public

Author: kidzik

Dockerfile

@@ -0,0 +1,85 @@
+FROM python:3.7-slim
+
+# Create a group and user to run our app
+ARG APP_USER=appuser
+RUN groupadd -r ${APP_USER} && useradd --no-log-init -r -g ${APP_USER} ${APP_USER}
+
+# Install packages needed to run your application (not build deps):
+#   mime-support -- for mime types when serving static files
+#   postgresql-client -- for running database commands
+# We need to recreate the /usr/share/man/man{1..8} directories first because
+# they were clobbered by a parent image.
+RUN set -ex \
+    && RUN_DEPS=" \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libpcre3 \
+    mime-support \
+    postgresql-client \
+    " \
+    && seq 1 8 | xargs -I{} mkdir -p /usr/share/man/man{} \
+    && apt-get update && apt-get install -y --no-install-recommends $RUN_DEPS \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy in your requirements file
+ADD requirements.txt /requirements.txt
+
+# OR, if you're using a directory for your requirements, copy everything (comment out the above and uncomment this if so):
+# ADD requirements /requirements
+
+# Install build deps, then run `pip install`, then remove unneeded build deps all in a single step.
+# Correct the path to your production requirements file, if needed.
+RUN set -ex \
+    && BUILD_DEPS=" \
+    build-essential \
+    libpcre3-dev \
+    libpq-dev \
+    " \
+    && apt-get update && apt-get install -y --no-install-recommends $BUILD_DEPS \
+    && pip install --no-cache-dir -r /requirements.txt \
+    && pip install --no-cache-dir uwsgi \
+    \
+    && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false $BUILD_DEPS \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy your application code to the container (make sure you create a .dockerignore file if any large files or directories should be excluded)
+RUN mkdir /code/
+WORKDIR /code/
+ADD . /code/
+
+# uWSGI will listen on this port
+EXPOSE 80
+
+# Add any static environment variables needed by Django or your settings file here:
+ENV DJANGO_SETTINGS_MODULE=motionlab.settings
+
+# Call collectstatic (customize the following line with the minimal environment variables needed for manage.py to run):
+# RUN DATABASE_URL='' python manage.py collectstatic --noinput
+
+RUN mkdir data ; python manage.py migrate ; python manage.py loaddata fixtures/startup-data.json
+
+# Tell uWSGI where to find your wsgi file (change this):
+ENV UWSGI_WSGI_FILE=motionlab/wsgi.py
+
+# Base uWSGI configuration (you shouldn't need to change these):
+ENV UWSGI_MASTER=1 UWSGI_HTTP_AUTO_CHUNKED=1 UWSGI_HTTP_KEEPALIVE=1 UWSGI_LAZY_APPS=1 UWSGI_WSGI_ENV_BEHAVIOR=holy
+ENV UWSGI_HTTP=0.0.0.0:80
+#ENV UWSGI_HTTPS=0.0.0.0:443,/keys/fullchain.pem,/keys/privkey.pem
+
+# Number of uWSGI workers and threads per worker (customize as needed):
+ENV UWSGI_WORKERS=2 UWSGI_THREADS=4
+
+# uWSGI static file serving configuration (customize or comment out if not needed):
+# ENV UWSGI_STATIC_MAP="/static/=/code/static/" UWSGI_STATIC_EXPIRES_URI="/static/.*\.[a-f0-9]{12,}\.(css|js|png|jpg|jpeg|gif|ico|woff|ttf|otf|svg|scss|map|txt) 315360000"
+
+# Deny invalid hosts before they get to Django (uncomment and change to your hostname(s)):
+# ENV UWSGI_ROUTE_HOST="^(?!localhost:8000$) break:400"
+
+# Change to a non-root user
+# USER ${APP_USER}:${APP_USER}
+
+# Uncomment after creating your docker-entrypoint.sh
+# ENTRYPOINT ["/code/docker-entrypoint.sh"]
+
+# Start uWSGI
+CMD ["uwsgi", "--show-config"]

Makefile

@@ -0,0 +1,21 @@
+.PHONY: docker
+docker:
+	docker build . -t stanfordnmbl/motionlab
+
+.PHONY: push
+push:
+	docker push stanfordnmbl/motionlab
+
+.PHONY: stop
+stop:
+	docker kill motionlab_openpose 2> /dev/null
+	docker rm motionlab_openpose 2> /dev/null
+	docker-compose down
+
+.PHONY: start
+start:
+	docker-compose up -d
+# -v $(pwd)/.env:/code/.env
+	docker run --name motionlab_openpose --link motionlab_redis_1:redis --link motionlab_www_1:www --net motionlab_default --gpus all -d --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 stanfordnmbl/motionlab-worker /bin/sh -c 'celery -A worker worker --loglevel=info --concurrency=1 --pool=solo'
+
+run: docker stop start

