build_BDD.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This script inspect a SPASE dataset folder (containing Granules, NumericalData, Instrument and
Observatory folders), then generate a SQL script which insert all the granules in a database,
formatted as epn-tap parameters.
See
http://spase-group.org/data/reference/spase-2_2_6/ for more information about spase specification,
and https://voparis-confluence.obspm.fr/display/VES/EPN-TAP+V2.0+parameters for more information
about epn-tap-v2 specification."""
import math
import re
import xml.etree.ElementTree as ElTr
import os.path as op
from os import walk
from datetime import datetime, timedelta
from typing import Tuple, List, Dict, Optional
import sys
# Type aliases
SQLDic = Dict[str, object]
SpaseDic = Dict[str, List[ElTr.Element]]
# Paths
WORKING_DIR = op.dirname(op.abspath(__file__)) # parent directory
OUTPUT_SQL_FILE_PATH = op.join(WORKING_DIR, 'DaCHS', 'amdadb_db.sql')
SPASE_DIR = op.join(WORKING_DIR, 'DATA')
LOG_FILE_PATH = op.join(WORKING_DIR, 'log', 'build_granules.log') # Set to None if you want to log in stdout instead of a file
# XML and SQL formats
XMLNS = 'http://www.spase-group.org/data/schema'
XML_DATE_FORMAT = '%Y-%m-%dT%H:%M:%SZ'
SQL_DATE_FORMAT = '%Y-%m-%d'
SEP = '#'
# Dictionaries of values
DATAPRODUCT_TYPE_DIC = {'Image': 'im', 'Plasmagram': 'ds', 'Spectrogram': 'ds', 'StackPlot': 'ts',
'TimeSeries': 'ts', 'time_series': 'ts', 'WaveForm': 'ts'}
PROCESSING_LEVEL_DIC = {'Calibrated': 3, 'Raw': 1, 'Uncalibrated': 5}
# Based on http://spase-group.org/
TARGET_CLASS_DIC = {'Heliosphere': 'interplanetary_medium', 'Interstellar': 'galaxy',
'Earth': 'planet', 'Saturn': 'planet', 'Mercury': 'planet', 'Uranus': 'planet',
'Mars': 'planet', 'Neptune': 'planet', 'Jupiter': 'planet', 'Venus': 'planet',
'Moon': 'satellite', 'Callisto': 'satellite', 'Europa': 'satellite',
'Ganymede': 'satellite', 'Dione': 'satellite', 'Enceladus': 'satellite',
'Mimas': 'satellite', 'Miranda': 'satellite', 'Phobos': 'satellite',
'Iapetus': 'satellite', 'Titania': 'satellite', 'Oberon': 'satellite',
'Puck': 'satellite', 'Deimos': 'satellite', 'Ariel': 'satellite',
'Umbriel': 'satellite', 'Rhea': 'satellite', 'Tethys': 'satellite',
'Titan': 'satellite', 'Io': 'satellite',
'Pluto': 'dwarf_planet',
'Comet': 'comet'
}
MIME_TYPE_LIST = {'AVI': 'video/x-msvideo',
'Binary': 'application/octet-stream',
'CDF': 'application/x-cdf-istp',
'CEF': 'application/x-cef1',
'CEF1': 'application/x-cef1',
'CEF2': 'application/x-cef2',
'Excel': 'application/vnd.ms-excel',
'FITS': 'application/x-fits-bintable',
'GIF': 'image/gif',
'HDF': 'application/x-hdf',
'HDF4': 'application/x-hdf',
'HDF5': 'application/x-hdf',
'HTML': 'text/html',
'Hardcopy': None,
'Hardcopy.Film': None,
'Hardcopy.Microfiche': None,
'Hardcopy.Microfilm': None,
'Hardcopy.Photograph': None,
'Hardcopy.PhotographicPlate': None,
'Hardcopy.Print': None,
'IDFS': None,
'IDL': 'application/octet-stream',
'JPEG': 'image/jpeg ',
'MATLAB_4': 'application/octet-stream',
'MATLAB_6': 'application/octet-stream',
'MATLAB_7': 'application/octet-stream',
'MPEG': 'video/mpeg',
'NCAR': None,
'NetCDF': 'application/x-netcdf',
'PDF': 'application/pdf',
'PNG': 'image/png',
'Postscript': 'application/postscript',
'QuickTime': 'video/quicktime',
'TIFF': 'image/tiff',
'Text': 'text/plain',
'Text.ASCII': 'text/plain',
'Text.Unicode': 'text/plain',
'UDF': None,
'VOTable': 'application/x-votable+xml',
'XML': 'text/xml'}
# All default SQL values for missing parameters in dataset
DEFAULT_DATASET_VALUES = {
'dataproduct_type': 'Unknown',
'target_name': 'Unknown',
'target_class': 'Unknown',
'target_region': None,
'spase_region': None,
'instrument_host_name': None,
'instrument_name': None,
'measurement_type': None,
'spatial_frame_type': None,
'processing_level': 0,
'time_sampling_step_min': None,
'time_sampling_step_max': None,
'time_exp_min': None,
'access_format': 'application/x-cdf-istp'
