Commit f5125041 authored by Andrea Giannetti's avatar Andrea Giannetti
Browse files

Adapted scripts for docker compose.

parent 42393340

Dockerfile

0 → 100644
+28 −0
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FROM python:3.9-slim





# STEP 1) Setting up environment

# apt packages

RUN apt-get update && \

    apt-get --yes upgrade && \

    apt-get install --yes libgomp1 && \

    apt-get install --yes postgresql-client && \

    apt-get install --yes --reinstall build-essential && \

    apt-get -y install curl vim less nano pip git && \

    apt-get -y install zip unzip



WORKDIR /usr/src/etl

RUN python -m pip install --upgrade pip

COPY etl/requirements.txt .

RUN pip install -r requirements.txt



COPY documentation/radmc3d_install.sh .

RUN chmod 755 radmc3d_install.sh

RUN ./radmc3d_install.sh

ENV PATH="/root/bin:${PATH}"

ENV PYTHONPATH="/root/bin/python:${PYTHONPATH}"



# STEP 2) Bundling app

COPY etl .



CMD python main.py
 
 No newline at end of file

etl/docker-compose.yaml→docker-compose.yaml

+38 −0
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@@ -2,6 +2,7 @@ version: '3.8' 
services:

  db:

    image: postgres:14.1-alpine

    container_name: db_container

    restart: always

    environment:

      - POSTGRES_DB=$DB_NAME
@@ -11,6 +12,27 @@ services: 
      - '5432:5432'

    volumes:

      - db:/var/lib/postgresql/data

    networks:

      - sak_network

    network_mode: 'bridge'



  etl:

    build:

      dockerfile: Dockerfile

    container_name: 'etl'

    image: 'sak_etl'

    depends_on:

      - db

    stdin_open: true

    tty: true

    networks:

      - sak_network

    network_mode: 'bridge'

    volumes:

      - ./etl:/usr/src/etl

volumes:

  db:

    driver: local

networks:

  sak_network:

    name: 'sak_app_network'
 
 No newline at end of file

documentation/radmc3d_install.sh

+5 −5
Original line number Diff line number Diff line 
#!/bin/bash

# Set PYCHARM_HOME, INSTALL_DEPENDENCIES environment variable

PYCHARM_HOME=${PYCHARM_HOME:=$HOME/PycharmProjects}

INSTALL_DEPENDENCIES="${INSTALL_DEPENDENCIES:=false}"

PYCHARM_HOME=${PYCHARM_HOME:=$HOME}

INSTALL_DEPENDENCIES="${INSTALL_DEPENDENCIES:=true}"

echo $PYCHARM_HOME

cd $PYCHARM_HOME

export RADMC_HOME=$PYCHARM_HOME/radmc3d-2.0
@@ -13,14 +13,14 @@ fi 


if $INSTALL_DEPENDENCIES

then

    sudo apt-get install gfortran

    apt-get install -y gfortran

fi



cd $RADMC_HOME/src

make

make install

echo "y\n y\n"| make install



# Add this to thee .bashrc configuration file (or equivalent)

# Add this to the .bashrc configuration file (or equivalent)

export PATH=$HOME/bin:$PATH

export PYTHONPATH=$HOME/bin/python:$PYTHONPATH

etl/main.py

+2 −2
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@@ -10,7 +10,7 @@ from prs.prs_inspect_results import main as prs_inspection_main 


def build_model_grid():

    stg_config = load_config_file(os.path.join('stg', 'config', 'config.yml'))

    pl_density_index = float(stg_config['density_powerlaw_idx'])

    pl_density_index = float(stg_config['grid']['density_powerlaw_idx'])

    _model_type = 'spherical' if pl_density_index != 0 else 'homogeneous'



    config = load_config_file(os.path.join('config', 'config.yml'))
@@ -24,7 +24,7 @@ def build_model_grid(): 


    grid_tarfiles = []



    density_keyword = 'central_density' if _model_type == 'homogeneous' else 'density_value_at_reference'

    density_keyword = 'central_density' if _model_type == 'homogeneous' else 'density_at_reference'



    for (tdust, nh2) in product(dust_temperatures, densities):

        overrides = {

etl/prs/prs_inspect_results.py

+3 −1
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@@ -37,7 +37,9 @@ def get_aggregated_ratio_from_db( 
                                                                                           or_(RatioMaps.mom_zero_map_1,

                                                                                               RatioMaps.mom_zero_map_2)).filter(

        and_(GridPars.dust_temperature == dust_temperature,

             GridPars.central_density == gas_density, or_(ModelPars.iline.in_(lines)))).all()

             GridPars.density_at_reference == gas_density,

             # GridPars.central_density == gas_density,

             or_(ModelPars.iline.in_(lines)))).all()

    assert len(results) == 1

    return results[0][1].aggregated_ratio