bika.lims 3.1.15

Description:

bika.lims 3.1.15

Bika LIMS
v3.1.15 (2017-05-27)

The meaning of Gaob
In the tradition of Chief Inkosi Bika LIMS 2 using a title for a release, this
edition is code-named Gaob Bika LIMS 3. Gaob, King, is taken from Khoi San Nama,
language of the world’s first people.


Installation

Installation Manual



Documentation

User Manual
GitHub Wiki



Feedback and support

Bika Users List: bika-users
Bika Developers List: bika-developers
LIMS design List: lims-design
Issue Tracker: http://jira.bikalabs.com/
IRC: irc://freenode.net/#bika
Slack: bikalims.slack.com




Installing Bika LIMS
The process should be similar for all systems on which Plone is supported.

Linux Installation Steps

Plone and Bika LIMS have some system dependencies

The following list of packages need to be installed. The package list is valid
for Ubuntu 14.04. If you use a different distribution, you may need to find the
versions of these packages which are provided with your system.
sudo apt-get install python-dev build-essential libffi-dev libpcre3-dev gcc
sudo apt-get install autoconf libtool pkg-config zlib1g-dev git-core libssl-dev
sudo apt-get install libexpat1-dev libxslt1.1 gnuplot libpcre3 libcairo2
sudo apt-get install libpango1.0-0 libgdk-pixbuf2.0-0


Install Plone

Download the latest stable version of the
Plone Unified Installer.
You should also read the
Plone Installation Documentation.
A basic command for installing a development environment in Linux:
./install.sh --target=/path/to/Plone --build-python --static-lxml zeo


Add Bika LIMS to your buildout.cfg

Change directory to Plone/zeocluster, and edit buildout.cfg.
Find the section beginning with eggs =, and add bika.lims to the existing
entries:
eggs =
Plone
Pillow
bika.lims
Indentation in buildout.cfg is important, and should be kept uniform for all lines.
Save the file, and then run bin/buildout again. Buildout will download and install
all remaining dependencies.
If the download is interrupted, simply run bin/buildout again. The process will
be resumed.
Spurious errors may occur while running buildout, and may be safely ignored. Verify
successful build from the output of the buildout script, which should include a
list of found versions like this:
*************** PICKED VERSIONS ****************
[versions]
Babel = 1.3
CairoSVG = 1.0.7
Products.ATExtensions = 1.1
Products.AdvancedQuery = 3.0.3
PyYAML = 3.11
Pygments = 1.6
Pyphen = 0.9.1
Werkzeug = 0.9.4
argh = 0.24.1
bpython = 0.13
cairocffi = 0.5.3
cffi = 0.8.2
collective.progressbar = 0.5
collective.wtf = 1.0b9
cssselect = 0.9.1
gpw = 0.2
i18ndude = 3.3.3
magnitude = 0.9.3
pathtools = 0.1.2
plone.api = 1.1.0
plone.jsonapi.core = 0.4
*************** /PICKED VERSIONS ***************
If the buildout finished successfully, an ‘adminPassword.txt’ will have been
created automatically inside the Plone instance folder. It contains the super-user
credentials you’ll need to create the Bika site.


Test your setup

First, start the ZEO Server:
bin/plonectl zeoserver start
Then you must start one ZEO Client in the foreground, noting error messages if any
and taking corrective action if so:
bin/plonectl client1 fg
If you see INFO Zope Ready to handle requests then the server is running.
Press Control+C to stop the foreground client.
To start the Plone server normally, use the following command:
bin/plonectl start


Add a new Plone/Bika instance.

Open a browser and go to http://localhost:8080/. Select “Add Plone Site”,
and ensure that the Bika LIMS option is checked, then submit the form.





Windows Installation Steps

Download and Install Plone

Currently Bika LIMS for Windows requires a Plone 4.3.1 installation.

Download the Windows Installer
Execute the installer and follow through the steps

For this guide we will assume the default location of C:Plone43
For more information visit: http://docs.plone.org/manage/installing/index.html


Installing Bika LIMS


Open C:\Plone43\buildout.cfg in a text editor
Find the section beginning with eggs =, and add bika.lims to the existing
entries:
eggs =
Plone
Pillow
bika.lims

Run buildout from cmd (press ⊞ Win, type cmd, press ↵ Enter):
C:> cd C:\Plone43
C:\Plone43> bin\buildout.exe

A successful buildout should output:
Updating run-instance.
Updating service.
*************** PICKED VERSIONS ****************
[versions]
bika.lims = 3.0
cairocffi = 0.5.4
cairosvg = 1.0.7
cssselect = 0.9.1
gpw = 0.2
magnitude = 0.9.3
products.advancedquery = 3.0.3
products.atextensions = 1.1
pycparser = 2.10
pyphen = 0.9.1
*************** /PICKED VERSIONS ***************


If you see the following errors: Error: Couldn't install: cffi 0.8.2 or
Error 5: Access is denied refer to Troubleshooting below.


Setting up Plone Services


Run cmd as Administrator (press ⊞ Win, type: cmd, press CTRL``+``⇧ Shift``+``↵ Enter)
Navigate to the Plone root directory:
C:\> cd C:\Plone43

Install, Start and bring your newly created instance to the Foreground
This should stop the default Plone 4.3 Service:
C:\Plone43> bin\instance.exe install
C:\Plone43> bin\instance.exe start
C:\Plone43> bin\instance.exe fg
If you see INFO Zope Ready to handle requests then the server is running




Add a new Plone/Bika instance.

