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Update Openspecimen to 6.3RC8#1

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ChristianMUG wants to merge 3286 commits intobibbox:masterfrom
krishagni:master
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Update Openspecimen to 6.3RC8#1
ChristianMUG wants to merge 3286 commits intobibbox:masterfrom
krishagni:master

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Getting the newest branch from openspecimen

…cify

the floating-point based range for all number filters...
…lts view

to navigate to the relevant CP overview page.
…enabled

in the specimen tree configuration (CP workflows JSON).

The derived specimen is hidden only if
a) hideDerivatives = true
b) all children of derived specimen are aliquot
1. return the resolved specimens or errors

2. allow the host view to set the input specimen labels / barcodes
The existing os-menu is useful for displaying static/fixed menu options
that are known at the build time.

The os-dynamic-menu is useful for displaying menu options that are
generated at run time.
1) Specimen description - added "showAliquotType" input parameter
When true, displays the aliquot type. Otherwise, just Aliquot
Separated it from "detailed" input parameter, which is for detailed
specimen description like XYZ collected in ABC container.

2) Exposed list view context for use in the filters context.

3) Updated <os-tag> with support for secondary type

4) Few missing i18n translation keys
…enabled

in the specimen tree configuration (CP workflows JSON).

The derived specimen is hidden only if
a) hideDerivatives = true
b) has one or more children and all of them are aliquots

This means the derived specimen is displayed if it has no aliquots or no children
Instruct the API, the input is UDN and not name.
1. When site based access is enabled then the user should have received
   access rights on one of the CP sites and one of the participant's MRN
   sites (if available)

2. When site based access is disabled then the user should have received
   access rights on one of the CP sites.
(missed to add the change in the last commit)
1) Participant, Visit, and Specimen overview/detail, edit page header - left and right titles
2) Specimen description
When event point is specified, ensure event point unit is mandatory

Ensure the sorting of events do not break/crash when event point unit
is not specified.
…ions

to bulk update:
1) Container Transfer Events
2) Specimen Disposal Events
3) Specimen Reserved Events
4) Cancel Specimen Reservation Events
5) Specimen Return Events
6) Specimen Transfer Events
…ations table

Older entries are deleted in chunks of 10K to keep the transaction size in check

The Old Files Backlog cleaner job can be configured to specify retention period
for different tables.

filesRetentionDays: Specifies the retention period for all kinds of files on the
file system - export / import files, query exported files, reporting files etc
When not specified a default retention period of 30 days is used.

apiLogsRetentionDays: Number of days to retain the API calls log. When not specified
default of 90 days retention is used.

notifRetentionDays: Number of days to retain the notifications. When not specified
a default retention period of 90 days is used.
…art IDs

in the sub-query that selects the carts eligible for read by the signed-in
user.
gracefully to prevent crashes during domain-to-interaction object conversion.
1) Switched from static table to expand/collapse accordion style table.
   Fixed the accordion table to handle all types of fields.

2) Displayed registration details when users click on one of the matched
   participant registration.

   Turned the table into clickable cards. When a matching card is clicked,
   a new card with participant registration details appear.

3) Displayed matching participant details using the dictionary configured
   for the registration CP.

4) Added ability to configure widgets within the matched participant details card.

   Implemented AQL backed tables.

   When no widgets are configured, the matched participant details card
   defaults to displaying collected specimens and aliquots count tables.

   Example configuration:

   {
     "name": "matching-participants",
     "data": {
       "detail-widgets": [
         {
           "title": "Primary Specimens",
           "aql": "select Specimen.type, Specimen.tissueSite, Specimen.spmnCollRecvDetails.collContainer, Specimen.availableQty where Specimen.lineage = \"New\" and Specimen.collectionStatus = \"Collected\" and Participant.id = :cprId",
           "params": {
             "dynamic": {
               "cprId": "cpr.id"
             }
           }
         },

         ...
       ]
     }
   }
As soon as the file was selected, the file uploader was unmounted.
However, the uploader runs the code assuming the file input is still
present in the view. As a result, the UI thread crashes with error
and no file is uploaded to the backend.
…tly parse

the multi-valued parameters cpShortTitle and dpShortTitle into an array.

For example
dpShortTile=A,B&dpShortTitle=C is translated to ["A,B", "C"]

Earlier it was translated to ["A", "B", "C"]
(Accidentally  committed the changes to master instead of VP_AI_EMBEDDINGS)

This reverts commit 22ef7f4.
…gning algorithm.

Problem: The logout request and the signature were encoded and sent as SAMLRequest.
SAMLRequest=<Logout Request + Signature on Logout Request>
Further, the URL also didn't specify the algorithm used to sign.

The required format is:
SAMLRequest=<Logout Request>&SigAlg=<Signing Algorithm>&Signature=<Covers both the Logout Request and signing algo>

Fixed the logout URL to conform to the above format.
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