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bika.lims's Introduction

Bika code moved to Senaite

Bika 1,2 and 3, from 2002 to 2017, established the foundation Senaite rests on. Senaite 1's initial design analysis went under the Bika 4 moniker, with an emphasis on performance and maintainability

The Bika team assisted in upgrading Bika 3 code top the Senaite repos where we continue to contribute code, as well as developing add-ons, see the main folder here, https://github.com/bikalims

After going global and attracting a wider group of participants, Bika LIMS suffered from a naming issue - the project and Cape Town founding company were both using Bika in their titles, unfair to other contributors

With so much invested, the Bika brand is maintained independently from Cape Town

See https://www.bikalims.org/frequently-asked-bika-lims-questions/how-does-senaite-lims-relate-to-bika

The bika.lims repo here, like the wiki, are for now maintained for historic purposes only

Basix workflow and objects were maintained and the wiki will ingeneral still hold true - the Bika Senaite user manual is being kept up to date, https://www.bikalims.org/manual

Please use the latest Senaite code for your core installation

Thanks, Lemoene

bika.lims's People

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bika.lims's Issues

Client Reference Ranges

  1. For easy reference for the client, the Reference Ranges of each analysis service should be displayed on the final report/AR view with the results.
    At present only an out of range marker is displayed, but it is very helpful to know how much over/under the normal range the result is. It is difficult to know at a glance in the current setup.

  2. The function to (via a button on Client specs, e.g. /clients/client_9/analysisspecs) to copy the lab specs did not survive the migration.

Publishing Problems

  • Date Published field is blank in Emailed report to the contact
  • Publication preference was set to Print in the contact but Printer dialog failed to start when the status was changed to "published"

Water. Final label layout

All label s are 7cm wide as they come of the printer roll, but short and long labels differ in height

The labels are laid out in 2 columns of 3.5 cm, no borders

In most cases field labels are not printed, only their values

Th short label abel is 7cm wide and 3 cm high, and carries:

Sample ID Hazardous Y/N Barcode
Sample type Preservation Sample point
Sampling date Sampler

as in

SW12-123456 <!! > |||||||||||||||||||||||
Sewage   Chill 4 deg C Pond 23A
12 Feb 2012 John Smith

The long label is similarly laid out from:
Sample ID Hazardous Y/N Barcode
Sample type Preservation Sample point
Composite/Grab Sampler
Date requested Sampling date Disposal date
Client Contact Client SID Client order ID
Client reference
Field Analysis 1 Field Analysis 2 Field Analysis 3

AR Add UI improvements

  • The (>>) copy values button must appear on mouseover of any cell, and then copy the value of that cell to all cells left of it's position.
  • The (>>) copy values buttons in analyses must be [X] select all checkboxes.
  • Sampling Date selection should raise a visual flag when future dates are selected.

Copy lab specs to client specs

The function to (via a button on Client specs, e.g. /clients/client_9/analysisspecs) to copy the lab specs did not survive the migration.

Mail-shot

Interlab's mail shot to client contacts function...

Site error on AR after calculation

logged by Ian

Home › Clients › Klaymore Fertilizer › AR- 0329-01
We’re sorry, but there seems to be an error…
The error has been logged as entry number 1322034433.310.676960266362 .

I entered a result of 3 * 10 and am now unable to see /open the AR to enter further results.

Water. AR and Sample IDs

as in svn BikaWater trunk:

SampleType gets a Prefix field

  • Samples get STPrefix-XXX
  • ARs get STPrefix-SSSS-AA

bika_setup's ID Server tab gets a "Sample 0-pad length" and "AR 0-pad length"

Easy. Page headers

/samples currently reads 'Samples:Samples' - should be just 'Samples'

/analysis requests reads 'Bika LIMS: Analysis requests - just Analysis Requests please

/worksheets , ditto Worksheets: Worksheets

Small. Padding on Worksheets

Worksheets, e.g: http://bika3dev.bikalabs.com/Plone/worksheets/WS-007

  1. the standard number of pixels padding around the analyst and instrument fields please
  2. could these 2 fields be on the same row please?
  3. in the attachments expansion box, default padding please between these fields and their drop down menus below them:
    All analyses of type, Analysis, Attachment Type and Keywords
  4. same for attachments expansion box on ARs please

Bulk/Corporate pricing

This has to be rooted out and cleaned up:

  • Replace 'Corporate price' with "Bulk discount"
  • On Clients, modify the Corporate/Non-Corporate tag to read "Client qualifies for bulk discount" Y/N
  • Member Discount might be included in whatever structure replaces "Corporate Price"?
    (the two are confusing atm).

Printing Worksheets

A properly laid out landscape format print in stead of the default browser print-out of the worksheet is available from the standard 'print this page' icon


Want to back this issue? Place a bounty on it! We accept bounties via Bountysource.

AR add. was: Water. Sample Point & Type relationship

In the Sample Point set-up, a field is provided where a Sample type can be selected from all the Sample types captured in the system

On forms where both Sample Point and Sample Type are required:

  1. The Sample Type is auto completed by the LIMS when the Sample Point is selected
  2. If the Sample Type is selected first, the list of available (and valid) Sample Points is restricted to those that comply with the Sample type

Electronic signature on reports

All users who scan their signatures into the system should have these included at the bottom of reports and results (the user compiling/publishing the report).

