Roslin EPAD DB Release History

Version: 12.1.0 22-02-2024 13:19:02
Up Since: 14-03-2025 00:05:19

Roslin EPAD Sample DB Web Application

Web application providing an Interface to the Roslin EPAD Database tracking participant samples banked as par of the EPAD project.

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

Current Release: 12.1.0 [built: Thu, Feb 22, 2024]


Release History


v12.1.0 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 in features from 11.1.0 - 11.3.0.

Bug Fixes

  • FIX bug with reporting null Boolean values.
  • Got rid of all <body onload=''> calls, putting calls in document.ready();
  • BUG FIX: checking sample request details text field is not empty.

v11.3.0 built: not known

New Features

  • Updated jquery, jqgrid, and highcharts javascript libraries and associated css files.
  • Removed superfluous gantt and maphilight javascript libraries.

v11.2.0 built: Fri, Sep 01, 2023

New Features

  • Sort retrieved FXTubes by volume, and display biggest in table of results grouped by Kit.
  • Exclude any 'NEVER USE' FXTubes from the tabulation above.
  • Implement 'export to excel' from this modified table (listing ONLY the largest volume FXTube).
  • Add coloured availability cell to the excel output of FXTube details.

v11.1.0 built: Fri, Aug 25, 2023

New Features

  • Relaxed some Sample tube queries so that tubes with no collection date etc will be found and displayed.

v11.0.0 built: Thu, May 25, 2023

New Features

  • Transferred the single LITE-KIT Sample set to a standard KIT representation.
  • Removed all LITE-KIT functionality.
  • Added Discard information to Excel reports of sample and collection tubes.

Bug Fixes

  • Tidied up the display when aliquoting Samples.
  • Fixed some dead URLs and http to https.

v10.0.0 built: Tue, May 16, 2023

New Features

  • Artifact dependencies updated to most recent release versions (compatible with java 11/tomcat9/spring5).
  • Improved searching for and management of sample tubes: 1 search by Box Barcode
  • Improved searching for and management of sample tubes: 2 search by Sample FluidX Barcodes
  • Improved searching for and management of sample tubes: 3 Discarded and Released Samples
  • Improved searching for and management of sample tubes: 4 Record Comment on Samples
  • Improved searching for and management of sample tubes: 5 Support Aliquoting of multiple Samples at once
  • Added ability to handle Freezer 15 storage locations.
  • Improved searching for and management of Collection Tubes: 1 Discard Collection Tubes

Bug Fixes

  • Force removal of storage coordinates when a Sample is discarded etc.

v9.0.0 built: Mon, Mar 20, 2023

New Features

  • Added a new sample type (PAX RNA 6.2) to handle returned samples.
  • Added support for this type throughout the app: searching, displaying, reporting, exporting.

v8.1.0 built: Fri, Aug 26, 2022

New Features

  • Changed queries and code to support FXTubes (e.g. aliquots) that aren't associated with a rack or freezer coordinate.

Bug Fixes

  • Fixed bug in code to count released FX tubes.

v8.0.0 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).

v7.1.1 built: Tue, Aug 09, 2022

Bug Fixes

  • Fix failure to read scan files where the first line (A1) has NO READ or NO TUBE value.
  • Allow 'current' scan files to be uploaded where there is no original scan record.
  • Allow for 'original' rack scans being incomplete (i.e. not 84 or 96 tubes) in 'update to current scan' logic. (There is now no tube-count integrity check when upload current scans.)

v7.0.0 built: Mon, May 30, 2022

New Features

  • Added lookup table for Aridhia IDs mapped to ECRF IDs.
  • Modified all queries to retrieve and display the Aridhia ID.
  • Expand data queries to allow searching by Aridhia ID.

v6.1.0 built: Tue, Mar 22, 2022

New Features

  • Improving all report queries to discount discarded kits/tubes and now only reports on explicitly stored (banked) samples.
  • Improved stock query and report.
  • Added detailed stock analysis of visit profiles for each sample type.

