bika.lims 3.1.15

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

Linux Installation Steps

1. 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

2. 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

3. 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.

4. 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

5. 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

1. 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

2. Installing Bika LIMS

   1. Open C:\Plone43\buildout.cfg in a text editor

   2. Find the section beginning with eggs =, and add bika.lims to the existing entries:

      eggs =
          Plone
          Pillow
          bika.lims

   3. Run buildout from cmd (press ⊞ Win, type cmd, press ↵ Enter):

      C:> cd C:\Plone43
      C:\Plone43> bin\buildout.exe

   4. 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.

3. Setting up Plone Services

   1. Run cmd as Administrator (press ⊞ Win, type: cmd, press CTRL``+``⇧ Shift``+``↵ Enter)

   2. Navigate to the Plone root directory:

      C:\> cd C:\Plone43

   3. 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

4. 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.

1. Backup

   Stop Plone, and make a full backup of your instance before continuing:

   bin/plonectl stop
   bin/fullbackup

2. Buildout

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

   bin/buildout -n

3. 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

4. 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.

1. Download source:

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

2. 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

3. Edit buildout.cfg:

   develop =
       src/bika.lims

4. 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:f9f7dd0163a74fbeac4e24a5123b3d39@sentry.bikalabs.com/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