Open a browser and go to http://localhost:8080/. Select “Add Plone Site”,
and ensure that the Bika LIMS option is checked, then submit the form.





Upgrading Bika LIMS
If a new release of the LIMS is made available, the following procedure will
upgrade your existing installation to use the new packages.

Backup

Stop Plone, and make a full backup of your instance before continuing:
bin/plonectl stop
bin/fullbackup


Buildout

Run buildout with the “-n” option, to retreive the latest version of Bika
LIMS and it’s dependencies:
bin/buildout -n


Restart Plone

Just as during the installation, it’s useful to start a single zeo client
in the foreground to check for errors:

bin/plonectl client1 stop
bin/plonectl client1 fg

To restart Plone issue a command like this:

bin/plonectl restart



Migrate

Go to site-setup, and click Add-ons. Find Bika LIMS in the list of
activated addons, and click the bika.lims upgrade button.





Installing Bika-LIMS source
You should already have Plone and Bika LIMS installed. The paths and commands
below are for Linux, but following along in windows is simple.

Download source:
cd Plone/zeocluster/src
git clone https://github.com/bikalabs/Bika-LIMS.git bika.lims

Select a git branch:
We use git-flow to manage the git repository, with some quirks. The ``next``
branch contains code for the next hotfix or release, and ``develop`` contains
unreleased code merged from ``feature/*`` branches. ::

git checkout develop

Edit buildout.cfg:
develop =
src/bika.lims

Restart Plone

bin/plonectl restart all



The Bika LIMS distribution in Plone/buildout-cache/eggs/bika.lims* will now be
ignored by Plone, and the copy in src/bika.lims is used instead.


Troubleshooting

(Windows) Dependencies
You need to install some dependencies manually
Download and install _bika_dependencies(Plone 4.3.1).exe_ from https://github.com/zylinx/bika.dependencies
This fixes the fact that Plone's buildout cannot compile the libraries required by weasyprint.
It installs the pre-compiled binaries into System32 and Plone's installation folder instead.
(Windows) Privileges
Open ``Explorer`` >> Navigate to ``C:\`` >> Right-Click on the ``Plone43`` directory >> select ``roperties``
Select the ``Security`` Tab >> Click ``Edit`` >> Check ``Full Control`` Allow for necessary User / Group
Click ``Apply``
(Windows) If you are having trouble starting bin\instance.exe fg as follows:
The program seems already to be running. If you believe not,
check for dangling .pid and .lock files in var/.

* You can try the following steps:

-Find the running process id by opening the .pid file within your instance's var/ directory.
-Open the Windows Task Manager and stop the running process with the above identifier.
-Delete all .pid and .lock files in your instance's var/ directory.
-Start your instance.

* OR::

-Run services.msc
-Search for Plone 4.3
-Try Starting or Stopping it along with your instance
To empty/reset the database, run the following:
rm -rf var/filestorage
bin/buildout
If your admin user does not exist or you forget the password:
bin/plonectl adduser admin admin
AttributeError: type object ‘IIdServer’ has no attribute ‘__iro__’
* The code for "bika.lims" not installed or not included
* Running buildout again usually fixes this



Log errors to sentry.bikalabs.com
Add raven to your buildout.cfg in the eggs = section:
eggs =
...
raven
Then add the following snippet to your [instance] section. If you are using a
ZEO configuration, add this to all [clientX] sections:
event-log-custom =
%import raven.contrib.zope
<logfile>
path ${buildout:directory}/var/client1/event.log
level INFO
max-size 5 MB
old-files 5
</logfile>
<sentry>
dsn http://90723864025d4520b084acee225ddb8a:[email protected]/2
level ERROR
</sentry>
Add raven 4.0.4 into [versions] section:
[versions]
...
raven = 4.0.4
Run bin/buildout, and restart Plone.


3.1.15 (2017-05-27)

Fixed broken Release



3.1.14 (2017-05-26)
Pinned Plone version to 4.3.11


3.1.13 (2016-12-28)
LIMS-2299: Add ui for editing ar_count in all analysisrequest lists
- Removed commented HTML that was causing Chameleon to choke when adding ARs.


3.1.12 (2016-12-15)
HEALTH-569 Bar code printing not working on sample registration
- Pinned CairoSVG to 1.0.20 (support for Python 2 removed in later versions)


3.1.11 (2016-04-22)
LIMS-2252: Partitions not submitted when creating AR if the form is submitted before partitions are calculated
LIMS-2223: Saving a recordswidget as hidden fails
LIMS-2225: Formatted results not displayed properly in Worksheet’s transposed layout
LIMS-2001: Duplicate for one analysis only
LIMS-1809: Typos. Perdiod an missing spaces
LIMS-2221: Decimal mark doesn’t work in Sci Notation
LIMS-2219: Using a SciNotation diferent from ‘aE+b / aE-b’ throws an error
LIMS-2220: Raw display of exponential notations in results manage views
LIMS-2216: Results below LDL are not displayed in reports
LIMS-2217: Specifications are not set in analyses on Analysis Request creation
LIMS-2218: Result is replaced by min or max specs when “<Min” or “>Max” fields are used
LIMS-2215: Decimal mark not working
LIMS-2203: ‘Comma’ as decimal mark doesnt work
LIMS-2212: Sampling round- Sampling round templates show all system analysis request templates
LIMS-2209: error in manage analyises
LIMS-1917: Inconsistencies related to significant digits in uncertainties
LIMS-2015: Column spacing on Client look-up
LIMS-1807: Validation for Start Date - End date relationship while creating invoices and price lists
LIMS-1991: Sort Order for Analysis Categories and Services
LIMS-1521: Date verified column for AR lists
LIMS-2194: Error when submitting a result
LIMS-2169: Cannot start instance
WINE-125: Client users receive unauthorized when viewing some published ARs