Bug Fixes

  • Change all uses of personal-index.html link to personal-index; the updated spring seems to fail to forward if use the .html suffix.

v6.0.1 built: Tue, Dec 14, 2021

Bug Fixes

  • Updated logging to safe version of Log4J (disallowing JNDI injection attacks).
  • Updated some deprecated classes and calls.

v6.0.0 built: Tue, Nov 09, 2021

New Features

  • Added methods to record and edit sample tube volumes.
  • Modified Stock reporting to include Aliquot usage.

Bug Fixes

  • Fixed some navigation problems after searching for sample tubes.

v5.1.1 built: Wed, Jun 09, 2021

Bug Fixes

  • VISIT numbers were being wrongly mapped.

v5.1.0 built: Fri, May 21, 2021

New Features

  • Added Sample Stock Overview page.
  • Added Graphical Sample Stock Detail page.
  • Added 'NEW FEATURES' to QUICK MENU.

v5.0.0 built: Tue, Mar 23, 2021

New Features

  • Implemented Sample Request Tracking.
  • Searching for samples matching Requests: Reserving and Noting Interest on samples.

Bug Fixes

  • Added missing VISIT# on table of FXTubes grouped by Kit.
  • Fixed buggy selection/cancel of Collection Tubes to move.
  • ReleaseDetails specified an aberrant extra local id property.

v4.3.0 built: Tue, Dec 15, 2020

New Features

  • Implemented aliquoting of FluidX Sample Tubes.

v4.1.0 built: Tue, Nov 17, 2020

New Features

  • New function to remove a fluidx box from the system if it is safe to do so (allowing re-use).
  • New function to upload a scan of new box with moved tubes, for either release or relocation.
  • Handle export/release (and relocation) of these new 'transfer' boxes, differing from the standard 3-kit boxes.
  • Simplified Error and Exception reporting to remove sensitive information.

v4.0.1 built: Fri, Oct 02, 2020

New Features

  • Updated the workflow for managing the release of banked FluidX Sample and Collection Tubes.
  • Queries to search for tubes to manage are stored and can be rerun.
  • CSV files of kit/participant IDs can be uploaded to form part of query.
  • FluidX Sample tubes listing can be atomic or grouped by kit.
  • Produces printable worksheets for Tube retrieval, sorted by freezer location.
  • Scans of tubes picked for release can be uploaded and checked against the search requirements etc.
  • Turned off most of the automatic reporting features of the system.

v4.0.0 built: Fri, Aug 28, 2020

New Features

  • Updated the workflow for managing the release of banked FluidX Sample and Collection Tubes.
  • 1 Queries to search for tubes to manage are stored and can be rerun.
  • 2 CSV files of kit/participant IDs can be uploaded to form part of query.
  • 3 FluidX Sample tubes listing can be atomic or grouped by kit.
  • 4 Produces printable worksheets for Tube retrieval, sorted by freezer location.
  • 5 Scans of tubes picked for release can be uploaded and checked against the search requirements etc.

v3.10.1 built: Mon, Mar 16, 2020

New Features

  • Removed all spaces from column titles in csv and excel export files.

Bug Fixes

  • Prevent saving empty comments.
  • Enable PBMC volume recording where appropriate (HotFIX since 2020-01-30).

v3.10.0 built: Mon, Jan 27, 2020

New Features

  • Modified and expanded CSV generating reports of samples returned, stored and released.
  • Added monthly cumulative email-report of returned samples.

v3.9.0 built: Fri, Dec 13, 2019

New Features

  • Removed block preventing users from editing data over a year old.
  • Added data capture and processing for return of the PBMC (4.1) Collection Tube. This is optional for centres that can't process the sample and aliquot to FluidX tubes.

v3.8.0 built: Tue, Aug 27, 2019

New Features

  • Added queries to report on banked and released kits.
  • Added monthly automatic email report of banked and released kits.
  • Added queries to extract logs of edits to Kits, Racks and Tubes.
  • Added weekly automatic email report of edit logs.
  • Relaxed allowed time period for completing data capture from 3 months to 1 year.
  • Update some dependencies to support Java-11.

