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Shipment of Specimens
- pooja kulkarni (Deactivated)
- Rohan Patwardhan
- Prayuja Teli (Unlicensed)
- 1 Introduction
- 2 Create Shipment/ Shipment Request
- 3 Receive
- 4 Edit (v7.1)
- 5 Shipment Report
- 5.1 Configure Report
- 6 Delete
- 7 Create in bulk
- 8 Pre-print primary specimens upon Shipment Receive
- 9 Pre-print child specimens upon Shipment Receive
- 10 External ID: Name and Value Configuration
Introduction
OpenSpecimen allows you to track the shipment of samples from one site to another. For example, collection site to the central repository. To ship boxes, refer to Shipment of Containers
Below are prerequisites to ship/receive specimens using OpenSpecimen:
The shipping site and receiving site should use the same instance of OpenSpecimen.
Both sites and the logged-in user should be part of the CP that has the specimens being shipped.
Cannot ship specimens from multiple sites in one shipment.
If the shipped specimens are stored in a container, the container's site should be sending site.
When receiving a shipment, the user can only store specimens in the containers of the receiving site.
The sending site should be the site to which specimens belong (Site under CP).
Difference between 'Distribution' & 'Shipping'
Create Shipment/ Shipment Request
You can create shipments/ shipment requests from multiple pages. The "Action" button now available on all specimen pages allows you to create shipments/ shipment requests without having to add specimens to the cart.
Pages where Action button is available
You can create a new shipment by going to the "Shipment" module and scanning or typing in the specimen labels. This works well when you already have the list of specimens to ship/ request.
Note
Shipment request feature is introduced from v10.3
From Home page navigate to 'Shipments'.
Click on the 'Create' button and select the option 'Specimens'
On the 'Create Shipment' page, you'll see option to generate shipment request. Fill all the details
Note
From v10.3 Unique shipment names will be auto-generated with the format
Regular Shipments: Shipment_<date>_<time>
Request Shipments: Shipment_Request_<date>_<time>
Add specimen labels/barcodes and click on "Add".
Selected specimens will appear on the next page. To confirm the shipment, click on 'Ship'.
Further, the users selected in 'Notify Users' will receive an email with a link to the shipment details.
A 'Shipment Shipped Event' is created under all shipped specimens.
If the shipment is requested, user can ship the requested specimens similar to creating regular shipment.
Once the shipment is “Shipped“/ "Requested", you cannot edit the “Notify Users“ field
You can see the “Notify Users“ field on the overview page for the Shipped shipments but cannot see it on the edit screen.
Ship from query
You can query specimens using the query interface and ship from the results page.
Go to the queries list page and click on 'Create'.
Create a query using any filters and click on 'View Records' to get the list of records.
Select the specimen rows or click on 'Select All' from the results page and click on 'Specimens' → 'Ship'.
Enter the further details and click 'Ship' to ship the specimens.
Ship from cart
You can create a cart of the specimens to be shipped and can ship from the cart.
Create a 'Specimen cart' or click on an existing cart from which the specimens must be shipped.
Click on the 'Actions' button → Ship.
Enter the further details and click on 'Ship' to ship the specimens.
Ship from other places
You can also ship specimens from the below-listed pages:
CP specimen list
Container specimen list
Reserved specimens list
Visit and specimen pages
Participant specimen list
E.g., Ship specimens from the participant's specimen list
Go to the overview page of the participant whose specimens have to be shipped.
Click on the 'Specimens' icon from the left-side menu.
Select the specimens from the list, and click on 'Actions' → 'Ship'.
The ‘Actions’ button will appear only after selecting at least one specimen from the specimen tree.
Enter the further details and click 'Ship' to ship the specimens
Similarly, you can ship specimens from any specimen list pages.
Request Status
From version 11.2, a new 'Request Status' feature has been added, enabling the site fulfilling the request to update the requester on the current status of their shipment. You can define status values in Extras → Dropdown Manager → Shipment Request Status. Changes to the request status are communicated via email to the requester, sender, and any users designated in the notify users field. This status is also visible in the Shipment list view and can be used as a filter.
Receive
The receiver can receive the shipment by clicking on the 'Receive' button from the shipment details page.
The user from receiving site logs in and selects 'Shipments' from the homepage to receive the specimens.
Select the shipment from the list and click on 'Receive'.
Review the shipment details and click on 'Next' to confirm the receipt of samples.
In the next step, you can choose the
Received sample quantity
Quality (e.g., acceptable, unacceptable, etc.).
Storage location: where the receiving site is storing the specimen
On saving, the system will create a 'Shipment Received Event' for each specimen in the shipment.
Once the shipment is ”Received”, you cannot edit the “Notify Users“ field.
You can see the “Notify Users“ field on the overview page for the Received shipments but cannot see it on the edit screen.
The email notifications will be sent to the users of the sending and receiving site who have minimum of ‘Update’ privilege to the 'Shipping and Tracking' resource.
Edit the specimen details while receiving a shipment
The specimens are often collected in multiple hospitals for different studies. These specimens are labeled and shipped to the receiving site facility for further processing and storage. For faster collection and data entry, the labeling at hospitals is done using generic labels like the randomly generated unique numbers, etc. However, when specimens are received at the receiving site, the biobankers relabel the received specimens based on their type, collection container, study, or other established practices for better organization and retrieval purposes.
