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 :)
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