}
# All default SQL values for missing parameters in granule
DEFAULT_GRANULE_VALUES = {
# obs_id: if missing, the script exits directly.
'time_min': 0.0,
'time_max': 0.0,
'access_url': None,
'access_estsize': 0,
'release_date': '01-01-0001'
}
# SQL code
SQL_HEADER = '''-- Generated by build_BDD.py on %s.
-- SQL procedure to define amdadb data table. Other parameters comes in the epn_core view.
-- Name: amdadb; Type: SCHEMA; Schema: amdadb; Owner: postgres
DROP SCHEMA IF EXISTS amdadb cascade;
CREATE SCHEMA amdadb;
SET search_path = public, pg_catalog;
SET default_tablespace = '';
SET default_with_oids = false;
SET client_encoding = 'UTF8';
-- Name: data_table; Type: TABLE; Schema: amdadb; Owner: postgres; Tablespace:
CREATE TABLE amdadb.data_table (
-- header parameters
id SERIAL PRIMARY KEY,
obs_id TEXT,
dataproduct_type TEXT,
target_name TEXT,
time_min DOUBLE PRECISION, -- date as JD
time_max DOUBLE PRECISION, -- date as JD
-- important parameters
access_url TEXT,
target_class TEXT,
target_region TEXT,
spase_region TEXT,
instrument_host_name TEXT,
instrument_name TEXT,
measurement_type TEXT,
spase_measurement_type TEXT,
spatial_frame_type TEXT,
processing_level INTEGER,
release_date DATE,
access_estsize INTEGER,
access_format TEXT,
time_sampling_step_min DOUBLE PRECISION, -- duration in seconds
time_sampling_step_max DOUBLE PRECISION, -- duration in seconds
time_exp_min DOUBLE PRECISION -- duration in seconds
);
''' % datetime.now().strftime('%c')
SQL_ROW = 'INSERT INTO amdadb.data_table(%s) VALUES (%s);\n'
SQL_FOOTER = '''REVOKE ALL ON SCHEMA "amdadb" FROM PUBLIC;
REVOKE ALL ON SCHEMA "amdadb" FROM postgres;
GRANT ALL ON SCHEMA "amdadb" TO postgres;
GRANT ALL PRIVILEGES ON SCHEMA amdadb TO gavo WITH GRANT OPTION;
GRANT ALL PRIVILEGES ON SCHEMA amdadb TO gavoadmin WITH GRANT OPTION;
GRANT ALL PRIVILEGES ON amdadb.data_table TO gavo WITH GRANT OPTION;
GRANT ALL PRIVILEGES ON amdadb.data_table TO gavoadmin WITH GRANT OPTION;'''
def log(message: str) -> None:
"""Log a warning in a log file or the stdout.
- ``message``: The message to display or to print in the log file.
"""
if log_file:
log_file.write(message + '\n')
else:
print(message)
def get_nb_files() -> int:
"""Get the number of files in the ``SPASE`` directory,
in order to be able to show a progress bar."""
return sum([len(walker[2]) for walker in walk(SPASE_DIR)])
def get_spase() -> Optional[SpaseDic]:
"""Get all the spase files
- ``return``: a dictionary, where:
- **key** = dataset type ('numerical_data', 'granules', etc) ;
- **value** = A list of spase ElementTree nodes.
