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Update docker
* Bump app version (#28) * build: bump app version --------- Co-authored-by: root <root@nes-dev.ime.usp.br> Co-authored-by: erico <erico@numec.prp.usp.br> * build: update first stage for NES * chore: remove wsgi from entrypoint * build: add second stage to build * chore: update WSGI to default * chore: remove wsgi.py from .gitignore * build: add missing dep * build: conditionally run migrations and db-related ops * build: add docker-compose.yml * chore: remove deprecated property from docker-compose.yml * build: add docker files * build: fix compose * build: simplify Dockerfile to single stage * build: create super user on entrypoint --------- Co-authored-by: Erico Silva <augusto.ericosilva@gmail.com> Co-authored-by: root <root@nes-dev.ime.usp.br> Co-authored-by: erico <erico@numec.prp.usp.br>
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Lines changed: 87 additions & 126 deletions

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‎docker/compose/nes/Dockerfile‎

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@@ -1,86 +1,44 @@
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FROM python:3.8-alpine3.12 as wheeler
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# sudo docker build -t nes:test -f docker/compose/nes/Dockerfile .
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# sudo docker run --rm -it nes:test /bin/bash
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FROM python:3.8-slim
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ENV PYTHONUNBUFFERED=1
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RUN apk update && \
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apk add --no-cache \
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libpng-dev \
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freetype-dev \
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build-base \
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git \
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postgresql-dev \
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openblas-dev \
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libjpeg-turbo-dev \
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hdf5-dev && \
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rm -rf /var/cache/apk/* && \
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ln -s /usr/include/locale.h /usr/include/xlocale.h
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ARG NES_TAG=unset
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ARG NES_BRANCH=unset
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ARG NES_DIR=/nes
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ENV NES_DIR=$NES_DIR
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RUN mkdir -p "$NES_DIR" && \
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if [ "$NES_TAG" != "unset" ]; then \
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echo Cloning tag "$NES_TAG" ;\
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wget https://github.com/neuromat/nes/archive/TAG-"${NES_TAG}".tar.gz -qO - | \
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tar xzv --strip-components=1 -C "$NES_DIR" ;\
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sed -i 's/\(psycopg2==\)[0-9.]\+/\12.7.5/' /nes/patientregistrationsystem/qdc/requirements.txt ;\
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sed -i '1isetuptools>=40.6.3' /nes/patientregistrationsystem/qdc/requirements.txt ;\
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sed -i '1ipip>=18.1' /nes/patientregistrationsystem/qdc/requirements.txt ;\
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echo 'mne>=0.17.0' >> /nes/patientregistrationsystem/qdc/requirements.txt ;\
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echo '-e "git+https://github.com/AllenInstitute/nwb-api.git#egg=nwb&subdirectory=ainwb"' >> /nes/patientregistrationsystem/qdc/requirements.txt ;\
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elif [ "$NES_BRANCH" != "unset" ]; then \
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echo Cloning "$NES_BRANCH" branch ;\
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git clone -j $(nproc) -b "$NES_BRANCH" https://github.com/neuromat/nes.git "$NES_DIR" ;\
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else \
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echo Cloning master branch ;\
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git clone -j $(nproc) https://github.com/neuromat/nes.git "$NES_DIR" ;\
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fi
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RUN mkdir -p /wheels/requirement && \
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cp "$NES_DIR"/patientregistrationsystem/qdc/requirements.txt /wheels/requirement
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WORKDIR /wheels
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RUN pip3 install -U pip setuptools wheel && \
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pip3 install -r requirement/requirements.txt && \
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pip3 wheel -r requirement/requirements.txt
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FROM alpine:3.12
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SHELL ["/bin/sh","-exc"]
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RUN apk update && \
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apk add --no-cache \
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git \
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libpq \
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openblas-dev \
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libjpeg-turbo-dev \
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python3 \
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py3-pip \
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graphviz \
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hdf5-dev && \
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rm -rf /var/cache/apk/*
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ARG NES_DIR=/nes
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ENV NES_DIR=$NES_DIR
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COPY --from=wheeler /wheels /wheels
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COPY --from=wheeler $NES_DIR $NES_DIR
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RUN pip3 install -U pip setuptools wheel && \
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pip3 install -r /wheels/requirement/requirements.txt -f /wheels && \
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rm -rf /wheels && \
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rm -rf /root/.cache/pip*
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VOLUME $NES_DIR
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COPY ./entrypoint.sh /
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ENV NES_IP ${NES_IP:-0.0.0.0}
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ENV NES_PORT ${NES_PORT:-8000}
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ENTRYPOINT [ "/entrypoint.sh" ]
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CMD [ "/bin/sh", "-c", "/usr/bin/python3 -u ${NES_DIR}/patientregistrationsystem/qdc/manage.py runserver -v3 $NES_IP:$NES_PORT" ]
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# System deps (build + runtime together)
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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git \
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build-essential \
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python3-distutils \
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libpq-dev \
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libpq5 \
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libopenblas-dev \
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libjpeg62-turbo-dev \
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libpng-dev \
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libfreetype6-dev \
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graphviz \
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libhdf5-dev && \
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rm -rf /var/lib/apt/lists/*
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# App location
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ENV NES_DIR=/nes
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WORKDIR $NES_DIR
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RUN git config --global --add safe.directory /nes
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# App source
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COPY . .
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# Python deps
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RUN pip install --no-cache-dir \
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-r patientregistrationsystem/qdc/requirements.txt
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# Runtime config
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ENV NES_IP=0.0.0.0
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ENV NES_PORT=8000
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COPY docker/compose/nes/entrypoint.sh /
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ENTRYPOINT ["/entrypoint.sh"]
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# CMD ["/bin/sh", "-c", "python -u patientregistrationsystem/qdc/manage.py runserver -v3 $NES_IP:$NES_PORT"]

