diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json deleted file mode 100644 index 30b66f8..0000000 --- a/.devcontainer/devcontainer.json +++ /dev/null @@ -1,51 +0,0 @@ -// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: -// https://github.com/microsoft/vscode-dev-containers/tree/v0.202.5/containers/docker-existing-dockerfile -{ - "name": "impatientdev", - "build": { "args": { "-t": "impatientdev:latest" } }, - // Sets the run context to one level up instead of the .devcontainer folder. - "context": "..", - - // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename. - "dockerFile": "../Dockerfile.dev", - - // Set *default* container specific settings.json values on container create. - "settings": {}, - - // Add the IDs of extensions you want installed when the container is created. - "extensions": [ - "eamodio.gitlens", - "ecmel.vscode-html-css", - "ms-toolsai.jupyter", - "ms-toolsai.jupyter-renderers", - "christian-kohler.path-intellisense", - "esbenp.prettier-vscode", - "ms-python.black-formatter", - "ms-python.vscode-pylance", - "ms-python.python", - "naumovs.color-highlight", - "njpwerner.autodocstring", - "James-Yu.latex-workshop", - "GrapeCity.gc-excelviewer", - "mutantdino.resourcemonitor", - "GitHub.copilot", - "albert.tabout", - "mechatroner.rainbow-csv", - "druideinformatique.antidote", - "analytic-signal.preview-tiff", - "vincaslt.highlight-matching-tag" - ], - - // Use 'forwardPorts' to make a list of ports inside the container available locally. - "forwardPorts": [5000], - // Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker. - "mounts": [ - "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" - ], - "workspaceMount": "source=${localWorkspaceFolder},target=/home/impatient,type=bind,consistency=cached", - "workspaceFolder": "/home/impatient", - "runArgs": ["--init", "--name", "impatientdev", "--rm", "-it"], - - // Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root. - "remoteUser": "impatient" -} diff --git a/.dvc/.gitignore b/.dvc/.gitignore deleted file mode 100644 index 528f30c..0000000 --- a/.dvc/.gitignore +++ /dev/null @@ -1,3 +0,0 @@ -/config.local -/tmp -/cache diff --git a/.dvc/config b/.dvc/config deleted file mode 100644 index 380d857..0000000 --- a/.dvc/config +++ /dev/null @@ -1,8 +0,0 @@ -[core] - remote = ssh_lbgi -['remote "ssh_lbgi"'] - user = meyer - url = ssh://ssh.lbgi.fr/home/meyer/dvc - ask_password = True -['remote "local_backup"'] - url = /tmp/dvcstore diff --git a/.dvc/plots/confusion.json b/.dvc/plots/confusion.json deleted file mode 100644 index af1b48d..0000000 --- a/.dvc/plots/confusion.json +++ /dev/null @@ -1,107 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "facet": { - "field": "rev", - "type": "nominal" - }, - "spec": { - "transform": [ - { - "aggregate": [ - { - "op": "count", - "as": "xy_count" - 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} - }, - "mark": "point", - "encoding": { - "opacity": { - "condition": { - "selection": "label", - "value": 1 - }, - "value": 0 - } - } - } - ] - }, - { - "transform": [ - { - "filter": { - "selection": "label" - } - } - ], - "layer": [ - { - "mark": { - "type": "rule", - "color": "gray" - }, - "encoding": { - "x": { - "field": "", - "type": "quantitative" - } - } - }, - { - "encoding": { - "text": { - "type": "quantitative", - "field": "" - }, - "x": { - "field": "", - "type": "quantitative" - }, - "y": { - "field": "", - "type": "quantitative" - } - }, - "layer": [ - { - "mark": { - "type": "text", - "align": "left", - "dx": 5, - "dy": -5 - }, - "encoding": { - "color": { - "type": "nominal", - "field": "rev" - } - } - } - ] - } - ] - } - ] -} diff --git a/.dvc/plots/scatter.json b/.dvc/plots/scatter.json deleted file mode 100644 index 9af9304..0000000 --- a/.dvc/plots/scatter.json +++ /dev/null @@ -1,104 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "width": 300, - "height": 300, - "layer": [ - { - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - }, - "layer": [ - { - "mark": "point" - }, - { - "selection": { - "label": { - "type": "single", - "nearest": true, - "on": "mouseover", - "encodings": [ - "x" - ], - "empty": "none", - "clear": "mouseout" - } - }, - "mark": "point", - "encoding": { - "opacity": { - "condition": { - "selection": "label", - "value": 1 - }, - "value": 0 - } - } - } - ] - }, - { - "transform": [ - { - "filter": { - "selection": "label" - } - } - ], - "layer": [ - { - "encoding": { - "text": { - "type": "quantitative", - "field": "" - }, - "x": { - "field": "", - "type": "quantitative" - }, - "y": { - "field": "", - "type": "quantitative" - } - }, - "layer": [ - { - "mark": { - "type": "text", - "align": "left", - "dx": 5, - "dy": -5 - }, - "encoding": { - "color": { - "type": "nominal", - "field": "rev" - } - } - } - ] - } - ] - } - ] -} diff --git a/.dvc/plots/smooth.json b/.dvc/plots/smooth.json deleted file mode 100644 index d497ce7..0000000 --- a/.dvc/plots/smooth.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://vega.github.io/schema/vega-lite/v4.json", - "data": { - "values": "" - }, - "title": "", - "mark": { - "type": "line" - }, - "encoding": { - "x": { - "field": "", - "type": "quantitative", - "title": "" - }, - "y": { - "field": "", - "type": "quantitative", - "title": "", - "scale": { - "zero": false - } - }, - "color": { - "field": "rev", - "type": "nominal" - } - }, - "transform": [ - { - "loess": "", - "on": "", - "groupby": [ - "rev" - ], - "bandwidth": 0.3 - } - ] -} diff --git a/.flaskenv b/.flaskenv index 2f67d30..7aa708e 100644 --- a/.flaskenv +++ b/.flaskenv @@ -1 +1 @@ -FLASK_APP=impatient.py +FLASK_APP=src/impatient/impatient_app.py diff --git a/.gitignore b/.gitignore index 20fcb71..9fef6d8 100644 --- a/.gitignore +++ b/.gitignore @@ -157,7 +157,7 @@ package-lock.json *.list joblib* *.back -app/static/viz/* +src/impatient/app/static/viz/* *.jar *.pdf git-filter-repo @@ -183,4 +183,5 @@ data/backup/* notebooks/* !notebooks/*.ipynb profile.json -profile.html \ No newline at end of file +profile.html +!src/* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 16a52f4..0000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,27 +0,0 @@ -# See https://pre-commit.com for more information -# See https://pre-commit.com/hooks.html for more hooks -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-yaml - - - repo: https://github.com/Lucas-C/pre-commit-hooks-bandit - rev: v1.0.5 - hooks: - - id: python-bandit-vulnerability-check - args: [., -ll, -r, -x, "./tests/*"] - - - repo: https://github.com/psf/black - rev: 21.12b0 - hooks: - - id: black - language_version: python3.9.5 - - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v2.5.1 - hooks: - - id: prettier - types_or: [css, javascript] diff --git a/.python-version b/.python-version index c8cfe39..fdcfcfd 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.10 +3.12 \ No newline at end of file diff --git a/.vscode/launch.json b/.vscode/launch.json deleted file mode 100644 index 895d706..0000000 --- a/.vscode/launch.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - // Use IntelliSense to learn about possible attributes. - // Hover to view descriptions of existing attributes. - // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 - "version": "1.0.0", - "configurations": [ - { - "name": "Debug Flask App (Docker)", - "type": "docker", - "request": "launch", - "preLaunchTask": "docker-run: debug", - "python": { - "pathMappings": [ - { - "localRoot": "${workspaceFolder}", - "remoteRoot": "/home/impatient" - } - ], - "projectType": "flask" - }, - "dockerServerReadyAction": { - "action": "openExternally", - "pattern": "Running on (http?://\\S+|[0-9]+)", - "uriFormat": "%s://localhost:%s/" - }, - }, - { - "name": "Debug Flask App (Linux)", - "type": "python", - "request": "launch", - "module": "flask", - "env": { - "FLASK_APP": "impatient.py", - "FLASK_ENV": "development", - "FLASK_DEBUG": "0" - }, - "args": [ - "run", - "--no-debugger", - "--no-reload" - ], - "jinja": true - }, - ] -} diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index eb20a5f..0000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "editor.defaultFormatter": null, - "[javascript]": { - "editor.defaultFormatter": "esbenp.prettier-vscode" - }, - "[css]": { - "editor.defaultFormatter": "esbenp.prettier-vscode" - }, - "[html]": { - "editor.defaultFormatter": "vscode.html-language-features" - }, - "python.linting.enabled": true, - "python.formatting.provider": "black", - "python.testing.pytestArgs": ["tests"], - "python.testing.unittestEnabled": false, - "python.testing.pytestEnabled": true, -} diff --git a/.vscode/tasks.json b/.vscode/tasks.json deleted file mode 100644 index 3e2e631..0000000 --- a/.vscode/tasks.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "version": "2.0.0", - "tasks": [ - { - "type": "docker-run", - "label": "docker-run: debug", - "dependsOn": ["docker-build"], - "dockerRun": { - "containerName": "impatientdev", - "image": "impatientdev:latest", - "env": { - "FLASK_APP": "/home/impatient/impatient.py", - "FLASK_ENV": "development" - }, - "volumes": [ - { - "containerPath": "/home/impatient", - "localPath": "${workspaceFolder}" - } - ], - "ports": [ - { - "containerPort": 5000, - "hostPort": 5000 - } - ] - }, - "python": { - "args": ["run", "--host", "0.0.0.0", "--port", "5000"], - "module": "flask" - } - }, - { - "label": "docker-build", - "type": "docker-build", - "dockerBuild": { - "context": "${workspaceFolder}", - "dockerfile": "${workspaceFolder}/Dockerfile.dev", - "tag": "impatientdev:latest" - } - } - ] - } diff --git a/Dockerfile b/Dockerfile index d5ec26f..1df2a70 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,29 +1,32 @@ -FROM python:3.9-slim +FROM python:3.12-slim-bullseye +COPY --from=ghcr.io/astral-sh/uv:0.5.30 /uv /bin/uv + +ENV UV_COMPILE_BYTECODE=1 +ENV UV_NO_CACHE=1 RUN useradd impatient WORKDIR /home/impatient -RUN apt update && apt install -y gcc git tesseract-ocr tesseract-ocr-osd tesseract-ocr-fra poppler-utils -COPY --chown=impatient:impatient pyproject.toml pyproject.toml -COPY --chown=impatient:impatient poetry.lock poetry.lock +RUN apt update && apt install -y gcc git tesseract-ocr tesseract-ocr-osd tesseract-ocr-fra poppler-utils cmake build-essential git-lfs +RUN git lfs install +ARG GIT_LFS_SKIP_SMUDGE=0 +RUN git clone https://huggingface.co/spaces/corentinm7/IMPatienT --depth 1 /home/impatient # To Get Git LFS files +RUN git lfs pull -RUN python -m pip install poetry -RUN python -m poetry config virtualenvs.create false -RUN python -m poetry install --no-root --no-interaction && rm -rf ~/.cache/pypoetry/{cache,artifacts} +COPY --chown=impatient:impatient pyproject.toml pyproject.toml +COPY --chown=impatient:impatient src /home/impatient/src -COPY --chown=impatient:impatient impatient.py config.py docker/boot.sh ./ -COPY --chown=impatient:impatient app app -COPY --chown=impatient:impatient migrations migrations -COPY --chown=impatient:impatient config config +RUN uv sync --no-install-project --no-sources --no-dev -RUN chown impatient:impatient /home/impatient +COPY --chown=impatient:impatient docker/boot.sh ./ +RUN chown -R impatient:impatient /home/impatient RUN chmod a+x boot.sh -ENV FLASK_APP impatient.py +ENV FLASK_APP=src/impatient/impatient_app.py RUN usermod -u 1000 impatient RUN usermod -G staff impatient USER impatient -EXPOSE 5000 +EXPOSE 7860 ENTRYPOINT ["./boot.sh"] diff --git a/Dockerfile.dev b/Dockerfile.dev index edd0e07..f835fb0 100644 --- a/Dockerfile.dev +++ b/Dockerfile.dev @@ -1,23 +1,23 @@ -FROM python:3.9-slim +FROM python:3.12-slim-bullseye +COPY --from=ghcr.io/astral-sh/uv:0.5.30 /uv /bin/uv + +ENV UV_COMPILE_BYTECODE=1 +ENV UV_NO_CACHE=1 RUN useradd impatient WORKDIR /home/impatient -RUN apt update && apt install -y gcc git tesseract-ocr tesseract-ocr-osd tesseract-ocr-fra poppler-utils +RUN apt update && apt install -y gcc git tesseract-ocr tesseract-ocr-osd tesseract-ocr-fra poppler-utils cmake build-essential COPY --chown=impatient:impatient pyproject.toml pyproject.toml -COPY --chown=impatient:impatient poetry.lock poetry.lock - -RUN python -m pip install poetry -RUN python -m poetry config virtualenvs.create false -RUN python -m poetry install --no-root --no-interaction && rm -rf ~/.cache/pypoetry/{cache,artifacts} +RUN uv sync --no-install-project --no-sources RUN chown impatient:impatient /home/impatient -ENV FLASK_ENV development -ENV FLASK_APP impatient.py -ENV SHELL /bin/bash +ENV FLASK_ENV=development +ENV FLASK_APP=src/impatient/impatient_app.py +ENV SHELL=/bin/bash USER impatient -EXPOSE 5000 +EXPOSE 7860 ENTRYPOINT ["./dev_boot.sh"] diff --git a/Makefile b/Makefile deleted file mode 100644 index f1be5b9..0000000 --- a/Makefile +++ /dev/null @@ -1,42 +0,0 @@ -black: - black app - black tests - -black-diff: - black app --diff - black tests --diff - -build: - poetry build - -install: - poetry install - pre-commit install - -mkserve: - mkdocs serve - -mypy: - mypy app/ --ignore-missing-imports - -pre-commit: black mypy ruff test - -publish: - poetry publish - -publish-release: pre-commit build publish - -ruff: - ruff app tests - -test: - pytest tests - -_update: - poetry update - -update-all: _update publish-release - -update-all-diff: - poetry update --dry-run | grep -i updat - diff --git a/README.md b/README.md index aecacbb..1de3ebe 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,23 @@ +--- +title: IMPatienT +emoji: 🗂️ +colorFrom: yellow +colorTo: red +sdk: docker +pinned: true +license: agpl-3.0 +header: mini +short_description: Annotate multimodal patient data web-app +tags: + - ontology + - myology + - biology + - histology + - muscle + - annotation + - myopathy +--- + ![Twitter Follow](https://img.shields.io/twitter/follow/corentinm_py?style=social) ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/lambda-science/impatient) ![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/lambda-science/IMPatienT) [![Build](https://github.com/lambda-science/IMPatienT/actions/workflows/docker-build-push.yml/badge.svg)](https://github.com/lambda-science/IMPatienT/actions/workflows/docker-build-push.yml) ![GitHub last commit](https://img.shields.io/github/last-commit/lambda-science/impatient) ![GitHub](https://img.shields.io/github/license/lambda-science/IMPatienT) # IMPatienT 🗂️: an integrated web application to digitize, process and explore multimodal patient data. @@ -9,7 +29,7 @@ **IMPatienT 🗂️** (**I**ntegrated digital **M**ultimodal **PATIEN**t da**T**a) **is a web application developped in the MYO-xIA project for patient data digitization and exploration.** It features a standard vocabulary creator, optical character recognition (OCR), natural language processing (NLP), image annotation and segmentation using machine learning, interactive visualizations and automatic diagnosis suggestion. -A demo version is currently deployed at: https://impatient.lbgi.fr/ +A demo version is currently deployed at: https://huggingface.co/spaces/corentinm7/IMPatienT This project is free and open-source under the AGPL license, feel free to fork and contribute to the development. Several guides are available at the bottom of this page for the production deployment and developer mode. ## Contact: @@ -36,22 +56,51 @@ Medical acts, such as imaging, generally lead to the production of several medic **Results** Here, we present IMPatienT (**I**ntegrated digital **M**ultimodal **PATIEN**t da**T**a), a free and open-source web application to digitize, process and explore multimodal patient data. IMPatienT has a modular architecture, including four components to: (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data by mapping it to a set of standard terms, (iii) annotate images and perform image segmentation, and (iv) generate an automatic visualization dashboard to provide insight on the data and perform automatic diagnosis suggestions. Finally, we demonstrate the usefulness of IMPatienT on a corpus of 40 simulated muscle biopsy reports of congenital myopathy patients. **Conclusions** -IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text data. As it relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as a patient registry for exploratory data analysis (EDA). A demo instance of the application is available at https://impatient.lbgi.fr. +IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text data. As it +relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as a patient +registry for exploratory data analysis (EDA). A demo instance of the application is available +at https://huggingface.co/spaces/corentinm7/IMPatienT. ## Setup guides -### (DOCKER) Developper Mode Setup (to contribute) +### Local Developer mode using Docker (to contribute) + +1. Clone the repository `git clone git@github.com:lambda-science/IMPatienT.git` +2. Build the docker image and run it using by running: `chmod +x docker/dev_build_run.sh` and + `./docker/dev_build_run.sh` + Congrats, the app is now running on `http://localhost:7860`! + Any modification you do to the code will be saved and applied directly to the app. + +### Deploy to Production using Docker + +1. Clone the repository `git clone git@github.com:lambda-science/IMPatienT.git` +2. Build the docker image: `chmod +x docker/build.sh` +3. Edit the configuration sample with your secrets: -[See the wiki page: Developper Mode Setup (DOCKER)]() +```bash +cp docker/run_sample.sh docker/run.sh +nano docker/run.sh +``` -### (DOCKER) Deploy to production & Maintain IMPatienT +4. Run the docker image: `./docker/run.sh` + Congrats, the app is now running on `http://localhost:7860` with demo database and ontology ! Use any reverse-proxy ( + like Nginx) to expose it to the internet. If you want to customize, see the note below about persistent data. -[See the wiki page: Deploy and maintain (DOCKER)]() +**Note about persistent data:** -### (LINUX) Deploy to production & Maintain IMPatienT +Currently, all your data are ephemeral inside the docker container and will be lost when you stop the container. By +default it runs a demo database and ontology is no data are provided. To solve this you can create a persistent volume +to store your actual data. -[See the wiki page: Deploy and maintain (LINUX)]() +⚠️ 🚨 **This is only needed for fresh/clean/new installations. This WILL delete all your previous IMPatienT database and +ontology as this creates a new volume and overwrite its content with the content of the current directory `data/`.** ⚠️ +🚨 -### (LINUX) Developper Mode Setup +1. Before running the container, create the volume by running: `./docker/create_volume.sh` +2. Run the docker image: `./docker/run.sh` -[See the wiki page: Developper Mode Setup (LINUX)]() +* **NB1:** If you have issues with permissions on data folder inside the docker. You might have to `chown -R 1000 data/` + before `./docker/create_volume.sh` +* **NB2:** This can also be used to deploy/inject/restore backup data to the container: as this script copy current + `data/` folder content to the volume. Simply add your `app.db` backup in `data/database/` and `ontology.json` backup + in `data/ontology` and your patient folders with images in `data/images/` before running the script. diff --git a/app/auth/__init__.py b/app/auth/__init__.py deleted file mode 100644 index 5b56d53..0000000 --- a/app/auth/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from flask import Blueprint - -bp = Blueprint("auth", __name__, template_folder="templates") - -from app.auth import routes diff --git a/app/auth/email.py b/app/auth/email.py deleted file mode 100644 index ce724c3..0000000 --- a/app/auth/email.py +++ /dev/null @@ -1,18 +0,0 @@ -from app.email import send_email -from flask import current_app, render_template - - -def send_password_reset_email(user): - """Sent a token by email to reset the password - - Args: - user (SQLAlchemy Object): The user who requested the password reset - """ - token = user.get_reset_password_token() - send_email( - ("[IMPatienT] Reset Your Password"), - sender=current_app.config["ADMINS_EMAIL"][0], - recipients=[user.email], - text_body=render_template("email_reset_password.txt", user=user, token=token), - html_body=render_template("email_reset_password.html", user=user, token=token), - ) diff --git a/app/auth/forms.py b/app/auth/forms.py deleted file mode 100644 index 4c7de0c..0000000 --- a/app/auth/forms.py +++ /dev/null @@ -1,93 +0,0 @@ -from flask_wtf import FlaskForm -from wtforms import BooleanField, PasswordField, StringField, SubmitField -from wtforms.validators import DataRequired, Email, EqualTo - - -class LoginForm(FlaskForm): - """Login - - Args: - FlaskForm (FlaskForm Class): The FlaskForm Class - """ - - username = StringField( - "Username", - validators=[ - DataRequired(), - ], - render_kw={"placeholder": "Username", "class": "form-control"}, - ) - password = PasswordField( - "Password", - validators=[DataRequired()], - render_kw={"placeholder": "Password", "class": "form-control"}, - ) - remember_me = BooleanField("Remember Me") - # submit = SubmitField("Sign In", render_kw={"class": "btn btn-primary"}) - - -class ResetPasswordRequestForm(FlaskForm): - """Reset Password Request Form - - Args: - FlaskForm (FlaskForm Class): The FlaskForm Class - """ - - email = StringField( - "Email", - validators=[DataRequired(), Email()], - render_kw={"placeholder": "Email", "class": "form-control"}, - ) - # submit = SubmitField( - # "Request Password Reset", render_kw={"class": "btn btn-primary"} - # ) - - -class ResetPasswordForm(FlaskForm): - """New password form - - Args: - FlaskForm (FlaskForm Class): The FlaskForm Class - """ - - password = PasswordField( - "Password", - validators=[DataRequired()], - render_kw={"placeholder": "Password", "class": "form-control"}, - ) - password2 = PasswordField( - "Repeat Password", - validators=[DataRequired(), EqualTo("password")], - render_kw={"placeholder": "Confirm Password", "class": "form-control"}, - ) - # submit = SubmitField( - # "Request Password Reset", render_kw={"class": "btn btn-primary"} - # ) - - -# class RegistrationForm(FlaskForm): -# """The form used for registration""" -# username = StringField('Username', -# validators=[ -# DataRequired(), -# Regexp(r'^[\w.@+-]+$'), -# Length(min=4, max=25) -# ]) -# email = StringField('Email', validators=[DataRequired(), Email()]) -# password = PasswordField('Password', validators=[DataRequired()]) -# password2 = PasswordField('Repeat Password', -# validators=[DataRequired(), -# EqualTo('password')]) -# submit = SubmitField('Register') -# -# def validate_username(self, username): -# """Function used to check if username already exist""" -# user = User.query.filter_by(username=username.data).first() -# if user is not None: -# raise ValidationError('Username already exists.') -# -# def validate_email(self, email): -# """Function used to check if email already exist""" -# user = User.query.filter_by(email=email.data).first() -# if user is not None: -# raise ValidationError('Email already used.') diff --git a/app/auth/routes.py b/app/auth/routes.py deleted file mode 100644 index 5c38246..0000000 --- a/app/auth/routes.py +++ /dev/null @@ -1,123 +0,0 @@ -from app import db, login_manager -from app.auth import bp -from app.auth.email import send_password_reset_email -from app.auth.forms import LoginForm, ResetPasswordForm, ResetPasswordRequestForm -from app.models import User -from flask import flash, redirect, render_template, request, url_for -from flask_login import current_user, login_required, login_user, logout_user -from werkzeug.urls import url_parse - - -@login_manager.unauthorized_handler -def handle_needs_login(): - flash("You have to be logged in to access this page.", "info") - return redirect(url_for("auth.login")) - - -@bp.route("/login", methods=["GET", "POST"]) -def login(): - """The login page - - Returns: - str: Login HTML Page - """ - # Already auth. user are redirected to index - if current_user.is_authenticated: - return redirect(url_for("index.index")) - form = LoginForm() - if form.validate_on_submit(): - # Check if password match - user = User.query.filter_by(username=form.username.data).first() - if user is None or not user.check_password(form.password.data): - flash("Invalid username or password", "danger") - return redirect(url_for("auth.login")) - # Log user if password matched, store username and redirect user - login_user(user, remember=form.remember_me.data) - flash("Login successful", "success") - return redirect(url_for("index.index")) - return render_template("login.html", title="Sign In", form=form) - - -@bp.route("/logout") -def logout(): - """Logout Page - - Returns: - str: Logout HTML Page - """ """View page to logout""" - flash("You were logged out", "info") - logout_user() - return redirect(url_for("auth.login")) - - -@bp.route("/reset_password_request", methods=["GET", "POST"]) -def reset_password_request(): - """Reset password request page - - Returns: - str: Reset password request HTML Page or redirection to login page - """ """View page to request password reset""" - # If Logged already: redirect to index - if current_user.is_authenticated: - return redirect(url_for("index.index")) - form = ResetPasswordRequestForm() - # If form validated, look for user in database and create the token & email for password reset - if form.validate_on_submit(): - user = User.query.filter_by(email=form.email.data).first() - if user: - send_password_reset_email(user) - flash( - "Check your email for the instructions to reset your password", - "success", - ) - else: - flash("No account found for this email.", "danger") - return redirect(url_for("auth.login")) - return render_template( - "reset_password_request.html", title="Reset Password", form=form - ) - - -@bp.route("/reset_password/", methods=["GET", "POST"]) -def reset_password(token): - """Create new password page - - Args: - token (str): JWT-Token to reset password - - Returns: - str: HTML Page to create new password or redirection to login page - """ - # If Logged already: redirect to index - if current_user.is_authenticated: - return redirect(url_for("index.index")) - # Filter user by verifying token. Redirect if not valid. Else new password form - user = User.verify_reset_password_token(token) - if not user: - return redirect(url_for("index.index")) - form = ResetPasswordForm() - # Save new password to DB - if form.validate_on_submit(): - user.set_password(form.password.data) - db.session.commit() - flash("Your password has been reset.") - return redirect(url_for("auth.login")) - return render_template("reset_password.html", form=form) - - -# @bp.route('/register', methods=['GET', 'POST']) -# def register(): -# """View page to register""" -# # Redirect if already logged -# if current_user.is_authenticated: -# return redirect(url_for('index.index')) -# form = RegistrationForm() -# # If form validated, register user to database -# if form.validate_on_submit(): -# user = User(username=form.username.data, email=form.email.data) -# user.set_password(form.password.data) -# db.session.add(user) -# db.session.commit() -# flash('Congratulations, you are now a registered user!', "success") -# return redirect(url_for('auth.login')) -# return render_template('register.html', title='Register', form=form) diff --git a/app/auth/templates/email_reset_password.html b/app/auth/templates/email_reset_password.html deleted file mode 100644 index 226ad7a..0000000 --- a/app/auth/templates/email_reset_password.html +++ /dev/null @@ -1,14 +0,0 @@ -