"""
spase_dic = {}
n_file = 0
for dir_path, _, files in walk(SPASE_DIR):
for file_path in [op.join(dir_path, file_name) for file_name in files]:
try:
root = ElTr.parse(file_path).getroot()
except FileNotFoundError:
print('\nThe spase file is not found on %s.\n' % file_path)
with open(file_path) as spase_file:
print(spase_file.read())
return
for child in root:
key = str(child.tag).split('}')[-1]
if key != 'Version':
if key not in spase_dic:
spase_dic[key] = []
spase_dic[key].append(child)
print('Parsed {:<23.23} {:<19.19} [{:<50.50}]'.format(
'%d/%d (%.2f%%)' % (n_file + 1, nb_files, 100 * float(n_file + 1) / nb_files),
op.splitext(op.basename(file_path))[0],
'.' * int((n_file + 1) / nb_files * 50)), end='\r')
n_file += 1
print()
if not spase_dic:
print('The SPASE dictionary is empty, please check the SPASE folder: %s.' % SPASE_DIR)
return
return spase_dic
def get_observatory(spase_dic: SpaseDic, observatory_id: str) -> ElTr.Element:
"""Given the ``observatory_id``, return the *observatory ElementTree node*
(by looking in the Observatory spase file).
"""
obs_ids = [obs.find('{%s}ResourceID' % XMLNS).text for obs in spase_dic['Observatory']]
return spase_dic['Observatory'][obs_ids.index(observatory_id)]
def get_instrument(spase_dic: SpaseDic, instrument_id: str) -> ElTr.Element:
"""Given the ``instrument_id``, return the *instrument ElementTree node*,
by looking in the Instrument spase file.
"""
instru_ids = [instru.find('{%s}ResourceID' % XMLNS).text for instru in spase_dic['Instrument']]
return spase_dic['Instrument'][instru_ids.index(instrument_id)]
def get_access_format(numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing the access format (mime-type)."""
access_formats = set()
for access_info in numerical_data_node.findall('{%s}AccessInformation' % XMLNS):
spase_format_node = access_info.find('{%s}Format' % XMLNS)
if spase_format_node and spase_format_node.text:
access_formats.add(spase_format_node.text)
access_format = SEP.join(access_formats)
try:
return {'access_format': MIME_TYPE_LIST[access_format]}
except KeyError:
return {'access_format': None}
def get_region_info(numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing:
- **target_class**: the ```target_class`` EPN-TAP parameter;
- **target_name**: the ```target_name`` EPN-TAP parameter;
- **target_region**: the ``target_region`` EPN-TAP parameter.
- **spase_region**: the ``spase_region`` parameter, added to the EPN-TAP parameters for the purposes of AMDA.
"""
target_name = set()
target_class = set()
target_region = set()
spase_region = set()
obs_regions = numerical_data_node.findall('{%s}ObservedRegion' % XMLNS)
for target in [o_reg.text.split('.') for o_reg in obs_regions if o_reg.text is not None]:
offset = 1 if len(target) >= 2 and target[1] in TARGET_CLASS_DIC \
and TARGET_CLASS_DIC[target[1]] == 'satellite' else 0
target_class.add(TARGET_CLASS_DIC[target[offset]])
target_name.add(target[offset] if target[offset] != 'Heliosphere' else 'Sun')
target_region.add('.'.join(target[offset + 1:]))
spase_region.add('.'.join(target))
return {'target_class': SEP.join(target_class) if target_class else None,
'target_name': SEP.join(target_name) if target_name else None,
'target_region': SEP.join(target_region) if target_region else None,
'spase_region': SEP.join(spase_region) if spase_region else None}
def get_instru_name_and_host_name(spase_dic: SpaseDic, numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing:
- **instrument_name**: the ``instrument_name`` EPN-TAP parameter;
- **instrument_host_name**: the ``instrument_host_name`` EPN-TAP parameter.
