astronomical_archives: astronomical

comparison astronomical_archives.py @ 1:667fc28d803c draft

planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ commit f9ba105adfaad1b2a16dd570652aa27c508d3c4d

author	astroteam
date	Tue, 24 Oct 2023 06:38:22 +0000
parents	0ddfc343f9f9
children	7398ea3d9ac4

comparison

equal deleted inserted replaced

-:0ddfc343f9f9
+:667fc28d803c
+import errno
+import functools
 import json
 import os
+import signal
 import sys
 import urllib
 from urllib import request
+from astropy.coordinates import SkyCoord
 import pyvo
 from pyvo import DALAccessError, DALQueryError, DALServiceError
 from pyvo import registry
 MAX_ALLOWED_ENTRIES = 100
 MAX_REGISTRIES_TO_SEARCH = 100
+class TimeoutException(Exception):
+pass
+def timeout(seconds=10, error_message=os.strerror(errno.ETIME)):
+def decorator(func):
+def _handle_timeout(signum, frame):
+raise TimeoutException(error_message)
+@functools.wraps(func)
+def wrapper(*args, **kwargs):
+signal.signal(signal.SIGALRM, _handle_timeout)
+signal.alarm(seconds)
+try:
+result = func(*args, **kwargs)
+finally:
+signal.alarm(0)
+return result
+return wrapper
+return decorator
 class Service:
 # https://pyvo.readthedocs.io/en/latest/api/pyvo.registry.Servicetype.html
 self.access_url = access_url
 self.initialized = False
 self.archive_service = None
 self.tables = None
+@timeout(10)
 def get_resources(self,
 query,
 number_of_results,
 url_field='access_url'):
 name = 'Unknown archive title'
 return name
+class ConeService(TapArchive):
+def _get_service(self):
+if self.access_url:
+self.archive_service = pyvo.dal.SCSService(self.access_url)
+def get_resources_from_service_list(self, service_list, target, radius):
+resource_list_hydrated = []
+for service in service_list:
+resources = service.search(target, radius)
+for i in range(resources.__len__()):
+resource_url = resources.getrecord(i).getdataurl()
+if resource_url:
+resource_list_hydrated.append(resource_url)
+return resource_list_hydrated
 class RegistrySearchParameters:
 def __init__(self, keyword=None, waveband=None, service_type=None):
 self.keyword = keyword
 self.waveband = waveband
 ivoa_registry.access_url)
 archive_list.append(archive)
 return archive_list
+class ConeServiceRegistry:
+def __init__(self):
+pass
+@staticmethod
+def search_services(keyword, number_of_registries):
+service_list = []
+service_list = registry.search(servicetype="scs", keywords=keyword)
+if service_list:
+service_list = service_list[:number_of_registries]
+return service_list
 class TapQuery:
 def __init__(self, query):
 self._output_html = output_html
 self._output_basic_html = output_basic_html
 self._output_error = output_error
 self._set_run_main_parameters()
 self._is_initialised, error_message = self._set_archive()
 if self._is_initialised and error_message is None:
 self._set_query()
 self._set_output()
 " parameters could be initialized"
 else:
 return False, error_message
-def _set_query(self):
+def _set_cone_service(self):
 qs = 'query_section'
 qsl = 'query_selection'
+csts = 'cone_search_target_selection'
+error_message = None
+is_service_initialised = True
+keyword = self._json_parameters[qs][qsl][csts]['keyword']
+service_list = ConeServiceRegistry.search_services(
+keyword,
+MAX_REGISTRIES_TO_SEARCH)
+if len(service_list) >= 1:
+self._services = service_list
+else:
+is_service_initialised = False
+error_message = "no services matching search parameters"