Dear {{ user.username }},

-

- To reset your password - - click here - -

-

- Alternatively, you can paste the following link in your browser's address bar: -

-

{{ url_for('auth.reset_password', token=token, _external=True) }}

-

If you have not requested a password reset simply ignore this message.

-

Sincerely,

-

The IMPatienT Team

diff --git a/app/auth/templates/email_reset_password.txt b/app/auth/templates/email_reset_password.txt deleted file mode 100644 index 0d6c281..0000000 --- a/app/auth/templates/email_reset_password.txt +++ /dev/null @@ -1,11 +0,0 @@ -Dear {{ user.username }}, - -To reset your password click on the following link: - -{{ url_for('auth.reset_password', token=token, _external=True) }} - -If you have not requested a password reset simply ignore this message. - -Sincerely, - -The IMPatienT Team diff --git a/app/auth/templates/login.html b/app/auth/templates/login.html deleted file mode 100644 index 9821a7c..0000000 --- a/app/auth/templates/login.html +++ /dev/null @@ -1,30 +0,0 @@ -{% extends "base.html" %} - -{% block content %} -
-

Sign In

-

New User? Contact an admin to create an account !

-
- {{ form.hidden_tag() }} - {% for error in form.errors %} - {{ error }}: {{form.errors[error]}} - {% endfor %} -

- {{ form.username.label(class="form-label") }}
- {{ form.username }} -

-

- {{ form.password.label(class="form-label") }}
- {{ form.password }} -

-

{{ form.remember_me() }} {{ form.remember_me.label }}

-

- Forgot Your Password? - Click to Reset It -

-

-
-
-{% endblock %} diff --git a/app/auth/templates/register.html b/app/auth/templates/register.html deleted file mode 100644 index f5aedb6..0000000 --- a/app/auth/templates/register.html +++ /dev/null @@ -1,37 +0,0 @@ -{% extends "base.html" %} {% block content %} - -{% endblock %} diff --git a/app/auth/templates/reset_password.html b/app/auth/templates/reset_password.html deleted file mode 100644 index ff2868e..0000000 --- a/app/auth/templates/reset_password.html +++ /dev/null @@ -1,23 +0,0 @@ -{% extends "base.html" %} {% block content %} -
-

Reset Your Password

-
- {{ form.hidden_tag() }} -

- {{ form.password.label(class="form-label") }}
- {{ form.password }}
- {% for error in form.password.errors %} - [{{ error }}] - {% endfor %} -

-

- {{ form.password2.label(class="form-label") }}
- {{ form.password2 }}
- {% for error in form.password2.errors %} - [{{ error }}] - {% endfor %} -

-

-
-
-{% endblock %} diff --git a/app/auth/templates/reset_password_request.html b/app/auth/templates/reset_password_request.html deleted file mode 100644 index f963fcb..0000000 --- a/app/auth/templates/reset_password_request.html +++ /dev/null @@ -1,16 +0,0 @@ -{% extends "base.html" %} {% block content %} -
-

Reset Password

-
- {{ form.hidden_tag() }} -

- {{ form.email.label(class="form-label") }}
- {{ form.email }}
- {% for error in form.email.errors %} - [{{ error }}] - {% endfor %} -

-

-
-
-{% endblock %} diff --git a/app/dashapp/static/segmentation-style.css b/app/dashapp/static/segmentation-style.css deleted file mode 100644 index 6d3b0e5..0000000 --- a/app/dashapp/static/segmentation-style.css +++ /dev/null @@ -1,27 +0,0 @@ -#app-title > * { - color: white; - margin: 0; - padding: 0; -} - -#howto-open { - white-space: nowrap; -} - -#gh-link { - white-space: nowrap; -} - -.card { - margin: 1em 0 1em 0; - min-width: auto; -} - -label { - display: block; - margin-bottom: 0; -} - -#transparent-loader-wrapper > div { - visibility: visible !important; -} diff --git a/app/errors/templates/404.html b/app/errors/templates/404.html deleted file mode 100644 index 2afb10e..0000000 --- a/app/errors/templates/404.html +++ /dev/null @@ -1,7 +0,0 @@ -{% extends "base.html" %} {% block content %} -

Error 404: Page not found

-

- This page has not been found. Please press the back button to go to the index: - Back -

-{% endblock %} diff --git a/app/errors/templates/413.html b/app/errors/templates/413.html deleted file mode 100644 index f4c08db..0000000 --- a/app/errors/templates/413.html +++ /dev/null @@ -1,7 +0,0 @@ -{% extends "base.html" %} {% block content %} -

Error 413: File is too large

-

- Uploaded file is too large. Please press the back button to go to the index: - Back -

-{% endblock %} diff --git a/app/errors/templates/500.html b/app/errors/templates/500.html deleted file mode 100644 index bdd57d4..0000000 --- a/app/errors/templates/500.html +++ /dev/null @@ -1,12 +0,0 @@ -{% extends "base.html" %} {% block content %} -

Error 500: An unexpected error has occurred

-

If this happened in the visualisation module, a common fix could be going to the Standard Vocabulary module and - press "Save tree" to re-generate files !

-

The administrator has been notified. Sorry for the inconvenience!

-

- Please press the back button to go to the index: - Back -

-

Traceback:

- 
{{ traceback_info }}
- {% endblock %} \ No newline at end of file diff --git a/app/historeport/static/slider.css b/app/historeport/static/slider.css deleted file mode 100644 index d84d6d5..0000000 --- a/app/historeport/static/slider.css +++ /dev/null @@ -1,62 +0,0 @@ -markneg { - background: rgb(112, 5, 5); - color: rgb(255, 255, 255); -} -markpos { - background: rgb(9, 158, 9); - color: rgb(255, 255, 255); -} - -/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#f0ad4e+10,d9534f+10,d9534f+30,5cb85c+30 */ -/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#f0ad4e+45,d9534f+45,d9534f+55,5cb85c+55 */ -/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#d9534f+5,f0ad4e+5,f0ad4e+5,f0ad4e+51,d2ffc9+51,0cf900+100 */ - -/* Mozilla */ -input[type="range"]::-moz-range-track { - background: -moz-linear-gradient( - left, - #f0ad4e 15%, - #d9534f 15%, - #d9534f 30%, - #5cb85c 30% - ); /* FF3.6-15 */ - background: linear-gradient( - to right, - #f0ad4e 15%, - #d9534f 15%, - #d9534f 30%, - #5cb85c 30% - ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ -} - -/* Chrome */ -input[type="range"]::-webkit-slider-runnable-track { - background: -webkit-linear-gradient( - left, - #f0ad4e 15%, - #d9534f 15%, - #d9534f 30%, - #5cb85c 30% - ); /* Chrome10-25,Safari5.1-6 */ - background: linear-gradient( - to right, - #f0ad4e 15%, - #d9534f 15%, - #d9534f 30%, - #5cb85c 30% - ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ -} - -/* IE*/ -input[type="range"]::-ms-fill-lower, -input[type="range"]::-ms-fill-upper { - background: #f0ad4e; /* Old browsers */ - background: linear-gradient( - to right, - #f0ad4e 15%, - #d9534f 15%, - #d9534f 30%, - #5cb85c 30% - ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ - filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#f0ad4e', endColorstr='#5cb85c',GradientType=1 ); /* IE6-9 */ -} diff --git a/app/historeport/templates/histo_index.html b/app/historeport/templates/histo_index.html deleted file mode 100644 index b01435f..0000000 --- a/app/historeport/templates/histo_index.html +++ /dev/null @@ -1,114 +0,0 @@ -{% extends "base.html"%} {% block content %} - - - - -
-
-

Digitize a new report

-
- - New Report - -
-
-
-
-
-

Digital Report Database

Download All Reports (.CSV) - - - - - - - - - - - - - - - - - - - {% for report in history %} - - - - - - - - - - {% endfor %} -
Biopsy IDPatient IDGeneDiagnosticBOQA PredictionBOQA Score (0-1)Action
{{ report.biopsie_id }}{{ report.patient_id }}{{ report.gene_diag }}{{ report.conclusion }}{{ report.BOQA_prediction }} - {{ report.BOQA_prediction_score }} - - - Resume - - - - - - -
-
-
- - - -{% endblock %} \ No newline at end of file diff --git a/app/historeport/templates/historeport.html b/app/historeport/templates/historeport.html deleted file mode 100644 index b03dc34..0000000 --- a/app/historeport/templates/historeport.html +++ /dev/null @@ -1,268 +0,0 @@ -{% extends "base.html"%} -{% block content %} - - - - - - - - - - - - -
-
-
-
-
-

Optional: Select a PDF and upload it to perform OCR/NLP analysis

- {% for error in pdf_form.errors %} - {{ error }}: {{pdf_form.errors[error]}} - {% endfor %} -
-
- {{ pdf_form.hidden_tag() }} - {{ pdf_form.pdf_file}} -
-
- {{ pdf_form.language}} -
-
- - - -
- -
-
- - -
-
- -
-
-

- -

-
-
-
-
-
-
-
-
-
-
-
-

- -

-
-
-
-
-
-
-
-
-
-
-
- -
- -
-
-
-

Patient Informations

- - {% for error in form.errors %} - {{ error }}: {{form.errors[error]}} - {% endfor %} - {{ form.hidden_tag() }} -
-
- {{ form.patient_id.label(class="form-label") }} - {{ form.patient_id }} -
-
- {{ form.biopsie_id.label(class="form-label") }} - {{ form.biopsie_id }}
-
- {{ form.date_envoie.label(class="form-label") }} - {{ form.date_envoie }}
-
- {{ form.muscle_prelev.label(class="form-label") }} - {{ form.muscle_prelev }}
-
-
-
- - {{ form.age_biopsie.label(class="form-label") }} - {{ form.age_biopsie }}
-
- {{ form.gene_diag.label(class="form-label") }} - {{ form.gene_diag }}
- {{ form.ontology_tree }} -
- - -
-
- - {{ form.pheno_terms.label(class="form-label") }} - {{ form.pheno_terms }}
-
- {{ form.mutation.label(class="form-label") }} - {{ form.mutation }}
-
- -
-
-
-

Vocabulary Tree

- - -
-
-
-

Absence/Presence Annotation

- - {% for error in form2.errors %} - {{ error }}: {{form2.errors[error]}} - {% endfor %} - {{ form2.hidden_tag() }} -
-
-
- {{ form2.preabsProba.label(class="form-label d-flex justify-content-center") }} - {{ form2.preabsProba }} -
-
-
-
- -
-
-

Vocabulary Properties

-
-
- {{ form2.onto_id_ext.label(class="form-label") }} - {{ form2.onto_id_ext }} -
-
- {{ form2.onto_name.label(class="form-label") }} - {{ form2.onto_name }} -
-
- {{ form2.synonymes.label(class="form-label") }} - {{ form2.synonymes }} - {{ form2.alternative_language.label(class="form-label") }} - {{ form2.alternative_language }} - {{ form2.hpo_datamined.label(class="form-label") }} - {{ form2.hpo_datamined }} - {{ form2.gene_datamined.label(class="form-label") }} - {{ form2.gene_datamined }} - {{ form2.phenotype_datamined.label(class="form-label") }} - {{ form2.phenotype_datamined }} - {{ form2.correlates_with.label(class="form-label") }} - {{ form2.correlates_with }} - {{ form2.description.label(class="form-label") }} - {{ form2.description }} - - -
-
-
-
- -
-
-
-
-

Final Vocabulary Annotation (Present)

-
-
-
-
-

Final Vocabulary Annotation (Negated)

-
-
- -
-
-
-
-

Commentaries and Conclusions

- {{form.comment}} - Diagnosis Prediction:
- Method BOQA (Stats):
-

- {{form.conclusion.label(class="form-label")}} - {{form.conclusion}} - -
-
-
-
- -
- -
- - - - -{% endblock %} \ No newline at end of file diff --git a/app/histostats/templates/histostats_index.html b/app/histostats/templates/histostats_index.html deleted file mode 100644 index 27feaec..0000000 --- a/app/histostats/templates/histostats_index.html +++ /dev/null @@ -1,90 +0,0 @@ -{% extends "base.html"%} {% block content %} - - - - -
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- -
-
-
-
-
-
-
-
-
-
-

Vocabulary Frequencies Per Genes

- - Download Table (.CSV) - {{df_per_gene | safe}} -
- -
-

Vocabulary Frequencies Per Diagnosis

- - Download Table (.CSV) - {{df_per_diag | safe}} -
-
-
-
- - - - - - - - - - - - -{% endblock %} diff --git a/app/imgupload/templates/create_img.html b/app/imgupload/templates/create_img.html deleted file mode 100644 index cf1e0a7..0000000 --- a/app/imgupload/templates/create_img.html +++ /dev/null @@ -1,39 +0,0 @@ -{% extends "base.html"%} -{% block content %} - - - - - - -
-
-
-

