v5.2 Release Notes


We are happy to announce that v5.2 is ready for download! As always, it has new features, improvements and bug fixes selected based on feedback from many of our current adopter. We would like to thank the following centers for inputs and funding features in this release:

  1. Memorial Sloan Kettering Cancer Center
  2. South Australian Health Research Center
  3. University of Basel
  4. Washington University
  5. University of Pittsburgh (Hillman Cancer Center)


Software/Hardware requirements

Review this page before attempting to upgrade for any changes: Software/Hardware Requirements.

Tomcat version upgrade

v5.2 needs Tomcat 8 or higher. Please upgrade if you using older version of Tomcat.

Audit Reports

Super admin can export audit information of specific or all users for specific time duration. The 'Audit Logs' option is available under 'Extras'.

Specify the duration and select the user for whom audit information needs to be downloaded:

Audit information includes any operations done in OpenSpecimen including on custom forms. Sample audit reports: 



Container Enhancements

Container custom fields

Custom fields can be created at container level now. While attaching the form, there is a new level that can be selected - 'Container Custom Fields'.

Custom fields added will appear on container add and edit page:

Print container labels

Print rules can be specified to print container labels including tokens like name, barcode, location, site and type. This will allow printing container labels for freezers and boxes based on these rules.

Collection Protocol Enhancements

Below enhancements are implemented in collection protocol module:

  • Ability to mark events and requirements as closed in collection protocol: This will keep the data already collected for previous participants for the closed events and requirements. But pending visit and specimens will not be displayed for the closed events and requirements for new participants
  • Allow to create aliquot requirements with zero quantity

Query Enhancements

Based on feedback, there are many enhancements in query module to enable more complex reports:

  • Scheduling queries
  • Filters on aggregate fields
  • Query on anticipated visit date
  • Parameterized subqueries

Scheduling queries

Saved queries can now be scheduled to run automatically at specified intervals like monthly, weekly, daily, etc. Specific users can be notified when the scheduled query is executed.

Refer to 'Scheduling Queries' for more details.

Filters on aggregate values

While creating queries, you can now add filters on aggregate values. For example, patients with family history of pancreatic cancer having more than 2 serum aliquots.

Similarly, condition can be specified on sum(specimen.availableQuantity), count(participant.id), count(visit.id) etc to get results of queries like:

  1. Patients having greater than 50 ml of Urine
  2. Protocols having more than 100 female participants
  3. Patients who have completed more than 3 followup visits

For more details, refer to 'Aggregate (Counts) Queries' for more details.

Parameterized subquery filters

While including results of another query as a filter in a query, it can now be specified a parameterized filter.

Consider for example, find patients having breast disorders but not thyroid cancer. User might want to choose from multiple diagnosis related to breast disorders while running the query. So, clinical diagnosis as a parameterized filter can be created as a saved query. This saved query can be used as input filter in the final query. This way, the clinical diagnosis will appear as filter in the results view for users to choose filter values at run time.

Refer to 'Parameterized Subqueries' for more details.

Query for anticipated specimens

Based on collection protocol time points, it is now possible to query for anticipated specimens. For example, query for expected specimens for participants of a protocol in next week.

Refer to 'Query for anticipated visits/specimens' for more details.

Parameterized filter support for entering many values

When text fields are parameterized in queries, by default all unique values of that text field are displayed in query results. This becomes a very long list for fields like PPID, label, barcode etc. To make this user friendly, in v5.2 user can choose to 'Hide options' for parameterized filters. This will allow them to filter based on multiple values on query results page at run time.

Refer to 'Hide options for parameterized filters' for more details.

Supplies Module

Supplies module has been enhanced to support more advanced features to support end to end workflow based on user feedback. Below are some of the enhancements:

  1. View supplies by supply types 
  2. Search supplies by collection protocol, name, location, site, vendor and item barcodes
  3. Clone supplies
  4. Specify location(in hierarchy way, e.g.Site->Building->Cupboard) where the supplies are stored
  5. Export supply details in CSV file
  6. Specify more details while creating type like vendor, expiry reminder interval, collection protocol etc
  7. Manually utilise supply items
  8. Alerts when supplies are nearing expiry date or are running low

Refer to 'Supply Management' for more details.

Advanced UI configurations

Below enhancements are implemented which can be configured using workflow JSON via REST API:

  1. Configure columns in aliquot and derivative creation pages
  2. Specify format of date fields in lists
  3. Restrict registration site on participant page to only sites associated to the corresponding collection protocol
  4. Configure columns in specimen list on order page

Download logs from UI

Super admins can access OpenSpecimen logs from UI under Extras→Errors:

All Improvements

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All bug fixes

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