Introduction
Surgical pathology reports (SPR), which are usually in file formats like pdf, text, etc., 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 uploading of surgical pathology reports for a visit. You can only view the ‘Surgical Pathology Reports’ tab on the visits page if the setting is ‘Enabled’.
- 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 |
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Enabled | Use System Setting | Yes | Enabled | Yes | Yes | Enabled | No | No | Disabled | Use System Setting | No | Disabled | Yes | Yes | Disabled | No | No |
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- 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’.
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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 the ‘Path Report’ tab from the left-hand side menu.
- Click on the 'Choose file' button, select the desired file by browsing and click on the ‘Upload’ button.
- You will be able to view the uploaded SPR on the same page.
The system does not show the ‘Path Report’ tab for the missed, not collected, or pending visits. |
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- Once uploaded, the system displays the path report icon in the occurred visits and visits side panel of the participant detail page.
- The 'Path Report' tab is also highlighted 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 de-identify the text, lock, or delete SPRs manually.
- 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.
Specific users can be given privileges to edit, lock, unlock and delete SPRs. Check under Roles table for more details. |
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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’.
- 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 |
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Enabled | Yes | Yes | Enabled | No | No | Disabled | Yes | Yes | Disabled | No | No |
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How to Extract text from SPR PDF Docs?
- Go to the 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, 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. |
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