Modify/Upload New Image


-
- {% for error in form.errors %} - {{ error }}: {{form.errors[error]}} - {% endfor %} - {{ form.hidden_tag() }} - {{ form.patient_ID.label(class="form-label") }} - {{ form.patient_ID }} -

Select an image file

- {{ form.image }}
- {{ form.biopsy_report_ID.label(class="form-label") }} - {{ form.biopsy_report_ID }} - {{ form.type_coloration.label(class="form-label") }} - {{ form.type_coloration }} - {{ form.age_histo.label(class="form-label") }} - {{ form.age_histo }} - {{ form.diagnostic.label(class="form-label") }} - {{ form.diagnostic }} - -
-
-
- -{% endblock %} diff --git a/app/imgupload/templates/img_index.html b/app/imgupload/templates/img_index.html deleted file mode 100644 index ac4dbb9..0000000 --- a/app/imgupload/templates/img_index.html +++ /dev/null @@ -1,81 +0,0 @@ -{% extends "base.html"%} {% block content %} - - - - -
-
-

Upload a new image

-
- New Image - -
-
-
-
-
-

Image Database

- Download All Images (.tar.gz) - - - - - - - - - {% for image in image_history %} - - - - - - - - {% endfor %} -
Biopsy IDPatient IDImage NameDiagnosticAction
{{ image.biopsy_id }}{{ image.patient_id }}{{ image.image_name }}{{ image.diagnostic }} - - Anotate - - - Modify - - - - - - -
-
-
- - - -{% endblock %} diff --git a/app/index/templates/index.html b/app/index/templates/index.html deleted file mode 100644 index a5f5795..0000000 --- a/app/index/templates/index.html +++ /dev/null @@ -1,122 +0,0 @@ -{% extends "base.html" %} {% block content %} -
-

- IMPatienT🗂️️: an integrated web application to digitize, process and explore multimodal patient data. -

-

- IMPatienT Banner -

-

- IMPatienT (Integrated digital Multimodal PATIENt - daTa) is a web application developped in the - MYO-xIA project for patient data digitization and exploration.
It features a standard - vocabulary - creator, optical character recognition (OCR), natural language processing - (NLP), image annotation and segmentation using machine learning, interactive - visualizations and automatic diagnosis prediction. -

-
-

Demo Usage Instructions

-

- If you are on the demo instance (https://impatient.lbgi.fr), you can login - on top - right with - login: demo ; password: demo
The application is - preloaded with a database of histology reports and a standard vocabulary for - muscle biopsy. Data on this demo instance is reset once every day.
- For the PDF automatic analysis, you can find a sample PDF - HERE - working with the preinstalled standard vocabulary. A sample image for image - annotation can be found - HERE. -

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Partners

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- - Partner Logo - -
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-

IMPatienT is developped and used in collaboration with the - Morphological Unit of the Institute of Myology of Paris. - A production instance is deployed to help discovering new relevant - features for congenital myopathies classification and diagnosis.

-
-
-
-

IMPatienT🗂️️ Abstract

-

- Background -
- Medical acts, such as imaging, generally lead to the production of several medical text reports that describe the - relevant findings. Such processes induce multimodality in patient data by linking image data to free-text data and - consequently, multimodal data have become central to drive research and improve diagnosis of patients. However, the - exploitation of patient data is challenging as the ecosystem of available analysis tools is fragmented depending on - the type of data (images, text, genetic sequences), the task to be performed (digitization, processing, exploration) - and the domain of interest (clinical phenotype, histology…). To address the challenges, the analysis tools need to - be integrated in a simple, comprehensive, and flexible platform. -
- Results -
- Here, we present IMPatienT (Integrated digital Multimodal PATIENt - daTa), a free and open-source web application to digitize, process and explore multimodal patient - data. IMPatienT has a modular architecture, including four components to: (i) create a standard vocabulary for a - domain, (ii) digitize and process free-text data by mapping it to a set of standard terms, (iii) annotate images and - perform image segmentation, and (iv) generate an automatic visualization dashboard to provide insight on the data - and perform automatic diagnosis suggestions. Finally, we demonstrate the usefulness of IMPatienT on a corpus of 40 - simulated muscle biopsy reports of congenital myopathy patients. -
- Conclusions -
- IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text data. As - it relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as a - patient registry for exploratory data analysis (EDA). A demo instance of the application is available at https://impatient.lbgi.fr. - -

-
-

MYO-xIA Project

-

- The MYO-xIA project aims to collect data from patients with - congenital myopathies in order to analyse them using - explainable AI approaches. In the field of congenital - myopathies research, there is an important need for - digitization and standardization of patient data in order - to use modern data analysis methods.
This project has tree mains - objectives: -

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  • - Gather and format patient data to be ready for automatic - exploitation (patient histology-report form, image annotation, OCR/NLP) -
    • -
  • - Help the - discovery of new phenotype-genotype-histology association - for each congenital myopathy subtype (standard vocabulary creation tool, - per gene and per class histology feature statistics) -
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  • - Provide tools for automatic diagnosis based on patient - data (live prediction of congenital myopathy subtype with histology - reports, images, genetic data and phenotype) -
    • -
-
-

Contact

-

- The main maintainer is:
Corentin Meyer - PhD Student @ - CSTB Team - iCube - University Of Strasbourg co.meyer@unistra.fr -

-
-

Citing IMPatienT🗂️

-

[placeholder]

-
-
-{% endblock %} \ No newline at end of file diff --git a/app/index/templates/index.md b/app/index/templates/index.md deleted file mode 100644 index 6032607..0000000 --- a/app/index/templates/index.md +++ /dev/null @@ -1,39 +0,0 @@ -# IMPatienT 🗂️: an integrated web application to digitize, process and explore multimodal patient data. - -**IMPatienT** 🗂️ is a web application developped in the **MYO-xIA project** for patient data digitization and exploration. -It features a standard vocabulary creator, optical character recognition (OCR), natural language processing (NLP), image annotation and segmentation using machine learning, interactive visualizations and automatic diagnosis prediction. - -## Demo Usage Instructions - -If you are on the demo instance (https://impatient.lbgi.fr), you can login on top right with **login: demo ; password: demo** -The application is preloaded with a database of histology reports and a standard vocabulary for muscle biopsy. Data on this demo instance is reset once every day. -For the PDF automatic analysis, you can find a sample PDF [HERE](https://www.lbgi.fr/~meyer/IMPatienT/sample_demo_report.pdf) working with the preinstalled standard vocabulary. A sample image for image annotation can be found [HERE](https://www.lbgi.fr/~meyer/IMPatienT/sample_image_histo.jpg). -## Partners -IMPatienT is developped and used in collaboration with the [Morphological Unit of the Institute of Myology of Paris](https://www.institut-myologie.org/en/recherche-2/neuromuscular-investigation-center/morphological-unit/). A production instance is deployed to help discovering new relevant features for congenital myopathies classification and diagnosis. - -## IMPatienT🗂️ Abstract - -**Background** -Medical acts, such as imaging, generally lead to the production of several medical text reports that describe the relevant findings. Such processes induce multimodality in patient data by linking image data to free-text data and consequently, multimodal data have become central to drive research and improve diagnosis of patients. However, the exploitation of patient data is challenging as the ecosystem of available analysis tools is fragmented depending on the type of data (images, text, genetic sequences), the task to be performed (digitization, processing, exploration) and the domain of interest (clinical phenotype, histology…). To address the challenges, the analysis tools need to be integrated in a simple, comprehensive, and flexible platform. -**Results** -Here, we present IMPatienT (d**I**gitize **M**ultimodal **PATIEN**t da**T**a), a free and open-source web application to digitize, process and explore multimodal patient data. IMPatienT has a modular architecture, including four components to: (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data by mapping it to a set of standard terms, (iii) annotate images and perform image segmentation, and (iv) generate an automatic visualization dashboard to provide insight on the data and perform automatic diagnosis suggestions. Finally, we demonstrate the usefulness of IMPatienT on a corpus of 40 simulated muscle biopsy reports of congenital myopathy patients. -**Conclusions** -IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text data. As it relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as a patient registry for exploratory data analysis (EDA). A demo instance of the application is available at https://impatient.lbgi.fr. - -## MYO-xIA Project - -The MYO-xIA project aims to collect data from patients with **congenital myopathies** in order to analyse them using **explainable AI approaches**. In the field of congenital myopathies research, there is an important need for **digitization and standardization of patient data** in order to use modern data analysis methods. -This project has tree mains objectives: - -- **Gather and format patient data** to be ready for automatic exploitation (patient histology-report form, image annotation, OCR/NLP) -- Help the **discovery of new phenotype-genotype-histology** association for each congenital myopathy subtype (standard vocabulary creation tool, per gene and per class histology feature statistics) -- Provide tools for **automatic diagnosis** based on patient data (live prediction of congenital myopathy subtype with histology reports, images, genetic data and phenotype) - -## Contact: - -The main maintainer is: -**Corentin Meyer** - PhD Student @ CSTB Team - iCube - University Of Strasbourg [co.meyer@unistra.fr](mailto:co.meyer@unistra.fr) - -## Citing IMPatienT🗂️ - -[placeholder] diff --git a/app/models.py b/app/models.py deleted file mode 100644 index 7978bef..0000000 --- a/app/models.py +++ /dev/null @@ -1,185 +0,0 @@ -import datetime -from time import time - -import jwt -from flask import current_app -from flask_login import UserMixin -from werkzeug.security import check_password_hash, generate_password_hash - -from app import db, login_manager - - -class User(UserMixin, db.Model): - """Database table for Users""" - - id = db.Column(db.Integer, primary_key=True) - username = db.Column( - db.String(64), - index=True, - unique=True, - nullable=False, - ) - email = db.Column(db.String(120), index=True, unique=True, nullable=False) - password_hash = db.Column(db.String(128), nullable=False) - images = db.relationship("Image", backref="creator", lazy="dynamic") - report = db.relationship("ReportHisto", backref="creator", lazy="dynamic") - - def __repr__(self): - return "".format(self.username, self.email) - - def set_password(self, password): - """Method to hash password to the database - - Args: - password (str): Plain-text password - """ - self.password_hash = generate_password_hash(password) - - def check_password(self, password): - """Method to check if the plain-text password matches the hashed one - - Args: - password (str): Plain-text password - - Returns: - bool: True if the password matches, False otherwise - """ - return check_password_hash(self.password_hash, password) - - def get_reset_password_token(self, expires_in=600): - """Generate a JWT Token to reset password. - - Args: - expires_in (int, optional): Token validity duration. Defaults to 600. - - Returns: - JWT Token: The generated token as string - """ - return jwt.encode( - {"reset_password": self.id, "exp": time() + expires_in}, - current_app.config["SECRET_KEY"], - algorithm="HS256", - ) - - @staticmethod - def verify_reset_password_token(token): - """Method to check if the token is valid - - Args: - token (JWT Token): The token to check - - Returns: - SQLAlchemy Obj: Return the user database entry object if the token is - valid, None otherwise - """ - try: - id = jwt.decode( - token, current_app.config["SECRET_KEY"], algorithms=["HS256"] - )["reset_password"] - except: - return - return User.query.get(id) - - @staticmethod - def create_admin_account(): - """Create a default admin account if no user is present in the database""" - user_entry = User.query.get(1) - if not user_entry: - user = User( - username=current_app.config["DEFAULT_ADMIN_USERNAME"], - email=current_app.config["DEFAULT_ADMIN_EMAIL"], - ) - user.set_password(current_app.config["DEFAULT_ADMIN_PASSWORD"]) - db.session.add(user) - db.session.commit() - - -@login_manager.user_loader -def load_user(id): - """Method to load current user in Flask-Login - - Args: - id (str): User ID in database - - Returns: - SQLAlchemy Obj: Return the user database entry object corresponding to the ID - """ - return User.query.get(int(id)) - - -class Image(db.Model): - """Database table for Image & annotations""" - - id = db.Column(db.Integer, primary_key=True) - image_name = db.Column(db.String(140), nullable=False) - expert_id = db.Column(db.Integer, db.ForeignKey("user.id"), nullable=False) - patient_id = db.Column(db.String(100), index=True, nullable=False) - biopsy_id = db.Column(db.String(100), index=True) - type_coloration = db.Column(db.String(140)) - age_at_biopsy = db.Column(db.Integer, default=-1) - image_path = db.Column(db.String(4096), unique=True, nullable=False) - image_background_path = db.Column(db.String(4096), unique=True) - sigma_range_min = db.Column(db.Float()) - sigma_range_max = db.Column(db.Float()) - diagnostic = db.Column(db.String(140), index=True) - seg_matrix_path = db.Column(db.String(4096), unique=True) - mask_image_path = db.Column(db.String(4096), unique=True) - blend_image_path = db.Column(db.String(4096), unique=True) - classifier_path = db.Column(db.String(4096), unique=True) - mask_annot_path = db.Column(db.String(4096), unique=True) - class_info_path = db.Column(db.String(4096), unique=True) - datetime = db.Column( - db.DateTime(), - onupdate=datetime.datetime.utcnow, - default=datetime.datetime.utcnow, - ) - - def __repr__(self): - return "".format(self.image_name, self.patient_id) - - def isduplicated(self): - """Method to check if the image is already in the - database (same name and patient ID) - - Returns: - bool: True if the image is already in the database, False otherwise - """ - if ( - Image.query.filter_by( - image_name=self.image_name, patient_id=self.patient_id - ).first() - is None - ): - return False - else: - return True - - -class ReportHisto(db.Model): - """Database table text reports""" - - id = db.Column(db.Integer, primary_key=True) - patient_id = db.Column(db.String(100), index=True) - expert_id = db.Column(db.Integer, db.ForeignKey("user.id"), nullable=False) - biopsie_id = db.Column(db.String(140)) - muscle_prelev = db.Column(db.String(140)) - age_biopsie = db.Column(db.Integer) - date_envoie = db.Column(db.String(10)) - gene_diag = db.Column(db.String(140), index=True) - mutation = db.Column(db.String(140)) - pheno_terms = db.Column(db.String(4096)) - ontology_tree = db.Column(db.JSON, default=[], nullable=False) - comment = db.Column(db.Text, default="") - conclusion = db.Column(db.String(140), index=True) - BOQA_prediction = db.Column(db.String(140), index=True) - BOQA_prediction_score = db.Column(db.Float()) - datetime = db.Column( - db.DateTime(), - onupdate=datetime.datetime.utcnow, - default=datetime.datetime.utcnow, - ) - - def __repr__(self): - return "".format( - self.id, self.patient_id, self.biopsie_id - ) diff --git a/app/ontocreate/templates/ontocreate.html b/app/ontocreate/templates/ontocreate.html deleted file mode 100644 index 575222a..0000000 --- a/app/ontocreate/templates/ontocreate.html +++ /dev/null @@ -1,136 +0,0 @@ -{% extends "base.html"%} {% block content %} - - - - - - - - -
-
-

Standard Vocabulary Tree

- Download Vocabulary (.JSON) - - Download Vocabulary - (.OBO) - - - - - - - - - -
- - - - - - - - - -
-
-

Vocabulary Properties

-
- {% for error in form.errors %} - {{ error }}: {{form.errors[error]}} - {% endfor %} - {{ form.hidden_tag() }} - {{ form.onto_id_ext.label(class="form-label") }} - {{ form.onto_id_ext }} - {{ form.onto_name.label(class="form-label") }} - {{ form.onto_name }} - {{ form.alternative_language.label(class="form-label") }} - {{ form.alternative_language }} - {{ form.synonymes.label(class="form-label") }} - {{ form.synonymes }} - {{ form.image_annotation.label(class="form-label") }} - {{ form.image_annotation }}
- {{ form.hpo_datamined.label(class="form-label") }} - {{ form.hpo_datamined }} - {{ form.gene_datamined.label(class="form-label") }} - {{ form.gene_datamined }} - {{ form.phenotype_datamined.label(class="form-label") }} - {{ form.phenotype_datamined }} - {{ form.correlates_with.label(class="form-label") }} - {{ form.correlates_with }} - {{ form.description.label(class="form-label") }} - {{ form.description }} - - -
-
-
- - -{% endblock %} \ No newline at end of file diff --git a/app/static/custom.css b/app/static/custom.css deleted file mode 100644 index 638ff8b..0000000 --- a/app/static/custom.css +++ /dev/null @@ -1,24 +0,0 @@ -.table tr { - line-height: 10px; - min-height: 10px; - height: 10px; -} - -.footer { - position: fixed; - left: 0; - bottom: 0; - width: 100%; - background-color: rgb(41, 43, 44); - color: white; - text-align: center; -} - -.obfuscate { - unicode-bidi: bidi-override; - direction: rtl; -} - -* { - font-family: "Nunito Sans", sans-serif; -} diff --git a/app/templates/base.html b/app/templates/base.html deleted file mode 100644 index 4fcedf8..0000000 --- a/app/templates/base.html +++ /dev/null @@ -1,136 +0,0 @@ - - - - - - IMPatienT - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- -
- - {% with messages=get_flashed_messages(with_categories=true) %} - - {% if messages %} - {% for category, message in messages %} - - - {% endfor %} - {% endif %} - {% endwith %} - - - - {% block content %} - {% endblock %} -
- -
-
-

Created by: Corentin Meyer at CSTB Team @ ICube, CNRS, Unistra. Code availiable here - Contact: rf.artsinu@reyem.oc