README.md

@@ -0,0 +1,22 @@
+# sit2stand.ai 
+
+[Sit2stand.ai](https://sit2stand.ai/) is a web-app for deriving health-related metrics from a mobile phone video. 
+
+## Quick start
+
+The platform is developped in django so it can be deployed as any other django application
+
+1. Install requirements with 
+```
+pip install -r requirements.txt
+```
+2. Check settings in `motionlab/settings.py`. In particular, make sure to configure it to run on your database and AWS S3 servers.
+3. Migrate the database with
+```
+python manage.py migrate
+```
+4. Start the server with
+```
+python manage.py runserver
+```
+5. Visit http://127.0.0.1:8000/ in your browser

docker-compose.yaml

@@ -0,0 +1,23 @@
+version: '3.3'
+
+services:
+    www:
+        image: stanfordnmbl/motionlab
+        ports:
+          - "80:80"
+        env_file:
+          - ".env"
+        depends_on:
+          - redis
+        volumes:
+          - ./data:/code/data
+          - ./keys:/keys
+    # http2https:
+    #     image: http2https
+    #     ports:
+    #       - "80:80"
+    redis:
+        image: redis
+        command: redis-server --requirepass ZXdLkEtzvjsye6
+        ports:
+          - "6379:6379"

fixtures/startup-data.json

@@ -0,0 +1 @@
+[{"model": "contenttypes.contenttype", "pk": 1, "fields": {"app_label": "admin", "model": "logentry"}}, {"model": "contenttypes.contenttype", "pk": 2, "fields": {"app_label": "auth", "model": "permission"}}, {"model": "contenttypes.contenttype", "pk": 3, "fields": {"app_label": "auth", "model": "group"}}, {"model": "contenttypes.contenttype", "pk": 4, "fields": {"app_label": "auth", "model": "user"}}, {"model": "contenttypes.contenttype", "pk": 5, "fields": {"app_label": "contenttypes", "model": "contenttype"}}, {"model": "contenttypes.contenttype", "pk": 6, "fields": {"app_label": "sessions", "model": "session"}}, {"model": "contenttypes.contenttype", "pk": 7, "fields": {"app_label": "motionlab", "model": "video"}}, {"model": "contenttypes.contenttype", "pk": 8, "fields": {"app_label": "motionlab", "model": "annotation"}}, {"model": "motionlab.video", "pk": 1, "fields": {"slug": "T8h7xpSW", "file": "output.mp4", "email": null}}, {"model": "motionlab.annotation", "pk": 1, "fields": {"video": 1, "file": "video.mp4", "response": {}, "status": "done"}}, {"model": "auth.permission", "pk": 1, "fields": {"name": "Can add log entry", "content_type": 1, "codename": "add_logentry"}}, {"model": "auth.permission", "pk": 2, "fields": {"name": "Can change log entry", "content_type": 1, "codename": "change_logentry"}}, {"model": "auth.permission", "pk": 3, "fields": {"name": "Can delete log entry", "content_type": 1, "codename": "delete_logentry"}}, {"model": "auth.permission", "pk": 4, "fields": {"name": "Can view log entry", "content_type": 1, "codename": "view_logentry"}}, {"model": "auth.permission", "pk": 5, "fields": {"name": "Can add permission", "content_type": 2, "codename": "add_permission"}}, {"model": "auth.permission", "pk": 6, "fields": {"name": "Can change permission", "content_type": 2, "codename": "change_permission"}}, {"model": "auth.permission", "pk": 7, "fields": {"name": "Can delete permission", "content_type": 2, "codename": "delete_permission"}}, {"model": "auth.permission", "pk": 8, "fields": {"name": "Can view permission", "content_type": 2, "codename": "view_permission"}}, {"model": "auth.permission", "pk": 9, "fields": {"name": "Can add group", "content_type": 3, "codename": "add_group"}}, {"model": "auth.permission", "pk": 10, "fields": {"name": "Can change group", "content_type": 3, "codename": "change_group"}}, {"model": "auth.permission", "pk": 11, "fields": {"name": "Can delete group", "content_type": 3, "codename": "delete_group"}}, {"model": "auth.permission", "pk": 12, "fields": {"name": "Can view group", "content_type": 3, "codename": "view_group"}}, {"model": "auth.permission", "pk": 13, "fields": {"name": "Can add user", "content_type": 4, "codename": "add_user"}}, {"model": "auth.permission", "pk": 14, "fields": {"name": "Can change user", "content_type": 4, "codename": "change_user"}}, {"model": "auth.permission", "pk": 15, "fields": {"name": "Can delete user", "content_type": 