+Logger.create_action_log(
+Logger.ACTION_ERROR,
+Logger.ACTION_TYPE_ARCHIVE_CONNECTION,
+error_message)
+return is_service_initialised, error_message
+def _set_query(self):
+qs = 'query_section'
+qsl = 'query_selection'
+csts = 'cone_search_target_selection'
+cs = 'cone_section'
+ts = 'target_selection'
+con = 'cone_object_name'
 if self._query_type == 'obscore_query':
 dataproduct_type = \
 self._json_parameters[qs][qsl]['dataproduct_type']
 t_max = \
 self._json_parameters[qs][qsl]['t_max']
 order_by = \
 self._json_parameters[qs][qsl]['order_by']
+if self._json_parameters[qs][qsl][cs][csts][ts] == 'coordinates':
+ra = self._json_parameters[qs][qsl][cs][csts]['ra']
+dec = self._json_parameters[qs][qsl][cs][csts]['dec']
+else:
+obs_target = self._json_parameters[qs][qsl][cs][csts][con]
+if obs_target != 'none' and obs_target is not None:
+target = CelestialObject(obs_target)
+target_coordinates = target.get_coordinates_in_degrees()
+ra = target_coordinates['ra']
+dec = target_coordinates['dec']
+else:
+ra = None
+dec = None
+radius = self._json_parameters[qs][qsl][cs]['radius']
+if (ra != '' and ra is not None)\
+and (dec != '' and dec is not None)\
+and (radius != '' and radius is not None):
+cone_condition = \
+ADQLConeSearchQuery.get_search_circle_condition(ra,
+dec,
+radius)
+else:
+cone_condition = None
 obscore_query_object = ADQLObscoreQuery(dataproduct_type,
 obs_collection,
 obs_title,
 obs_id,
 facility_name,
 obs_publisher_id,
 s_fov,
 calibration_level,
 t_min,
 t_max,
+cone_condition,
 order_by)
 self._adql_query = obscore_query_object.get_query()
 elif self._query_type == 'raw_query':
 tap_table,
 where_field,
 where_condition)
 else:
 self._adql_query = ADQLObscoreQuery.base_query
+def _set_cone_query(self):
+qs = 'query_section'
+qsl = 'query_selection'
+csts = 'cone_search_target_selection'
+ts = 'target_selection'
+con = 'cone_object_name'
+search_radius = self._json_parameters[qs][qsl]['radius']
+time = None
+if self._json_parameters[qs][qsl][csts][ts] == 'coordinates':
+ra = self._json_parameters[qs][qsl][csts]['ra']
+dec = self._json_parameters[qs][qsl][csts]['dec']
+time = self._json_parameters[qs][qsl][csts]['time']
+else:
+target = CelestialObject(self._json_parameters[qs][qsl][csts][con])
+target_coordinates = target.get_coordinates_in_degrees()
+ra = target_coordinates['ra']
+dec = target_coordinates['dec']
+cone_query_object = ADQLConeSearchQuery(ra, dec, search_radius, time)
+self._adql_query = cone_query_object.get_query()
 def _set_output(self):
 self._number_of_files = \
 int(
 self._json_parameters['output_section']['number_of_files']
 archive_name = self._archives[0].get_archive_name(
 self._archive_type)
 for archive in self._archives:
-_file_url, error_message = archive.get_resources(
+try:
-self._adql_query,
+_file_url, error_message = archive.get_resources(
-self._number_of_files,
+self._adql_query,
-self._url_field)
+self._number_of_files,
+self._url_field)
-file_url.extend(_file_url)
+file_url.extend(_file_url)
+except TimeoutException:
+error_message = \
+"Archive is taking too long to respond (timeout)"
+Logger.create_action_log(
+Logger.ACTION_ERROR,
+Logger.ACTION_TYPE_ARCHIVE_CONNECTION,
+error_message)
 if len(file_url) >= int(self._number_of_files):
 file_url = file_url[:int(self._number_of_files)]
 break
 else:
 summary_file += error_message
 FileHandler.write_file_to_output(summary_file,
 self._output_error)