3.1.10 (2016-01-13)

Updated Plone to 4.3.7
Dashboard: replace multi-bar charts by stacked-bar charts

LIMS-2177: template_set error when no template has been selected
HEALTH-410: AR Create. Auto-complete Contact field if only 1
LIMS-2175: “NaN” is shown automatically for result fields that have AS with “LDL” enabled and then an error is shown after submitting a result
LIMS-1917: Inconsistencies related to significant digits in uncertainties
LIMS-2143: Statements vs Invoices
LIMS-1989: Retracting a published AR fails if one or more ASs has been retracted before publishing
LIMS-2071: Can’t generate Invoice Batch/Monthly Statements
WINE-71: Instrument. BBK WS export to FIA fails
WINE-72: Instrument. BBK WineScan Auto Import fails
WINE-58: Instrument. BBK FIAStar import fails
WINE-76: WineScan FT120 Import warnings incorrect?
LIMS-1906: Spaces should be stripped out of the keywords coming from the Instrument
LIMS-2117: Analysis Categories don’t expand on Analysis Specification creation
LIMS-1933: Regression: Selecting secondary AR in client batches, fails.
LIMS-2075: Ensure hiding of pricing information when disabled in site-setup
LIMS-2081: AR Batch Import WorkflowException after edit
LIMS-2106: Attribute error when creating AR inside batch with no client.
LIMS-2080: Correctly interpret default (empty) values in ARImport CSV file
LIMS-2115: Error rises when saving a Calculation
LIMS-2116: JSONAPI throws an UnicodeDecodeError
LIMS-2114: AR Import with Profiles, no Analyses are created
LIMS-2132: Reference Analyses got the same ID
LIMS-2133: Once in a while, specs var is going empty in results reports
LIMS-2136: Site Error on AR Verification
LIMS-2121: Fix possible Horiba ICP csv handling errors
LIMS-2042: Improving Horiba ICP to avoid Element Symbols as keywords
LIMS-2123: Analysis Categories don’t expand in Worksheet Templates
LIMS-1993: Existing Sample look-up for AR Create in Batch does not work
LIMS-2124: QR missing on sticker preview
LIMS-2147: Add ARImport schema fields when creating ARs
LIMS-409: ShowPrices setting was getting ignored in some contexts
LIMS-2062: Cancelled ARs no longer appear in analysisrequest folder listings
LIMS-2076: Cancelled batches appear in listing views
LIMS-2154: Hide inactive ARs from BatchBook view
LIMS-2134: Inactive services appear in AR Create
LIMS-2139: WS Blank and Control Selection renderes whole page
LIMS-2156: Ignore blank index values when calculating ReferenceAnalysesGroupID
LIMS-2157: Cancelled ARs appear in AR listing inside Batches
LIMS-2042: Horiba ICP: Missing ‘DefaultResult’ for imported rows
LIMS-2030: Assign ARs in alphabetical ID order to WS
LIMS-2167: Cannot assign a QC analysis to an invalid instrument
LIMS-2067: Prevent initial method/instrument query for each analysis
WINE-82: Ignore invalid entry in Sample field during AR creation
LIMS-1717: Workflow transitions in edit context do not take effect
WINE-111: Do not attempt formatting of ‘nan’ analysis result values
WINE-114: Some users cannot view published ARs (unauthorised)
WINE-122: Transposed worksheet layout failed while rendering empty slots
LIMS-2149: Missing analyses can cause error accessing worksheet
LIMS-1521: Date verified column for AR lists
LIMS-2015: Column spacing on Client look-up