-
-
- - - - \ No newline at end of file diff --git a/data/database/app.db.dvc b/data/database/app.db.dvc deleted file mode 100644 index 4ddee90..0000000 --- a/data/database/app.db.dvc +++ /dev/null @@ -1,4 +0,0 @@ -outs: -- md5: 7d1dee26d7094c36ceda6f1430d9da9b - size: 10362880 - path: app.db diff --git a/data/ontology/ontology.json.dvc b/data/ontology/ontology.json.dvc deleted file mode 100644 index 7c390f4..0000000 --- a/data/ontology/ontology.json.dvc +++ /dev/null @@ -1,4 +0,0 @@ -outs: -- md5: d733325e28672cbbbf13376351bdaf67 - size: 102388 - path: ontology.json diff --git a/data/ontology/ontology_default.json b/data/ontology/ontology_default.json deleted file mode 100644 index d97d216..0000000 --- a/data/ontology/ontology_default.json +++ /dev/null @@ -1,87 +0,0 @@ -[ - { - "id": "MHO:000001", - "text": "Sample Keyword", - "icon": true, - "data": { - "description": "", - "synonymes": "", - "phenotype_datamined": "", - "gene_datamined": "", - "alternative_language": "Sample Keyword", - "hex_color": "#c7ef34", - "hpo_datamined": "", - "correlates_with": "", - "image_annotation": false - }, - "parent": "#" - }, - { - "id": "MHO:000004", - "text": "Keyword Image Annotation", - "icon": true, - "data": { - "description": "", - "synonymes": "", - "phenotype_datamined": "UNCLEAR", - "gene_datamined": "N/A", - "alternative_language": "", - "correlates_with": "", - "image_annotation": true, - "hex_color": "#77e3a4", - "hpo_datamined": "" - }, - "parent": "MHO:000001" - }, - { - "id": "MHO:000005", - "text": "Keyword Image Annotation 2", - "icon": true, - "data": { - "description": "", - "synonymes": "", - "phenotype_datamined": "", - "gene_datamined": "", - "alternative_language": "", - "correlates_with": "", - "image_annotation": true, - "hex_color": "#094f6a", - "hpo_datamined": "" - }, - "parent": "MHO:000001" - }, - { - "id": "MHO:000002", - "text": "Sample Keyword Child", - "icon": true, - "data": { - "description": "", - "synonymes": "", - "phenotype_datamined": "", - "gene_datamined": "", - "alternative_language": "", - "correlates_with": "", - "image_annotation": false, - "hex_color": "#14cd17", - "hpo_datamined": "" - }, - "parent": "MHO:000001" - }, - { - "id": "MHO:000003", - "text": "Sample Keyword Child 2", - "icon": true, - "data": { - "description": "", - "synonymes": "", - "phenotype_datamined": "", - "gene_datamined": "", - "alternative_language": "", - "correlates_with": "", - "image_annotation": false, - "hex_color": "#d9eab9", - "hpo_datamined": "" - }, - "parent": "MHO:000001" - } -] diff --git a/deploy_hf_space.py b/deploy_hf_space.py new file mode 100644 index 0000000..e028141 --- /dev/null +++ b/deploy_hf_space.py @@ -0,0 +1,64 @@ +from huggingface_hub import HfApi + +api = HfApi() +repo_id = "corentinm7/IMPatienT" + +api.add_space_secret(repo_id=repo_id, key="SECRET_KEY", value="XXXXXX") +api.add_space_secret(repo_id=repo_id, key="MAIL_SERVER", value="XXXXXX") +api.add_space_secret(repo_id=repo_id, key="MAIL_PORT", value="25") +api.add_space_secret(repo_id=repo_id, key="MAIL_USERNAME", value="XXXXXX") +api.add_space_secret(repo_id=repo_id, key="MAIL_PASSWORD", value="XXXXXX") +api.add_space_secret(repo_id=repo_id, key="ADMINS_EMAIL", value="XXXXXX") + +api.upload_folder( + folder_path=".", + repo_id=repo_id, + repo_type="space", + allow_patterns=[ + "data", + "docker", + "src", + ".flaskenv", + ".gitattributes", + ".gitignore", + ".python-version", + "deploy_hf_space.py", + "requirements.txt", + "README.md", + "pyproject.toml", + "uv.lock", + "dev_boot.sh", + "Dockerfile", + "LICENSE", + "*.demo", + "*.js", + "*.css", + "*.html", + "*.py", + "*.sh", + "*.json", + "*.jpg", + "*.png", + "*.pkl", + "*.json", + "*.npy", + "*.txt", + "*.md", + "*.ini", + "*.mako", + "README", + ".gitkeep", + ], + ignore_patterns=[ + ".venv", + ".github", + "dpcs", + "flask_session", + "joblib_cache", + "logs", + "notebooks", + "tests", + "libcairo.2.dylib", + "ontology.json", + ], +) diff --git a/dev_boot.sh b/dev_boot.sh index ba9cf02..a2764dc 100755 --- a/dev_boot.sh +++ b/dev_boot.sh @@ -2,7 +2,7 @@ # this script is used by ./docker/dev_build_run.sh to boot the app for developpement FILE="data/ontology/ontology.json" if [ ! -f $FILE ]; then - cp data/ontology/ontology_default.json data/ontology/ontology.json + cp data/ontology/ontology.json.demo data/ontology/ontology.json fi DB="data/database/app.db" @@ -10,12 +10,5 @@ if [ ! -f $DB ]; then cp data/database/app.db.demo data/database/app.db fi -# Check if running in a container or not. -if [ -f /.dockerenv ]; then - flask db upgrade - flask run --host=0.0.0.0; -else - source .venv/bin/activate - flask db upgrade - flask run -fi +uv run flask db upgrade -d src/impatient/migrations +uv run flask --debug run --host=0.0.0.0 --port=7860; diff --git a/docker/boot.sh b/docker/boot.sh index 41bd336..8fee8f4 100755 --- a/docker/boot.sh +++ b/docker/boot.sh @@ -1,17 +1,22 @@ #!/bin/bash # this script is used to boot a Docker container -source /home/impatient/.venv/bin/activate while true; do FILE="data/ontology/ontology.json" if [ ! -f $FILE ]; then - cp data/ontology/ontology_default.json data/ontology/ontology.json + cp data/ontology/ontology.json.demo data/ontology/ontology.json fi - flask db upgrade + DB="data/database/app.db" + if [ ! -f $DB ]; then + cp data/database/app.db.demo data/database/app.db + fi + + uv run flask db upgrade -d src/impatient/migrations + if [[ "$?" == "0" ]]; then break fi echo Deploy command failed, retrying in 5 secs... sleep 5 done -exec gunicorn -b :5000 --access-logfile - --error-logfile - --timeout 900 --workers 4 --threads 8 --preload impatient:app +exec uv run gunicorn -b :7860 --access-logfile - --error-logfile - --timeout 900 --workers 4 --threads 8 --preload src.impatient.impatient_app:app diff --git a/docker/dev_build_run.sh b/docker/dev_build_run.sh index d3c94b4..4de7cef 100755 --- a/docker/dev_build_run.sh +++ b/docker/dev_build_run.sh @@ -1,2 +1,2 @@ docker build . -f Dockerfile.dev -t impatientdev:latest -docker run --rm -it --name impatientdev -p 5000:5000 -v $(pwd):/home/impatient/ impatientdev:latest +docker run --rm -it --name impatientdev -p 7860:7860 -v $(pwd):/home/impatient/ impatientdev:latest diff --git a/docker/run_sample.sh b/docker/run_sample.sh index ca57edc..2a1b113 100755 --- a/docker/run_sample.sh +++ b/docker/run_sample.sh @@ -1,20 +1,14 @@ -SECRET_KEY= -MAIL_SERVER= -MAIL_PORT= -MAIL_USERNAME= -MAIL_PASSWORD= -APP_PORT=8000 -DEFAULT_ADMIN_USERNAME= -DEFAULT_ADMIN_EMAIL= -DEFAULT_ADMIN_PASSWORD= -ADMINS_EMAIL= +SECRET_KEY=xxxxxx +MAIL_SERVER=xxxxxx +MAIL_PORT=25 +MAIL_USERNAME=xxxxxx +MAIL_PASSWORD=xxxxxx +APP_PORT=7860 +ADMINS_EMAIL=xxxxxx -docker run --name impatient -d -p $APP_PORT:5000 -it -e SECRET_KEY=$SECRET_KEY \ +docker run --name impatient -d -p $APP_PORT:7860 -it -e SECRET_KEY=$SECRET_KEY \ -e MAIL_SERVER=$MAIL_SERVER -e MAIL_PORT=$MAIL_PORT -e MAIL_USE_TLS=true \ -e MAIL_USERNAME=$MAIL_USERNAME -e MAIL_PASSWORD=$MAIL_PASSWORD \ - -e DEFAULT_ADMIN_USERNAME=$DEFAULT_ADMIN_USERNAME \ - -e DEFAULT_ADMIN_EMAIL=$DEFAULT_ADMIN_EMAIL \ - -e DEFAULT_ADMIN_PASSWORD=$DEFAULT_ADMIN_PASSWORD \ -e ADMINS_EMAIL=$ADMINS_EMAIL \ -v dataimpatient:/home/impatient/data \ --restart unless-stopped impatient:latest diff --git a/notebooks/Vocab_datamining.ipynb b/notebooks/Vocab_datamining.ipynb index a10467d..503494d 100644 --- a/notebooks/Vocab_datamining.ipynb +++ b/notebooks/Vocab_datamining.ipynb @@ -10,7 +10,6 @@ "import sys\n", "\n", "sys.path.append(\"..\")\n", - "import sqlite3\n", "\n", "import numpy as np\n", "import pandas as pd\n", diff --git a/notebooks/Vocab_properties_migration.ipynb b/notebooks/Vocab_properties_migration.ipynb index 537ff6c..a3e9a48 100644 --- a/notebooks/Vocab_properties_migration.ipynb +++ b/notebooks/Vocab_properties_migration.ipynb @@ -45,8 +45,8 @@ "sys.path.append(\"..\")\n", "import json\n", "\n", - "from app import create_app, db\n", - "from app.models import ReportHisto\n", + "from impatient.app import create_app, db\n", + "from impatient.app import ReportHisto\n", "from sqlalchemy.orm.attributes import flag_modified\n", "\n", "# Create instance of app\n", @@ -98,7 +98,7 @@ "translator = deepl.Translator(\"xxxxxxxxxxxx:fx\")\n", "\n", "list_terms = []\n", - "with open(\"../config/negex_en.txt\", \"r\") as fp:\n", + "with open(\"../src/impatient/config/negex_en.txt\", \"r\") as fp:\n", " for lines in fp.readlines():\n", " list_terms.append(lines.strip(\"\\n\"))\n", "\n", @@ -114,7 +114,7 @@ "metadata": {}, "outputs": [], "source": [ - "textfile = open(\"../config/negex_fr.txt\", \"w\")\n", + "textfile = open(\"../src/impatient/config/negex_fr.txt\", \"w\")\n", "for element in list_terms_fr:\n", " textfile.write(element + \"\\n\")\n", "textfile.close()" diff --git a/notebooks/import_ontology.ipynb b/notebooks/import_ontology.ipynb index a20b909..f8d1c17 100644 --- a/notebooks/import_ontology.ipynb +++ b/notebooks/import_ontology.ipynb @@ -8,9 +8,11 @@ "source": [ "import json\n", "import random\n", + "\n", "from pronto import Ontology, Definition\n", "\n", - "class ImpatientVocab():\n", + "\n", + "class ImpatientVocab:\n", " def __init__(self) -> None:\n", " self.used_colors: list[str] = []\n", " self.impatient_json: list[dict] = []\n", @@ -20,11 +22,11 @@ " def load_json(self, path: str) -> list[dict]:\n", " self.impatient_json = json.load(open(path, \"r\"))\n", " return self.impatient_json\n", - " \n", + "\n", " def load_ontology(self, path: str) -> Ontology:\n", " self.impatient_onto = Ontology(path)\n", " return self.impatient_onto\n", - " \n", + "\n", " def json_to_onto(self) -> Ontology:\n", " self.impatient_onto = Ontology()\n", " for term in self.impatient_json:\n", @@ -36,11 +38,13 @@ " if term[\"data\"][\"description\"] != \"\":\n", " added_term.definition = Definition(term[\"data\"][\"description\"])\n", " if term[\"parent\"] != \"#\":\n", - " added_term.superclasses().add(self.impatient_onto[term[\"parent\"].replace(\"_\", \":\")])\n", - " \n", + " added_term.superclasses().add(\n", + " self.impatient_onto[term[\"parent\"].replace(\"_\", \":\")]\n", + " )\n", + "\n", " self.list_of_terms.append(added_term)\n", " return self.impatient_onto\n", - " \n", + "\n", " def onto_to_json(self) -> list[dict]:\n", " self.impatient_json = []\n", " index = 0\n", @@ -55,8 +59,12 @@ " \"text\": term.name,\n", " \"icon\": True,\n", " \"data\": {\n", - " \"description\": term.definition if term.definition is not None else \"\",\n", - " \"synonymes\": \",\".join([syn.description for syn in term.synonyms]),\n", + " \"description\": term.definition\n", + " if term.definition is not None\n", + " else \"\",\n", + " \"synonymes\": \",\".join(\n", + " [syn.description for syn in term.synonyms]\n", + " ),\n", " \"phenotype_datamined\": \"\",\n", " \"gene_datamined\": \"\",\n", " \"alternative_language\": term.name,\n", @@ -65,12 +73,14 @@ " \"hex_color\": self._generate_hex_color(),\n", " \"hpo_datamined\": \"\",\n", " },\n", - " \"parent\": relationships[0].replace(\"_\", \":\") if relationships != [] else \"#\"\n", + " \"parent\": relationships[0].replace(\"_\", \":\")\n", + " if relationships != []\n", + " else \"#\",\n", " }\n", " )\n", " index += 1\n", " return self.impatient_json\n", - " \n", + "\n", " def _generate_hex_color(self):\n", " while True:\n", " # Generate a random hex color\n", @@ -80,7 +90,7 @@ " # Add the color to the list of used colors and return it\n", " self.used_colors.append(color)\n", " return color\n", - " \n", + "\n", " def dump_onto(self, path: str) -> None:\n", " with open(path, \"wb\") as f:\n", " self.impatient_onto.dump(f, format=\"obo\")\n", diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index f8a0fea..0000000 --- a/poetry.lock +++ /dev/null @@ -1,4474 +0,0 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. - -[[package]] -name = "alembic" -version = "1.9.2" -description = "A database migration tool for SQLAlchemy." -category = "main" -optional = false -python-versions = ">=3.7" -files = [ - {file = "alembic-1.9.2-py3-none-any.whl", hash = "sha256:e8a6ff9f3b1887e1fed68bfb8fb9a000d8f61c21bdcc85b67bb9f87fcbc4fce3"}, - {file = "alembic-1.9.2.tar.gz", hash = "sha256:6880dec4f28dd7bd999d2ed13fbe7c9d4337700a44d11a524c0ce0c59aaf0dbd"}, -] - -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} -importlib-resources = {version = "*", markers = "python_version < \"3.9\""} -Mako = "*" -SQLAlchemy = ">=1.3.0" - 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"1.7.0" description = "IMPatienT: an integrated web application to digitize, process and explore multimodal patient data" -authors = ["Corentin Meyer "] -license = "AGPL" +authors = [{ name = "Corentin Meyer", email = "contact@cmeyer.fr" }] +maintainers = [ + { name = "Corentin Meyer", email = "contact@cmeyer.fr" } +] +requires-python = ">= 3.10" -[tool.poetry.dependencies] -python = ">=3.8,<3.11" -pip = "*" -setuptools = "*" -wheel = "*" -scikit-learn = "^1" -scikit-image = "^0" -dash = "^2" -Flask = "^2" -Flask-WTF = "^0" -WTForms = "^2" -wtforms-validators = "^1" -Flask-Login = "^0" -Flask-SQLAlchemy = "^2" -Flask-Mail = "^0" -python-dotenv = "^0" -pandas = "^1.3" -numpy = "^1" -plotly = "^5" -CairoSVG = "^2" -Pillow = "^9" -joblib = "^1" -dash-core-components = "^2" -dash-bootstrap-components = "^1" -Flask-Migrate = "^4" -Flask-Session = "^0" -pytesseract = "^0" -pdf2image = "^1" -spacy = "^3" -thefuzz = "^0" -email-validator = "^1" -dash-html-components = "^2" -gunicorn = "^20" -opencv-python-headless = "^4" -python-Levenshtein = "^0.12.2" -PyJWT = "^2.3.0" -en_core_web_sm = { url = "https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.2.0/en_core_web_sm-3.2.0-py3-none-any.whl" } -fr_core_news_sm = { url = "https://github.com/explosion/spacy-models/releases/download/fr_core_news_sm-3.2.0/fr_core_news_sm-3.2.0-py3-none-any.whl" } -Flask-Cors = "^3.0.10" -textacy = "^0.12.0" -bleach = "^5.0.1" -pronto = "^2.5.5" -jsonschema = "^4.19.0" -scalene = "^1.5.31.1" +dependencies = [ + "scikit-learn<2", + "scikit-image<1", + "dash<4", + "Flask<4", + "Flask-WTF<2", + "WTForms<3", + "wtforms-validators<2", + "Flask-SQLAlchemy<4", + "Flask-Mail<1", + "python-dotenv<1", + "pandas<3", + "numpy<2", + "plotly<7", + "Pillow<12", + "joblib<2", + "dash-core-components<3", + "dash-bootstrap-components<2", + "Flask-Migrate<5", + "Flask-Session<1", + "pytesseract<1", + "pdf2image<2", + "spacy<=3.8.7", + "thefuzz<1", + "email-validator<3", + "dash-html-components<3", + "gunicorn<24", + "opencv-python-headless<5", + "python-Levenshtein<0.27.1", + "PyJWT<2.4.0", + "en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.8.0/en_core_web_sm-3.8.0-py3-none-any.whl", + "fr_core_news_sm @ https://github.com/explosion/spacy-models/releases/download/fr_core_news_sm-3.8.0/fr_core_news_sm-3.8.0-py3-none-any.whl", + "Flask-Cors<7", + "textacy<1", + "bleach<5.1.1", + "pronto<2.6.5", + "jsonschema<4.20.0", + "cairosvg<3.0.0", + "huggingface-hub>=0.33.0", +] -[tool.poetry.group.dev.dependencies] -ruff = "^0.0.221" -mkdocs-material = "^9.0.5" -black = {extras = ["jupyter"], version = "*"} -ipykernel = "^6" -unittest2 = "^1" -pytest = "^6.2.5" -bandit = "^1.7.1" -pre-commit = "^2.16.0" -mypy = "^0.991" -mkdocstrings = "^0.19.1" +[dependency-groups] +dev = [ +] [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.hatch.metadata] +allow-direct-references = true + +[tool.hatch.build.targets.wheel] +packages = ["src/impatient"] diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..20e1a86 --- /dev/null +++ b/src/__init__.py @@ -0,0 +1 @@ +# This file makes the src directory a Python package diff --git a/app/src/__init__.py b/src/impatient/__init__.py similarity index 100% rename from app/src/__init__.py rename to src/impatient/__init__.py diff --git a/app/__init__.py b/src/impatient/app/__init__.py similarity index 76% rename from app/__init__.py rename to src/impatient/app/__init__.py index c53555f..2ba98d6 100644 --- a/app/__init__.py +++ b/src/impatient/app/__init__.py @@ -3,10 +3,8 @@ from logging.handlers import RotatingFileHandler, SMTPHandler import dash -from config import Config -from flask import Flask, current_app -from flask.helpers import get_root_path -from flask_login import LoginManager, login_required +from impatient.config import Config +from flask import Flask from flask_mail import Mail from flask_migrate import Migrate from flask_session import Session @@ -26,9 +24,6 @@ metadata = MetaData(naming_convention=convention) db = SQLAlchemy(metadata=metadata) migrate = Migrate() -login_manager = LoginManager() -login_manager.login_view = "auth.login" -login_manager.login_message_category = "info" mail = Mail() session = Session() cors = CORS() @@ -46,48 +41,44 @@ def create_app(config_class=Config): """ app = Flask(__name__) app.config.from_object(config_class) + os.makedirs(app.config["VIZ_FOLDER"], exist_ok=True) db.init_app(app) with app.app_context(): if db.engine.url.drivername == "sqlite": migrate.init_app(app, db, render_as_batch=True) else: migrate.init_app(app, db) - login_manager.init_app(app) mail.init_app(app) session.init_app(app) cors.init_app(app) register_dashapps(app) # Configuration of our various flask-blueprint folders - from app.errors import bp as errors_bp + from impatient.app.errors import bp as errors_bp app.register_blueprint(errors_bp) - from app.auth import bp as auth_bp - - app.register_blueprint(auth_bp) - - from app.index import bp as index_bp + from impatient.app.index import bp as index_bp app.register_blueprint(index_bp) - from app.ontocreate import bp as ontocreate_bp + from impatient.app.ontocreate import bp as ontocreate_bp app.register_blueprint(ontocreate_bp) - from app.historeport import bp as historeport_bp + from impatient.app.historeport import bp as historeport_bp app.register_blueprint(historeport_bp) - from app.histostats import bp as histostats_bp + from impatient.app.histostats import bp as histostats_bp app.register_blueprint(histostats_bp) - from app.dashapp import bp as dashapp_bp + from impatient.app.dashapp import bp as dashapp_bp app.register_blueprint(dashapp_bp) - from app.imgupload import bp as imgupload_bp + from impatient.app.imgupload import bp as imgupload_bp app.register_blueprint(imgupload_bp) @@ -145,8 +136,8 @@ def register_dashapps(app): Args: app (Flask Application Object): Our flask application object. """ - from app.dashapp.callbacks import register_callbacks - from app.dashapp.layout import get_external_stylesheets, layout + from impatient.app.dashapp.callbacks import register_callbacks + from impatient.app.dashapp.layout import get_external_stylesheets, layout # Meta tags for viewport responsiveness meta_viewport = { @@ -166,20 +157,6 @@ def register_dashapps(app): dashapp.layout = layout register_callbacks(dashapp) app.config["DASHAPP"] = dashapp - _protect_dashviews(dashapp) - - -def _protect_dashviews(dashapp): - """Function to protect the dash views behind the login mecanism. - - Args: - dashapp (Dash Application Object): Our Dash Application Object - """ - for view_func in dashapp.server.view_functions: - if view_func.startswith(dashapp.config.url_base_pathname): - dashapp.server.view_functions[view_func] = login_required( - dashapp.server.view_functions[view_func] - ) -from app import models +from impatient.app import models diff --git a/app/dashapp/__init__.py b/src/impatient/app/dashapp/__init__.py similarity index 81% rename from app/dashapp/__init__.py rename to src/impatient/app/dashapp/__init__.py index 1a4f218..421890e 100644 --- a/app/dashapp/__init__.py +++ b/src/impatient/app/dashapp/__init__.py @@ -8,4 +8,4 @@ static_url_path="/static/dashapp", ) -from app.dashapp import routes +from impatient.app.dashapp import routes diff --git a/app/dashapp/callbacks.py b/src/impatient/app/dashapp/callbacks.py similarity index 97% rename from app/dashapp/callbacks.py rename to src/impatient/app/dashapp/callbacks.py index ee7764f..58dfb7b 100644 --- a/app/dashapp/callbacks.py +++ b/src/impatient/app/dashapp/callbacks.py @@ -1,41 +1,34 @@ -import io import base64 +import io import json import os -import dash import pickle # nosec import traceback - -from flask import current_app from urllib import parse -from joblib import Memory - -import numpy as np -import pandas as pd import PIL.Image -from skimage import io as skio -from dash.dependencies import Input, Output, State -from dash import html -from dash import dcc +import dash import dash_bootstrap_components as dbc +import numpy as np +from dash import html +from dash.dependencies import Input, Output, State +from flask import current_app +from joblib import Memory +from skimage import io as skio -from app import db -import app.dashapp.plot_common as plot_common -from app.models import Image -import app.dashapp.common_func as common_func -from app.dashapp.shapes_to_segmentations import ( +import impatient.app.dashapp.common_func as common_func +import impatient.app.dashapp.plot_common as plot_common +from impatient.app import db +from impatient.app.dashapp.shapes_to_segmentations import ( compute_segmentations, blend_image_and_classified_regions_pil, ) +from impatient.app.dashapp.trainable_segmentation import multiscale_basic_features +from impatient.app.models import Image -from app.dashapp.trainable_segmentation import multiscale_basic_features - - -memory = Memory("./joblib_cache", bytes_limit=500000000, verbose=1) +memory = Memory("./joblib_cache", verbose=1) compute_features = memory.cache(multiscale_basic_features) - onto_tree_imgannot = common_func.load_onto() class_label_colormap = { int(term["id"].split(":")[1]): term["data"]["hex_color"] diff --git a/app/dashapp/common_func.py b/src/impatient/app/dashapp/common_func.py similarity index 64% rename from app/dashapp/common_func.py rename to src/impatient/app/dashapp/common_func.py index 34ac3b7..4ce46b1 100644 --- a/app/dashapp/common_func.py +++ b/src/impatient/app/dashapp/common_func.py @@ -1,9 +1,11 @@ -import os import json +import os def load_onto(): - with open(os.path.join("data/ontology", "ontology.json"), "r") as fp: + with open( + os.path.join("/home/impatient/data/ontology/", "ontology.json"), "r" + ) as fp: onto_tree = json.load(fp) onto_tree_imgannot = [i for i in onto_tree if i["data"]["image_annotation"] == True] return onto_tree_imgannot diff --git a/app/dashapp/layout.py b/src/impatient/app/dashapp/layout.py similarity index 98% rename from app/dashapp/layout.py rename to src/impatient/app/dashapp/layout.py index c5b19a1..5a56cb1 100644 --- a/app/dashapp/layout.py +++ b/src/impatient/app/dashapp/layout.py @@ -1,11 +1,12 @@ +import os + +import dash_bootstrap_components as dbc from dash import dcc from dash import html -import dash_bootstrap_components as dbc -import os -from app.dashapp import bp -import app.dashapp.plot_common as plot_common -import app.dashapp.common_func as common_func -import json + +import impatient.app.dashapp.common_func as common_func +import impatient.app.dashapp.plot_common as plot_common +from impatient.app.dashapp import bp DEFAULT_STROKE_WIDTH = 3 # gives line width of 2^3 = 8 diff --git a/app/dashapp/plot_common.py b/src/impatient/app/dashapp/plot_common.py similarity index 100% rename from app/dashapp/plot_common.py rename to src/impatient/app/dashapp/plot_common.py diff --git a/app/dashapp/routes.py b/src/impatient/app/dashapp/routes.py similarity index 82% rename from app/dashapp/routes.py rename to src/impatient/app/dashapp/routes.py index e011971..5c83460 100644 --- a/app/dashapp/routes.py +++ b/src/impatient/app/dashapp/routes.py @@ -1,17 +1,14 @@ from flask import send_from_directory, current_app -from flask_login import login_required -from app.dashapp import bp +from impatient.app.dashapp import bp # @bp.route(bp.static_folder + "/") -# @login_required # def image_folder_seg(filename): # """Serve files located in patient subfolder inside folder""" # return send_from_directory(bp.static_folder, filename) @bp.route("/data/images/") -# @login_required def images_folder(filename): """Serve files located in patient subfolder inside folder""" return send_from_directory(current_app.config["IMAGES_FOLDER"], filename) diff --git a/app/dashapp/shape_utils.py b/src/impatient/app/dashapp/shape_utils.py similarity index 98% rename from app/dashapp/shape_utils.py rename to src/impatient/app/dashapp/shape_utils.py index 6ef5d1c..c55119d 100644 --- a/app/dashapp/shape_utils.py +++ b/src/impatient/app/dashapp/shape_utils.py @@ -1,8 +1,9 @@ -from cairosvg import svg2png -import skimage -import PIL.Image import io + +import PIL.Image import numpy as np +import skimage +from cairosvg import svg2png def shape_to_svg_code(shape, fig=None, width=None, height=None): @@ -38,9 +39,7 @@ def shape_to_svg_code(shape, fig=None, width=None, height=None): fill-opacity="0" /> -""".format( - **fmt_dict - ) +""".format(**fmt_dict) def shape_to_png(fig=None, shape=None, width=None, height=None, write_to=None): diff --git a/app/dashapp/shapes_to_segmentations.py b/src/impatient/app/dashapp/shapes_to_segmentations.py similarity index 97% rename from app/dashapp/shapes_to_segmentations.py rename to src/impatient/app/dashapp/shapes_to_segmentations.py index 3113a86..e5c85d0 100644 --- a/app/dashapp/shapes_to_segmentations.py +++ b/src/impatient/app/dashapp/shapes_to_segmentations.py @@ -1,14 +1,16 @@ +from time import time + import PIL.Image import numpy as np +import plotly.express as px import skimage -import skimage.util -import skimage.io import skimage.color -import app.dashapp.shape_utils as shape_utils -from app.dashapp.trainable_segmentation import fit_segmenter -import plotly.express as px +import skimage.io +import skimage.util from sklearn.ensemble import RandomForestClassifier -from time import time + +import impatient.app.dashapp.shape_utils as shape_utils +from impatient.app.dashapp.trainable_segmentation import fit_segmenter def img_to_ubyte_array(img): diff --git a/app/dashapp/static/explanations.md b/src/impatient/app/dashapp/static/explanations.md similarity index 63% rename from app/dashapp/static/explanations.md rename to src/impatient/app/dashapp/static/explanations.md index d7824ab..de70e51 100644 --- a/app/dashapp/static/explanations.md +++ b/src/impatient/app/dashapp/static/explanations.md @@ -1,4 +1,5 @@ -The code of this app is [available here](https://github.com/plotly/dash-sample-apps/blob/master/apps/dash-image-segmentation/app.py). +The code of this app +is [available here](https://github.com/plotly/dash-sample-apps/blob/master/apps/dash-image-segmentation/app.py). This app uses machine learning in order to compute the segmentation of an image, given user-provided annotations. In addition to plotly and Dash, the app @@ -11,8 +12,10 @@ To build the training set, we use the [new shape drawing capabilities of plotly.py](https://eoss-image-processing.github.io/2020/05/06/shape-drawing.html) and in particular the `drawopenpath` dragmode which can used to draw "squiggles" on parts of the image which you want to label. You can adjust the width of the squiggle with a Dash -`dcc.Slider` to make it possible to annotate features of different sizes. Each time a new annotation is drawn, it is captured by the plotly figure's -[relayoutData event, which triggers a callback](https://dash.plotly.com/interactive-graphing). You should select a different color for every type of object you wish to segment. +`dcc.Slider` to make it possible to annotate features of different sizes. Each time a new annotation is drawn, it is +captured by the plotly figure's +[relayoutData event, which triggers a callback](https://dash.plotly.com/interactive-graphing). You should select a +different color for every type of object you wish to segment. ### Computation of features @@ -34,4 +37,10 @@ and are relatively fast, since they operate on local neighbourhoods. ## Model training and prediction -Features are extracted for the annotated pixels, and passed to a scikit-learn [Random Forest Classifier](https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html). This estimator belongs to the class of [ensemble methods](https://scikit-learn.org/stable/modules/ensemble.html), where the predictions by several base estimators are combined to improve the generalizability or robustness of the prediction. After the model is trained, its prediction is computed on unlabeled pixels, resulting in a segmentation of the image. It is possible to add more annotations to improve the segmentation if some pixels are wrongly classified. Furthermore, one can download the estimator in order to classify new images of the same type (for example, a time series). +Features are extracted for the annotated pixels, and passed to a +scikit-learn [Random Forest Classifier](https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html). +This estimator belongs to the class of [ensemble methods](https://scikit-learn.org/stable/modules/ensemble.html), where +the predictions by several base estimators are combined to improve the generalizability or robustness of the prediction. +After the model is trained, its prediction is computed on unlabeled pixels, resulting in a segmentation of the image. It +is possible to add more annotations to improve the segmentation if some pixels are wrongly classified. Furthermore, one +can download the estimator in order to classify new images of the same type (for example, a time series). diff --git a/app/dashapp/static/sample.png b/src/impatient/app/dashapp/static/sample.png similarity index 100% rename from app/dashapp/static/sample.png rename to src/impatient/app/dashapp/static/sample.png diff --git a/src/impatient/app/dashapp/static/segmentation-style.css b/src/impatient/app/dashapp/static/segmentation-style.css new file mode 100644 index 0000000..186a76f --- /dev/null +++ b/src/impatient/app/dashapp/static/segmentation-style.css @@ -0,0 +1,27 @@ +#app-title > * { + color: white; + margin: 0; + padding: 0; +} + +#howto-open { + white-space: nowrap; +} + +#gh-link { + white-space: nowrap; +} + +.card { + margin: 1em 0 1em 0; + min-width: auto; +} + +label { + display: block; + margin-bottom: 0; +} + +#transparent-loader-wrapper > div { + visibility: visible !important; +} diff --git a/app/dashapp/trainable_segmentation.py b/src/impatient/app/dashapp/trainable_segmentation.py similarity index 99% rename from app/dashapp/trainable_segmentation.py rename to src/impatient/app/dashapp/trainable_segmentation.py index a7c894e..41c96a0 100644 --- a/app/dashapp/trainable_segmentation.py +++ b/src/impatient/app/dashapp/trainable_segmentation.py @@ -1,9 +1,10 @@ -from itertools import combinations_with_replacement import itertools +from itertools import combinations_with_replacement + import numpy as np +from joblib import Parallel, delayed from skimage import filters, feature from skimage import img_as_float32 -from joblib import Parallel, delayed try: from sklearn.exceptions import NotFittedError diff --git a/app/dashapp/use_ml_image_segmentation_classifier.py b/src/impatient/app/dashapp/use_ml_image_segmentation_classifier.py similarity index 92% rename from app/dashapp/use_ml_image_segmentation_classifier.py rename to src/impatient/app/dashapp/use_ml_image_segmentation_classifier.py index bd3b172..38d406c 100644 --- a/app/dashapp/use_ml_image_segmentation_classifier.py +++ b/src/impatient/app/dashapp/use_ml_image_segmentation_classifier.py @@ -13,18 +13,20 @@ """ +import base64 +import io +import json import os -import app.dashapp.plot_common as plot_common -import app.dashapp.shapes_to_segmentations as shapes_to_segmentations -from app.dashapp.trainable_segmentation import ( +import pickle # nosec + +import skimage.io + +import impatient.app.dashapp.plot_common as plot_common +import impatient.app.dashapp.shapes_to_segmentations as shapes_to_segmentations +from impatient.app.dashapp.trainable_segmentation import ( multiscale_basic_features, predict_segmenter, ) -import pickle # nosec -import base64 -import io -import skimage.io -import json def getenv(e): diff --git a/app/email.py b/src/impatient/app/email.py similarity index 96% rename from app/email.py rename to src/impatient/app/email.py index 12c725d..127dd17 100644 --- a/app/email.py +++ b/src/impatient/app/email.py @@ -3,7 +3,7 @@ from flask import current_app from flask_mail import Message -from app import mail +from impatient.app import mail def send_async_email(app, msg): diff --git a/app/errors/__init__.py b/src/impatient/app/errors/__init__.py similarity index 69% rename from app/errors/__init__.py rename to src/impatient/app/errors/__init__.py index bd7d2ea..c89d9ca 100644 --- a/app/errors/__init__.py +++ b/src/impatient/app/errors/__init__.py @@ -2,4 +2,4 @@ bp = Blueprint("errors", __name__, template_folder="templates") -from app.errors import handlers +from impatient.app.errors import handlers diff --git a/app/errors/handlers.py b/src/impatient/app/errors/handlers.py similarity index 93% rename from app/errors/handlers.py rename to src/impatient/app/errors/handlers.py index 06c8687..a157843 100644 --- a/app/errors/handlers.py +++ b/src/impatient/app/errors/handlers.py @@ -1,5 +1,5 @@ -from app import db -from app.errors import bp +from impatient.app import db +from impatient.app.errors import bp from flask import render_template import traceback diff --git a/src/impatient/app/errors/templates/404.html b/src/impatient/app/errors/templates/404.html new file mode 100644 index 0000000..48e4590 --- /dev/null +++ b/src/impatient/app/errors/templates/404.html @@ -0,0 +1,7 @@ +{% extends "base.html" %} {% block content %} +