 else:
 summary_file = Logger.create_log_file("Archive",
 self._adql_query)
-summary_file += "Unable to initialize archive"
+summary_file += "Unable to initialize archives"
 FileHandler.write_file_to_output(summary_file,
 self._output_error)
 obs_publisher_id,
 s_fov,
 calibration_level,
 t_min,
 t_max,
+cone_condition,
 order_by):
 super().__init__()
 if calibration_level == 'none':
 if em_max == 'None' or em_max is None:
 em_max = ''
 if dataproduct_type == 'none' or dataproduct_type is None:
 dataproduct_type = ''
+if cone_condition is not None:
+self.cone_condition = cone_condition
+else:
+self.cone_condition = None
 self.parameters = {
 'dataproduct_type': dataproduct_type,
 'obs_collection': obs_collection,
 'obs_title': obs_title,
 'em_min': em_min,
 'em_max': em_max,
 'target_name': target_name,
 'obs_publisher_id': obs_publisher_id,
 's_fov': s_fov,
-'calibration_level': calibration_level,
+'calib_level': calibration_level,
 't_min': t_min,
-'t_max': t_max
+'t_max': t_max,
 }
 self.order_by = order_by
 def get_query(self):
 obscore_order_type = ADQLObscoreQuery.order_by_field[order_type]
 return super()._get_order_by_clause(obscore_order_type)
 def get_where_statement(self):
-return self._get_where_clause(self.parameters)
+where_clause = self._get_where_clause(self.parameters)
+if where_clause == '' and self.cone_condition is not None:
+where_clause = 'WHERE ' + self.get_cone_condition()
+elif where_clause != '' and self.cone_condition is not None:
+where_clause += 'AND ' + self.get_cone_condition()
+return where_clause
 def _get_where_clause(self, parameters):
 return super()._get_where_clause(parameters)
+def get_cone_condition(self):
+return self.cone_condition
 class ADQLTapQuery(BaseADQLQuery):
 base_query = 'SELECT TOP '+str(MAX_ALLOWED_ENTRIES)+' * FROM '
 ' WHERE ' + \
 str(where_field) + ' = ' + '\'' + \
 str(where_condition) + '\''
 else:
 return ADQLTapQuery.base_query + str(table)
+class ADQLConeSearchQuery:
+base_query = "SELECT TOP 100 * FROM ivoa.obscore"
+def __init__(self, ra, dec, radius, time=None):
+self.ra = ra
+self.dec = dec
+self.radius = radius
+self.time = time
+self._query = ADQLObscoreQuery.base_query
+if self.ra and self.dec and self.radius:
+self._query += " WHERE "
+self._query += self._get_search_circle(ra, dec, radius)
+if self.time:
+self._query += self._get_search_time()
+def _get_search_circle(self, ra, dec, radius):
+return "(CONTAINS" \
+"(POINT('ICRS', s_ra, s_dec), " \
+"CIRCLE('ICRS', "+str(ra)+", "+str(dec)+", "+str(radius)+")" \
+") = 1)"
+def _get_search_time(self):
+return " AND t_min <= "+self.time+" AND t_max >= "+self.time
+def get_query(self):
+return self._query
+@staticmethod
+def get_search_circle_condition(ra, dec, radius):
+return "(CONTAINS" \
+"(POINT('ICRS', s_ra, s_dec)," \
+"CIRCLE('ICRS', "+str(ra)+", "+str(dec)+", "+str(radius)+")" \
+") = 1) "
+class CelestialObject:
+def __init__(self, name):
+self.name = name
+self.coordinates = None
+self.coordinates = SkyCoord.from_name(self.name)
+def get_coordinates_in_degrees(self):
+coordinates = {
+'ra': '',
+'dec': ''
+}
+ra_dec = self.coordinates.ravel()
+coordinates['ra'] = ra_dec.ra.degree[0]
+coordinates['dec'] = ra_dec.dec.degree[0]
+return coordinates
 class HTMLReport:
 _html_report_base_header = ''
 _html_report_base_body = ''

Mercurial > repos > astroteam > astronomical_archives

comparison astronomical_archives.py @ 1:667fc28d803c draft