"""
instru_names = set()
instru_host_names = set()
for instru_id in [i.text for i in numerical_data_node.findall('{%s}InstrumentID' % XMLNS)]:
instru = get_instrument(spase_dic, instru_id)
instru_names.add(instru.find('{%s}ResourceHeader' % XMLNS).find('{%s}ResourceName' % XMLNS).text)
observatory = get_observatory(spase_dic, instru.find('{%s}ObservatoryID' % XMLNS).text)
instru_host_names.add(observatory.find('{%s}ResourceHeader' % XMLNS).find('{%s}ResourceName' % XMLNS).text)
return {'instrument_name': SEP.join(instru_names) if instru_names else None,
'instrument_host_name': SEP.join(instru_host_names) if instru_host_names else None}
def get_types(numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing:
- **dataproduct_type**: the ``dataproduct_type`` EPN-TAP parameter;
- **spatial_frame_type**: the ``spatial_frame_type`` EPN-TAP parameter;
- **measurement_type**: the ``measurement_type`` EPN-TAP parameter.
- **spase_measurement_type**: the ``spase_measurement_type`` parameter,
added to the EPN-TAP parameters for the purposes of AMDA.
"""
with open('log', 'w') as f_out:
dataproduct_types = set()
sp_frame_types = set()
measurement_types = set()
spase_measurement_type = getattr(numerical_data_node.find('{%s}MeasurementType' % XMLNS), 'text', None)
for param in numerical_data_node.findall('{%s}Parameter' % XMLNS):
hints = param.findall('{%s}RenderingHints' % XMLNS)
dt_nodes = [hint.find('{%s}DisplayType' % XMLNS) for hint in hints]
for display in [display.text for display in dt_nodes if display is not None and display.text is not None]:
dataproduct_types.add(DATAPRODUCT_TYPE_DIC[display])
coord_sys = param.find('{%s}CoordinateSystem' % XMLNS)
if coord_sys is not None:
sp_frame_types.add(coord_sys.find('{%s}CoordinateRepresentation' % XMLNS).text.lower())
measurement_type = param.find('{%s}Ucd' % XMLNS)
if measurement_type is not None and measurement_type.text is not None:
f_out.write(measurement_type.text)
measurement_types.add(measurement_type.text)
return {'dataproduct_type': SEP.join(dataproduct_types) if dataproduct_types else None,
'spatial_frame_type': SEP.join(sp_frame_types) if sp_frame_types else None,
'measurement_type': SEP.join(measurement_types) if measurement_types else None,
'spase_measurement_type': spase_measurement_type}
def get_times_min_max(numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing:
- **time_sampling_step_min**: the ``time_sampling_step_min`` EPN-TAP parameter;
- **time_sampling_step_max**: the ``time_sampling_step_max`` EPN-TAP parameter;
- **time_exp_min**: the ``time_exp_min`` EPN-TAP parameter.
"""
temporal_description_node = numerical_data_node.find('{%s}TemporalDescription' % XMLNS)
if temporal_description_node is None:
return {'time_sampling_step_min': None, 'time_sampling_step_max': None, 'time_exp_min': None}
return {'time_sampling_step_min': str(xml_duration_to_seconds(getattr(temporal_description_node.find(
'{%s}%s' % (XMLNS, 'Cadence_Min')), 'text', None))),
'time_sampling_step_max': str(xml_duration_to_seconds(getattr(temporal_description_node.find(
'{%s}%s' % (XMLNS, 'Cadence_Max')), 'text', None))),
'time_exp_min': str(xml_duration_to_seconds(getattr(temporal_description_node.find(
'{%s}%s' % (XMLNS, 'Exposure')), 'text', None)))
}
def get_processing_lvl(numerical_data_node: ElTr.Element) -> SQLDic:
"""Given the ``NumericalData`` node, return a dictionary containing:
- **processing_level**: the ``processing_level`` EPN-TAP parameter;
"""
proc_lvl = getattr(numerical_data_node.find('{%s}ProcessingLevel' % XMLNS), 'text', None)
return {'processing_level': PROCESSING_LEVEL_DIC.get(proc_lvl, None)}
def get_granule_and_parent(gr_node: ElTr.Element) -> Tuple[str, SQLDic]:
"""Given a Granule node, return a dictionary containing all the parameters inside it:
- **obs_id**: the ``obs_id`` EPN-TAP parameter;
- **creation_date**: the ``creation_date`` EPN-TAP parameter;
- **release_date**: the ``release_date`` EPN-TAP parameter;
- **time_min**: the ``time_min`` EPN-TAP parameter;
- **time_max**: the ``time_max`` EPN-TAP parameter;
- **access_url**: the ``access_url`` EPN-TAP parameter;
- **access_estsize**: the ``access_estsize`` EPN-TAP parameter.