Error 404: Page not found

+

+ This page has not been found. Please press the back button to go to the index: + Back +

+{% endblock %} diff --git a/src/impatient/app/errors/templates/413.html b/src/impatient/app/errors/templates/413.html new file mode 100644 index 0000000..655d253 --- /dev/null +++ b/src/impatient/app/errors/templates/413.html @@ -0,0 +1,7 @@ +{% extends "base.html" %} {% block content %} +

Error 413: File is too large

+

+ Uploaded file is too large. Please press the back button to go to the index: + Back +

+{% endblock %} diff --git a/src/impatient/app/errors/templates/500.html b/src/impatient/app/errors/templates/500.html new file mode 100644 index 0000000..f80cfd1 --- /dev/null +++ b/src/impatient/app/errors/templates/500.html @@ -0,0 +1,12 @@ +{% extends "base.html" %} {% block content %} +

Error 500: An unexpected error has occurred

+

If this happened in the visualisation module, a common fix could be going to the Standard Vocabulary module and + press "Save tree" to re-generate files !

+

The administrator has been notified. Sorry for the inconvenience!

+

+ Please press the back button to go to the index: + Back +

+

Traceback:

+ 
{{ traceback_info }}
+{% endblock %} \ No newline at end of file diff --git a/app/historeport/__init__.py b/src/impatient/app/historeport/__init__.py similarity index 80% rename from app/historeport/__init__.py rename to src/impatient/app/historeport/__init__.py index 1896811..5f1fafa 100644 --- a/app/historeport/__init__.py +++ b/src/impatient/app/historeport/__init__.py @@ -8,4 +8,4 @@ static_url_path="/static/historeport", ) -from app.historeport import routes +from impatient.app.historeport import routes diff --git a/app/historeport/boqa.py b/src/impatient/app/historeport/boqa.py similarity index 100% rename from app/historeport/boqa.py rename to src/impatient/app/historeport/boqa.py diff --git a/app/historeport/forms.py b/src/impatient/app/historeport/forms.py similarity index 99% rename from app/historeport/forms.py rename to src/impatient/app/historeport/forms.py index e22874d..a2d8a66 100644 --- a/app/historeport/forms.py +++ b/src/impatient/app/historeport/forms.py @@ -1,7 +1,5 @@ import json -import os -import app.src.common as Common from flask_wtf import FlaskForm from flask_wtf.file import FileAllowed, FileField, FileRequired from wtforms import SelectField, StringField, SubmitField, TextAreaField, fields diff --git a/app/historeport/ocr.py b/src/impatient/app/historeport/ocr.py similarity index 99% rename from app/historeport/ocr.py rename to src/impatient/app/historeport/ocr.py index 9a69cda..46b42d1 100644 --- a/app/historeport/ocr.py +++ b/src/impatient/app/historeport/ocr.py @@ -1,7 +1,5 @@ -import collections import json import os -from shlex import join import cv2 import numpy as np @@ -9,8 +7,8 @@ import spacy from flask import current_app from pdf2image import convert_from_bytes -from thefuzz import fuzz from textacy.extract.basics import ngrams +from thefuzz import fuzz class TextReport: diff --git a/app/historeport/onto_func.py b/src/impatient/app/historeport/onto_func.py similarity index 98% rename from app/historeport/onto_func.py rename to src/impatient/app/historeport/onto_func.py index f8b710f..a7e0341 100644 --- a/app/historeport/onto_func.py +++ b/src/impatient/app/historeport/onto_func.py @@ -1,8 +1,9 @@ +import io import json import random -from pronto import Ontology, Definition -import io + from flask_wtf.file import FileField +from pronto import Ontology, Definition class ImpatientVocab: @@ -35,9 +36,7 @@ def load_ontology_f(self, file: FileField) -> Ontology: def json_to_onto(self) -> Ontology: self.impatient_onto = Ontology() - term_mapping = ( - {} - ) # A dictionary to store term IDs and their corresponding created terms + term_mapping = {} # A dictionary to store term IDs and their corresponding created terms # First pass: Create terms without adding superclasses for term in self.impatient_json: diff --git a/app/historeport/routes.py b/src/impatient/app/historeport/routes.py similarity index 92% rename from app/historeport/routes.py rename to src/impatient/app/historeport/routes.py index 4d13d9b..b3ebd25 100644 --- a/app/historeport/routes.py +++ b/src/impatient/app/historeport/routes.py @@ -1,39 +1,37 @@ -import json from contextlib import suppress -from app import db -from app.historeport import bp -from app.historeport.boqa import * -from app.historeport.forms import ( + +from flask import ( + current_app, + flash, + redirect, + render_template, + request, + url_for, + make_response, +) + +from impatient.app import db +from impatient.app.historeport import bp +from impatient.app.historeport.boqa import * +from impatient.app.historeport.forms import ( DeleteButton, RepredictReports, OntologyDescriptPreAbs, ReportForm, PdfUpload, ) - -from app.histostats.vizualisation import ( +from impatient.app.historeport.ocr import TextReport +from impatient.app.historeport.onto_func import StandardVocabulary +from impatient.app.histostats.vizualisation import ( db_to_df, table_to_df, generate_stat_per, process_df, ) -from app.historeport.ocr import TextReport -from app.historeport.onto_func import StandardVocabulary -from app.models import ReportHisto -from flask import ( - current_app, - flash, - redirect, - render_template, - request, - url_for, - make_response, -) -from flask_login import current_user, login_required +from impatient.app.models import ReportHisto @bp.route("/historeport", methods=["GET", "POST"]) -@login_required def histoindex(): """View function for the text report index @@ -49,14 +47,15 @@ def histoindex(): @bp.route("/historeport/repredict_reports", methods=["GET"]) -@login_required def repredict_reports(): """Route for to trigger the reprediction of all reports in the DB with latest data. Returns: redirect: Redirect to the historeports index HTML page """ - with open(os.path.join("data/ontology", "ontology.json"), "r") as fp: + with open( + os.path.join("/home/impatient/data/ontology/", "ontology.json"), "r" + ) as fp: onto_tree = json.load(fp) df = db_to_df() df, features_col = table_to_df(df, onto_tree) @@ -80,9 +79,10 @@ def repredict_reports(): @bp.route("/historeport/download", methods=["GET"]) -@login_required def histo_download(): - with open(os.path.join("data/ontology", "ontology.json"), "r") as fp: + with open( + os.path.join("/home/impatient/data/ontology/", "ontology.json"), "r" + ) as fp: onto_tree = json.load(fp) df = db_to_df() df, features_col = table_to_df(df, onto_tree) @@ -94,7 +94,6 @@ def histo_download(): @bp.route("/historeport/new", methods=["GET", "POST"]) -@login_required def historeport(): """View function for the text report registration form. Or modify an existing report. @@ -109,7 +108,6 @@ def historeport(): if report_request is not None: form = ReportForm( patient_id=report_request.patient_id, - expert_id=report_request.expert_id, biopsie_id=report_request.biopsie_id, muscle_prelev=report_request.muscle_prelev, age_biopsie=report_request.age_biopsie, @@ -159,7 +157,6 @@ def historeport(): "value" ] report_entry.ontology_tree = onto_jstree.clean_tree() - report_entry.expert_id = current_user.id try: results = get_boqa_pred(json.dumps(report_entry.ontology_tree)) except: @@ -195,7 +192,6 @@ def historeport(): ] onto_jstree = StandardVocabulary(report_entry.ontology_tree) report_entry.ontology_tree = onto_jstree.clean_tree() - report_entry.expert_id = current_user.id db.session.add(report_entry) try: results = get_boqa_pred(json.dumps(report_entry.ontology_tree)) @@ -225,7 +221,6 @@ def historeport(): @bp.route("/delete_report/", methods=["POST"]) -@login_required def delete_report(id_report): """Route for the deletion of a registered text report. @@ -251,7 +246,6 @@ def delete_report(id_report): @bp.route("/predict_diag_boqa/", methods=["POST"]) -@login_required def predict_diag_boqa(): """API POST route for the prediction of a text report class using BOQA. @@ -274,7 +268,6 @@ def predict_diag_boqa(): @bp.route("/ocr_pdf", methods=["POST"]) -@login_required def ocr_pdf(): """API POST route for the OCR/NLP of a PDF file. diff --git a/app/historeport/static/histo_index.js b/src/impatient/app/historeport/static/histo_index.js similarity index 100% rename from app/historeport/static/histo_index.js rename to src/impatient/app/historeport/static/histo_index.js diff --git a/app/historeport/static/historeport.js b/src/impatient/app/historeport/static/historeport.js similarity index 100% rename from app/historeport/static/historeport.js rename to src/impatient/app/historeport/static/historeport.js diff --git a/src/impatient/app/historeport/static/slider.css b/src/impatient/app/historeport/static/slider.css new file mode 100644 index 0000000..350ff71 --- /dev/null +++ b/src/impatient/app/historeport/static/slider.css @@ -0,0 +1,63 @@ +markneg { + background: rgb(112, 5, 5); + color: rgb(255, 255, 255); +} + +markpos { + background: rgb(9, 158, 9); + color: rgb(255, 255, 255); +} + +/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#f0ad4e+10,d9534f+10,d9534f+30,5cb85c+30 */ +/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#f0ad4e+45,d9534f+45,d9534f+55,5cb85c+55 */ +/* Permalink - use to edit and share this gradient: https://colorzilla.com/gradient-editor/#d9534f+5,f0ad4e+5,f0ad4e+5,f0ad4e+51,d2ffc9+51,0cf900+100 */ + +/* Mozilla */ +input[type="range"]::-moz-range-track { + background: -moz-linear-gradient( + left, + #f0ad4e 15%, + #d9534f 15%, + #d9534f 30%, + #5cb85c 30% + ); /* FF3.6-15 */ + background: linear-gradient( + to right, + #f0ad4e 15%, + #d9534f 15%, + #d9534f 30%, + #5cb85c 30% + ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ +} + +/* Chrome */ +input[type="range"]::-webkit-slider-runnable-track { + background: -webkit-linear-gradient( + left, + #f0ad4e 15%, + #d9534f 15%, + #d9534f 30%, + #5cb85c 30% + ); /* Chrome10-25,Safari5.1-6 */ + background: linear-gradient( + to right, + #f0ad4e 15%, + #d9534f 15%, + #d9534f 30%, + #5cb85c 30% + ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ +} + +/* IE*/ +input[type="range"]::-ms-fill-lower, +input[type="range"]::-ms-fill-upper { + background: #f0ad4e; /* Old browsers */ + background: linear-gradient( + to right, + #f0ad4e 15%, + #d9534f 15%, + #d9534f 30%, + #5cb85c 30% + ); /* W3C, IE10+, FF16+, Chrome26+, Opera12+, Safari7+ */ + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#f0ad4e', endColorstr='#5cb85c', GradientType=1); /* IE6-9 */ +} diff --git a/src/impatient/app/historeport/templates/histo_index.html b/src/impatient/app/historeport/templates/histo_index.html new file mode 100644 index 0000000..9b6d1ca --- /dev/null +++ b/src/impatient/app/historeport/templates/histo_index.html @@ -0,0 +1,122 @@ +{% extends "base.html" %} {% block content %} + + + + +
+
+

Digitize a new report

+
+ + New Report + +
+
+
+
+
+

Digital Report Database

Download All Reports (.CSV) + + + + + + + + + + + + + + + + + + + {% for report in history %} + + + + + + + + + + {% endfor %} +
Biopsy IDPatient IDGeneDiagnosticBOQA PredictionBOQA Score (0-1)Action
{{ report.biopsie_id }}{{ report.patient_id }}{{ report.gene_diag }}{{ report.conclusion }}{{ report.BOQA_prediction }} + {{ report.BOQA_prediction_score }} + + + Resume + + + + + + +
+
+
+ + + +{% endblock %} \ No newline at end of file diff --git a/src/impatient/app/historeport/templates/historeport.html b/src/impatient/app/historeport/templates/historeport.html new file mode 100644 index 0000000..919fb13 --- /dev/null +++ b/src/impatient/app/historeport/templates/historeport.html @@ -0,0 +1,276 @@ +{% extends "base.html" %} +{% block content %} + + + + + + + + + + + + +
+
+
+
+
+

Optional: Select a PDF and upload it to perform OCR/NLP analysis

+ {% for error in pdf_form.errors %} + {{ error }}: {{ pdf_form.errors[error] }} + {% endfor %} +
+
+ {{ pdf_form.hidden_tag() }} + {{ pdf_form.pdf_file }} +
+
+ {{ pdf_form.language }} +
+
+ + + +
+ +
+
+ + +
+
+ +
+
+

+ +

+
+
+
+
+
+
+
+
+
+
+
+

+ +

+
+
+
+
+
+
+
+
+
+
+
+ +
+ +
+
+
+

Patient Informations

+ + {% for error in form.errors %} + {{ error }}: {{ form.errors[error] }} + {% endfor %} + {{ form.hidden_tag() }} +
+
+ {{ form.patient_id.label(class="form-label") }} + {{ form.patient_id }} +
+
+ {{ form.biopsie_id.label(class="form-label") }} + {{ form.biopsie_id }}
+
+ {{ form.date_envoie.label(class="form-label") }} + {{ form.date_envoie }}
+
+ {{ form.muscle_prelev.label(class="form-label") }} + {{ form.muscle_prelev }}
+
+
+
+ + {{ form.age_biopsie.label(class="form-label") }} + {{ form.age_biopsie }}
+
+ {{ form.gene_diag.label(class="form-label") }} + {{ form.gene_diag }}
+ {{ form.ontology_tree }} +
+ + +
+
+ + {{ form.pheno_terms.label(class="form-label") }} + {{ form.pheno_terms }}
+
+ {{ form.mutation.label(class="form-label") }} + {{ form.mutation }}
+
+ +
+
+
+

Vocabulary Tree

+ + +
+
+
+

Absence/Presence Annotation

+ + {% for error in form2.errors %} + {{ error }}: {{ form2.errors[error] }} + {% endfor %} + {{ form2.hidden_tag() }} +
+
+
+ {{ form2.preabsProba.label(class="form-label d-flex justify-content-center") }} + {{ form2.preabsProba }} +
+
+
+
+ +
+
+

Vocabulary Properties

+
+
+ {{ form2.onto_id_ext.label(class="form-label") }} + {{ form2.onto_id_ext }} +
+
+ {{ form2.onto_name.label(class="form-label") }} + {{ form2.onto_name }} +
+
+ {{ form2.synonymes.label(class="form-label") }} + {{ form2.synonymes }} + {{ form2.alternative_language.label(class="form-label") }} + {{ form2.alternative_language }} + {{ form2.hpo_datamined.label(class="form-label") }} + {{ form2.hpo_datamined }} + {{ form2.gene_datamined.label(class="form-label") }} + {{ form2.gene_datamined }} + {{ form2.phenotype_datamined.label(class="form-label") }} + {{ form2.phenotype_datamined }} + {{ form2.correlates_with.label(class="form-label") }} + {{ form2.correlates_with }} + {{ form2.description.label(class="form-label") }} + {{ form2.description }} + + +
+
+
+
+ +
+
+
+
+

Final Vocabulary Annotation (Present)

+
+
+
+
+

Final Vocabulary Annotation (Negated)

+
+
+ +
+
+
+
+

Commentaries and Conclusions

+ {{ form.comment }} + Diagnosis Prediction: + +
+ Method BOQA (Stats): +
+
+
+ {{ form.conclusion.label(class="form-label") }} + {{ form.conclusion }} + +
+
+
+
+ +
+ +
+ + + + +{% endblock %} \ No newline at end of file diff --git a/app/histostats/__init__.py b/src/impatient/app/histostats/__init__.py similarity index 80% rename from app/histostats/__init__.py rename to src/impatient/app/histostats/__init__.py index ec9a8a7..6db2a80 100644 --- a/app/histostats/__init__.py +++ b/src/impatient/app/histostats/__init__.py @@ -8,4 +8,4 @@ static_url_path="/static/histostats", ) -from app.histostats import routes +from impatient.app.histostats import routes diff --git a/app/histostats/routes.py b/src/impatient/app/histostats/routes.py similarity index 86% rename from app/histostats/routes.py rename to src/impatient/app/histostats/routes.py index 10f7c01..91b838b 100644 --- a/app/histostats/routes.py +++ b/src/impatient/app/histostats/routes.py @@ -1,14 +1,10 @@ -import json -import os - -from app.histostats import bp -from app.histostats.vizualisation import * from flask import current_app, render_template -from flask_login import login_required + +from impatient.app.histostats import bp +from impatient.app.histostats.vizualisation import * @bp.route("/histostats", methods=["GET", "POST"]) -@login_required def statsindex(): """View function for the automatic dashboard visualization @@ -16,7 +12,9 @@ def statsindex(): str: Dashboard HTML Page """ # Up to stat_per_diag to move in the historeport part to not always regenerate - with open(os.path.join("data/ontology", "ontology.json"), "r") as fp: + with open( + os.path.join("/home/impatient/data/ontology/", "ontology.json"), "r" + ) as fp: onto_tree = json.load(fp) df = db_to_df() df, features_col = table_to_df(df, onto_tree) diff --git a/src/impatient/app/histostats/templates/histostats_index.html b/src/impatient/app/histostats/templates/histostats_index.html new file mode 100644 index 0000000..6e50884 --- /dev/null +++ b/src/impatient/app/histostats/templates/histostats_index.html @@ -0,0 +1,93 @@ +{% extends "base.html" %} {% block content %} + + + + +
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ +
+
+
+
+
+
+
+
+
+
+

Vocabulary Frequencies Per Genes

+ + Download Table (.CSV) + {{ df_per_gene | safe }} +
+ +
+

Vocabulary Frequencies Per Diagnosis

+ + Download Table (.CSV) + {{ df_per_diag | safe }} +
+
+
+
+ + + + + + + + + + + + +{% endblock %} diff --git a/app/histostats/vizualisation.py b/src/impatient/app/histostats/vizualisation.py similarity index 95% rename from app/histostats/vizualisation.py rename to src/impatient/app/histostats/vizualisation.py index a9579c4..4bd1b41 100644 --- a/app/histostats/vizualisation.py +++ b/src/impatient/app/histostats/vizualisation.py @@ -3,15 +3,15 @@ import numpy as np import pandas as pd -import plotly import plotly.express as px import plotly.figure_factory as ff import plotly.graph_objs as go -from app import db -from app.models import ReportHisto from flask import current_app from sklearn.metrics import confusion_matrix +from impatient.app import db +from impatient.app.models import ReportHisto + def id_to_name(onto, ids_list, mode="full"): """Map a list of ID of ontology term to their names @@ -54,21 +54,20 @@ def table_to_df(df, onto_tree): for index, row in df.iterrows(): tree_as_dict.setdefault("id", []).append(row[0]) tree_as_dict.setdefault("patient_id", []).append(row[1]) - tree_as_dict.setdefault("expert_id", []).append(row[2]) - tree_as_dict.setdefault("biopsie_id", []).append(row[3]) - tree_as_dict.setdefault("muscle_prelev", []).append(row[4]) - tree_as_dict.setdefault("age_biopsie", []).append(row[5]) - tree_as_dict.setdefault("date_envoie", []).append(row[6]) - tree_as_dict.setdefault("gene_diag", []).append(row[7]) - tree_as_dict.setdefault("mutation", []).append(row[8]) - tree_as_dict.setdefault("pheno_terms", []).append(row[9]) - tree_as_dict.setdefault("comment", []).append(row[11]) - tree_as_dict.setdefault("conclusion", []).append(row[12]) - tree_as_dict.setdefault("BOQA_prediction", []).append(row[13]) - tree_as_dict.setdefault("BOQA_prediction_score", []).append(row[14]) - tree_as_dict.setdefault("datetime", []).append(row[15]) - - my_tree = row[10] + tree_as_dict.setdefault("biopsie_id", []).append(row[2]) + tree_as_dict.setdefault("muscle_prelev", []).append(row[3]) + tree_as_dict.setdefault("age_biopsie", []).append(row[4]) + tree_as_dict.setdefault("date_envoie", []).append(row[5]) + tree_as_dict.setdefault("gene_diag", []).append(row[6]) + tree_as_dict.setdefault("mutation", []).append(row[7]) + tree_as_dict.setdefault("pheno_terms", []).append(row[8]) + tree_as_dict.setdefault("comment", []).append(row[10]) + tree_as_dict.setdefault("conclusion", []).append(row[11]) + tree_as_dict.setdefault("BOQA_prediction", []).append(row[12]) + tree_as_dict.setdefault("BOQA_prediction_score", []).append(row[13]) + tree_as_dict.setdefault("datetime", []).append(row[14]) + + my_tree = row[9] # my_tree = dict((item['text'], item) for item in row[8]) for feature in onto_tree: # node = my_tree[feature["text"]] @@ -88,7 +87,7 @@ def db_to_df(): Returns: Dataframe: Dataframe representation of the SQLite table for text reports """ - df = pd.read_sql(db.session.query(ReportHisto).statement, db.session.bind) + df = pd.read_sql(db.session.query(ReportHisto).statement, db.engine) return df diff --git a/app/imgupload/__init__.py b/src/impatient/app/imgupload/__init__.py similarity index 80% rename from app/imgupload/__init__.py rename to src/impatient/app/imgupload/__init__.py index 59937bb..3584b0a 100644 --- a/app/imgupload/__init__.py +++ b/src/impatient/app/imgupload/__init__.py @@ -8,4 +8,4 @@ static_url_path="/static/imgupload", ) -from app.imgupload import routes +from impatient.app.imgupload import routes diff --git a/app/imgupload/forms.py b/src/impatient/app/imgupload/forms.py similarity index 98% rename from app/imgupload/forms.py rename to src/impatient/app/imgupload/forms.py index 63b1d64..9bae6eb 100644 --- a/app/imgupload/forms.py +++ b/src/impatient/app/imgupload/forms.py @@ -1,6 +1,3 @@ -import os - -import app.src.common as Common from flask_wtf import FlaskForm from flask_wtf.file import FileAllowed, FileField, FileRequired from wtforms import SelectField, StringField, SubmitField diff --git a/app/imgupload/routes.py b/src/impatient/app/imgupload/routes.py similarity index 94% rename from app/imgupload/routes.py rename to src/impatient/app/imgupload/routes.py index d09eac0..7bb8772 100644 --- a/app/imgupload/routes.py +++ b/src/impatient/app/imgupload/routes.py @@ -1,10 +1,10 @@ +import json import os +import tarfile from contextlib import suppress -import json -from app import db -from app.imgupload import bp -from app.imgupload.forms import DeleteButton, ImageForm -from app.models import Image + +import pandas as pd +from PIL import Image as PILImage from flask import ( current_app, flash, @@ -13,18 +13,17 @@ request, send_from_directory, url_for, - make_response, ) -from flask_login import current_user, login_required from werkzeug.datastructures import FileStorage from werkzeug.utils import secure_filename -from PIL import Image as PILImage -import pandas as pd -import tarfile + +from impatient.app import db +from impatient.app.imgupload import bp +from impatient.app.imgupload.forms import DeleteButton, ImageForm +from impatient.app.models import Image @bp.route("/data/images/") -@login_required def images_folder(filename): """Route to serve files located in the data/images folder. @@ -38,7 +37,6 @@ def images_folder(filename): @bp.route("/img_index", methods=["GET", "POST"]) -@login_required def img_index(): """View function for the image index @@ -51,7 +49,6 @@ def img_index(): @bp.route("/img_index/download", methods=["GET"]) -@login_required def img_download(): df = pd.read_sql(db.session.query(Image).statement, db.session.bind) df.to_csv( @@ -68,7 +65,6 @@ def img_download(): @bp.route("/delete_img/", methods=["POST"]) -@login_required def delete_img(id_img): """Route for the deletion of an image from the database and data folder. @@ -104,7 +100,6 @@ def delete_img(id_img): @bp.route("/create_img", methods=["GET", "POST"]) -@login_required def create_img(): """View function for the image upload page. @@ -155,7 +150,6 @@ def create_img(): # Create our new Image & Patient database entry image = Image( image_name=filename, - expert_id=current_user.id, patient_id=form.patient_ID.data, biopsy_id=form.biopsy_report_ID.data, type_coloration=form.type_coloration.data, diff --git a/app/imgupload/static/img_index.js b/src/impatient/app/imgupload/static/img_index.js similarity index 100% rename from app/imgupload/static/img_index.js rename to src/impatient/app/imgupload/static/img_index.js diff --git a/app/imgupload/static/imgupload.js b/src/impatient/app/imgupload/static/imgupload.js similarity index 100% rename from app/imgupload/static/imgupload.js rename to src/impatient/app/imgupload/static/imgupload.js diff --git a/src/impatient/app/imgupload/templates/create_img.html b/src/impatient/app/imgupload/templates/create_img.html new file mode 100644 index 0000000..feedd08 --- /dev/null +++ b/src/impatient/app/imgupload/templates/create_img.html @@ -0,0 +1,39 @@ +{% extends "base.html" %} +{% block content %} + + + + + + +
+
+
+