3.1.9 (2015-10-8)
LIMS-2068: LIMS-2068 Urgent. Analysis Catgories don’t expand
LIMS-1875: Able to deactivate instruments and reference samples without logging in
LIMS-2049: Displaying lists doesn’t work as expected in 319
LIMS-1908: Navigation tree order
LIMS-1543: Add “Security Seal Intact Y/N” checkbox for partition container
LIMS-1544: Add “File attachment” field on Sample Point
LIMS-1949: Enviromental conditions
LIMS-1549: Sampling Round Templates privileges and permissions
LIMS-1564: Cancelling a Sampling Round
LIMS-2020: Add Sampling Round - Department not available for selection
LIMS-1545: Add “Composite Y/N” checkbox on AR Template
LIMS-1547: AR Templates tab inside Sampling Round Template
LIMS-1561: Editing a Sampling Round
LIMS-1558: Creating Sampling Rounds
LIMS-1965: Modified default navtree order for new installations
LIMS-1987: AR Invoice tab should not be shown if pricing is toggled off
LIMS-1523: Site Error when transitioning AR from ‘Manage Analyses’ or ‘Log’ tab
LIMS-1970: Analyses with AR Specifications not displayed properly in AR Add form
LIMS-1969: AR Add error when “Categorise analysis services” is disabled
LIMS-1397: Fix Client Title accessor to prevent catalog error when data is imported
LIMS-1996: On new system with no instrument data is difficult to get going.
LIMS-2005: Click on Validations tab of Instruments it give error
LIMS-1806: Instrument Interface. AQ2. Seal Analytical - Error
LIMS-2002: Error creating Analysis Requests from batch.
LIMS-1996: On new system with no instrument data it is difficult to get going. The warnings could be confusing
LIMS-1312: Transposed Worksheet view, ARs in columns
LIMS-1760: Customised AR Import spreadsheets (refactored, support importing to Batch)
LIMS-1548: Client-specific Sampling Round Templates
LIMS-1546: Sampling Round Template Creation and Edit view
LIMS-1944: Prevent concurrent form submissions from clobbering each other’s results
LIMS-1930: AssertionError: Having an orphan size, higher than batch size is undefined
LIMS-1959: Not possible to create an AR
LIMS-1956: Error upgrading to 319
LIMS-1934: Hyperlinks in invoices
LIMS-1943: Stickers preview and custom stickers templates support
LIMS-1855: Small Sticker layout. QR-code capabilities
LIMS-1627: Pricing per Analysis Profile
HEALTH-279: AS IDs to be near top of page. Columns in AS list
LIMS-1625: Instrument tab titles and headers do not correspond
LIMS-1924: Instrument tab very miss-titled. Internal Calibration Tests
LIMS-1922: Instrument out of date typo and improvement
HEALTH-175: Supplier does not resolve on Instrument view page
LIMS-1887: uniquefield validator doesn’t work properly
LIMS-1869: Not possible to create an Analysis Request
LIMS-1867: Auto-header, auto-footer and auto-pagination in results reports
LIMS-1743: Reports: ISO (A4) or ANSI (letter) pdf report size
LIMS-1695: Invoice export function missing
LIMS-1812: Use asynchronous requests for expanding categories in listings
LIMS-1811: Refactor AR Add form Javascript, and related code.
LIMS-1818: Instrument Interface. Eltra CS-2000
LIMS-1817: Instrument Interface. Rigaku Supermini XRF
- New System Dashboard for LabManagers and Admins


3.1.8.3 (2015-10-01)
LIMS-1755: PDF writer should be using a world-writeable tmp location
LIMS-2041: Resolve ${analysis_keyword) in instrument import alert.
LIMS-2041: Resolve translation syntax error in instrument import alert
LIMS-1933: Secondary Sample selection in Client Batches does not locate samples


3.1.8.2 (2015-09-27)
LIMS-1996: On new system with no instrument data is difficult to get going.
LIMS-1760: Customised AR Import spreadsheets (refactored, support importing to Batch)
LIMS-1930: AssertionError: Having an orphan size, higher than batch size is undefined
LIMS-1818: Instrument Interface. Eltra CS-2000
LIMS-1817: Instrument Interface. Rigaku Supermini XRF
LIMS-2037: Gracefully anticipate missing analysis workflow history
LIMS-2035: Prevent Weasyprint flooding due to asyncronous publish


3.1.8.1 (2015-06-23)
LIMS-1806: Instrument Interface. AQ2. Seal Analytical - Error
LIMS-1760: Customised AR Import spreadsheets (refactored, support importing to Batch)
Fix portlets.xml for Plone 4.3.6 compatibility


3.1.8 (2015-06-03)
LIMS-1923: Typo InstrumentCalibration
HEALTH-287: Hyperlink in Instrument messages
LIMS-1929: Translation error on Instrument Document page
LIMS-1928 Asset Number on Instruments’ Certificate tab should use Instrument’s default
LIMS-1929: Translation error on Instrument Document page
LIMS-1773: Instrument. Thermo Fisher ELISA Spectrophotometer
LIMS-1697: Error updating bika.lims 317 to 318 via quickinstaller
LIMS-1820: QC Graphs DateTime’s X-Axis not well sorted
LIMS-280 : System IDs starting from a specific value
LIMS-1819: Bika LIMS in footer, not Bika Lab Systems
LIMS-1808: Uncertainty calculation on DL
LIMS-1522: Site Error adding display columns to sorted AR list
LIMS-1705: Invoices. Currency unit overcooked
LIMS-1806: Instrument Interface. AQ2. Seal Analytical
LIMS-1770: FIAStar import ‘no header’
LIMS-1771: Instrument. Scil Vet abc Plus
LIMS-1772: Instrument. VetScan VS2
LIMS-1507: Bika must notify why is not possible to publish an AR
LIMS-1805: Instrument Interface. Horiba JY ICP
LIMS-1710: UnicodeEncode error while creating an Invoice from AR view
WINE-44: Sample stickers uses Partition ID only if ShowPartitions option is enabled
LIMS-1634: AR Import fields (ClientRef, ClientSid) not importing correctly
LIMS-1474: Disposed date is not shown in Sample View
LIMS-1779: Results report new fields and improvements
LIMS-1775: Allow to select LDL or UDL defaults in results with readonly mode
LIMS-1769: Allow to use LDL and UDL in calculations.
LIMS-1700: Lower and Upper Detection Limits (LDL/UDL). Allow manual input
LIMS-1379: Allow manual uncertainty value input
LIMS-1324: Allow to hide analyses in results reports
LIMS-1754: Easy install for LIMS’ add-ons was not possible
LIMS-1741: Fixed unwanted overlay when trying to save supply order
LIMS-1748: Error in adding supply order when a product has no price
LIMS-1745: Retracted analyses in duplicates
LIMS-1629: Pdf reports should split analysis results in different pages according to the lab department
Some new ID Generator’s features, as the possibility of select the separator type
LIMS-1738: Regression. ‘NoneType’ object has no attribute ‘getResultsRangeDict’
LIMS-1739: Error with results interpretation field of an AR lacking departments
LIMS-1740: Error when trying to view any Sample
LIMS-1724: Fixed missing start and end dates on reports
LIMS-1628: There should be a results interpretation field per lab department
LIMS-1737: Error when adding pricelists of lab products with no volume and unit
LIMS-1696: Decimal mark conversion is not working with “<0,002” results type
LIMS-1729: Analysis Specification Not applying to Sample when Selected
LIMS-1507: Do not cause exception on SMTPServerDisconnect when publishing AR results.


