Repository Sync

Owned by Bijoy George
Last updated: Oct 22, 2024 by Bijoy George
6 min read

BioMS to OpenSpecimen Sync (forward Sync)


A general rule applied on the sync of entities from BMS to OpenSpecimen is that entities are only synced to OpenSpecimen (OS) hosting those repositories where the entity would physically belong or is referenced by an entity that physically belong. E.g Specimen status updates are synced only to those OS repositories where the specimen would be shipped to.

Study


A study built in BMS will be synced to repositories on an explicit sync action from the Study Manager. When a study is completely built and is ready to be send to repositories Study manger will initiate a sync action by clicking the 'Synchronize Study' on build study UI. All study data except the following will be synced. These attributes/relations could not be synced because they are not captured in the OS domain model.

  • Coincident Epoch

  • Coincident CPE

  • Alternate Specimen

  • Equivalent Specimen

  • SpecimenRequirement. tubeType

  • SpecimenRequirement.repository

  • SpecimenRequirement.shippingType

  • SpecimenRequirement.specimenForms

  • SpecimenRequirement.preparationInstruction

  • SpecimenRequirement.shippingInstruction


Note: A Study would be synced (in its entirety) to only those repositories which receive at least one specimen from the study.

Participant


Participant data comes from the mayo RadoNode as part of the participant registration message. Whenever a new registration message is received from the RandoNode and new participant data is inserted into BioMS, the participant is synced to all the repositories. All the attributes (listed below) of the participant would be synced to all repositories linked to BioMS.

  • firstname

  • middleName

  • lastName

  • DOB

  • race

  • Ethnicity

  • gender

  • genomeType

Study Registration

StudyRegistration data comes from the Mayo RandoNode. Registration message contains a registration of a participant to Study and participant is automatically registered to all Epochs and Arms of the study. Participant registration messages are synced to those repositories where the study was originally synced. The following attributes of participarnt registration are synced

  • protocolParticipantID (PPID)

  • registrationDate

  • participant

  • protocol

When study registration is synced, all SCG and anticipated specimens for the participant stud registration is created in the OS repository. In each repository, specimen targeted (shipped to) that repository are mapped in the entity mapping table and all other anticipated specimens are marked 'Closed' and not mapped. The repository staff is not supposed to modify the specimen's marked closed, any modifications to those closed unmapped specimens will not be synced back to BioMS.
Note: For testing participant registration can be created in BMS using the temporary patientRegistration page. The participant registration page can be accessed at <bioms- base-url>/participantRegistration.

Specimen


Whenever specimen status changes in BioMS the updated specimen data is synced to the repository caTissue to which the specimen would be shipped to.

Specimen Collected


When a specimen is marked Collected by a CRA in BioMS, the following attributes of the specimen would be synced to the repository which would hold the specimen

  • availableQuantiy

  • initialQuantity

  • collectionStatus (set to Collected)

  • createdOnDate


Specimen CollectionEventParameter also will be added to the specimen with the following information.

  • performedBy ( set to CRA who collected the specimen)

  • timestamp

  • container (set to the TubeType specified in the SpecimenRequirement)

  • collectionProcedure (set to Not Specified)

The specimen would put in a storage position create on the BMS_Site_Container. BMS_Site_Container will hold the specimen until the specimen is moved to a 'InTransit' container, which happens when the specimen is shipped by collection site to a repository.

Specimen Pending


When the specimen is moved back to Pending state from collected in BMS the following attributes of the specimen would be updated

  • availableQuantiy (set to 0)

  • initialQuantity (set to 0)

  • collectionStatus (set to Pending)

All other attribute will remain same including the collection event parameter.

Specimen Not Collected


When a specimen is marked Not Collected in BMS , the specimen status and the comment that captures the reason for not collected are synced to repository.