Modify/Upload New Image


+
+ {% for error in form.errors %} + {{ error }}: {{ form.errors[error] }} + {% endfor %} + {{ form.hidden_tag() }} + {{ form.patient_ID.label(class="form-label") }} + {{ form.patient_ID }} +

Select an image file

+ {{ form.image }}
+ {{ form.biopsy_report_ID.label(class="form-label") }} + {{ form.biopsy_report_ID }} + {{ form.type_coloration.label(class="form-label") }} + {{ form.type_coloration }} + {{ form.age_histo.label(class="form-label") }} + {{ form.age_histo }} + {{ form.diagnostic.label(class="form-label") }} + {{ form.diagnostic }} + +
+
+
+ +{% endblock %} diff --git a/src/impatient/app/imgupload/templates/img_index.html b/src/impatient/app/imgupload/templates/img_index.html new file mode 100644 index 0000000..721e6ed --- /dev/null +++ b/src/impatient/app/imgupload/templates/img_index.html @@ -0,0 +1,87 @@ +{% extends "base.html" %} {% block content %} + + + + +
+
+

Upload a new image

+
+ New Image + +
+
+
+
+
+

Image Database

+ Download All Images (.tar.gz) + + + + + + + + + {% for image in image_history %} + + + + + + + + {% endfor %} +
Biopsy IDPatient IDImage NameDiagnosticAction
{{ image.biopsy_id }}{{ image.patient_id }}{{ image.image_name }}{{ image.diagnostic }} + + Anotate + + + Modify + + + + + + +
+
+
+ + + +{% endblock %} diff --git a/app/index/__init__.py b/src/impatient/app/index/__init__.py similarity index 70% rename from app/index/__init__.py rename to src/impatient/app/index/__init__.py index 9c360fd..662cfa4 100644 --- a/app/index/__init__.py +++ b/src/impatient/app/index/__init__.py @@ -2,4 +2,4 @@ bp = Blueprint("index", __name__, template_folder="templates") -from app.index import routes +from impatient.app.index import routes diff --git a/app/index/routes.py b/src/impatient/app/index/routes.py similarity index 85% rename from app/index/routes.py rename to src/impatient/app/index/routes.py index 6d61d05..3722a9c 100644 --- a/app/index/routes.py +++ b/src/impatient/app/index/routes.py @@ -1,4 +1,4 @@ -from app.index import bp +from impatient.app.index import bp from flask import render_template diff --git a/src/impatient/app/index/templates/index.html b/src/impatient/app/index/templates/index.html new file mode 100644 index 0000000..ddf9668 --- /dev/null +++ b/src/impatient/app/index/templates/index.html @@ -0,0 +1,134 @@ +{% extends "base.html" %} {% block content %} +
+

+ IMPatienT🗂️️: an integrated web application to digitize, process and explore multimodal patient data. +

+

+ IMPatienT Banner +

+

+ IMPatienT (Integrated digital Multimodal + PATIENt + daTa) is a web application developped in the + MYO-xIA project for patient data digitization and exploration.
It features a standard + vocabulary + creator, optical character recognition (OCR), natural language processing + (NLP), image annotation and segmentation using machine learning, interactive + visualizations and automatic diagnosis prediction. +

+
+

Demo Usage Instructions

+

+ The application is + preloaded with a database of histology reports and a standard vocabulary for + muscle biopsy. Data on this demo instance is reset once every day.
+ For the PDF automatic analysis, you can find a sample PDF + HERE + working with the preinstalled standard vocabulary. A sample image for image + annotation can be found + HERE. +

+
+

Partners

+
+
+ + Partner Logo + +
+
+

IMPatienT is developped and used in collaboration with the + Morphological Unit of the Institute of Myology of Paris. + A production instance is deployed to help discovering new relevant + features for congenital myopathies classification and diagnosis.

+
+
+
+

IMPatienT🗂️️ Abstract

+

+ Background +
+ Medical acts, such as imaging, generally lead to the production of several medical text reports that + describe the + relevant findings. Such processes induce multimodality in patient data by linking image data to free-text + data and + consequently, multimodal data have become central to drive research and improve diagnosis of patients. + However, the + exploitation of patient data is challenging as the ecosystem of available analysis tools is fragmented + depending on + the type of data (images, text, genetic sequences), the task to be performed (digitization, processing, + exploration) + and the domain of interest (clinical phenotype, histology…). To address the challenges, the analysis tools + need to + be integrated in a simple, comprehensive, and flexible platform. +
+ Results +
+ Here, we present IMPatienT (Integrated digital Multimodal + PATIENt + daTa), a free and open-source web application to digitize, process and explore multimodal + patient + data. IMPatienT has a modular architecture, including four components to: (i) create a standard vocabulary + for a + domain, (ii) digitize and process free-text data by mapping it to a set of standard terms, (iii) annotate + images and + perform image segmentation, and (iv) generate an automatic visualization dashboard to provide insight on the + data + and perform automatic diagnosis suggestions. Finally, we demonstrate the usefulness of IMPatienT on a corpus + of 40 + simulated muscle biopsy reports of congenital myopathy patients. +
+ Conclusions +
+ IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text + data. As + it relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as + a + patient registry for exploratory data analysis (EDA). A demo instance of the application is available at https://huggingface.co/spaces/corentinm7/IMPatienT. + +

+
+

MYO-xIA Project

+

+ The MYO-xIA project aims to collect data from patients with + congenital myopathies in order to analyse them using + explainable AI approaches. In the field of congenital + myopathies research, there is an important need for + digitization and standardization of patient data in order + to use modern data analysis methods.
This project has tree mains + objectives: +

+
+
    +
  • + Gather and format patient data to be ready for automatic + exploitation (patient histology-report form, image annotation, OCR/NLP) +
    • +
  • + Help the + discovery of new phenotype-genotype-histology association + for each congenital myopathy subtype (standard vocabulary creation tool, + per gene and per class histology feature statistics) +
    • +
  • + Provide tools for automatic diagnosis based on patient + data (live prediction of congenital myopathy subtype with histology + reports, images, genetic data and phenotype) +
    • +
+
+

Contact

+

+ The main maintainer is:
Corentin Meyer, PhD contact@cmeyer.fr +

+
+

Citing IMPatienT🗂️

+

[placeholder]

+
+
+{% endblock %} \ No newline at end of file diff --git a/src/impatient/app/index/templates/index.md b/src/impatient/app/index/templates/index.md new file mode 100644 index 0000000..9805168 --- /dev/null +++ b/src/impatient/app/index/templates/index.md @@ -0,0 +1,68 @@ +# IMPatienT 🗂️: an integrated web application to digitize, process and explore multimodal patient data. + +**IMPatienT** 🗂️ is a web application developped in the **MYO-xIA project** for patient data digitization and +exploration. +It features a standard vocabulary creator, optical character recognition (OCR), natural language processing (NLP), image +annotation and segmentation using machine learning, interactive visualizations and automatic diagnosis prediction. + +## Demo Usage Instructions + +The application is preloaded with a database of histology reports and a standard vocabulary for muscle biopsy. Data on +this demo instance is reset once every day. +For the PDF automatic analysis, you can find a sample +PDF [HERE](https://www.lbgi.fr/~meyer/IMPatienT/sample_demo_report.pdf) working with the preinstalled standard +vocabulary. A sample image for image annotation can be +found [HERE](https://www.lbgi.fr/~meyer/IMPatienT/sample_image_histo.jpg). + +## Partners + +IMPatienT is developped and used in collaboration with +the [Morphological Unit of the Institute of Myology of Paris](https://www.institut-myologie.org/en/recherche-2/neuromuscular-investigation-center/morphological-unit/). +A production instance is deployed to help discovering new relevant features for congenital myopathies classification and +diagnosis. + +## IMPatienT🗂️ Abstract + +**Background** +Medical acts, such as imaging, generally lead to the production of several medical text reports that describe the +relevant findings. Such processes induce multimodality in patient data by linking image data to free-text data and +consequently, multimodal data have become central to drive research and improve diagnosis of patients. However, the +exploitation of patient data is challenging as the ecosystem of available analysis tools is fragmented depending on the +type of data (images, text, genetic sequences), the task to be performed (digitization, processing, exploration) and the +domain of interest (clinical phenotype, histology…). To address the challenges, the analysis tools need to be integrated +in a simple, comprehensive, and flexible platform. +**Results** +Here, we present IMPatienT (d**I**gitize **M**ultimodal **PATIEN**t da**T**a), a free and open-source web application to +digitize, process and explore multimodal patient data. IMPatienT has a modular architecture, including four components +to: (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data by mapping it to a set of +standard terms, (iii) annotate images and perform image segmentation, and (iv) generate an automatic visualization +dashboard to provide insight on the data and perform automatic diagnosis suggestions. Finally, we demonstrate the +usefulness of IMPatienT on a corpus of 40 simulated muscle biopsy reports of congenital myopathy patients. +**Conclusions** +IMPatienT is a platform to digitize, process and explore patient data that can handle image and free-text data. As it +relies on a user-designed vocabulary, it can be adapted to fit any domain of research and can be used as a patient +registry for exploratory data analysis (EDA). A demo instance of the application is available +at https://huggingface.co/spaces/corentinm7/IMPatienT. + +## MYO-xIA Project + +The MYO-xIA project aims to collect data from patients with **congenital myopathies** in order to analyse them using * +*explainable AI approaches**. In the field of congenital myopathies research, there is an important need for * +*digitization and standardization of patient data** in order to use modern data analysis methods. +This project has tree mains objectives: + +- **Gather and format patient data** to be ready for automatic exploitation (patient histology-report form, image + annotation, OCR/NLP) +- Help the **discovery of new phenotype-genotype-histology** association for each congenital myopathy subtype (standard + vocabulary creation tool, per gene and per class histology feature statistics) +- Provide tools for **automatic diagnosis** based on patient data (live prediction of congenital myopathy subtype with + histology reports, images, genetic data and phenotype) + +## Contact: + +The main maintainer is: +**Corentin Meyer**, PhD [contact@cmeyer.fr](mailto:contact@cmeyer.fr) + +## Citing IMPatienT🗂️ + +[placeholder] diff --git a/src/impatient/app/models.py b/src/impatient/app/models.py new file mode 100644 index 0000000..696bfa0 --- /dev/null +++ b/src/impatient/app/models.py @@ -0,0 +1,79 @@ +import datetime + +from impatient.app import db + + +class Image(db.Model): + """Database table for Image & annotations""" + + id = db.Column(db.Integer, primary_key=True) + image_name = db.Column(db.String(140), nullable=False) + patient_id = db.Column(db.String(100), index=True, nullable=False) + biopsy_id = db.Column(db.String(100), index=True) + type_coloration = db.Column(db.String(140)) + age_at_biopsy = db.Column(db.Integer, default=-1) + image_path = db.Column(db.String(4096), unique=True, nullable=False) + image_background_path = db.Column(db.String(4096), unique=True) + sigma_range_min = db.Column(db.Float()) + sigma_range_max = db.Column(db.Float()) + diagnostic = db.Column(db.String(140), index=True) + seg_matrix_path = db.Column(db.String(4096), unique=True) + mask_image_path = db.Column(db.String(4096), unique=True) + blend_image_path = db.Column(db.String(4096), unique=True) + classifier_path = db.Column(db.String(4096), unique=True) + mask_annot_path = db.Column(db.String(4096), unique=True) + class_info_path = db.Column(db.String(4096), unique=True) + datetime = db.Column( + db.DateTime(), + onupdate=datetime.datetime.utcnow, + default=datetime.datetime.utcnow, + ) + + def __repr__(self): + return "".format(self.image_name, self.patient_id) + + def isduplicated(self): + """Method to check if the image is already in the + database (same name and patient ID) + + Returns: + bool: True if the image is already in the database, False otherwise + """ + if ( + Image.query.filter_by( + image_name=self.image_name, patient_id=self.patient_id + ).first() + is None + ): + return False + else: + return True + + +class ReportHisto(db.Model): + """Database table text reports""" + + id = db.Column(db.Integer, primary_key=True) + patient_id = db.Column(db.String(100), index=True) + biopsie_id = db.Column(db.String(140)) + muscle_prelev = db.Column(db.String(140)) + age_biopsie = db.Column(db.Integer) + date_envoie = db.Column(db.String(10)) + gene_diag = db.Column(db.String(140), index=True) + mutation = db.Column(db.String(140)) + pheno_terms = db.Column(db.String(4096)) + ontology_tree = db.Column(db.JSON, default=[], nullable=False) + comment = db.Column(db.Text, default="") + conclusion = db.Column(db.String(140), index=True) + BOQA_prediction = db.Column(db.String(140), index=True) + BOQA_prediction_score = db.Column(db.Float()) + datetime = db.Column( + db.DateTime(), + onupdate=datetime.datetime.utcnow, + default=datetime.datetime.utcnow, + ) + + def __repr__(self): + return "".format( + self.id, self.patient_id, self.biopsie_id + ) diff --git a/app/ontocreate/__init__.py b/src/impatient/app/ontocreate/__init__.py similarity index 80% rename from app/ontocreate/__init__.py rename to src/impatient/app/ontocreate/__init__.py index 2cf3e23..74734a9 100644 --- a/app/ontocreate/__init__.py +++ b/src/impatient/app/ontocreate/__init__.py @@ -8,4 +8,4 @@ static_url_path="/static/ontocreate", ) -from app.ontocreate import routes +from impatient.app.ontocreate import routes diff --git a/app/ontocreate/forms.py b/src/impatient/app/ontocreate/forms.py similarity index 97% rename from app/ontocreate/forms.py rename to src/impatient/app/ontocreate/forms.py index b87856c..e97ebc9 100644 --- a/app/ontocreate/forms.py +++ b/src/impatient/app/ontocreate/forms.py @@ -1,6 +1,5 @@ from flask_wtf import FlaskForm -from flask_wtf.file import FileAllowed, FileField, FileRequired -from wtforms.validators import DataRequired +from flask_wtf.file import FileAllowed, FileField from wtforms import StringField, SubmitField, TextAreaField, BooleanField diff --git a/app/ontocreate/routes.py b/src/impatient/app/ontocreate/routes.py similarity index 87% rename from app/ontocreate/routes.py rename to src/impatient/app/ontocreate/routes.py index ac23718..b210cda 100644 --- a/app/ontocreate/routes.py +++ b/src/impatient/app/ontocreate/routes.py @@ -1,21 +1,7 @@ import json import os -import jsonschema -from jsonschema import validate import bleach -from werkzeug.utils import secure_filename -from app import db -from app.historeport.onto_func import StandardVocabulary, ImpatientVocab -from app.models import ReportHisto -from app.ontocreate import bp -from app.ontocreate.forms import InvertLangButton, OntologyDescript, OntoUpload -from app.histostats.vizualisation import ( - db_to_df, - table_to_df, - process_df, - generate_stat_per, -) from flask import ( current_app, redirect, @@ -24,12 +10,27 @@ send_from_directory, url_for, ) -from flask_login import login_required +from jsonschema import validate from sqlalchemy.orm.attributes import flag_modified +from impatient.app import db +from impatient.app.historeport.onto_func import StandardVocabulary, ImpatientVocab +from impatient.app.histostats.vizualisation import ( + db_to_df, + table_to_df, + process_df, + generate_stat_per, +) +from impatient.app.models import ReportHisto +from impatient.app.ontocreate import bp +from impatient.app.ontocreate.forms import ( + InvertLangButton, + OntologyDescript, + OntoUpload, +) + @bp.route("/ontology/") -@login_required def onto_json(filename): """Route to serve the standard vocabulary JSON file. Used internally by JSTree. @@ -43,7 +44,6 @@ def onto_json(filename): @bp.route("/ontocreate", methods=["GET", "POST"]) -@login_required def ontocreate(): """View function for the standard vocabulary creator module. @@ -87,11 +87,11 @@ def ontocreate(): import importlib import sys - importlib.reload(sys.modules["app.dashapp.callbacks"]) - import app.dashapp.layout + importlib.reload(sys.modules["impatient.app.dashapp.callbacks"]) + import impatient.app.dashapp.layout - importlib.reload(app.dashapp.layout) - dashapp.layout = app.dashapp.layout.layout + importlib.reload(impatient.app.dashapp.layout) + dashapp.layout = impatient.app.dashapp.layout.layout return redirect(url_for("ontocreate.ontocreate")) return render_template( "ontocreate.html", form=form, form2=form2, form_onto=form_onto @@ -99,7 +99,6 @@ def ontocreate(): @bp.route("/modify_onto", methods=["PATCH"]) -@login_required def modify_onto(): """API PATCH route to update the standard vocabulary JSON file with modifications. PATCH AJAX Requestion from JSTree. @@ -151,16 +150,15 @@ def modify_onto(): import importlib import sys - importlib.reload(sys.modules["app.dashapp.callbacks"]) - import app.dashapp.layout + importlib.reload(sys.modules["impatient.app.dashapp.callbacks"]) + import impatient.app.dashapp.layout - importlib.reload(app.dashapp.layout) - dashapp.layout = app.dashapp.layout.layout + importlib.reload(impatient.app.dashapp.layout) + dashapp.layout = impatient.app.dashapp.layout.layout return json.dumps({"success": True}), 200, {"ContentType": "application/json"} @bp.route("/download_onto", methods=["GET"]) -@login_required def download_onto(): """Route to download the standard vocabulary JSON file. @@ -173,7 +171,6 @@ def download_onto(): @bp.route("/upload_onto", methods=["POST"]) -@login_required def upload_onto(): """Route to upload an ontology in place as JSON, OWL or OBO file.""" return send_from_directory( @@ -182,7 +179,6 @@ def upload_onto(): @bp.route("/download_onto_as_obo", methods=["GET"]) -@login_required def download_onto_as_obo(): """Route to download the standard vocabulary JSON file. @@ -203,7 +199,6 @@ def download_onto_as_obo(): @bp.route("/invert_lang", methods=["POST"]) -@login_required def invert_lang(): """API POST route to invert the language of the standard vocabulary JSON file. @@ -253,10 +248,10 @@ def invert_lang(): import importlib import sys - importlib.reload(sys.modules["app.dashapp.callbacks"]) - import app.dashapp.layout + importlib.reload(sys.modules["impatient.app.dashapp.callbacks"]) + import impatient.app.dashapp.layout - importlib.reload(app.dashapp.layout) - dashapp.layout = app.dashapp.layout.layout + importlib.reload(impatient.app.dashapp.layout) + dashapp.layout = impatient.app.dashapp.layout.layout return redirect(url_for("ontocreate.ontocreate")) diff --git a/app/ontocreate/static/ontocreate.js b/src/impatient/app/ontocreate/static/ontocreate.js similarity index 100% rename from app/ontocreate/static/ontocreate.js rename to src/impatient/app/ontocreate/static/ontocreate.js diff --git a/src/impatient/app/ontocreate/templates/ontocreate.html b/src/impatient/app/ontocreate/templates/ontocreate.html new file mode 100644 index 0000000..c7093d3 --- /dev/null +++ b/src/impatient/app/ontocreate/templates/ontocreate.html @@ -0,0 +1,147 @@ +{% extends "base.html" %} {% block content %} + + + + + + + + +
+
+

Standard Vocabulary Tree

+ Download Vocabulary + (.JSON) + + Download + Vocabulary + (.OBO) + + + + + + + + + +
+ + + + + + + + + +
+
+

