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Specimen Requirements CSV

Owned by Prayuja Teli (Unlicensed)
Last updated: Jul 30, 2024 by Neha Nimgire
3 min read

Steps to Import CSV

  1. Log in and go to the CP overview page.

  2. Click on the 'More' button and select 'Import Specimen Requirements' from the dropdown.

3. Click on 'Download Template File' to download the template file from the 'Import Specimen Requirements' page.

4. Enter all valid data in the template file as mentioned in the 'Data Dictionary' table.

5. Upload the filled template file in the 'Input Records File' field, select 'Import Type' as 'Create' to create or 'Update' to update events.

6. Click on the 'Validate and Import' button.

7. Refer to 'Import status' to check the status of the import job.

 

Copy Specimen Requirements (SRs) from one environment to other

We come across use cases where SRs in live Collection Protocols (CPs) need to be updated, or client analysts make changes across multiple CPs and need to move them into other environments. From v10.3 it is possible to export-import SRs across single/multiple/all collection protocols.

Steps:

  1. Select collection protocol/s from the list view from env 1 (e.g.Test)

  2. Export SRs which you need to update

  3. Remove the 'Identifier' column in CSV

  4. Import into env 2 (e.g.Prod )(if CP short title/event name matches, system will update SRs)

  5. In Prod, 'Close' all the SRs which you don't want people to use

OpenSpecimen does allow you to update the events for existing collection protocols. If there are any associated visits/ specimens collected, you will not be able to delete event. However, you have an option to close current event and start collecting using new event.

Sample CSV

Data Directory

Column Name

Data type

Mandatory? (Create)

Mandatory? (Update)

Description

Permissible Values

Validations

Column Name

Data type

Mandatory? (Create)

Mandatory? (Update)

Description

Permissible Values

Validations

Identifier

Number

No

Yes

System auto-generated unique number for every specimen requirement.

 

Mandatory while updating specimen requirements.

CP Short Title

String

Yes

Yes

CP Short Title, in which the specimen requirement needs to be added.

 

It should be unique within the system.

Event Label

String

Yes

No

Event Name.

 

 

Parent Code

String

Depends

No

It links the child specimens (derivatives/aliquots) to their parent specimen.

 

Mandatory for creating the child specimens.

Name

String

No

No

Specimen Requirement Name

 

 

 

Code

String

Depends

No

Specimen Requirement Code

 

Mandatory only when you create the child specimen under the parent.

Lineage

String

No

No

The lineage of the specimen

  • New

  • Derived

  • Aliquot

If left blank, the system will add lineage as 'New' by default

Specimen Class

String

Yes

Yes

 

  • Tissue

  • Molecular

  • Cell

  • Fluid

 

 

Specimen Type

String

Yes

Yes

 

Permissible values for specimen class-type

Should be a valid value from the list

Anatomic Site

 String

Yes

Yes

 

Permissible values for anatomic Site

Anatomic Site is mandatory only for the primary specimens.

It should be a valid value from the list.

Default value: 'Not Specified.'

Laterality

 String

Yes

Yes

 

  •  Left

  • Right

  • Not Applicable

  • Not Specified

Laterality is mandatory only for the primary specimens.

Default value: 'Not Specified.'

Pathology

 String

Yes

Yes

 

  • Non-Malignant

  • Non-Malignant, Diseased

  • Pre-Malignant

  • Malignant, Pre-Invasive

  • Malignant, Invasive

  • Malignant

  • Metastatic

  • Not Specified

Pathology is mandatory only for the primary specimens.

It should be the valid value from the list.

Default value: 'Not Specified.'

Storage Type

String

Yes

Yes

 

  • Virtual (if the specimen is not stored in the repository)

  • Manual (if the specimen is stored in the repository)

 

Initial Quantity

Double

No

No

 

 

If the left blank system will add 'Not Specified' by default.

Concentration

Double

No

No

 

 

 

Collector#Email Address

String

No

No

 

 

The user should exist within OpenSpecimen.

Collection Container

String

Yes

Yes

Type of container used for specimen collection

  • ACD Vacutainer

  • Citrate Vacutainer

  • CPT

  • EDTA Vacutainer

  • Heparin Vacutainer

  • No Additive Vacutainer

  • Paxgene

  • Serum Separator Vacutainer

  • Sterile Specimen Container

  • Streck

  • Not Specified

Collection Container is mandatory only for the primary specimens.

Should be a valid value from the list

Collection Procedure

String

Yes

Yes

The procedure used during specimen collection.

  • Lavage Needle

  • Aspirate

  • Needle Core Biopsy

  • Venipuncture

  • Indwelling Catheter

  • Surgical Resection

  • Not Specified

Collection Procedure is mandatory only for the primary specimens.

It should be a valid value from the list.

Receiver#Email Address

String

No

No

 

 

The user should exist within OpenSpecimen.

Label Format

String

No

No

 

 

 

Label Auto Print Mode

String

No

No

 

  • ON_RECEIVE

  • PRE_PRINT

  • ON_COLLECTION

  • NONE

 

 

Label Print Copies

Integer

No

No

 

 

 

Sort Order

Integer

No

No

 

 

 

Activity Status

String

No

No

Used to Disable the requirements of the specimen in bulk.

  • Active

  • Closed

  • Disabled

The value should be 'Disabled' to delete the specimens.

Values are case-sensitive.

 

Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com