Unable to upload images for the report when calling ipr_report.

[faruqsandi]

Describe the bug Unable to upload images for the report when calling ipr_report.

To Reproduce Steps to reproduce the behavior:

1. Run command  ipr_report
2. with input:

   {
       "patientId": "Faruq-Test-Build-Report",
       "kbDiseaseMatch": "colorectal cancer",
       "project": "TEST",
       "template": "genomic",
       "ageOfConsent": 35,
       "alternateIdentifier": "fhir-patiet-id-here",
       "biopsyDate": "2021-06-04T16:36:37.279Z",
       "biopsyName": "colon",
       "ploidy": "diploid",
       "presentationDate": "2021-06-04T16:36:37.279Z",
       "subtyping": "adenocarcinoma",
       "images": [
           {
               "key": "mutationBurden.density_snv.primary",
               "path": "/absolute/path/to/pori_suite/mutationBurden.density_snv.primary.png",
               "title": "Mock Data",
               "caption": "Mock Data"
           }
   }

3. See error (unnecessary details omitted):

   {'error': {'message': 'Error processing report image mutationBurden.density_snv.primary.png Error: Input file is missing: /home/bit/Playground/xnalabs/pori_suite/mutationBurden.density_snv.primary.png'}}

Expected behaviour I expected that the image would be successfully uploaded. I see that function post_images never actually called besides in test cases.

Versions (please complete the following information):  - OS: Windows 11, WSL 2, Ubuntu 22.04.4 LTS.  - Python: 3.11.9  - Version: pori_python==0.1.2  - GraphKB URL: local  - IPR URL: local

Additional context I tried to construct a complete JSON for ipr_report that will produce a complete report in each section.

[dustinbleile]

Input file is missing: /home/bit/Playground/xnalabs/pori_suite/mutationBurden.density_snv.primary.png The error is showing this file as missing or inaccessible.

Are read permissions restricted on that file? Is the directory correct.

[faruqsandi]

Yes, paths are guaranteed to be OK and accessible using terminal.

My current workaround is to remove the "images" from the payload for individual upload after report created.

images = report_payload.pop()

ipr_conn = IprConnection(
    username=username, password=password, url=myurl
)

for image in images:
    image_key = image["key"]
    files = {
        f"{image_key}": image["path"],
    }
    data = {
        f"{image_key}.title": image["title"],
        f"{image_key}.caption": image["caption"],
    }
    try:
        response_image = ipr_conn.post_images(
            report_id=report_id, files=files, data=data
        )
        print(image_key, response_image)
    except Exception:
        print(f"Failed to upload image {image_key}")
        continue

Here is my json: example_report.json