3.1.7 (2015-02-26)
LIMS-1693: Error trying to save a new AR
LIMS-1570: Instrument interface: Roche Cobas Taqman 48
LIMS-1520: Allow to invalidate verified ARs
LIMS-1690: Typo. Instrument page
LIMS-1688: After AR invalidation, ARs list throws an error
LIMS-1569: Instrument interface: Beckman Coulter Access 2
LIMS-1689: Error while creating a new invoice batch
LIMS-1266: Sampling date format error
LIMS-1365: Batch search parameters on Work sheets/Work sheets insides Batches
LIMS-1428: After receiving a sample with Sampling Workflow enable is not possible to input results
LIMS-1540: When accent characters are used in a “Sample Type” name, it is not possible to create a new AR
LIMS-1617: Error with bin/test
LIMS-1571: Instrument interface: Sysmex XS-1000i
LIMS-1574: Fixed AR and Analysis attachments
LIMS-1670: Fixed windows incompatibility in TAL (referencewidget.pt)
LIMS-1594: Added option to select landing page for clients in configuration registry
LIMS-1594: Re-ordered tabs on Client home page
LIMS-1520: Allow to invalidate verified ARs
LIMS-1539: Printable Worksheets. In both AR by row or column orientations
LIMS-1199: Worksheet totals in WS lists
LIMS-257: Set Blank and Warning icons in Reference Sample main view
LIMS-1636: Batch Sample View crash
LIMS-1524: Invalidate email does not have variables populated
LIMS-1572: Instrument interface: Sysmex XS-500i
LIMS-1575: Thermo Arena 20XT
LIMS-1423: Save details when AR workflow action kicked off
LIMS-1624: Import default test.xlsx fails
LIMS-1614: Error when selecting Analysis Administration Tab after receiving a sample with Sampling Workflow enabled
LIMS-1605: Tescan TIMA interface
LIMS-1604: BioDrop uLite interface
LIMS-1603: Life Technologies Qubit interface
LIMS-1517: Storage field tag untranslated?
LIMS-1518: Storage Location table
LIMS-1527: CC Contact on AR view (edit) offers all contacts in system
LIMS-1536: Add button [Add], to alow quickly addings in referencewidget
LIMS-1587: Better support for extension of custom sample labels
LIMS-1622: Version Check does not correctly check cache
LIMS-1623: Implement bika-frontpage as a BrowserView


3.1.6 (2014-12-17)
LIMS-1530: Scrambled Analysis Category order in Published Results
LIMS-1529: Error while inserting an AR with container-based partitioning is required
LIMS-1460: Additional field in AR for comments or results interpretation
LIMS-1441: An error message related to partitions unit is shown when selecting analysis during AR creation
LIMS-1470: AS Setup. File attachment field tag is missing
LIMS-1422: Results doesn’t display yes/no once verified but 1 or 0
LIMS-1486: Typos in instrument messages
LIMS-1498: Published Results not Showing for Logged Clients
LIMS-1445: Scientific names should be written in italics in published reports
LIMS-1389: Units in results publishing should allow super(sub)script format, for example in cm2 or m3
LIMS-1500: Alere Pima’s Instrument Interfice
LIMS-1457: Exponential notation in published AR pdf should be formatted like a×10^b instead of ae^+b
LIMS-1334: Calculate result precision from Uncertainty value
LIMS-1446: After retracting a published AR the Sample gets cancelled
LIMS-1390: More workflow for Batches
LIMS-1378: Bulking up Batches
LIMS-1479: new-version and upgrade-steps should be python viewlets
LIMS-1362: File attachment uploads to Batches
LIMS-1404: New Batch attributes (and their integration with existing ones on Batch views)
LIMS-1467: Sample Point Lookup doesn’t work on AR modify
LIMS-1363: Batches per Client
LIMS-1405: New Sample and AR attributes
LIMS-1085: Allow Clients to add Attachments to ARs
LIMS-1444: In AR published report accredited analysis services are not marked as accredited
LIMS-1443: In published reports the publishing date is not shown in the pdf
LIMS-1420: Status filter is not kept after moving to next page
LIMS-1442: Sample Type is not filtred by Sample Point
LIMS-1448: Reports: when you click on “Analysis turnaround time” displays others
LIMS-1440: Error when trying to publish with analysis from different categories
LIMS-1459: Error when checking instrument validity in manage_results
LIMS-1430: Create an AR from batch allows you to introduce a non existent Client and Contacts don’t work properly

After modifying analysis Category, reindex category name and UID for all subordinate analyses
Setup data import improvements and fixes
Simplify installation with a custom Plone overview and add site



