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Table of Contents

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Below are prerequisites to ship/receive specimens using OpenSpecimen:

  1. The shipping site and receiving site should use the same instance of OpenSpecimen.
  2. Both sites and the logged-in user should be part of the CP that has the specimens being shipped.
  3. Cannot ship specimens from multiple sites in one shipment.
  4. If the shipped specimens

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  1. are stored in a container, the container's site

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  1. should be sending site.
  2. When receiving a shipment, the user can only store specimens in the containers of the receiving site.
  3. The sending site should be the site to which specimens belong (Site under CP).
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titleDifference between 'Distribution' & 'Shipping'

Refer to Difference between distribution and shipment

Create Shipment/ Shipment Request

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You can create shipments/ shipment requests from multiple pages. The "Action" button now available

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on all specimen pages allows you to create shipments/ shipment requests without having to add specimens to the cart.

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Pages where Action button is available

Gliffy
imageAttachmentIdatt287997987
baseUrlhttps://openspecimen.atlassian.net/wiki
migration1
nameShipment
diagramAttachmentIdatt288194590
containerId14811246
timestamp

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1697454682691



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titleExpand to view steps..

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.

Info
titleNote

From v7.1 onwards, users will be able to create shipments with past/future dates.

Go to the home page and click on the 'Shipments' card

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, fill in the details and click on 'Next'.
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  • you'll see option to generate shipment request. Fill all the details

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Info
titleNote

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/barcode 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 that were shipped.
Info
  1. If the shipment is requested, user can ship the requested specimens similar to creating regular shipment.
  2. Once the shipment is “Shipped“/ "Requested", you cannot edit the “Notify Users“ field
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  2. 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 can ship from the results page.

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titleClick here to view the steps...
  • 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.

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titleClick here to view the steps...
  • Create a 'Specimen cart' or click on an existing cart from which the specimens have to must be shipped.
  • Click on the 'Actions' button and select the option '→ Ship'.

  • Enter the further details and click on 'Ship' to ship the specimens.

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titleClick here to view the steps...
  • 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'.



Note

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.

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titleClick here to view the steps...
  • To receive the specimens, 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
    1. Received sample quantity 
    2. Quality (e.g., acceptable, unacceptable, etc.).
    3. 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.
Info
  • 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.



Note

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

Many a time, the The specimens are often collected in multiple hospitals for different studies. These specimens are labeled and then shipped to the receiving site facility for further processing and storage purposes. 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. 

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There is a A system-level setting that 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 along with and other details while receiving the shipment. From the shipped shipments overview page, click on the 'Receive' button→ Click on the 'Next' button,button → Next → Change the specimen labels or other details, and click on the 'Receive' button.

Edit

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(v7.1

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)

Shipments in the draft, shipped, or received mode modes can be edited. 

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Fields allowed to be edited are mentioned below,

  1. Shipment name
  2. Tracking URL
  3. Courier name
  4. Sender/receiver comments
  5. Shipped and received dates
  6. Received quality

The following attributes are not editable:

  1. Sending and receiving sites cannot be modified after the shipment is shipped.
  2. Specimens cannot be added or removed from the shipment after it is shipped.
  3. Specimen location and quantity cannot be modified after the shipment is received.

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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 have to must define the columns you wish to include in the CSV.

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titleClick here to view the steps...
  • 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

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  • 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. 
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  • 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.

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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.
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  • When you keep the above configuration the toggle print checkbox is auto-checked as below. 
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  • 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.

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titleEnable the pre-print setting...

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.

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  • Under 'MISCELLANEOUS SETTINGS' → Create Pending Specimens → On Shipment Receive. Refer to the wiki page for more details.

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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:

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The below table lists the example expressions which you can use:

ExpressionDescription
^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 QuantityPre-prints child specimen labels for three qualities: Acceptable, Acceptable - Clotted, and Acceptable - Insufficient Quantity
AcceptablePre-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"


Info
  1. By default, all shipment received quality values are considered as 'Acceptable', and it pre-prints child specimen labels for all values.
  2. The specimen labels should be auto-generated for the CP.
  3. Only Super Admins can change the system-level settings.

External ID: Name and Value Configuration

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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.
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By configuring the above details below two fields will be displayed on the ‘Receive Specimen’ page.

  • External ID: Name

  • External ID: Value

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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)'
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When both values are provided for the received specimen it's displayed below

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Set Default External ID: Name If the user sets the 'External ID" Name' as the Default name in system settings as below.

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Only one column - External ID: Value (optional) is displayed on the shipment receive page as below.

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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.

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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.