"""
parent_id = getattr(gr_node.find('{%s}ParentID' % XMLNS), 'text', None)
obs_id = getattr(gr_node.find('{%s}ResourceID' % XMLNS), 'text', '').split('/')[-1]
if not obs_id:
print('Can not get the ResourceID content of a granule. Exiting here.')
sys.exit()
release_date = getattr(gr_node.find('{%s}ReleaseDate' % XMLNS), 'text', None)
tim_min = xml_date_to_jd(getattr(gr_node.find('{%s}StartDate' % XMLNS), 'text', None))
time_max = xml_date_to_jd(getattr(gr_node.find('{%s}StopDate' % XMLNS), 'text', None))
src_n = gr_node.find('{%s}Source' % XMLNS)
access_url = getattr(src_n.find('{%s}URL' % XMLNS), 'text', None) if src_n else None
data_extent_node = src_n.find('{%s}DataExtent' % XMLNS) if src_n else None
access_estsize = getattr(data_extent_node.find('{%s}Quantity' % XMLNS), 'text', None)
return parent_id, {'obs_id': obs_id,
'release_date': release_date,
'time_min': tim_min,
'time_max': time_max,
'access_url': access_url,
'access_estsize': int(access_estsize) if access_estsize else None}
def xml_date_to_jd(xml_date: str) -> Optional[float]:
"""Convert a *XML date* to *Julian day*."""
try:
output_date = datetime.strptime(xml_date, XML_DATE_FORMAT)
except ValueError: # Date is not well formatted
return None
if output_date.month == 1 or output_date.month == 2:
year_p = output_date.year - 1
month_p = output_date.month + 12
else:
year_p = output_date.year
month_p = output_date.month
# this checks where we are in relation to October 15, 1582, the beginning
# of the Gregorian calendar.
if ((output_date.year < 1582) or
(output_date.year == 1582 and output_date.month < 10) or
(output_date.year == 1582 and output_date.month == 10 and output_date.day < 15)):
j_day = 0
else:
j_day = 2 - math.trunc(year_p / 100.) + math.trunc(math.trunc(year_p / 100.) / 4.)
j_day += math.trunc((365.25 * year_p) - 0.75) if year_p < 0 else math.trunc(365.25 * year_p)
j_day += math.trunc(30.6001 * (month_p + 1)) + output_date.day + 1720994.5
j_day += output_date.hour/24 + output_date.minute/1440 + output_date.second/86400
return j_day
def xml_date_to_sql_date(xml_date: str) -> str:
"""Convert a *XML date* to a *SQL date*."""
return datetime.strptime(xml_date, XML_DATE_FORMAT).strftime(SQL_DATE_FORMAT)
def xml_duration_to_seconds(xml_duration: str) -> int:
"""Convert a *XML duration* to seconds."""
if not xml_duration:
return 0
regex = re.compile(r'(?P<sign>-?)P(?:(?P<years>\d+)Y)?(?:(?P<months>\d+)M)?(?:(?P<days>\d+)D)?' +
r'(?:T(?:(?P<hours>\d+)H)?(?:(?P<minutes>\d+)M)?(?:(?P<seconds>\d+)S)?)?')
time = regex.match(xml_duration.upper()).groupdict(0)
delta = timedelta(
days=int(time['days']) + (int(time['months']) * 30) + (int(time['years']) * 365),
hours=int(time['hours']),
minutes=int(time['minutes']),
seconds=int(time['seconds']))
return (delta * -1 if time['sign'] == "-" else delta).total_seconds()
def get_parameters(spase_dic: SpaseDic) -> List[SQLDic]:
"""Get all the parameters of the entire dataset.