3.1.5 (2014-10-06)
LIMS-1082: Report Barcode. Was images for pdf/print reports etc
LIMS-1159: reapply fix for samplepoint visibility
LIMS-1325: WSTemplate loading incompatible reference analyses
LIMS-1333: Batch label replace with standard Plone keyword widget
LIMS-1335: Reference Definitions don’t sort alphabetically on WS Template lay-outs
LIMS-1345: Analysis profiles don’t sort
LIMS-1347: Analysis/AR background colour to be different to for Receive and To be Sampled
LIMS-1360: Number of analyses in ARs folder view
LIMS-1374: Auto label printing does not happen for an AR drop-down receive
LIMS-1377: Error when trying to publish after updating branch hotfix/next or develop
LIMS-1378: Add AR/Sample default fields to Batch
LIMS-1395: front page issue tracker url
LIMS-1402: If no date is chosen, it will never expire.” not been accomplished
LIMS-1416: If a sample point has a default sample type the field is not pulled automatically during AR template creation
LIMS-1425: Verify Workflow (bika_listing) recursion

added ‘getusers’ method to JSON API
Added ‘remove’ method to JSON API
Added AR ‘Copy to new’ action in more contexts
Added basic handling of custom Sample Preparation Workflows
Added decimal mark configuration for result reports
Added help info regards to new templates creation
Added IAcquireFieldDefaults - acquire field defaults through acquisition
Added IATWidgetVisibility - runtime show/hide of AT edit/view widgets
Added watermark on invalid reports
Added watermark on provisional reports
Alert panel when upgrades are available
All relevant specification ranges are persisted when copying ARs or adding analyses
Allow comma entry in numbers for e.g. German users
Bika LIMS javascripts refactoring and optimization
Fix ZeroDivisionError in variation calculation for DuplicateAnalysis
Fixed spreadsheet load errors in Windows.
Fixed template rendering errors in Windows
JSONAPI update: always use field mutator if available
JSONAPI: Added ‘remove’ and ‘getusers’ methods.
Refactored ARSpecs, and added ResultsRange field to the AR



3.1.4.1-2 (2014-07-24)
3.1.4 release was broken, simple ARs could not be created.


3.1.4.1 (2014-07-24)
3.1.4 release was broken, simple ARs could not be created.
LIMS-1339: Published reports should use “±” symbol instead of “+/-”
LIMS-1327: Instrument from worksheet
LIMS-1328: Instrument calibration test graphs do not work on multiple samples
LIMS-1347: Analysis/AR background colour to be different to for Receive and To be Sampled
LIMS-1353: Analyses don’t sort in Attachment look-up

Preview for Results reports

Single/Multi-AR preview
Allows to cancel the pre-publish/publish process
Allows to make visible/invisible the QC analyses
Allows to add new custom-made templates
JS machinery allowed for pdf reporting





3.1.4 (2014-07-23)
LIMS-113: Allow percentage value for AS uncertainty
LIMS-1087: Prevent listing of empty categories
LIMS-1203: Fix Batch-AnalysisRequests query
LIMS-1207: LIMS-113 Allow percentage value for AS uncertainty
LIMS-1221: use folder icon for ARImports in nav
LIMS-1240: fix permissions for “Copy To New” in AR lists
LIMS-1330: handle duplicate of reference analysis
LIMS-1340: soft-cache validator results
LIMS-1343: Prevent sudden death if no version information is available
LIMS-1352: SamplingWorkflow not saved to sample
LIMS-334: Add Service/ExponentialFormatPrecision
LIMS-334: Added ExponentialFormatThreshold setting
LIMS-334: Allow exponential notation entry in numeric fields
LIMS-334: Exponent Format used for analysis Result
LIMS-334: Remove duplicate getFormattedResult code
LIMS-83: Update Method->calculation reference version when Calculation changes

Formula statements can be written on multiple lines for clarity.
Replace kss-bbb ajax-spinner with a quieter one
bika.lims.utils.log logs location url correctly



3.1.3 (2014-07-17)
Missing fixes from 3.1.2
LIMS-671: Preferred/Restricted client categories
LIMS-1251: Supply order permission error
LIMS-1272: Currency in Price Lists
LIMS-1310: Broken AnalysisProfile selector in AR Add form.


3.1.2 (2014-07-15)
LIMS-1292: UI fix Retracted ARs workfow: Warning msg on “full” retract.
LIMS.1287: UI fix Report parameter formatting
LIMS-1230: UI fix Livesearch’s box
LIMS-1257: UI fix Long titles in Analysis Profiles, Sample Points, etc.
LIMS-1214: UI fix More columns
LIMS-1199: UI fix Worksheet listing: better columns
LIMS-1303: jsi18n strings must be added to bika-manual.pot. i18ndude cannot find.
LIMS-1310: Filter SamplePoints by client in AR Template Edit View
LIMS-1256: Client objects included in AR-Add filters for Sample Point etc.
LIMS-1290: Allows Analyst to retract analyses, without giving extra permissions.
LIMS-1218: Slightly nicer monkey patch for translating content object ID’s and titles.
LIMS-1070: Accreditation text can be customised in bika_setup
LIMS-1245: off-by-one in part indicators in ar_add
LIMS-1240: Hide “copy to new” from Analyst users

LIMS-1059: Added worksheet rejection workflow
RejectAnalysis (Analysis subclass (has IAnalysis!)) workflow transition.

Does not retract individual Analysis objects - instead, forces their state
back to “Received”, and assigns them onto newly created WS.

