Clinical Sample Management App: Release History

Version: 5.2.01 15-04-2024 15:50:04
Up Since: 14-03-2025 00:05:14

ARRNC Clinical Sample Management Web Application

Web application providing an interface to the ARRNC Sample Management Database tracking clinical samples banked as part of the MND-SMART, Future MS and other Studies.

Developed By: Bioinformatics Group, The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, EH25 9RG    ROSLIN

Current Release: 5.2.0 [built: Mon, Apr 15, 2024]


Release History


v5.2.0 built: Mon, Apr 15, 2024

New Features

  • Handle different and extra appointment names for MNDSMART study.


v5.1.1 built: Thu, Apr 11, 2024

New Features

  • Allow superusers to grant (but not revoke) superuser permission.

Bug Fixes

  • Fixed bug processing available FXTubes for a 'colocated' Study Centre.


v5.0.1 built: Fri, Apr 05, 2024

New Features

  • Added new study 'Precision MS' tracking Serum sample records.

Bug Fixes

  • Fixed minor error in recording no Saliva sample for FMS participants.
  • Fixed multi-study permission control.


v4.1.0 built: Thu, Feb 22, 2024

New Features

  • Updated to Java to JDK 17, Jakarta EE, Tomcat 10.1 and the Spring Framework and Security 6.0.
  • Merged SPRING5 dev branches in to version 3.11.0.


v4.0.0 built: Thu, Aug 17, 2023

New Features

  • Updated to Java to JDK 17, Jakarta EE, Tomcat 10.1 and the Spring Framework and Security 6.0.
  • Merged SPRING5 dev branches in to version 3.11.0.


v3.12.0 built: Thu, Jan 25, 2024

New Features

  • Provide export of 1 or more sample tube details per appointment, from the 1 row per appointment search result page.
  • Added Quick Menu option to search for samples by their FluidX Barcode (in a file or typed or pasted).
  • Added Quick Menu option to search for samples on a Rack using its FluidX Barcode.

Bug Fixes

  • Tidied up some javascript jqgrid multiselect GUIs.
  • Fixed bug with reporting null Boolean values.


v3.11.0 built: Tue, Nov 07, 2023

New Features

  • Allow for 'Re-Use' of a 'Discarded' Saliva Tube.
  • Updated jquery and jqgrid javascript libraries and associated css files.
  • Removed superfluous gantt and maphilight javascript libraries.

Bug Fixes

  • Fixed some info messages for actions on pages displaying tables of sample records, these were failing to list samples correctly due to a missing attribute.


v3.10.0 built: Mon, Sep 25, 2023

New Features

  • Added some JS buttons to speed completion of the bank and move sample tubes forms.
  • Added new page to scan saliva tube IDs directly into sample boxes.
  • Now warns if 'relocating' a tube with a position already recorded in the system.


v3.9.0 built: Mon, Jul 31, 2023

New Features

  • Relaxed control that was preventing Sample Racks to be MOVED when there is no current Location stored.


v3.8.0 built: Thu, May 18, 2023

New Features

  • Artifact dependencies updated to most recent release versions (compatible with java 11/tomcat9/spring5).
  • Added optional logging to email of stock tube scans.

Bug Fixes

  • Wipe location data of removed tubes (ticket 10039).
  • Improve tubes in stock query.


v3.7.0 built: Thu, Apr 20, 2023

Bug Fixes

  • Fixed some report queries that had omitted FMS INITIAL samples.


v3.6.1 built: Thu, Apr 13, 2023

New Features

  • Artifact dependencies updated to most recent release versions (compatible with java 11/tomcat9/spring5).
  • Improved sample searches - for different types of tube,sample and study; and the display, printing and export of the retrieved records.
  • Added grouping of search results by patient/visit.
  • Improved accuracy and format of REPORT page queries.

Bug Fixes

  • Record missing Study reference when an FX tube is added to a patient appointment.
  • Wipe Study allocation when return FX tubes for re-use.
  • Fixed buggy editing of Saliva Tube values.
  • Fixed logic bug in javascript check when creating a new freezer box with a location (added as hot fix to previous release).
  • Fixed bug in sample_tube update sql.
  • Disallow erasure of Saliva Tube barcode.
  • Add help comment when rolling back to NO SAMPLING after recording times.


v3.5.0 built: Fri, Feb 10, 2023

New Features

  • Added a page listing all Freezer Coordinates and Rack and Box occupancy.
  • Added page to edit existing Freezer Box properties.
  • Relaxed Freezer Box property: Freezer Coordinates to allow this to be unset.

Bug Fixes

  • Attempting to fix bugs when moving freezer location of sample tubes: problems when working across multiple Studies


v3.4.0 built: Tue, Dec 20, 2022

New Features

  • Tightened some Read Only Restrictions.


v3.3.0 built: Tue, Aug 16, 2022

New Features

  • Switched to using the Authenticated Mail Relay service - because we are moving hosting to the Azure cloud.