Return a list containing the granules, where each granule is a dictionary, with:
- **keys**: the EPN-TAP parameter name;
- **values**: the EPN-TAP value corresponding to the parameter name.
"""
datasets = {}
missing_parameters = {}
nb_elements = len(spase_dic['NumericalData']) + len(spase_dic['NumericalOutput']) + len(spase_dic['Granule'])
n_dataset = 0
for numerical_data_node in spase_dic['NumericalData'] + spase_dic['NumericalOutput']:
print('Dataset %d/%d' % (n_dataset, nb_elements), end=' ' * 99 + '\r')
n_dataset += 1
try:
dataset_key = getattr(numerical_data_node.find('{%s}ResourceID' % XMLNS), 'text', None).split('/')[-1]
except AttributeError:
print('Can not get the ResourceID content of a dataset. Exiting here.')
sys.exit()
dataset = get_region_info(numerical_data_node)
dataset.update(get_instru_name_and_host_name(spase_dic, numerical_data_node))
dataset.update(get_types(numerical_data_node))
dataset.update(get_access_format(numerical_data_node))
dataset.update(get_times_min_max(numerical_data_node))
dataset.update(get_processing_lvl(numerical_data_node))
# Looking for None parameters in each dataset
for parameter, default_value in DEFAULT_DATASET_VALUES.items():
if not dataset[parameter]:
dataset[parameter] = default_value
if dataset_key not in missing_parameters:
missing_parameters[dataset_key] = set()
missing_parameters[dataset_key].add(parameter)
datasets[dataset_key] = dataset
granules_list = []
for granule_node in spase_dic['Granule']:
parent_id, granule = get_granule_and_parent(granule_node)
dataset_key = parent_id.split('/')[-1]
print('Granule {:<23.23} {:<18.18} [{:<50.50}]'.format(
'%d/%d (%.2f%%)' % (n_dataset + 1, nb_elements, 100 * float(n_dataset + 1) / nb_elements),
dataset_key,
'.' * int((n_dataset + 1) / nb_files * 50)), end='\r')
# Looking for None parameters in each granule
for parameter, default_value in DEFAULT_GRANULE_VALUES.items():
if not granule[parameter]:
granule[parameter] = default_value
if dataset_key not in missing_parameters:
missing_parameters[dataset_key] = set()
missing_parameters[dataset_key].add(parameter)
try:
granule.update(datasets[dataset_key])
except KeyError:
print('The parent id "%s" of the granule "%s" is not found in the dataset dictionary.'
% (parent_id, granule['access_url']))
granules_list.append(granule)
n_dataset += 1
print()
for bad_dataset, missings in missing_parameters.items():
log('%s\tmissing %s' % (bad_dataset, ', '.join(missings)))
return granules_list
def write_sql(granules_list):
"""Write a SQL script which insert all the granules in the database."""
with open(OUTPUT_SQL_FILE_PATH, 'w') as sql_file:
sql_file.write(SQL_HEADER)
for gr in granules_list:
keys = ', '.join(gr.keys())
values = ', '.join(['NULL' if param is None else "'%s'" % param if isinstance(param, str) else
str(param) for param in gr.values()])
sql_file.write(SQL_ROW % (keys, values))
sql_file.write(SQL_FOOTER)
if __name__ == '__main__':
log_file = open(LOG_FILE_PATH, 'w+') if LOG_FILE_PATH else None
print('Getting number of files in %s...' % SPASE_DIR)
nb_files = get_nb_files()
print('Parsing %d files...' % nb_files)
spase = get_spase()
print('Done. Found these types of data: %s.' % ', '.join([key for (key, val) in spase.items()]))
print('Loading numerical data...')
granules = get_parameters(spase)
print('Creating SQL script...')
write_sql(granules)
import subprocess
subprocess.Popen(['notify-send', 'The SQL script %s has been generated.' % OUTPUT_SQL_FILE_PATH])