The footer also includes title, name, email, phone.

Dry Matter results don't work

Logged by Benchmark's Chris:

I created sample AR-0379-01, added moisture to the profile, yet I cannot get it to calculated the dry matter values for the listed analysis. Perhaps I didn't create this properly but thought you should know. Do you know whether Dry Matter was set as a dependent analysis in your list of analysis services - dependent on the moisture analysis value?

Mail Templates

  • Results Publication SMS
  • Results Publication CSV
  • Results Publication Regular email
  • AR Query results
  • Order Query results
  • Invoice Query results
  • Pricelist Email
  • Reference Samples email
  • Reference Definitions email

Site colour scheme to be manageable

To easily customise and brand new sites, it'll be great to have the most prominent features handy for changes in either base_properties (the way inkosi used to work) or a custom css in the custom folder

Elements to be included:

  1. All the green edit bar items we identified earlier and put in a ploneCustom.css before:
    #edit-bar {
    background-color: #00793c !important;
    border: 0.25em solid #00793c !important;}
    #contentActionMenus {
    background: none repeat scroll 0 0 #00793c !important;}
    #contentActionMenus dl.actionMenu a, #contentActionMenus dl.actionMenu.activated dd {
    background-color: #00793c !important;}
    #content-views {
    background-color: #00793c !important;}

I dont know where to find the rests of the elements (got to learn Firebug...)

  1. The grey menu bar (similar to the green one above) for set-up items, currently #dddddd

  2. The category name background in analysis lists, currently #dddddd

  3. For tables, currentlly in base_properties:

    evenRowBackgroundColor, #ffffff

    oddRowBackgroundColor, currently #eeeeee

    table header row, currently #dddddd

  4. Alerts header row bg, #dddddd

  5. Late analysis header row bg, #ff0000

  6. copyright row' just above footer colophonm #dddddd

Water. method on Worksheet and ARs

Analysis method needs to be captured per analyses on worksheets and ARs. The method defaults to the one set-up for the corresponding analysis service

To be displayed in Sample, AR and Worksheet views

Certified Footer for results reports

The following text, editable in the system setup, is displayed at the bottom of all results views and publications. Fields, and signatures for print, are auto completed by the LIMS from set-up items configurable by lab managers

Deviation from sampling method xxx
xxxxxxxxx xxxxxxxx
Laboratory Supervisor Head Scientific Services
email xxxxxxxxx email xxxxxxxxx
tel xxxxxxxxxx tel xxxxxxxxxx

Note: Results pertain to samples as supplied/taken.
Denotes the method is accredited and included in the xxxxxx Schedule of Accreditation for this laboratory.
This Analytical Test Report may only be produced in full unless written approval is given by Head: xxxxxxxxxxx
UoM = Estimated uncertainty at a level of confidence of xxxxx

Water. Capturing instruments used for analyses

The lab needs to track analyses back to which instruments were used for analyses

In the LIMS set-up, and instrument is assigned to each analysis service. 'manual' is the default.

On Worksheets and AR manage results tabs, the instruments used for the analyses are to be captured, defaulting to the instrument configured in the set-up

Worksheet. Selecting all analyses per position

bika listing should cater for cell-level select checkboxes, so that an additional check box per WS position (at far left) will select all the analyses in that slot (say to remove all analyses from a certain slot). Analyses in the same slot can still be individually selected from their own check boxes, moved a few columns to the right to just to the left of the Analyses column

Use buildout properly (automate everywhere possible)

"Create an idserver start script, similar to below: Use the python from the bin/plonectl script:"

After all these years! Nooo! Look at how other recipes create scripts such as
snapshotbackup, maildropctl, zope_health_watcher, zopepy, etc. etc. and
follow their example.

Water. Sampling deviation on Worksheet and ARs

"Sample deviation" needs to be captured per Sample (if not routine samplers) from a drop-down setup with possible sampling deviations.

To be displayed in Sample, AR and Worksheet views

Bika Listing search filters

  1. Please make the filters case insensitive
  2. Remove it for uncatalogued fields, e.g. descriptions
  3. Could the [clear filters] URL be on a button?

Accreditation logo upload in set-up

The accreditation portlet refers to ++resource++/accreditation_logo.png - it should be settable in the UI.

  • /bika_setup/laboratory [Accreditation]

_("Please upload the logo you are authorised to use on your website and results reports by your accreditation body. Maximum size is 175 x 175 pixels"),

Automated sample label printing

When ARs/Samples are added or received, the sample label printing process must kick off automatically:

  1. /analysisrequests
  2. ARs on /clients/client_#/analysisrequests
  3. /samples
  4. Samples on /clients/client_#/samples

Automated label printing is not required when receiving ARs or Samples from their individual views since the labels can be printed from the label icons on these views

Print / Email / Fullscreen actions

  • The default Plone print/fullscreen/email document actions don't display.
  • print/email actions should exist and be configurable for each bika listing instance.

This was implemented in bika 2 for reference definitions (Print and Email buttons above list).

Water. Sample and AR prefixes for Sample Points

Could be done like this in Bika 3 too:

Samples and ARs are prefixed using an abbreviation per sample type, e.g. borehole water (BHW) will see its samples ant ARs prefixed BHW12-0001-01, etc

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