4, "codename": "delete_user"}}, {"model": "auth.permission", "pk": 16, "fields": {"name": "Can view user", "content_type": 4, "codename": "view_user"}}, {"model": "auth.permission", "pk": 17, "fields": {"name": "Can add content type", "content_type": 5, "codename": "add_contenttype"}}, {"model": "auth.permission", "pk": 18, "fields": {"name": "Can change content type", "content_type": 5, "codename": "change_contenttype"}}, {"model": "auth.permission", "pk": 19, "fields": {"name": "Can delete content type", "content_type": 5, "codename": "delete_contenttype"}}, {"model": "auth.permission", "pk": 20, "fields": {"name": "Can view content type", "content_type": 5, "codename": "view_contenttype"}}, {"model": "auth.permission", "pk": 21, "fields": {"name": "Can add session", "content_type": 6, "codename": "add_session"}}, {"model": "auth.permission", "pk": 22, "fields": {"name": "Can change session", "content_type": 6, "codename": "change_session"}}, {"model": "auth.permission", "pk": 23, "fields": {"name": "Can delete session", "content_type": 6, "codename": "delete_session"}}, {"model": "auth.permission", "pk": 24, "fields": {"name": "Can view session", "content_type": 6, "codename": "view_session"}}, {"model": "auth.permission", "pk": 25, "fields": {"name": "Can add video", "content_type": 7, "codename": "add_video"}}, {"model": "auth.permission", "pk": 26, "fields": {"name": "Can change video", "content_type": 7, "codename": "change_video"}}, {"model": "auth.permission", "pk": 27, "fields": {"name": "Can delete video", "content_type": 7, "codename": "delete_video"}}, {"model": "auth.permission", "pk": 28, "fields": {"name": "Can view video", "content_type": 7, "codename": "view_video"}}, {"model": "auth.permission", "pk": 29, "fields": {"name": "Can add annotation", "content_type": 8, "codename": "add_annotation"}}, {"model": "auth.permission", "pk": 30, "fields": {"name": "Can change annotation", "content_type": 8, "codename": "change_annotation"}}, {"model": "auth.permission", "pk": 31, "fields": {"name": "Can delete annotation", "content_type": 8, "codename": "delete_annotation"}}, {"model": "auth.permission", "pk": 32, "fields": {"name": "Can view annotation", "content_type": 8, "codename": "view_annotation"}}, {"model": "auth.user", "pk": 1, "fields": {"password": "pbkdf2_sha256$180000$1QXPT26MLfPo$nEdMIhCaK3jGxxGdWCWQ/x3cGJbehqlRfCRxyVxnBtk=", "last_login": null, "is_superuser": true, "username": "admin", "first_name": "", "last_name": "", "email": "", "is_staff": true, "is_active": true, "date_joined": "2020-10-03T18:51:28.156Z", "groups": [], "user_permissions": []}}]

manage.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'motionlab.settings')
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError as exc:
+        raise ImportError(
+            "Couldn't import Django. Are you sure it's installed and "
+            "available on your PYTHONPATH environment variable? Did you "
+            "forget to activate a virtual environment?"
+        ) from exc
+    execute_from_command_line(sys.argv)
+
+
+if __name__ == '__main__':
+    main()

motionlab/__init__.py

@@ -0,0 +1,7 @@
+from __future__ import absolute_import, unicode_literals
+
+# This will make sure the app is always imported when
+# Django starts so that shared_task will use this app.
+from .celery import app as celery_app
+
+__all__ = ('celery_app',)

motionlab/admin.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+from motionlab.models import Video, Annotation
+
+class AnnotationAdmin(admin.ModelAdmin):
+    list_display = ('video', 'file', 'status')
+
+class VideoAdmin(admin.ModelAdmin):
+    readonly_fields = ["slug",]
+    fields = ["slug","recordid","file","email",]
+    list_display = ('pk','recordid', 'slug', 'file', 'email')
+
+admin.site.register(Annotation, AnnotationAdmin)
+admin.site.register(Video, VideoAdmin)

motionlab/asgi.py

@@ -0,0 +1,16 @@
+"""
+ASGI config for gaitlab project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/3.0/howto/deployment/asgi/
+"""
+
+import os
+
+from django.core.asgi import get_asgi_application
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'motionlab.settings')
+
+application = get_asgi_application()