Bug Fixes

  • Switch to using 'catalina.base' property to specify locate Tomcat conf and log directories (necessary on Azure).


v3.2.0 built: Wed, Jul 27, 2022

New Features

  • Improved ability to edit/clear Sampling Time/No Sampling record.
  • Allow 'co-located' FMS/MNDSMART clinical sites to use either stock of FluidX racks (as well as FluidX Tubes).
  • Improve editability of collection data: 'No Sample' is now revertable, and Sample Tube barcode is editable.
  • Improve validation of Freezer co-ordinates.
  • Code dependencies updated.

Bug Fixes

  • Fixed fatal error in generating LIST SCAN DISCREPANCIES report.


v3.1.0 built: Mon, May 02, 2022

New Features

  • Modified Freezer location map and handling to allow either FluidX Racks or Freezer Boxes to be stored in Area B.
  • Added ability to search for tubes by Freezer location (coordinate), or Rack/Box barcode or name.
  • Added reports covering Freezer usage.

Bug Fixes

  • Fixed bug in reports that were filtering on a specified clinical centre.
  • Fixed bug on collection pages preventing 'safeback' if participant has been withdrawn.


v3.0.3 built: Tue, Apr 05, 2022

Bug Fixes

  • Fixed bug preventing entering Rack barcode for completed collections.
  • Fixed bug preventing successful use of FluidX tubes from the stock of a colocated centre (e.g. Edinburgh FMS and MND).


v3.0.0 built: Thu, Mar 31, 2022

New Features

  • Expanded the application to record freezer banking details for 'General Studies'.
  • Allow definition and editing of Studies: which include defined Appointments and Sample Types.
  • Converted Collection Type (Visit) from an enumeration to an Appointment class, allowing users to define specific Appointments for a Study.
  • Renamed MNDSMART/FMS patient sampling points from 'Samples' to 'Collections', to disambiguate from the actual Samples (i.e. Tubes). (In the code these are still modelled as 'Kits').
  • In the underlying code (but hidden from the user) there are three types of samples: FluidX tubes and Sample Tubes (that both belong to Collections) and General Sample tubes that are not part of Collections.
  • Implemented search functions for available and released Sample Tubes, and the functionality to record Sample release.
  • Control access to General Study sample records via the granting of MULTI USER: GENERAL permission to a User.
  • Started squirreling away final locations of sample tubes when released or disposed of, so that they can be recovered in an emergency.
  • Implemented functionality to record relocation of sample tubes in freezer boxes (and log movements so that they can be recovered in an emergency).
  • Added facility to associate lab users with more than one Centre (they can already be associated with multiple Studies).
  • Added fine control of Centre/Study permissions when a user logs in, to ensure they are working with permitted and appropriate combinations.
  • Allow users to switch Study/Centre, and this controls both their data view (e.g. for 'searches') and their editing permissions.
  • Allow dual centres (i.e. 5 Scottish Cities) to use FX tubes from the 'wrong' Study.
  • Allow searches for 'ALL' sample tube types together (except FMS Saliva...).
  • Added manual functions to set a collection record as complete/incomplete.

Bug Fixes

  • Modified Freezer Box Name/Barcode to force capitalisation and standardize spacing.
  • Fixed SQL reporting on incomplete collections to discount discarded collections.
  • Fixed bug failing to check all combinations of FMS Saliva Tube record.
  • Set autocomplete=off across all forms.
  • Fixed buggy check that a new appointment is not earlier than existing ones.
  • Fixed bug preventing deletion of an FMS collection if it has a Saliva Tube.


v2.0.0 built: Mon, Feb 14, 2022

New Features

  • Expanded application to provide blood and saliva sample tracking for FutureMS Study.
  • Rebranded site from MNDSMART to ARRNC.
  • Added Permission control and processing to determine working Study context.
  • Implemented tracking freezer storage of FluidX racks and Saliva Tubes in Freezer Boxes.
  • Minor logic change to allow duplicate (replacement) patient sample points if the original is discarded first.
  • Refactored tests to use Mockito in place of Unitils mocking.
  • Allow Users to be associated directly with 1 or more Studies.
  • Introduced separate concepts of 'Sampling' and 'Non-Sampling' (i.e General ARRNC Biobank) Studies.
  • Relaxed requirement for a rack ID for returning samples, and allow ARRNC Biobank to assign new racks to allow banking.
  • Force clinical centre users to select a Current Study if not automatically restricted.
  • Updated Demo to work for both FMS and MNDSMART patient collections, and preload a consumable pack for the Demo Centre.
  • Added V2.0 Clinical Centre User Notes, and Demo User Notes to Training page.
  • Add specific email address for Future-MS Study, and use appropriate address for automated Alert and Report emails.