‎docker/compose/nes/docker-compose.yml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
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# sudo docker compose -f docker/compose/nes/docker-compose.yml up
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services:
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db:
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image: postgres:15
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environment:
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POSTGRES_DB: nes_db
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POSTGRES_USER: nes_user
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POSTGRES_PASSWORD: nes_password
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volumes:
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- pgdata:/var/lib/postgresql/data
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web:
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build:
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context: ../../..
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dockerfile: docker/compose/nes/Dockerfile
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command: python manage.py runserver 0.0.0.0:8000
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ports:
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- "8000:8000"
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environment:
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NES_DB_HOST: db
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NES_DB: nes_db
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NES_DB_USER: nes_user
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NES_DB_PASSWORD: nes_password
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depends_on:
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- db
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volumes:
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pgdata:

‎docker/compose/nes/entrypoint.sh‎

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Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@ NES_DB_PORT=${NES_DB_PORT:-'5432'}
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NES_DB_PASSWORD=${NES_DB_PASSWORD:-'nes_password'}
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# External LimeSurvey settings
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LIMESURVEY_HOST=${LIMESURVEY_HOST:-'localhost'}
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LIMESURVEY_PORT=${LIMESURVEY_PORT:-'8080'}
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LIMESURVEY_API_URL=${LIMESURVEY_API_URL:-'http://localhost:8080'}
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LIMESURVEY_WEB_URL=${LIMESURVEY_WEB_URL:-'http://localhost:8080'}
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LIMESURVEY_ADMIN_USER=${LIMESURVEY_ADMIN_USER:-'limesurvey_admin'}
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LIMESURVEY_ADMIN_PASSWORD=${LIMESURVEY_ADMIN_PASSWORD:-'limesurvey_admin_password'}
2020

