darwinai/pl-pdfgeneration

COVID-Net ChRIS plugin for PDF report generation.

pl-pdfgeneration

Table of Contents

• Abstract
• Synopsis
• Description
• Agruments
• Local Build
• Run

Abstract

An app that takes in prediction results and generates PDF

Synopsis

python pdfgeneration.py                                           \
    [-v <level>] [--verbosity <level>]                          \
    [--version]                                                 \
    [--man]                                                     \
    [--meta]                                                    \
    <inputDir>
    <outputDir>

Description

pdfgeneration.py is a ChRIS-based application that...

Agruments

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number.

[--man]
If specified, print (this) man page.

[--meta]
If specified, print plugin meta data.

[--imagefile]
required field, the name of the patient chest X-Ray image

[--patientId]
patient's id

Local Build

DOCKER_BUILDKIT=1 docker build -t local/pl-covidnet-pdfgeneration .

Run

docker run --rm -u $(id -u):$(id -g) \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw \
    darwinai/pl-covidnet covidnet \
    --imagefile ex-covid.jpg /incoming /outgoing

docker run --rm -u $(id -u):$(id -g) \
    -v $PWD/out:/incoming:ro -v $PWD/out:/outgoing:rw \
    darwinai/pl-covidnet-pdfgeneration pdfgeneration \
    --imagefile ex-covid.jpg --patientId 12345678 /incoming /outgoing

pl-pdfgeneration's Issues

Pdf generation causes notification to show up in notification drawer that corresponds with analysis of image

Describe the bug
Currently, all plugin jobs, both model and PDF generation, are treated the same for the notifications drawer. Since the PDF generation plugin’s output is different, we need to add a case for this plugin if we want to show it.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Docker (please complete the following information):

• Docker version: [e.g. 20.10.10, build b485636]
• docker-compose version: [e.g. 1.29.2, build 5becea4c]

Additional context
Add any other context about the problem here.

Prevent pdfgeneration from causing the same processing animation in the PastAnalyses table as running a prediction

Describe the bug
Prevent PDF generation from causing the same processing animation in the PastAnalyses table as running a prediction.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Docker (please complete the following information):

• Docker version: [e.g. 20.10.10, build b485636]
• docker-compose version: [e.g. 1.29.2, build 5becea4c]

Additional context
Add any other context about the problem here.

Address other PDF generation concerns related to simplicity and compatibility

Describe the bug
Two bugs:

• not working on PowerPC
• result PDF does not contain strings, i.e. cannot use pdfgrep, strings, text is not highlightable nor copy-paste-able

Moreover, Webkit is rather bloated (overkill for this task).
A re-implementation with LaTeX or just leaving the output as HTML is preferred.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
Ability to select and/or highlight texts in generated PDFs.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Docker (please complete the following information):

• Docker version: [e.g. 20.10.10, build b485636]
• docker-compose version: [e.g. 1.29.2, build 5becea4c]

Additional context
FNNDSC/pl-covidnet-pdfgeneration