  • collectionStatus (set to Not Collected)

  • comment (capturing the reason for not collected)

 

Shipment


Shipments created in BioMS are synced to the repository were the shipment is addressed to. The shipment is synced to repository when the CRA sends the shipment in BioMS. The following attributes of the shipment are synced.

  • label (set to 'BMS shipment <shipment id>' )

  • sendDate

  • senderSite

  • receiverSite

  • senderContactPerson

  • receiverContactPerson

  • specimens

  • activiityStatus (set to 'In Transit')

Specimen Forms


When a Study Manager(SM) defines specimen form for BioMS via caTissue running on BioMS DB, SM manager has to share the form details to all the repository OS admins. Repository OS admins should define the forms in their OS. The form name and form attribute names, type and other constraints should match exactly with the form created in the BioMS. Whenever a CRA, enter data on the specimen form in the checklist view, the form data is synced to repository to which the specimen gets synced. All attributes of the specimen form are synced and attached to the specimen via SpecimenRecordEntry. Once the form is synced from BioMS, repository users would be able to see the form data in the Annotations tab for the specimen in the OS.

User

Whenever a CRA User is created/updated in BioMS as part of Sync of user data from Mayo DB, the user is synced to all the repositories. The user is synced to repository only for referential integrity and the CRA users will not be able login to repository OS. The User is used in reference for collected user, shipped by User etc. The CRA user won't have any role or privileges assigned in caTissue. The following attributes (all) of the User are synced.

  • loginName

  • lastName

  • firstName

  • emailAddress

  • Institution

  • Adrress

  • activityStatus

Site

When a new collection site is created/update in BMS as part of sync of Site data from Mayo DB, the Site data is synced to all repositories. All the sites from mayo DB are created as Collection Site is BMS and OS. The following (all) attributes of Site are synced.

  • name

  • type

  • Address

  • activityStatus

 

OS to BMS Sync (reverse Sync)


Whenever specimen data originally synced from BioMS changes in the repository, the updates are synced back to BioMS to keep the data in sync. But Study , Participant and Participant Registration data doesn't get synced back to BioMS because, BioMS is the source of record for that data and repository users are not allowed to change that data.

Study


Studies that were created in OS as sync from BMS are not reverse synced because the BMS should be source of record for the Study definition and repositories should not be changing the study. If we allow reverse sync study modifications it could cause conflicts in BMS when different repositories make different kinds of modifications to the Study

Participant

Participants are created in BMS as part of processing RandoNode registrations. Reverse syncing of modifications (e.g participant name) to Participant should not be synced back to BMS because that could cause conflicts in BMS when multiple repositories change the values. Also the source of record for the participant data should be the registration system and the data should not be changes either in BMS or repository.

Study Registration

Study registrations are creates in BioMS as part of processing RandoNode registrations. Modifications (e.g PPID) to registration should not be synced back to BioMS because that could cause conflicts in BioMS when multiple repositories change the values.

Specimen

Any modifications to Specimens that are originally synced from BMS are reverse synced to BMS. Here are the attributes that are reverse synced to BMS. Since each specimen is held only at one repository all the changes should come from only one repo and should not cause any conflicts in BioMS. Here are the list of attributes that are reverse synced to BMS.

Once the specimen is received at the repository label, barcode, availableQuantity, initialQuantity, globalSpecimenIdentifier (if assigned at caTissue) and ReceivedEventParameters will be synced to BMS. BMS wont have these values assigned until the shipment containing the specimen is received at repository.

Shipment

When a shipment sent from BMS is received at a repository, the status of the Shipment is updated and synced back to BMS.
The activityStatus of the shipment and all specimens contained in the shipment is set to 'Received' in BMS.

Specimen Collection Group

Specimen collection groups are created in caTissue during the participant registration sync. Repository users should not be creating any new collection groups.
Repository users can make modifications to Specimen Collection Group and the modifications would be synced back. The following attributes of the SCG will be synced back.

  • activityStatus

  • collectionStatus

  • encounterTimeStamp

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