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exit 1
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fi
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if [ -f "${NES_SETUP_PATH}"/wsgi.py ]
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then
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echo "INFO: NES wsgi.py file already provisioned"
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else
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echo "INFO: Creating NES wsgi.py file"
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cat <<-EOF > "${NES_SETUP_PATH}"/wsgi.py
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import os
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import sys
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import site
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paths = ["$NES_PROJECT_PATH", "$NES_DIR", "/usr/local", "/usr/bin", "/bin",]
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for path in paths:
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if path not in sys.path:
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sys.path.append(path)
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os.environ.setdefault("DJANGO_SETTINGS_MODULE", "qdc.settings")
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from django.core.wsgi import get_wsgi_application
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application = get_wsgi_application()
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EOF
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chown -R nobody "${NES_SETUP_PATH}"/wsgi.py
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fi
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if [ -f "${NES_SETUP_PATH}"/settings_local.py ]
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then
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echo "INFO: NES settings_local.py file already provisioned"
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}
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}
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LIMESURVEY = {
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"URL_API": "http://$LIMESURVEY_HOST:$LIMESURVEY_PORT",
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"URL_WEB": "http://$LIMESURVEY_HOST:$LIMESURVEY_PORT",
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"URL_API": "$LIMESURVEY_API_URL",
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"URL_WEB": "$LIMESURVEY_WEB_URL",
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"USER": "$LIMESURVEY_ADMIN_USER",
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"PASSWORD": "$LIMESURVEY_ADMIN_PASSWORD"
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}
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chown -R nobody "${NES_SETUP_PATH}"/settings_local.py
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fi
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while ! nc -z "$NES_DB_HOST" "$NES_DB_PORT"
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do
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sleep 0.2
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done
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# while ! nc -z "$NES_DB_HOST" "$NES_DB_PORT"
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# do
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# sleep 0.2
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# done
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if [ -f "${NES_DIR}"/.nes_initialization.placeholder ]
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then
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echo "INFO: NES data has already been initialized"
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else
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if [ ! -f "${NES_DIR}"/.nes_initialized.placeholder ]; then
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echo "INFO: Initializing NES data (migrations, initial, superuser, ICD)"
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cd "$NES_PROJECT_PATH"
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EOF
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python3 -u manage.py migrate
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# Different versions may have different commands
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python3 -u manage.py shell < add_initial_data.py || true
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python3 -u manage.py loaddata load_initial_data.json || true
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python3 -u manage.py shell < /tmp/create_superuser.py || true
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python3 -u manage.py import_icd_cid --file icd10cid10v2017.csv || true
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python3 -u manage.py createcachetable || true
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python3 -u manage.py shell < /tmp/create_superuser.py
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rm /tmp/create_superuser.py
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# If NES was installed from a release it won't have a .git directory
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chown -R nobody "${NES_DIR}"/.git || true
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chown -R nobody "${NES_DIR}"/patientregistrationsystem
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touch "${NES_DIR}"/.nes_initialization.placeholder
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touch "${NES_DIR}"/.nes_initialized.placeholder
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fi
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# If NES was installed from a release it won't have a .git directory
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chown -R nobody "${NES_DIR}"/.git || true
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chown -R nobody "${NES_DIR}"/patientregistrationsystem
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exec "$@"

‎patientregistrationsystem/qdc/.gitignore‎

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.idea
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qdc/settings_local.py
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*.DS_Store
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qdc/wsgi.py
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db.sqlite3
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__pycache__/
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geckodriver.log

‎patientregistrationsystem/qdc/qdc/settings.py‎

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except ImportError:
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pass
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VERSION = '1.72.7'
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VERSION = '1.73.0'

patientregistrationsystem/qdc/qdc/wsgi_default.py renamed to patientregistrationsystem/qdc/qdc/wsgi.py

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https://docs.djangoproject.com/en/1.6/howto/deployment/wsgi/
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"""
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import os
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os.environ.setdefault("DJANGO_SETTINGS_MODULE", "qdc.settings")
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from django.core.wsgi import get_wsgi_application
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application = get_wsgi_application()
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os.environ.setdefault("DJANGO_SETTINGS_MODULE", "qdc.settings")
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application = get_wsgi_application()

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