Bug Fixes

  • Fixed Firefox-specific display issue with 'copy-down' button on sampling input page.
  • Changed email search in user table to allow for invisible enclosing html.

v3.7.0 built: Wed, Apr 03, 2019

New Features

  • Update all dependencies etc. (GIT dc2bbf6)
  • Extract and report Server and Manifest information (DBA only view).
  • Change table column filters to typically default to 'contains' rather than 'equals' [or '>='(after) for dates].
  • Added a permission-restricted function for cleaning Demo Kit data.
  • Modified the Sample recording page to
    require active selection of either NO SAMPLE or PROCESSING TIME
    prevent recording a processing timepoint if no sample stored
    restrict the allowed date range for timepoints
    check entered timepoints for valid format
  • Added DBA-only button to allow editing all tubes without scanning.

Bug Fixes

  • Changed mail methods to use streams rather than files for attachments.
  • Turned autocomplete off for DatePickers to prevent them occasionally obscuring the calendar.
  • Improved handling of apostrophes in emails.
  • Changed to use Bulk Mail Relay to solve grey list problems. rt 8857,8859.

v3.6.1 built: Wed, Sep 12, 2018

New Features

  • Added new Visit types (3,4,5 +DNA,PBMC) to allow recording of these samples on return visits. RT8626
  • Improved search functions for reporting Kit and Tube usage. RT8626
  • Layout of Results Tables improved. RT8626

Bug Fixes

  • Improved graceful fail of login if LDAP authentication service unavailable.
  • Added logging of authentication failures.
  • Fixed problem if dismiss an unused 'Remaining Tubes: No Sample' window.

v3.5.0 built: Fri, Aug 10, 2018

New Features

  • Architecture: Updated to Spring Framework version 5.
  • Added pages to search for and display released sample tubes (results can be exported to Excel).

Bug Fixes

  • Minor display modifications to handle any ambiguities in data imported from Sharepoint.

v3.4.0 built: Mon, May 07, 2018

New Features

  • Added ability to record change in Freezer Location of stored FluidX Boxes. RT8480
  • Added new report listing current Freezer Locations of FluidX Boxes.

v3.3.1 built: Wed, Apr 25, 2018

New Features

  • Added unreturned tubes report. RT8455

v3.3.0 built: Wed, Apr 18, 2018

New Features

  • Added ability to allow independent saving of Returned Kits (i.e Boxes) and Collection Tubes. RT8442
  • Modified storage comment to be displayed per Kits, and update-able. RT8443

v3.2.0 built: Fri, Mar 23, 2018

New Features

  • Added ability for Centres to return incomplete Boxes (i.e. containing only 1 or 2 completed kits).
  • Added ability for EPAD to record storage details of incomplete Boxes (i.e. containing only 1 or 2 completed kits).
  • Disable email confirmation to Centres upon receipt/storage of returned kits.
  • Add facility to move freezer location of collection tubes.
  • Add facility to search for CSF-LITE collection tubes.
  • Add facilities to move or release CSF-LITE collection tubes.
  • Added 'MISSING' query to find outstanding kits not returned with their incomplete box.

Bug Fixes

  • Added permission for data browsers to download Users Details spreadsheet.
  • Fixed bug displaying multiple users sharing exact same name.
  • Fixed bug if saving just the local study on a lite-kit.

v3.1.0 built: Wed, Feb 14, 2018

New Features

  • Added missing field to save Amyloid Beta concentration for CSF-LITE kits. RT8357

v3.0.0 built: Tue, Feb 13, 2018

New Features

  • Added functionality for working with CSF LITE kits: at EPAD Edinburgh and Clinical Centres. Added new (LITE) Kit type and Local Studies, with Menus to drive the handling and recording of Kits sampling. RT8201
  • Added Help Notes for the CSF-LITE kit sample recording.
  • Added handling of 'RETEST' Visit types. RT8304
  • Added system to add and display alerts on home page.

