.1804 (Core), then added senaite.lims 1.2.0 to the system (via eggs section of buildout.cfg). When Senaite was launched, I noticed that for nearly every kind of object, there is a corresponding “Add” button to create/add an object, except Samples. The “Add” button for “Samples” seems missing.

Does anybody has similar experience? How to enable the “Add” button for “Samples”? Or maybe there were some installation issues related to this problem? I did see a number of “warnings” or “errors” when doing " sudo -u plone_buildout bin/buildout " after adding “senaite.lims” to the eggs section of buildout.cfg.

By the way, are there some documentation or tutorial about Senaite/Bika LIMS?

Thanks a lot in advance! – Lei


#2

Hi Lei,

Welcome to Senaite!

If Senaite has been installed, you should not fear those warnings when running bin/buildout.

So far, the system does not allow to create a sample without creating an analysis request at the same time. Each time you create an analysis request, a sample is created and binded to the same analysis request and the analyses.

But, while you are creating an analysis request, you can reuse an already created sample and all its fields will be automatically filled (date sampled, sample type, environmental conditions, container, etc). See the attached image:

About documentation, you can take advantage of Bika LIMS documentation for now. One milestone in the Seniate roadmap is to create a dedicated website for documentation and to provide an add-on that integrates the context-aware documentation within Senaite.

Regards,


#3

Worth to mention that some time ago, an effort to allow users to create Samples without the need of creating their Analysis Request counterparts were done. See this Pull Request: Standalone samples and sample creation form. That pull request hasn’t been accepted yet and it might require exhaustive refactoring due to the changes performed in AR Add submit form and in the javascript logic behind. Nevertheless, don’t miss the comments, cause there are some functional reasonings about why would be interesting to have such a functionality.


#4

I now see how my mails go missing, I need to reply online…

Main reason to have Sample registration only would be for bioinformatics/biobanks where most samples are done without any clear indication whether they’ll be tested immediately - they are registered, prepared and separated, aliquotted, genetic material extracted and frozen.

Bika Biobank / Baobab is stirring, Senaite Health in the cross hairs, stand by


#5

Espurna, xispa, and lemoene,

I really appreciate your knowledge input and explanations!

Actually I have been trying to create a ‘Analysis Request’ for two days, but kept getting error message
“Field ‘Analyses’ is required”.

I don’t see Field ‘Analyses’ in the input form, and don’t see anywhere I can add it in the website, including “Site Setup” section, where it seems that anything related to “Analyses” is not working.

I also re-installed senaite.lims 1.2.0 based on Plone-4.3.17, but got the same result.

Maybe I have missed something?I will try to find some clue in the old documentation.

Thanks a lot again! – Lei


#6

At least you have to select one analysis per Analysis Request. In AR Add form, click to “Lab Analyses” section (in blue background) located at the bottom, just above “Subtotal” field, and choose the Analysis/es you want to include. If no analyses for selection are displayed there, then you have to create one Analysis Service first: go to “Site Setup > Analysis Services” and create a new one.


#7

Damn, that is a known bug too - when the user does not have any Analyses selected when submitting the AR, the system reports Field Analysis is required, should just say A minimum of one Analysis is required

Would you mind logging @fatfatcoyote? If not there already, https://github.com/senaite/senaite.core/issues. Appreciated


#8

I followed xispa’s guidelines and created a new analysis service, then successfully created an AR. But it took me several hours to create a new analysis service, because it seems it is difficult to pick up an analysis category/type written in Chinese, so I had to add a new analysis category/type in English.

I also logged the issue per lemoene at:
https://github.com/senaite/senaite.core/issues/876

Here is its content:

"When a user does not have any Lab Analyses selected when submitting a AR, the system reports “Field ‘Analysis’ is required”.

First all, when a brand new system is built up, there is no Lab Analyses set up yet, thus the “Lab Analyses” section (in blue background, located above “Subtotal” field) is not visible in AR form at all. New users will have no idea about what the error means and how to fix it.

Second, maybe the error message can be changed to something like “A minimum of one Analysis is required. If you have not done so, please go to “Site Setup > Analysis Services” to create at one Analysis Service”.

Thanks a lot for your hard and excellent work!"