Sets attributes on src and dst worksheets:
WS instance rejected worksheet attribute: .replaced_by = UID
WS instance replacement worksheet attribute: .replaces_rejected_worksheet:UID




Fixed some i18n and encoding snags, and updated translations.


3.1.1 (2014-06-29)
Some bugs which only appear while running Windows, have been fixed.
LIMS-1281: Fix Restricted and Default categories in ar_add
LIMS-1275: Fix lax Aalyst permissions
LIMS-1301: jsonapi can set ReferenceField=””
LIMS-1221: Icon for ARImports folder in Navigation
LIMS-1252: AR Published Results Signature Block formatting
LIMS-1297: Update frontpage


3.1 (2014-06-23)

Product and Analysis specifications per AR
Incorrect published results invalidation workflow
Improved re-testing workflow
Adjustment factors on worksheets
Using ‘< n’ and ‘> n’ results values
Sample Storage locations
Sample Categories
Analysis Prioritisation
Bulk AR creation from file
Results reports inclusion of relevant QC results
Supply Inventory and Orders
JSON interface
Management Reports export to CSV
Enhancements to AR Batching
Enhancements to Results Reports
Instrument management module

Calibration certificates, maintenance, Instrument QC
Method, Instrument and Analysis integrity


Instrument interfaces

Agilent MS ‘Masshunter Quant’
Thermo Gallery
Foss Winescan FT 120, Auto


Invoices

Per AR, Analysis per Invoice line.
Per Supply Order, inventory item per Invoice line
Invoices by email
Invoice ‘batches’ for selected time period, ARs aand Orders per Invoice line
Invoice batch export to accounts systems
Price lists. Analysis Services and Supplies





3.1.3036 (2014-05-30)
Added two checboxes in BikaSetup > Security:
- Allow access to worksheets only to assigned analysts (Y/N)
- Only lab managers can create and amange new worksheets (Y/N)
** IMPORTANT NOTES **
The 3036 upgrade sets the above options to true by default, so after
being upgraded, only the labmanagers will be able to manage WS and the
analysts will only have access to the worksheets to which they are
assigned. These defaults can be changed in BikaSetup > Security.


3.0 (2014-03-15)

Fix some out-dated dependencies that prevented the app from loading.
Development of the current bika 3.0 code has slowed, and our efforts have been focused on
the 3.01a branch for some time.



3.0rc3.5.1 (2013-10-25)
Fix CSS AR Publication error
Fix error displaying client sample views


3.0rc3.5 (2013-10-24)
Requires Plone 4.3. For information on upgrading Plone, visit
http://plone.org/documentation/manual/upgrade-guide

Fix a serious error saving Analysis results.
Improve upgrade handling in genericsetup profile
Fix errors in setupdata loader
Force UTF-8 encoding of usernames (imported client contacts can now login)
Removed outdated test setup data
Handle duplicate request values in bika_listing
ID server handles changes in ID schemes without error
Remove folder-full-view from front-page view
Updated workflow and permissions to prevent some silly errors
Add robot tests
Add default robots.txt



3.0rc3.2 (2013-06-28)

Fix site-error displaying upgraded instruments
Fix spinner (KSS is not always enabled)
Add extra save button in ar_add
Label Printing: “Return to list” uses browser history
Bold worksheet position indicators
Remove version.txt (use only setup.py for version)



3.0rc3.1 (2013-06-27)

Fix permission name in upgrade step



3.0rc3 (2013-06-25)

Many instrument management improvements! (Merge branch ‘imm’)
Removed ReferenceManufacturer (use of generic Manufacturer instead)
Removed ReferenceSupplier (use Supplier instead)
Improve service/calculation interim field widgets
Allows service to include custom fields (without calculation selected)
Fix services display table categorisation in Analysis Specification views
Stop focusing the search gadget input when page load completes. (revert)
Limit access to Import tab (BIKA: Manage Bika)
New permission: “BIKA: Import Instrument Results”
New permission: “BIKA: Manage Login Details” - edit contact login details
Some late changes to better handle the updates to ID creation
Plone 4.3 compatibility (incomplete)
Use Collections as a base for Queries (incomplete)
Many many bugfixes.



3.0rc2.3 (2013-01-29)

Fix bad HTML



3.0rc2.2 (2013-01-28)

Fix an error during AR Publish



3.0rc2.1 (2013-01-21)

Fix bad HTML
Pin collective.js.jqueryui version to 1.8.16.9



3.0rc2 (2013-01-21)

Updated all translations and added Brazilian Portuguese
RecordsWidget: subfield_types include “date”
RecordsWidget: Automatic combogrid lookups
Added all bika types to Search and Live Search
Transition SamplePartition IDs to new format (SampleType-000?-P?
Always handle non-ASCII characters: UTF-8 encoding everywhere
Accept un-floatable (text) results for analyses
Hidden InterimFields in Calculations
Added InterimFields on AnalysisServices for overriding Calculation Interimfields.
Disable KSS inline-validation
Categorized analyses in AR views
Added remarks for individual analyses
Improved Javascript i18n handling
Improved default permissions

New reports

Added ‘Analysis summary per department’ (merge of ‘Analyses lab department weekly’ and ‘Analyses request summary by date range’
Added ‘Analyses performed as % of total’ report
Added Analyses per lab department report
Added ‘Samples received vs. samples reported’ report
Added Daily Samples Received report




Many many bugfixes.