Bug Fixes

  • Fixed various look and feel issues.
  • Improved reporting on unexpected sample tubes when uploading FluidX rack scans.


v1.4.1 built: Tue, Dec 14, 2021

Bug Fixes

  • Updated logging to safe version of Log4J (disallowing JNDI injection attacks).
  • Corrected schema directives in TLD file.
  • Updated some deprecated classes and calls.


v1.4.0 built: Fri, Aug 20, 2021

New Features

  • Updated all code dependencies.

Bug Fixes

  • Added missing Sampled date to Excel export of kits.


v1.3.2 built: Thu, Jun 10, 2021

New Features

  • Improved and expanded Reports.
  • Altered 'COUNTS OF ALIQUOTS COLLECTED' report to return all sampled kits, whether returned or not.
  • Renamed 'PARTICIPANT SUMMARY' report to 'PARTICIPANT SAMPLE DETAILS' and now returns all sample dates, even if not yet returned.
  • New 'SAMPLE & PATIENT STATS' report with sample and patient statistics for each centre.

Bug Fixes

  • When a kit listing only contains 1 kit, display it in a list anyway, so that workflow functionality is not lost.


v1.3.1 built: Tue, Mar 30, 2021

New Features

  • Improvements to jqgrid table display.
  • Improved Exception handling and logging.

Bug Fixes

  • Fixed email alerts of uncompleted sample kits.
  • Fixed setting of sample technician on kit creation.


v1.3.0 built: Wed, Apr 29, 2020

New Features

  • Added Drag and Drop facility to 'File Upload' dialogues.
  • Improved verification of returned Rack scan files: reporting and logging inconsistencies, and automatic email of queries.
  • Added User Documentation to HELP & TRAINING page.
  • Added several reporting functions to REPORTS page.
  • Implement 'Experimental Features' to work with sample tubes and their release.
  • Improved email alert of incomplete records to attach a spreadsheet highlighting missing data.

Bug Fixes

  • Fixed distinction between INITIAL scan and RESCAN file uploads.
  • Fixed retrieval of tube data necessary for printing a Returned Samples checklist.
  • Fixed broken query to print out checklist of returned samples and their tubes.
  • Altered logic to mark records as complete if consent has been withdrawn.
  • Handle edge cases where sample tubes are split across multiple Racks.
  • Fixed search by Rack barcode to work even for samples split across multiple Racks.


v1.2.0 built: Mon, Mar 02, 2020

New Features

  • Added a button on the Participant/Appointment collection page to either delete an unused record or to discard the Samples for this record.
  • Improved explicit functions to return Sample Tubes to stock if unused.
  • Improved constraints on FluidX barcode format.

Bug Fixes

  • Corrected query for counting racks in stock and whether currently in use.
  • Fixed potential sql bug comparing values to null.
  • Resolved cross-browser display issues with Chrome and Firefox, but Edge can only be supported for Clinical Centre recording.


v1.1.1 built: Fri, Feb 14, 2020

New Features

  • Added search function for Samples that are Banked but not yet Scanned.

Bug Fixes

  • Fixed bug in search for Returned Samples function, that broke empty tube csv upload.
  • Fixed chrome display bug for acknowledge pack button.
  • Fixed bug saving 'No Samples' for Serum.


v1.1.0 built: Thu, Feb 13, 2020

New Features

  • Added new data field to capture the start time for Plasma sample centrifugation.
  • Removed use and reference to Institutions throughout the Admin pages.
  • Added 'Set Alert' and 'Reset DB' actions to Super-Users menu.
  • Centre Code now enforced to be capitalised and not allowed spaces.
  • Automated email sent when a Centre acknowledges receipt of consumable Pack.
  • Removed permission for MNDSMART Sample Bank team to administrate Users and Centres etc.
  • Improved Quick Menu for MNDSMART Sample Bank team.
  • Improved table displaying Users to include active Permissions.
  • Fixed and improved the options on Sample Search page.

Bug Fixes

  • Fixed error in calculating sample completion where no FXTubes have been added, but all else complete.
  • Fixed problem if withdraw consent before record Sample is initialized.
  • Changes to wording COMMIT->SAVE, KIT->SAMPLE, WTCRF->PARTICIPANT, and various typos.
  • Removed text about sample 'exemption' from Sample return manifest.
  • Fixed editing locks to work on all fields in the Sample recording page.
  • Filter out ClientAbortExceptions from logging.
  • Fixed search page filtering by Appointment number.
  • Fixed failure to catch a tube count error on uploading new sample tube scans.


v1.0.0 built: Thu, Feb 06, 2020

New Features

  • Beta-Release of the MND-SMART Sample Management Webapp.

Bug Fixes

  • FIRST PRODUCTION RELEASE....this WILL be buggy :)