Commit 3705f0f6 authored by Eugenio Schisano's avatar Eugenio Schisano
Browse files

Commit crappy dabatase with FITS files from density structure

parent 8402e3d0

etl/stg/stg_build_db_structure.py

+13 −0
Original line number Diff line number Diff line
@@ -17,6 +17,19 @@ Base = declarative_base() 


engine = get_pg_engine(logger=logger)



class GridFiles(Base):

    __tablename__ = "grid_files"

    __table_args__ = (

        ForeignKeyConstraint(

            ('zipped_grid_name', 'run_id'),

            ['grid_parameters.zipped_grid_name', 'grid_parameters.run_id']

        ),

    )

    zipped_grid_name = Column(String(150), primary_key=True)

    quantity = Column(String(30), primary_key=True)

    fits_grid_name = Column(String)

    created_on = Column(DateTime)

    run_id = Column(String, primary_key=True)



class GridPars(Base):

    __tablename__ = "grid_parameters"

etl/stg/stg_radmc_input_generator.py

+44 −3
Original line number Diff line number Diff line 
import logging

import uuid



import numpy as np

import os

import shutil
@@ -20,9 +22,10 @@ from assets.commons import (compute_power_law_radial_profile, 
from assets.constants import (mean_molecular_mass,

                              radmc_input_headers,

                              radmc_lines_mode_mapping)

from stg.stg_build_db_structure import GridPars

from stg.stg_build_db_structure import GridPars, GridFiles

from astropy import units as u

from astropy import constants as cst

from astropy.io import fits



logger = setup_logger(name='STG')
@@ -155,7 +158,8 @@ def get_profiles(grid_metadata: dict) -> dict: 
        'escprob_lengthscale': {

            'central_value': min((np.max(grid_metadata['grid_size']) *

                                  u.Unit(grid_metadata['grid_size_units'][np.argmax(grid_metadata['grid_size'])]))

            .to(u.cm).value, (2 * grid_metadata['maximum_radius'] * u.Unit(grid_metadata['maximum_radius_unit']))

                                 .to(u.cm).value,

                                 (2 * grid_metadata['maximum_radius'] * u.Unit(grid_metadata['maximum_radius_unit']))

                                 .to(u.cm).value),

            'power_law_index': 0,

            'value_at_reference': None,
@@ -252,6 +256,14 @@ def write_molecular_number_density_profiles(profiles: dict, 
                          grid_metadata=grid_metadata)





def save_fits_grid_profile(quantity,

                           grid_metadata,

                           filename,

                           path=None):

    _path = validate_parameter(path, default=os.path.join('prs', 'fits', 'grids'))

    fits.writeto(os.path.join(_path, filename), quantity)





def convert_dimensional_unit(value: Union[float, None, str],

                             current_unit: str,

                             desired_unit: str) -> Union[float, None]:
@@ -360,6 +372,21 @@ def populate_grid_table(config: dict, 
    return output_filename





def populate_grid_files(quantity : str,

                        engine: sqla_engine,

                        tgz_filename : str,

                        filename : str,

                        run_id : str):

    raw_insert_entry = {'zipped_grid_name': tgz_filename, 'quantity': quantity, 'fits_grid_name': filename,

                        'created_on': datetime.now(), 'run_id': run_id}

    upsert(

        table_object=GridFiles,

        row_dict=raw_insert_entry,

        conflict_keys=[GridFiles.zipped_grid_name, GridFiles.quantity, GridFiles.run_id],

        engine=engine

    )





def main(run_id: str,

         override_config: Union[dict, None] = None,

         path_radmc_files: Union[str, None] = None) -> str:
@@ -383,6 +410,7 @@ def main(run_id: str, 
    write_radmc_lines_input(line_config=config['lines'],

                            path=input_files_dir,

                            logger=logger)



    write_molecular_number_density_profiles(profiles=profiles,

                                            grid_metadata=grid_metadata,

                                            line_config=config['lines'],
@@ -391,6 +419,19 @@ def main(run_id: str, 
                                       engine=engine,

                                       grid_metadata=grid_metadata,

                                       run_id=run_id)



    grid_file_name = f'{str(uuid.uuid4())}.fits'

    save_fits_grid_profile(quantity=profiles['gas_number_density'],

                           grid_metadata=grid_metadata,

                           filename=grid_file_name

                           )



    populate_grid_files(quantity='gas_number_density',

                        engine=engine,

                        tgz_filename=tgz_filename,

                        filename=grid_file_name,

                        run_id=run_id)



    make_tarfile(output_filename=tgz_filename,

                 source_dir=input_files_dir,

                 archive_path=os.path.join('stg', 'archive'))