A system-level setting will allow you to relabel the shipped specimens while receiving the shipment. To enable/disable this setting, go to 'Settings' → 'Administrative' module → 'Relabel Shipment Specimens' → Select option 'Enabled' and click on the 'Update' button.
Once enabled, you can edit the specimen labels and other details while receiving the shipment. From the shipped shipments overview page, click on the 'Receive' button → Next → Change the specimen labels or other details, and click on 'Receive'.
Edit (v7.1)
Shipments in the draft, shipped, or received modes can be edited.
Shipment Report
It is a CSV file that you can download from the shipment page. The system comes with a default report and can be customized by the super-admin.
You can download a shipment report as a CSV file with all the details of the shipment events and sample information from the shipments overview page.
Go to the shipments list page.
Click on the shipment whose report has to be downloaded.
Click on 'Download Report' from the overview page.
Configure Report
If you want to customize the shipment report, you will have to create a saved query using the query interface. In the query results, you must define the columns you wish to include in the CSV.
Login as super admin and go to the homepage.
Click on the 'Settings' → 'Common' module.
Click on the property 'Shipment Report'.
Specify the identifier of the saved query and update the property.
Delete
The delete feature is supported to delete the shipments created by mistakes by users, or the shipments of which the record is not necessary.
Users can delete the shipments in all pending, shipped, and received statuses.
- Users with sending site access only can delete the shipment which is in ‘Shipped’ status.
- Users with receiving site access only can delete the shipment which is in ‘Received’ status.To delete the shipment navigate to the shipment → Delete → Yes.
When the ‘Shipped’ status shipments are deleted, the corresponding ‘Shipment Shipped Event’ from all the shipment specimens is deleted as well.
When ‘Received’ status shipments are deleted, the corresponding ‘Shipment Shipped Event’ and 'Shipment Received Event’ from all the shipment specimens is deleted as well.
The original location of the specimens that were part of the deleted shipment will not be restored.
Create in bulk
You can create specimens shipment in bulk through bulk operation; for more details, refer to 'Create/Update Specimens Shipment'.
Pre-print primary specimens upon Shipment Receive
To support the primary specimen printing on receive the toggle checkbox is introduced on the 'Receive Specimen' page.
The setting is available at the CP level. Follow the below steps to enable:
Navigate to any 'Collection Protocol'.
Click on the 'Event' tab → Specimen Requirement → Set 'When to Print' as 'On Receive' as below.
When you keep the above configuration the toggle print checkbox is auto-checked as below.
If you don't configure the above specimen requirement setup then the toggle checkbox appears as unchecked. You can manually select and print the specimens.
Pre-print child specimens upon Shipment Receive
You can pre-print the child specimens when the parent specimens are shipped and received at the lab. Upon enabling this setting at the CP level, the child specimens will be created in a pending state and their labels are printed.
The setting is available at the CP level. Follow the below steps to enable:
Navigate to any 'Collection Protocol'.
Click on the 'Settings' tab → Label Format and Print.
Under 'MISCELLANEOUS SETTINGS' → Create Pending Specimens → On Shipment Receive. Refer to the wiki page for more details.
You can also choose for which 'Quality' you want to pre-print the child specimen labels by adding one or more values. This can be done by going to system-level 'Settings' → Biospecimen → Shipment Received Quality:
The below table lists the example expressions which you can use:
Expression | Description |
|---|---|
^Acceptable.* | Pre-prints child specimen labels for Shipment Received Quality = Acceptable, Acceptable - Clotted. i.e., It will pre-print labels for all specimens where the received quality starts with 'Acceptable'. |
Acceptable|Acceptable - Clotted|Acceptable - Insufficient Quantity | Pre-prints child specimen labels for three qualities: Acceptable, Acceptable - Clotted, and Acceptable - Insufficient Quantity |
Acceptable | Pre-print child specimen labels for Shipment Received Quality = Acceptable. |
^((?!Unacceptable).)*$ | Pre-prints child specimen labels for any Shipment Received Quality that does not include the word "Unacceptable" |
By default, all shipment received quality values are considered as 'Acceptable', and it pre-prints child specimen labels for all values.
The specimen labels should be auto-generated for the CP.
Only Super Admins can change the system-level settings.
External ID: Name and Value Configuration
Many biobanks use specimen external IDs while receiving the specimens. To support this the 'External ID: Name' and 'External ID: Value' fields are made configurable on the 'Receive Specimen' page.
Configuration- To add the External ID section user will need to enable the ‘Add External IDs’ setting in system settings.
By configuring the above details below two fields will be displayed on the ‘Receive Specimen’ page.
External ID: Name
External ID: Value
Both fields External ID: Name and External ID: Value fields are optional, but If the value in one field is provided then another field becomes mandatory. If the value is not provided system will throw the error 'One or more specimen external IDs do not have either name or value or both. (SPECIMEN_EXT_ID_NO_NAME_VALUE)'
When both values are provided for the received specimen it's displayed below
Set Default External ID: Name If the user sets the 'External ID" Name' as the Default name in system settings as below.
Only one column - External ID: Value (optional) is displayed on the shipment receive page as below.
The newly specified external IDs are added to the specimen’s existing external IDs list. This happens when you add the same specimen in two different shipments with a unique ‘External Id: Name’ value.
If the ‘External ID: Name' matches with any of the existing IDs of that specimen, then the value of matched 'External ID: Value' is overwritten by the new value specified by the user during shipment received.
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