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Import Records
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Import Records

This feature is implemented in OpenSpecimen v9.0 to provide the auto bulk import feature from the User Interface. In the older version(Auto Bulk Import) the user has to connect to the server and put the file on the server etc.

Import Records feature supports all the objects like Collection Protocol, Participant, Specimens, etc. The user needs to use the same template specified on the Bulk Import Template wiki page.

Advantages of this feature:

  1. Supported to importing Participant/Specimen centric collection protocol

  2. Can import multiple bulk import files in one go by adding those in ZIP

  3. Schedule the auto bulk import based on the timestamp specified in the file name

  4. Users do not need to use the auto bulk import feature to schedule import jobs.

 

How does the Import Record feature work?

  1. Once the user uploads the file, OpenSpecimen picks the file and import based on the timestamp specified in the file name.

  2. The most recent timestamp file will be picked first and import

 

You need the Super Admin privileges to access this feature.

How to access this feature?

  1. Login to the OpenSpecimen; Go to the Extras → Click on the Imports Records card.

  2. Select the CSV/Zip file and Import

  3. Download the import report

If your ZIP file has multiple CSV like Participant, Visits and Specimens, OpenSpecimen will import the files based on the timestamp added in the CSV file name. So, your participant CSV should be earlier timestamp than your visits and specimens.

Below, an example ZIP file contains – Three files Participant, Visits, and Specimen. OpenSpecimen picks the file based on the timestamp added to that file name.

Rules for the import file naming:

The Import Records features accepted the specific naming conversion files as below.

Data

Format

Description

Data

Format

Description

Standard entities (e.g. Collection Protocol, Participant, Specimen, etc) 

<object_type>_<operation>_<timestamp>_[<csv_type>].csv

  1. object_type: Entity name specified in bulk import schema file (see list below)

  2. operation: Operation to perform, valid values are "create" or "update".

  3. timestamp: In yyyyMMddHHmmssSSS".

  4. csv_type (optional): Specify "m" in case of "Order" and "Shipment"

  5. Examples

    • cp_create_20160511162033124.csv

    • distributionOrder_create_20160511162033124.csv

Custom fields

<entity>_<operation>_<timestamp>_cpId_<cpId>.csv

  1. entity: cpr, visit, specimen.

  2. operation - Operation to be performed, "create" or "update"

  3. timestamp - In "yyyyMMddHHmmssSSS" format

  4. cpId - Specifying Identifier of collection protocol. 

  5. <cpId> - Identifier of collection protocol. You can get this identifier via DB or from the browser URL on the collection protocol overview page.

  6. Example: Specimen custom field level update file

    specimen_update_20200925115950000_cpId_4292.csv

Custom forms

extensions_<attached_level><form_name><operation>_<timestamp>.csv

  1. extensions: Static word to identify a custom form.

  2. attached_level: Level at which form is attached. 

    1. Participant

    2. SpecimenCollectionGroup (i.e Visit)

    3. Specimen

    4. SpecimenEvent

  3. form_name - System generated 'Form Name' of the custom form.

  4. operation - Operation to be performed, "create" or "update"

  5. timestamp - In "yyyyMMddHHmmssSSS" format

  6. Example: extensions_Participant_familyHistoryAnnotation_create_20160511162246252.csv

 

Following is the list of object types for OpenSpecimen entities

Entity

Object Type