Introduction

Surgical pathology reports (SPR), usually in PDF, text, etc. files, can be uploaded in OpenSpecimen under the participant's visit. This can be downloaded for reference.

An interface plugin can be implemented to load these reports from external pathology systems automatically.

Settings to Upload SPR

There is a system-level setting to enable or disable the uploading of surgical pathology reports for a visit. If the setting is ' Enabled ', you can only view the ‘Surgical Pathology Reports’ tab on the visits page.

Navigate to ‘Settings’. Search for the property ‘Path Reports’ and select the option ‘Enabled’ in the ‘New Value’ field. System & CP level settings to enable/disable SPR: System-level setting CP level setting Allow uploading SPR Enabled Use System Setting Yes Enabled Yes Yes Enabled No No Disabled Use System Setting No Disabled Yes Yes Disabled No No

By default value for ‘Path Reports’ under the ‘Biospecimen’ module is disabled.
In the CP level setting default value for ‘Store SPRs’ is ‘Use System Setting’.

Upload SPR

To upload the file manually, follow the below steps:

Navigate to the visit for which you need to upload the SPR, click on the ‘Path Report’ tab Click on the 'Upload' button Select the desired file in the pop up by clicking the ‘Choose’ button. You will be able to view the uploaded SPR on the same page. The system does not show the ‘Path Report’ tab for missed, not collected, or pending visits.

Edit SPR

To edit the SPR file to de-identify the text from UI, follow the below steps:

Navigate to the ‘Path Report’ tab and click on ‘Edit’ button You can change the details of the uploaded file and click on ‘Update’ once done.

Lock/Unlock SPR

To lock the SPR file to restrict the users from editing the text, follow the below steps:

Steps to lock the path report Navigate to the ‘Path Report’ tab and click on ‘Lock’ button This will restrict the users from editing the report. Unless unlocked by the user Steps to lock the path report Navigate to the ‘Path Report’ tab and click on the ‘Unlock’ button Once done, you can edit the path report

Delete SPR

To delete the SPR file to de-identify the from UI, follow the below steps:

To delete the report, click on the delete icon. Specific users can be given privileges to edit, lock, unlock and delete SPRs. Check under Roles table for more details.

Settings to Extract Text from SPR PDF Docs

There is a system-level setting to enable or disable ‘Extract Text from SPR PDF Docs’. This can be overridden at the CP level.

If enabled, OpenSpecimen will try to extract text from the PDF file and store it as plain text, rather than storing the PDF file itself. The advantage of this is that the text will be visible on the page without having to downloading the file.

Important notes about “‘Extract Text from SPR PDF Docs’ setting:

This setting should be enabled only if you are uploading PDFs in simple text format.
OpenSpecimen cannot extract the text if the SPR contains images or formatted text.
In that case, disable “Extract Text from SPR”. You will be able to upload and download the PDF as a PDF (i.e., without extracting text).
Currently, if OpenSpecimen is unable to extract text, it will store a blank file. This bug will be fixed in future releases.

Navigate to ‘Settings’. Search for the property ‘Extract Text from SPR PDF Docs’ under the ‘Biospecimen’ module. Click on the property ‘Extract Text from SPR PDF Docs’ and select the option ‘Enabled’ of the ‘New Value’ field. System and CP level settings to enable/disable Extract Text from SPR files: System-level setting CP level setting Extract text from SPR Enabled Yes Yes Enabled No No Disabled Yes Yes Disabled No No

How to Extract Text from SPR PDF Docs?

Go to the CP edit page. Select option 'Yes' for the 'Extract Text from SPR PDF Docs?' field and save. When a file in text format is uploaded in the SPR tab, the file is processed and displayed on the same page. The user can set the ‘Extract SPR’ setting as ‘No’ if the uploaded SPR file is not in text like scanned documents or images. In such cases, the system displays the page as follows: If the report is in text format, then the text is displayed on the user interface. By default value for ‘Extract Text from SPR PDF Docs’ under the ‘Settings → Biospecimen’ module is Disabled.