Bug Fixes

  • Allow users with 'Data Browser' permission to view but not edit the Centres, Users, Releasees pages.

v2.2.0 built: Tue, Oct 24, 2017

New Features

  • Remove Urine Processing Field: this should never have been added and is not required for data completion. RT8172
  • Added count of completed racks to Centre Kit reports. RT8173

Bug Fixes

  • Fixed permission bug with autoemail queries run as system.RT8124
  • Fixed query for available FX Sample tubes.

v2.1.0 built: Mon, Oct 16, 2017

New Features

  • Added autoemail reply when returned kits are received at Edinburgh. RT 8125
  • Added autoemail alert when a centre's kit stock falls below 8. RT 8124
  • Added report functions for kit summary statistics by centre, and kits returned timeline. RT8069

Bug Fixes

  • Code for handling emails refactored. RT8118
  • Changed column labels: 'COLLECTED' to 'PROCESSED (START)' and 'TIME PROCESSED' to 'START PROCESSING'. RT8128

v2.0.1 built: Tue, Sep 26, 2017

New Features

  • Major updates to software architecture and dependencies. RT8079
  • Added workflow functions for finding and releasing banked collection & fluidx tubes. RT8066
  • Locked down read/edit access for centres to kits returned within previous fortnight. RT8068
  • Altered PAX gene RNA data to return collection tube not aliquoted sample tubes. RT8089
  • Updated help manual and links on training page. RT8094

v1.4.1 built: Fri, Aug 18, 2017

New Features

  • Introduced new Read-Only permission architecture with Centre restricted permissions. RT 8027
  • Improved summary Kits report exported to Excel, with more detail and now Kits for reporting can be selected by checkbox. RT 8027
  • Introduced two new detailed Kits reports exported to Excel: one with sample tube details, the other with collection tube details. RT 8027
  • New WYSIWYG print function on Kit detail page. RT 8027

Bug Fixes

  • Fixed bug creating normal (non-read-only) user.

v1.3.0 built: Thu, Jul 27, 2017

New Features

  • Change 'Collected' fields for tubes to 'Time Processed', and made all of these capture/display timestamps not bare dates.
  • Added two new data fields: incubation duration for PAX RNA Sample & processing duration for Urine Sample.

v1.2.2 built: Tue, Jul 18, 2017

Bug Fixes

  • Gave User creation/editing rights to superusers.

v1.2.1 built: Wed, Jul 05, 2017

New Features

  • Added HELP & TRAINING page hosting YouTube videos and Help document.

v1.2.0 built: Mon, Jul 03, 2017

New Features

  • Worked up procedures to perform on receipt of returned sample boxes.
  • Added printable checklist for returned sample boxes.
  • Added new tube discard reason: 'Missing from Return'.

v1.1.0 built: Thu, Jun 15, 2017

New Features

  • Modifications in response to user demo and initial pilot study feedback.
  • Removed any last uses of Patient (Participant) and Rack (Box).
  • ECRF ID entry and editing more robust: matches the format ddd-ddddd, with ddd = centre code prefilled for centre staff.
  • Manifest now pre-calculates max volume in parcel.
  • New comment type 'not applicable' for No Sample.
  • Automated marking of DNA/PBMCs as not applicable for Visits 3,4 and 5.
  • Reinstated timestamp recording (and display) for Cortisol samples.

Bug Fixes

  • Improved bottom menu layout of jqgrid tables.

v1.0.01 built: Mon, May 22, 2017

New Features

  • First release of Roslin EPAD DB Webapp, for local pilot study.

Bug Fixes

  • Improved expiring tube alerts.

v0.05 built: Fri, Apr 28, 2017

New Features

  • Pre Release of the Roslin EPAD DB Webapp.

Bug Fixes

  • FIXING SOME BUGS/FEATURES AFTER DEMOING WITH NEIL RT7759

v0.04 built: Thu, Apr 13, 2017

New Features

  • Pre Release of the Roslin EPAD DB Webapp.

Bug Fixes

  • BUGGY FIRST RELEASE....