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Table of Contents

Introduction

...

  1. Download the CSV template file
  2. Upload the CSV file
  3. Create and run the import job
  4. Check the job status
  5. Download the job report

Download the CSV template file

...

application/json

...

Follow the below steps to download the template file:

Login to OpenSpecimen → Navigate To → Collection Protocols → More → Import Biospecimen Data (CSV) → Choose the Record Type → Click on Download Template

Image Added 

Upload the CSV file

AttributeValue
URLhttp://<host>:<port>/openspecimen/rest/ng/import-jobs/input-file
MethodPOST
Request Type

form-data

Response


Code Block
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{
    "fileId": "fa8e7401-0495-443b-bedc-99a43e0738f5"
}


...

Note

Note down the 'fileId' as this will be used in step #3

Create and run the import job

AttributeValue
URLhttp://<host>:<port>/openspecimen/rest/ng/import-jobs
MethodPOST
Request Type

application/json

Request


Code Block
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{
  "objectType" : <objectType>,
  "importType" : <operationType>,
  "inputFileId" : <fileId>,
  "dateFormat": <dateFormat>,
  "timeFormat": <timeFormat>
}


...

Note
  1. Replace '<objectType>' with the schemaName for the corresponding Bulk Import entity. (Find here the schema name to entity mapping)
  2. Replace '<operationType>' with 'CREATE' or 'UPDATE' for bulk creating or bulk updating entities respectively.
  3. Replace '<fileId>' with the fileId retrieved from the step #2
  4. Date and time formats are optional. When not specified the system configured formats are used. Specify dateFormat and timeFormat when your input CSV uses date and times that are incompatible with the system configuration.

Check the job status

AttributeValue
URLhttp://<host>:<port>/openspecimen/rest/ng/import-jobs/{job-id}
MethodGET
Request Type

application/json

Download the job report/output

...

CodeApplies toStatus Message
200All requestsBulk Import request was successfully processed.
401All requestsAuthorisation failed, user doesn’t have the authority.
500All requestsInternal server error, encountered server error while performing operations.

Sample Code

The below is the sample python code to do bulk import for Specimen Events:

View file
namebulk_import.py
height250

How to run?

Info

python3 bulk_import.py <CSV_FILE_NAME>