motionlab/celery.py

@@ -0,0 +1,10 @@
+import os
+from celery import Celery
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'proj.settings')
+
+app = Celery('motionlab')
+
+app.config_from_object('django.conf:settings', namespace='CELERY')
+
+app.autodiscover_tasks()

motionlab/custom_storages.py

@@ -0,0 +1,8 @@
+from django.conf import settings
+from storages.backends.s3boto3 import S3Boto3Storage
+
+class StaticStorage(S3Boto3Storage):
+    location = settings.STATICFILES_LOCATION
+
+class MediaStorage(S3Boto3Storage):
+    location = settings.MEDIAFILES_LOCATION

motionlab/forms.py

@@ -0,0 +1,27 @@
+from django import forms
+from django.forms import ModelForm
+from motionlab.models import Video
+from django import forms
+from django.utils.safestring import mark_safe
+from django.forms import ModelForm, FileInput
+
+class VideoForm(ModelForm):
+#    terms_confirmed = forms.BooleanField(label=mark_safe("I've read and accept <a href='#license'>the terms of use</a>."))
+    
+    class Meta:
+        model = Video
+        fields = ["file", "recordid"]
+        widgets = {
+#            'file': FileInput(attrs={'class': "dropzone"}),
+        }
+
+class ContactForm(forms.Form):
+    your_email = forms.EmailField(required=True)
+    subject = forms.CharField(required=True)
+    message = forms.CharField(widget=forms.Textarea(attrs={'style': 'min-height: 7em;'}), required=True)
+
+class ApplicationForm(forms.Form):
+    your_name = forms.CharField(required=True)
+    your_email = forms.EmailField(required=True)
+    your_state = forms.CharField(required=True)
+    how = forms.CharField(widget=forms.Textarea(attrs={'style': 'min-height: 7em;'}), required=True, label="How you heard about the study?")

motionlab/migrations/0001_initial.py

@@ -0,0 +1,37 @@
+# Generated by Django 3.0.8 on 2021-01-27 19:44
+
+from django.db import migrations, models
+import django.db.models.deletion
+import jsonfield.fields
+import randomslugfield.fields
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Video',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('slug', randomslugfield.fields.RandomSlugField(blank=True, editable=False, length=8, max_length=8, unique=True)),
+                ('file', models.FileField(upload_to='', verbose_name='Video file')),
+                ('email', models.EmailField(max_length=254, null=True)),
+                ('recordid', models.CharField(max_length=32, unique=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Annotation',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('file', models.FileField(null=True, upload_to='')),
+                ('response', jsonfield.fields.JSONField(blank=True, null=True)),
+                ('status', models.CharField(choices=[('submitted', 'Submitted'), ('processing', 'Processing'), ('done', 'Done'), ('error', 'Error')], default='submitted', max_length=10)),
+                ('video', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='motionlab.Video')),
+            ],
+        ),
+    ]

motionlab/migrations/0002_auto_20210310_0503.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.0.8 on 2021-03-10 05:03
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('motionlab', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='video',
+            name='recordid',
+            field=models.CharField(max_length=32),
+        ),
+    ]

motionlab/migrations/__init__.py

@@ -0,0 +1,40 @@
+from django.db import models
+import jsonfield
+from randomslugfield import RandomSlugField
+from django.urls import reverse
+
+import uuid
+import os
+
+def get_file_path(directory):
+    def func(instance, filename):
+        ext = filename.split('.')[-1]
+        filename = "%s.%s" % (uuid.uuid4(), ext)
+        return os.path.join(directory, filename)
+    return func
+
+STATUS_CHOICES = [
+    ("submitted","Submitted"),
+    ("processing","Processing"),
+    ("done","Done"),
+    ("error","Error"),
+]
+
+class Video(models.Model):
+    slug = RandomSlugField(length=8)
+    file = models.FileField("Video file", upload_to=get_file_path("inputs"))
+    email = models.EmailField(null=True)
+    recordid = models.CharField(null=False, max_length=32)
+
+    def get_absolute_url(self):
+        return reverse('analysis', args=[str(self.slug)])
+
+    def __str__(self):
+        return self.slug.__str__()
+
+class Annotation(models.Model):
+    video = models.ForeignKey(Video, on_delete=models.CASCADE)
+    file = models.FileField(upload_to=get_file_path("outputs"),
+                            null=True)
+    response = jsonfield.JSONField(null=True, blank=True)
+    status = models.CharField(max_length=10, choices=STATUS_CHOICES, default='submitted')