Vocabulary Properties

+
+ {% for error in form.errors %} + {{ error }}: {{ form.errors[error] }} + {% endfor %} + {{ form.hidden_tag() }} + {{ form.onto_id_ext.label(class="form-label") }} + {{ form.onto_id_ext }} + {{ form.onto_name.label(class="form-label") }} + {{ form.onto_name }} + {{ form.alternative_language.label(class="form-label") }} + {{ form.alternative_language }} + {{ form.synonymes.label(class="form-label") }} + {{ form.synonymes }} + {{ form.image_annotation.label(class="form-label") }} + {{ form.image_annotation }}
+ {{ form.hpo_datamined.label(class="form-label") }} + {{ form.hpo_datamined }} + {{ form.gene_datamined.label(class="form-label") }} + {{ form.gene_datamined }} + {{ form.phenotype_datamined.label(class="form-label") }} + {{ form.phenotype_datamined }} + {{ form.correlates_with.label(class="form-label") }} + {{ form.correlates_with }} + {{ form.description.label(class="form-label") }} + {{ form.description }} + + +
+
+
+ + +{% endblock %} \ No newline at end of file diff --git a/app/static/viz/.gitkeep b/src/impatient/app/src/__init__.py similarity index 100% rename from app/static/viz/.gitkeep rename to src/impatient/app/src/__init__.py diff --git a/app/src/common.py b/src/impatient/app/src/common.py similarity index 100% rename from app/src/common.py rename to src/impatient/app/src/common.py diff --git a/app/static/banner.png b/src/impatient/app/static/banner.png similarity index 100% rename from app/static/banner.png rename to src/impatient/app/static/banner.png diff --git a/app/static/checkmark-32.png b/src/impatient/app/static/checkmark-32.png similarity index 100% rename from app/static/checkmark-32.png rename to src/impatient/app/static/checkmark-32.png diff --git a/src/impatient/app/static/custom.css b/src/impatient/app/static/custom.css new file mode 100644 index 0000000..3449903 --- /dev/null +++ b/src/impatient/app/static/custom.css @@ -0,0 +1,24 @@ +.table tr { + line-height: 10px; + min-height: 10px; + height: 10px; +} + +.footer { + position: fixed; + left: 0; + bottom: 0; + width: 100%; + background-color: rgb(41, 43, 44); + color: white; + text-align: center; +} + +.obfuscate { + unicode-bidi: bidi-override; + direction: rtl; +} + +* { + font-family: "Nunito Sans", sans-serif; +} diff --git a/app/static/favicon.ico b/src/impatient/app/static/favicon.ico similarity index 100% rename from app/static/favicon.ico rename to src/impatient/app/static/favicon.ico diff --git a/app/static/institute_partner_sm.png b/src/impatient/app/static/institute_partner_sm.png similarity index 100% rename from app/static/institute_partner_sm.png rename to src/impatient/app/static/institute_partner_sm.png diff --git a/app/static/question-mark-16.png b/src/impatient/app/static/question-mark-16.png similarity index 100% rename from app/static/question-mark-16.png rename to src/impatient/app/static/question-mark-16.png diff --git a/app/static/x-mark-32.png b/src/impatient/app/static/x-mark-32.png similarity index 100% rename from app/static/x-mark-32.png rename to src/impatient/app/static/x-mark-32.png diff --git a/src/impatient/app/templates/base.html b/src/impatient/app/templates/base.html new file mode 100644 index 0000000..d7d7c26 --- /dev/null +++ b/src/impatient/app/templates/base.html @@ -0,0 +1,128 @@ + + + + + + IMPatienT + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+ + {% with messages=get_flashed_messages(with_categories=true) %} + + {% if messages %} + {% for category, message in messages %} + + + {% endfor %} + {% endif %} + {% endwith %} + + + + {% block content %} + {% endblock %} +
+ + + + + + \ No newline at end of file diff --git a/config.py b/src/impatient/config.py similarity index 84% rename from config.py rename to src/impatient/config.py index dd3ae11..5bad925 100644 --- a/config.py +++ b/src/impatient/config.py @@ -2,8 +2,6 @@ from dotenv import load_dotenv -import app.src.common as Common - # Get base working directory and load env variables basedir = os.path.abspath(os.path.dirname(__file__)) load_dotenv(os.path.join(basedir, ".env")) @@ -12,16 +10,15 @@ class Config(object): """Class to load all config parameters of the Flask App""" - DEFAULT_ADMIN_USERNAME = os.environ.get("DEFAULT_ADMIN_USERNAME") or "admin" - DEFAULT_ADMIN_EMAIL = os.environ.get("DEFAULT_ADMIN_EMAIL") or "admin@admin.admin" - DEFAULT_ADMIN_PASSWORD = os.environ.get("DEFAULT_ADMIN_PASSWORD") or "admin" SECRET_KEY = os.environ.get("SECRET_KEY") or "myverylongsecretkey" - DATA_FOLDER = os.path.join(basedir, "data") - ONTOLOGY_FOLDER = os.path.join(basedir, "data", "ontology") - IMAGES_FOLDER = os.path.join(basedir, "data", "images") - CONFIG_FOLDER = os.path.join(basedir, "config") - VIZ_FOLDER = os.path.join(basedir, "app", "static", "viz") + DATA_FOLDER = os.path.join("/home/impatient", "data") + ONTOLOGY_FOLDER = os.path.join("/home/impatient/", "data", "ontology") + IMAGES_FOLDER = os.path.join("/home/impatient", "data", "images") + CONFIG_FOLDER = os.path.join("/home/impatient", "src", "impatient", "config") + VIZ_FOLDER = os.path.join( + "/home/impatient", "src", "impatient", "app", "static", "viz" + ) negex_en = open(os.path.join(CONFIG_FOLDER, "negex_en.txt"), "r") negex_fr = open(os.path.join(CONFIG_FOLDER, "negex_fr.txt"), "r") @@ -45,7 +42,7 @@ class Config(object): # DB connection settings SQLALCHEMY_DATABASE_URI = "sqlite:///" + os.path.join( - basedir, "data", "database", "app.db" + "/home/impatient", "data", "database", "app.db" ) SQLALCHEMY_TRACK_MODIFICATIONS = False diff --git a/config/negex_en.txt b/src/impatient/config/negex_en.txt similarity index 100% rename from config/negex_en.txt rename to src/impatient/config/negex_en.txt diff --git a/config/negex_fr.txt b/src/impatient/config/negex_fr.txt similarity index 100% rename from config/negex_fr.txt rename to src/impatient/config/negex_fr.txt diff --git a/config/negex_sep_en.txt b/src/impatient/config/negex_sep_en.txt similarity index 100% rename from config/negex_sep_en.txt rename to src/impatient/config/negex_sep_en.txt diff --git a/config/negex_sep_fr.txt b/src/impatient/config/negex_sep_fr.txt similarity index 100% rename from config/negex_sep_fr.txt rename to src/impatient/config/negex_sep_fr.txt diff --git a/impatient.py b/src/impatient/impatient_app.py similarity index 60% rename from impatient.py rename to src/impatient/impatient_app.py index 5d5b5a4..b3b87c4 100644 --- a/impatient.py +++ b/src/impatient/impatient_app.py @@ -1,22 +1,15 @@ -from app import create_app, db -from app.models import Image, ReportHisto, User +from impatient.app import create_app, db +from impatient.app.models import Image, ReportHisto # Create instance of app app = create_app() -@app.before_first_request -def create_admin(): - """Create admin user if no user registered""" - User.create_admin_account() - - @app.shell_context_processor def make_shell_context(): """Add DB object in the flask shell""" return { "db": db, - "User": User, "Image": Image, "ReportHisto": ReportHisto, } diff --git a/migrations/README b/src/impatient/migrations/README similarity index 100% rename from migrations/README rename to src/impatient/migrations/README diff --git a/src/impatient/migrations/__init__.py b/src/impatient/migrations/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/migrations/alembic.ini b/src/impatient/migrations/alembic.ini similarity index 100% rename from migrations/alembic.ini rename to src/impatient/migrations/alembic.ini diff --git a/migrations/env.py b/src/impatient/migrations/env.py similarity index 97% rename from migrations/env.py rename to src/impatient/migrations/env.py index b8333a4..7e9722a 100644 --- a/migrations/env.py +++ b/src/impatient/migrations/env.py @@ -3,11 +3,10 @@ import logging from logging.config import fileConfig +from alembic import context +from flask import current_app from sqlalchemy import engine_from_config from sqlalchemy import pool -from flask import current_app - -from alembic import context # this is the Alembic Config object, which provides # access to the values within the .ini file in use. @@ -28,6 +27,7 @@ ) target_metadata = current_app.extensions["migrate"].db.metadata + # other values from the config, defined by the needs of env.py, # can be acquired: # my_important_option = config.get_main_option("my_important_option") @@ -82,7 +82,7 @@ def process_revision_directives(context, revision, directives): connection=connection, target_metadata=target_metadata, process_revision_directives=process_revision_directives, - **current_app.extensions["migrate"].configure_args + **current_app.extensions["migrate"].configure_args, ) with context.begin_transaction(): diff --git a/migrations/script.py.mako b/src/impatient/migrations/script.py.mako similarity index 100% rename from migrations/script.py.mako rename to src/impatient/migrations/script.py.mako diff --git a/migrations/versions/78a123694ce2_bland_to_blend.py b/src/impatient/migrations/versions/78a123694ce2_bland_to_blend.py similarity index 100% rename from migrations/versions/78a123694ce2_bland_to_blend.py rename to src/impatient/migrations/versions/78a123694ce2_bland_to_blend.py index fb0686d..0a6fc21 100644 --- a/migrations/versions/78a123694ce2_bland_to_blend.py +++ b/src/impatient/migrations/versions/78a123694ce2_bland_to_blend.py @@ -5,9 +5,9 @@ Create Date: 2022-02-10 11:21:13.884534 """ -from alembic import op -import sqlalchemy as sa +import sqlalchemy as sa +from alembic import op # revision identifiers, used by Alembic. revision = "78a123694ce2" diff --git a/src/impatient/migrations/versions/__init__.py b/src/impatient/migrations/versions/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/migrations/versions/b27118dec823_class_info_path_for_images.py b/src/impatient/migrations/versions/b27118dec823_class_info_path_for_images.py similarity index 100% rename from migrations/versions/b27118dec823_class_info_path_for_images.py rename to src/impatient/migrations/versions/b27118dec823_class_info_path_for_images.py index 9ec8374..1d6c588 100644 --- a/migrations/versions/b27118dec823_class_info_path_for_images.py +++ b/src/impatient/migrations/versions/b27118dec823_class_info_path_for_images.py @@ -5,9 +5,9 @@ Create Date: 2022-03-24 17:54:11.594913 """ -from alembic import op -import sqlalchemy as sa +import sqlalchemy as sa +from alembic import op # revision identifiers, used by Alembic. revision = "b27118dec823" diff --git a/src/impatient/migrations/versions/cc394f0a8f7d_.py b/src/impatient/migrations/versions/cc394f0a8f7d_.py new file mode 100644 index 0000000..196fb9f --- /dev/null +++ b/src/impatient/migrations/versions/cc394f0a8f7d_.py @@ -0,0 +1,67 @@ +"""empty message + +Revision ID: cc394f0a8f7d +Revises: b27118dec823 +Create Date: 2025-06-23 10:15:40.155812 + +""" + +import sqlalchemy as sa +from alembic import op + +# revision identifiers, used by Alembic. +revision = "cc394f0a8f7d" +down_revision = "b27118dec823" +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table("user", schema=None) as batch_op: + batch_op.drop_index(batch_op.f("ix_user_email")) + batch_op.drop_index(batch_op.f("ix_user_username")) + + with op.batch_alter_table("image", schema=None) as batch_op: + batch_op.drop_constraint( + batch_op.f("fk_image_expert_id_user"), type_="foreignkey" + ) + batch_op.drop_column("expert_id") + + with op.batch_alter_table("report_histo", schema=None) as batch_op: + batch_op.drop_constraint( + batch_op.f("fk_report_histo_expert_id_user"), type_="foreignkey" + ) + batch_op.drop_column("expert_id") + + op.drop_table("user") + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table("report_histo", schema=None) as batch_op: + batch_op.add_column(sa.Column("expert_id", sa.INTEGER(), nullable=False)) + batch_op.create_foreign_key( + batch_op.f("fk_report_histo_expert_id_user"), "user", ["expert_id"], ["id"] + ) + + with op.batch_alter_table("image", schema=None) as batch_op: + batch_op.add_column(sa.Column("expert_id", sa.INTEGER(), nullable=False)) + batch_op.create_foreign_key( + batch_op.f("fk_image_expert_id_user"), "user", ["expert_id"], ["id"] + ) + + op.create_table( + "user", + sa.Column("id", sa.INTEGER(), nullable=False), + sa.Column("username", sa.VARCHAR(length=64), nullable=False), + sa.Column("email", sa.VARCHAR(length=120), nullable=False), + sa.Column("password_hash", sa.VARCHAR(length=128), nullable=False), + sa.PrimaryKeyConstraint("id", name=op.f("pk_user")), + ) + with op.batch_alter_table("user", schema=None) as batch_op: + batch_op.create_index(batch_op.f("ix_user_username"), ["username"], unique=1) + batch_op.create_index(batch_op.f("ix_user_email"), ["email"], unique=1) + + # ### end Alembic commands ### diff --git a/migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py b/src/impatient/migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py similarity index 100% rename from migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py rename to src/impatient/migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py index e838511..abb15c5 100644 --- a/migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py +++ b/src/impatient/migrations/versions/d3f5d79b9f94_update_with_new_fields_and_date.py @@ -5,9 +5,9 @@ Create Date: 2022-01-13 15:24:22.767508 """ -from alembic import op -import sqlalchemy as sa +import sqlalchemy as sa +from alembic import op # revision identifiers, used by Alembic. revision = "d3f5d79b9f94" diff --git a/migrations/versions/e6337fb0fc1c_column_name_rectification.py b/src/impatient/migrations/versions/e6337fb0fc1c_column_name_rectification.py similarity index 100% rename from migrations/versions/e6337fb0fc1c_column_name_rectification.py rename to src/impatient/migrations/versions/e6337fb0fc1c_column_name_rectification.py index 76c2df8..7cd50fc 100644 --- a/migrations/versions/e6337fb0fc1c_column_name_rectification.py +++ b/src/impatient/migrations/versions/e6337fb0fc1c_column_name_rectification.py @@ -5,9 +5,9 @@ Create Date: 2022-01-14 14:41:23.774582 """ -from alembic import op -import sqlalchemy as sa +import sqlalchemy as sa +from alembic import op # revision identifiers, used by Alembic. revision = "e6337fb0fc1c" diff --git a/migrations/versions/f7981800ac1e_v1_0.py b/src/impatient/migrations/versions/f7981800ac1e_v1_0.py similarity index 99% rename from migrations/versions/f7981800ac1e_v1_0.py rename to src/impatient/migrations/versions/f7981800ac1e_v1_0.py index edb2295..20bebef 100644 --- a/migrations/versions/f7981800ac1e_v1_0.py +++ b/src/impatient/migrations/versions/f7981800ac1e_v1_0.py @@ -1,13 +1,13 @@ """V1_0 Revision ID: f7981800ac1e -Revises: +Revises: Create Date: 2021-10-30 00:37:27.797639 """ -from alembic import op -import sqlalchemy as sa +import sqlalchemy as sa +from alembic import op # revision identifiers, used by Alembic. revision = "f7981800ac1e" diff --git a/tests/test_auth.py b/tests/test_auth.py deleted file mode 100644 index d436f81..0000000 --- a/tests/test_auth.py +++ /dev/null @@ -1,106 +0,0 @@ -import os -import sys -import unittest - -topdir = os.path.join(os.path.dirname(__file__), "..") -sys.path.append(topdir) - -from app import create_app, db -from app.models import User -from config import Config - - -class TestConfig(Config): - """Basic App configuration for testing environnement""" - - TESTING = True - ADMINS_EMAIL = ["test@test.test"] - SQLALCHEMY_DATABASE_URI = "sqlite://" - SECRET_KEY = "testingsecretkey" - WTF_CSRF_ENABLED = False - - -class UserModelCase(unittest.TestCase): - """Class for User authentification test case""" - - def setUp(self): - self.app = create_app(TestConfig) - self.app_context = self.app.app_context() - self.client = self.app.test_client() - self.app_context.push() - db.create_all() - user = User(username="test", email="test@test.test") - user.set_password("azerty") - db.session.add(user) - db.session.commit() - - def tearDown(self): - db.session.remove() - db.drop_all() - self.app_context.pop() - - def test_password_hashing(self): - user = User.query.get(1) - self.assertFalse(user.check_password("qwerty")) - self.assertTrue(user.check_password("azerty")) - - def test_reset_token(self): - user = User.query.get(1) - token = user.get_reset_password_token() - assert user == User.verify_reset_password_token(token) - assert User.verify_reset_password_token("abcd") is None - - def test_login(self): - rv = self.client.post( - "/login", - data=dict(username="test", password="fakepwd"), - follow_redirects=True, - ) - assert rv.status_code == 200 - assert b"Invalid username or password" in rv.data - - rv = self.client.post( - "/login", - data=dict(username="test", password="azerty"), - follow_redirects=True, - ) - assert rv.status_code == 200 - assert b"Login successful" in rv.data - - def test_logout(self): - rv = self.client.get("/logout", follow_redirects=True) - assert rv.status_code == 200 - assert b"You were logged out" in rv.data - - def test_reset_password_request(self): - rv = self.client.post( - "/reset_password_request", - data=dict(email="test@test.test"), - follow_redirects=True, - ) - assert rv.status_code == 200 - assert b"Check your email" in rv.data - - rv = self.client.post( - "/reset_password_request", - data=dict(email="azerty@azerty.azerty"), - follow_redirects=True, - ) - assert rv.status_code == 200 - assert b"No account found for this email" in rv.data - - def test_reset_password(self): - user = User.query.get(1) - token = user.get_reset_password_token() - rv = self.client.get("/reset_password/" + token, follow_redirects=True) - assert rv.status_code == 200 - assert b"Reset Your Password" in rv.data - - rv = self.client.post( - "/reset_password/" + token, - data=dict(password="qwerty", password2="qwerty"), - follow_redirects=True, - ) - assert rv.status_code == 200 - assert b"Your password has been reset" in rv.data - self.assertTrue(user.check_password("qwerty")) diff --git a/tests/test_historeport.py b/tests/test_historeport.py index fd93b26..62d35b5 100644 --- a/tests/test_historeport.py +++ b/tests/test_historeport.py @@ -6,10 +6,9 @@ topdir = os.path.join(os.path.dirname(__file__), "..") sys.path.append(topdir) -from app import create_app, db -from app.historeport.onto_func import StandardVocabulary -from app.models import User -from config import Config +from impatient.app import create_app, db +from impatient.app.historeport.onto_func import StandardVocabulary +from impatient.config import Config class TestConfig(Config): @@ -30,9 +29,6 @@ def setUp(self): self.client = self.app.test_client() self.app_context.push() db.create_all() - user = User(username="test", email="test@test.test") - user.set_password("azerty") - db.session.add(user) db.session.commit() self.client.post( "/login", diff --git a/tests/test_index.py b/tests/test_index.py index b72eb69..ff6379f 100644 --- a/tests/test_index.py +++ b/tests/test_index.py @@ -5,9 +5,8 @@ topdir = os.path.join(os.path.dirname(__file__), "..") sys.path.append(topdir) -from app import create_app, db -from app.models import User -from config import Config +from impatient.app import create_app +from impatient.config import Config class TestConfig(Config): diff --git a/uv.lock b/uv.lock new file mode 100644 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