3.0rc1 (2012-10-01)

Removed Bika Health data from released egg
Remove remarks from portal_factory screens
Add Month/Year selectors to default datetime widget
ClientFolder default sorting.
Date formats for jquery datepicker
Don’t overwrite the Title specified in @@plone-addsite
Bug fixes



3.0rc1 (2012-09-25)
### Changes

Requires Python 2.7 (Plone 4.2)
Add GNUPlot dependency
Added client sample points
Added Sampling Deviation selections
Added Ad-Hoc sample flag
Added Sample Matrices (Sampletype categorisation)
Added custom ResultsFooter field in bika setup
Added PDF Attachments to published results
Electronic signature included in Results and Reports
Login details form to create users for LabContacts
Sampling workflow is disabled by default
Methods are versioned by default
Methods are publicly accessible by default
Queries WIP
Reports WIP
Modified label layouts for easier customisation
Cleaned print styles
Use plonelocales for handling Date/Time formats
SMS and Fax setup items are disabled by default



2012-06-21

Partitioning & Preservation automation
Reports
Sample point & types relations in UI
AR template enhancements
Sample and AR layout improvements
Labels
Configuration logs
Faster indexing
JavaScript optimisation
Better IE compatibility
Set-up worksheet improvements
Updated translations
Workflow tweaks
Tweaks to Icons, Views & Lists



2012-04-23

Optional sampling and preservation workflows and roles.
Sample partitioning.
AR templates - Sample point & Sample type restrictions.
Reports - framework only. ‘Analysis per service’ shows what is planned.
Improved i18n handling, and updated strings from Transifex.
Numerous performance enhancements
Analysis Service & Method associations.
An improved Analysis Service pop-up window.
Sample Type and Sample Point relationship.
Currency selection from zope locales
Combined AR View and Edit tabs.
Re-factored AR ‘Add/Remove Analyses’ screen
Store the date of capture for analysis results
Append only remarks fields on more objects.



2012-01-23


Made Bika compatible with Plone 4.1
Sampler and Preserver roles, users and permissions
Sampling and Preservation workflows
Inactive and Cancellation Workflows
Pre-preserved Containers
Automatic versioning for some bika_setup types
Analyst and Instrument on Worksheet templates
XLSX setup data loader
Sample disposal date based on date sampled, not date received.
Internal ID Server by default
user defined calculations and interim fields
Dry Matter results option does not appear until enabled in Site Setup
Accreditation portlet disabled until enabled in Site Setup
BikaListingView
New icons
(mostly) usable at 800x600
Column display toggles
Future dated samples and ARs
Accreditation template: i18n in locales/manual.pot/accreditation_*
intermediate workflow state for analyses requiring attachments
Labmanager has Site Administrator role (not Manager)
‘Indeterminate’ results
use portal_factory everywhere
working test suite
static resource directories
Merged BikaMembers types
CoordinateField/Widget
DurationField/Widget
CustomRecordsWidget




2.3.3 Bug fix release


Inclusion of BikaMembers 0.0.3. No changes to bika code, version bumped
to facilitate release of new BikaMembers version.




2.3


Analysis categories introduced
Analysis service result restrictions - specification of possible results
Allow site and client specification of email and fax subject line content
Additional instrument/export formats:
WinescanFT120, WinescanAuto, FIAStar and Bartelt’s data-collector
Export worksheet analyses to instruments
PDF as a result output option
SMS result output option
Result publication options synchronized and signatures added to emails
Email batching of query results conforms to result mailing
IDServer batching of unique id request
Optmization of worksheet searching on selection criteria
Extract tab added with extract for analysis services or profiles
Batch update of analysis service prices
German translation module added
Added a light query form which excludes analysis category and service
Batch size setting in analysis request lists
BikaMembers replaces UpfrontContacts
ATSchemaEditor removed
Significant performance improvements
Resolve client action conflicts
Sampled date validation
Drymatter formatting on output corrected
Correct default none workflows
Review portlet optimization
Pricelist prints blank for analysis service with price not defined




2.2


Attachments permitted on analysis requests and analyses
Worksheet resequencing, and sort order for worksheet analysis selection
Worksheet deletion only available for open worksheets
Portlet to provide export of analysis services and analysis profiles
Requirement for unique analysis service names, analysis service keywords,
instrument import keywords and analysis profile keywords enforced.
Report headings and formats standardized accross different reports
AR import alternative layout provided with selection, including profiles
Progress bar introduced for long running processes




2.1.1


Disposal Date for Samples and Retention Period per Sample Type added.
Various new search criteria added.
Standard Manufacturers introduced.
Labels for Standard Samples introduced.
“Print” and “Email” facilities introduced for lists of Standard Samples and Standard Stocks.
“Duplicate” facility for Analysis Services introduced.
Addresses added to top of emailed query results.
Labels for Samples and Analysis Requests changed.
Analysis Services can have multiple Methods.
Change log introduced for Methods.
Methods added to left navigation bar.
List of Methods included in pop-up for Analyses.
Documents may be uploaded for Methods.




2.1


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




1.2.1


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


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-
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.

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
1418473: Updated start-id-server.bat for Win2K & Win XP




1.1.2


1423205: Show logs to labmanager set-up
1291750: Added default ID prefixes for Order and Statement
1424589: Late analysis alert to be calulated on date received




1.1.1


Updated portlets with Plone 2.1 style definition list markup
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)




Authors and maintainers

Bika Lab Systems, http://bikalabs.com
Naralabs, http://naralabs.com
RIDING BYTES, http://ridingbytes.com