Introduction
Surgical pathology reports (SPR) which are usually in file formats like pdf, text etc. can be uploaded in OpenSpecimen under a visit of the participant. This can be downloaded for reference. An interface plugin can be implemented to automatically load these reports from external pathology systems.
Settings to upload SPR
There is a system level setting to enable or disable uploading of surgical pathology reports for a visit. The user can view the ‘Surgical Pathology Reports’ tab on the visits page only if the setting is ‘Enabled’.
By default value for ‘Surgical Pathology Reports’ under ‘Biospecimen’ module is disabled and in CP level setting default value for ‘Store SPRs’ is ‘Use System Setting’.
Upload Surgical Pathology Report for a visit
To upload the file manually, follow the below steps:
- Click on any participants from the list for which you are going to add SPR for a visit
- Click on any of the occurred visits from the list and go to the overview page of that visit
- Click on ‘Path Report’ tab from the left-hand side menu
- Click on 'Browse' button, select the desired file by browsing and click on ‘Upload’ button
- The user will be able to view the uploaded SPR on the same page
The system does not show the ‘Path Report’ tab for the missed or pending visits.
Once uploaded, from v5.1 the system displays the path report icon in the occurred visits and visits side panel of the participant detail page. 
And highlights the 'Path Report' tab in blue color on the visits' overview page.
On clicking that icon, the system navigates you to the path reports overview page.
How to Edit, Lock/Unlock and Delete SPR
You might want to edit SPRs to manually de-identify the text, lock or delete SPRs. Follow the below steps to do so:
- To edit SPR, click on the edit icon, edit the details and click on the tick sign to save.
- To lock/unlock click on the lock button. This will prevent other users from editing the SPR.
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’. While enabling the ‘Extract Text From SPR PDF Docs’ user can view ‘Surgical Pathology Report’.
How to Extract text from SPR PDF Docs?
Follow the steps to extract text from SPR PDF docs:
- Go to CP edit page
- Select option 'Yes' for 'Extract Text from SPR PDF Docs?' field and save
- When a file in text format is uploaded in the SPR tab then the file is processed and displayed on the same page
- The user can set ‘Extract SPR’ setting as ‘No’ if the uploaded SPR file is in 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 ‘Settings->Biospecimen’ module is Disabled.