Update Openspecimen to 6.3RC8 #1
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…rticipant medical identifiers. 1. Nullify all the existing MRNs with empty/blank strings. Otherwise, unique constraint will fail (1, '') and (1, '') are the same for DB. But for app, they are different PMIs with the same site. Converted above tuples to (1, null) and (1, null) 2. Oracle: Added function based unique index. For Oracle, (1, null) and (1, null) are the same. 3. Fixed the API to trim whitespaces from the MRN.
The new column will track the rule that was used for printing the labels. Fixed the command files API to pick only those files generated by the rule instead of all files in the print directory. The filename format of the label/command file is changed from <object_type>_<tstmp>_<counter>_<copy>.txt to <object_type>_<rule_id>_<tstmp>_<counter>_<copy>.txt
…nstraint changeset. Need to remove the duplicate tuples.
…c692c787a4f Re-enable the participant (site, MRN) unique constraint changeset.
…insensitive) dropdown values are created. 1. Added an unique constraint on PV (attribute name, value) columns. 2. Oracle: Added function based unique index on PV (attribute name, lower(value)) columns.
… selected or not, display CP custom fields when the "Collection Protocol" form is selected for adding filter.
…box that no longer have direct access to Java classes like Runtime etc
…th_random(), rtMath.floor() etc
is not displayed when searching or selecting a new PV.
…sting duplicate PVs from the test server.
…sing the lookup key (form_id, record_id) The materialised table is kept in sync with the actual data table using triggers. The problem with the original solution of directly looking up in the data table using record ID was that the record ID is not unique and may be repeated for different forms.
users create import jobs either from the CPs list view or participants list view.
… the specimen actions on specimens selected from the result views.
Removed the extra "\n" that is added when both the comments and reason fields are empty.
Added support for export user profile form records as well.
order, container, shipment related specimens tab.
…t to the new UI app.
1) Scheduled job runs 2) Orders
… API interaction object. These variables can be used to specify the field on which the list should be sorted and sort direction - asc or desc
1. Processor metrics - CPU utilisation etc 2. File descriptor metrics - count of open files etc 3. Uptime 4. Count of classes loaded 5. JVM threads - busy, idle, waiting, blocked 6. JVM memory - heap and buffer 7. JVM GC - GC details 8. Disk space usage 9. Error rates 10. HTTP requests - by method, and module
…ocess The date only fields are exported and imported using the system or user selected date formats.
…ected from the specimen actions button of the cart view.
back to the specimen object to ensure compatibility with existing label formats and rules. The objects are kind of proxy to the collection and received attributes of the main specimen object. Removed the migration script. With this change, both the new and old variable naming convention can be used in the labels generation.
…cked ones. 1) Record the API call even before working on it with status = 000 2) After completion of the API call, record its response status and end time 3) This approach helps to trace the thread leaks, stuck API calls etc
…back to the system level format for visit names generation. The API will not bother about whether the system level format is set or not as long as there is a format specified at the CP level. When no format is specified at both CP and system level, an error is raised.
…late (more granular) instead of module wise (coarse).
…vailable for the plugin post processors.
services using the requirement template. As before, there is no support for partial update of specimen requirement.
…IDs of one or more registrations.
… bundle is not loaded yet.
…han 90 days (by default). Users can configure the scheduled job to specify a different retention period For example: apiLogsRetentionDays=100
…ecimen process. rest/ng/metrics/live-heap rest/ng/metrics/threads-dump
… date in yyyy-MM-dd format. The problem was - for both date only and date & time fields, the UI was initialising the default value to milliseconds elapsed since Epoch. While this was correct for date & time fields, the API rejected it as invalid value for the date only fields because it represented a moment in the time rather than the specific day start/boundary.
The problem was - the form designer was a separate standalone VueJS based UI module. It had its own set of reusable components like toasts among others. When it was merged with the new VueJS based OpenSpecimen UI, the toasts hook was not removed. As a result, the same error message appeared twice.
…dating forms via JSON based input payment or XML based file import. This ensures the same access control rules are applied in both the cases.
until a deletion confirmation is received from the backend / API.
…ecked out from a dimensionless container.
1) When no files are selected or validation fails and 2) the file is uploaded asynchronously to the server
time of unarchive to the container API.
when the message is processed successfully.
listing of containers based on the restrictions on the leaf node containers. Used virtual columns to auto compute free spaces in the container.
500 storage container objects in-memory irrespective of the depth and width of the container tree/hierarchy.
…m both container and specimen perspective. Earlier the API was clearing the position only from the container perspective. This was causing the position to be resaved by the specimen resulting in stale update error.
Supports 2 OAuth workflows: 1. Client Credentials Flow: The client obtains JWT by authenticating itself with the OAuth provider (without involving OpenSpecimen) and then uses the JWT as a Bearer token for subsequent communication with OpenSpecimen (invoking APIs). 2. Authorization Code Flow using PKCE: In this case, OpenSpecimen redirects (human) users to the respective OAuth providers in order to get consents for sharing their account details (openid) for accessing OpenSpecimen resources and APIs. 3. JWT Validation: OpenSpecimen validates and resolves the JWT to a valid user. The validation involves ensuring the token is: 3.1: Issued by an OAuth provider registered with OpenSpecimen 3.2: Not expired 3.3: Intended for accessing OpenSpecimen The public keys required for verification of the JWT signature are fetched from the respective OAuth providers at periodic intervals and cached in-memory. The resolution includes mapping the received subject claims to the user record in OpenSpecimen database by performing lookup on the login_name attribute. Tested the implementations using Auth0 and Google OAuth providers. TODO: Okta and Azure AD.
commit 88a6881 Author: Vinayak Pawar <vinayakapawar@gmail.com> Date: Sat Jan 24 17:12:10 2026 +0530 Invalidate any active (servlet) session and delete all cookies on user logout or session timeout/expiry.
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Getting the newest branch from openspecimen