def get_investigations_for_instrument_in_facility_cycle(
client, instrument_id, facilitycycle_id, filters, count_query=False,
):
"""
Given Instrument and Facility Cycle IDs, get investigations that use the given
instrument in the given cycle
:param client: ICAT client containing an authenticated user
:type client: :class:`icat.client.Client`
:param instrument_id: ID of the instrument from the request
:type instrument_id: :class:`int`
:param facilitycycle_id: ID of the facilityCycle from the request
:type facilitycycle_id: :class:`int`
:param filters: The list of filters to be applied to the request
:type filters: List of specific implementations :class:`QueryFilter`
:param count_query: Flag to determine if the query in this function should be used
as a count query. Used for
`get_investigations_for_instrument_in_facility_cycle_count()`
:type count_query: :class:`bool`
:return: A list of Investigations that match the query
"""
log.info(
"Getting a list of investigations from the specified instrument and facility"
" cycle, for ISIS",
)
query_aggregate = "COUNT:DISTINCT" if count_query else "DISTINCT"
query = ICATQuery(client, "Investigation", aggregate=query_aggregate)
query.isis_endpoint = True
instrument_id_check = PythonICATWhereFilter(
"facility.instruments.id", instrument_id, "eq",
)
investigation_instrument_id_check = PythonICATWhereFilter(
"investigationInstruments.instrument.id", instrument_id, "eq",
)
facility_cycle_id_check = PythonICATWhereFilter(
"facility.facilityCycles.id", facilitycycle_id, "eq",
)
facility_cycle_start_date_check = PythonICATWhereFilter(
"facility.facilityCycles.startDate", "o.startDate", "lte",
)
facility_cycle_end_date_check = PythonICATWhereFilter(
"facility.facilityCycles.endDate", "o.startDate", "gte",
)
required_filters = [
instrument_id_check,
investigation_instrument_id_check,
facility_cycle_id_check,
facility_cycle_start_date_check,
facility_cycle_end_date_check,
]
filters.extend(required_filters)
filter_handler = FilterOrderHandler()
filter_handler.manage_icat_filters(filters, query.query)
data = query.execute_query(client, True)
return data
def get_count_with_filters(client, entity_type, filters):
"""
Get the number of results of a given entity, based on the filters provided in the
request. This acts very much like `get_entity_with_filters()` but returns the number
of results, as opposed to a JSON object of data.
:param client: ICAT client containing an authenticated user
:type client: :class:`icat.client.Client`
:param entity_type: The type of entity requested to manipulate data with
:type entity_type: :class:`str`
:param filters: The list of filters to be applied to the request
:type filters: List of specific implementations :class:`QueryFilter`
:return: The number of records of the given entity (of type integer), using the
filters to restrict the result of the query
"""
log.info(
"Getting the number of results of %s, also using the request's filters",
entity_type,
)
query = ICATQuery(client, entity_type, aggregate="COUNT")
filter_handler = FilterOrderHandler()
filter_handler.manage_icat_filters(filters, query.query)
data = query.execute_query(client, True)
# Only ever 1 element in a count query result
return data[0]
def test_add_filter(self, icat_query):
test_handler = FilterOrderHandler()
test_filter = PythonICATWhereFilter("id", 2, "eq")
test_handler.add_filter(test_filter)
assert test_handler.filters == [test_filter]
def test_add_filters(self):
test_handler = FilterOrderHandler()
id_filter = PythonICATWhereFilter("id", 2, "eq")
name_filter = PythonICATWhereFilter("name", "New Name", "like")
filter_list = [id_filter, name_filter]
test_handler.add_filters(filter_list)
assert test_handler.filters == filter_list
def test_invalid_field(self, icat_query):
test_filter = PythonICATOrderFilter("unknown_field", "DESC")
filter_handler = FilterOrderHandler()
filter_handler.add_filter(test_filter)
with pytest.raises(FilterError):
filter_handler.apply_filters(icat_query)
filter_handler.clear_python_icat_order_filters()
def test_filter_applied_to_query(self, icat_query):
test_filter = PythonICATOrderFilter("id", "DESC")
filter_handler = FilterOrderHandler()
filter_handler.add_filter(test_filter)
filter_handler.apply_filters(icat_query)
assert icat_query.order == [("id", "DESC")]
filter_handler.clear_python_icat_order_filters()
def test_result_order_appended(self, icat_query):
id_filter = PythonICATOrderFilter("id", "ASC")
title_filter = PythonICATOrderFilter("title", "DESC")
filter_handler = FilterOrderHandler()
filter_handler.add_filters([id_filter, title_filter])
filter_handler.apply_filters(icat_query)
assert PythonICATOrderFilter.result_order == [("id", "ASC"),
("title", "DESC")]
filter_handler.clear_python_icat_order_filters()
def get_rows_by_filter(table, filters):
"""
Given a list of filters supplied in json format, returns entities that match the
filters from the given table
:param table: The table to checked
:param filters: The list of filters to be applied
:return: A list of the rows returned in dictionary form
"""
with ReadQuery(table) as query:
filter_handler = FilterOrderHandler()
return get_filtered_read_query_results(filter_handler, filters, query)
def get_facility_cycles_for_instrument(instrument_id, filters):
"""
Given an instrument_id get facility cycles where the instrument has investigations
that occur within that cycle
:param filters: The filters to be applied to the query
:param instrument_id: The id of the instrument
:return: A list of facility cycle entities
"""
with InstrumentFacilityCyclesQuery(instrument_id) as query:
filter_handler = FilterOrderHandler()
return get_filtered_read_query_results(filter_handler, filters, query)
def test_limit_and_skip_merge_correctly(self, icat_query, skip_value, limit_value):
"""
Skip and limit values are set together in Python ICAT, limit value should match
max entities allowed in one transaction in ICAT as defined in ICAT properties
"""
skip_filter = PythonICATSkipFilter(skip_value)
limit_filter = PythonICATLimitFilter(limit_value)
filter_handler = FilterOrderHandler()
filter_handler.add_filters([skip_filter, limit_filter])
filter_handler.merge_python_icat_limit_skip_filters()
filter_handler.apply_filters(icat_query)
assert icat_query.limit == (skip_value, limit_value)
def test_invalid_direction(self, icat_query):
test_filter = PythonICATOrderFilter("id", "up")
filter_handler = FilterOrderHandler()
filter_handler.add_filter(test_filter)
with pytest.raises(FilterError):
filter_handler.apply_filters(icat_query)
def test_remove_filter(self):
test_filter = PythonICATWhereFilter("id", 2, "eq")
test_handler = FilterOrderHandler()
test_handler.add_filter(test_filter)
test_handler.remove_filter(test_filter)
assert test_handler.filters == []
def get_entity_with_filters(client, entity_type, filters):
"""
Gets all the records of a given entity, based on the filters provided in the request
:param client: ICAT client containing an authenticated user
:type client: :class:`icat.client.Client`
:param entity_type: The type of entity requested to manipulate data with
:type entity_type: :class:`str`
:param filters: The list of filters to be applied to the request
:type filters: List of specific implementations :class:`QueryFilter`
:return: The list of records of the given entity, using the filters to restrict the
result of the query
"""
log.info("Getting entity using request's filters")
query = ICATQuery(client, entity_type)
filter_handler = FilterOrderHandler()
filter_handler.manage_icat_filters(filters, query.query)
data = query.execute_query(client, True)
return data
def test_multiple_conditions_per_field(self, icat_query):
lt_filter = PythonICATWhereFilter("id", 10, "lt")
gt_filter = PythonICATWhereFilter("id", 5, "gt")
filter_handler = FilterOrderHandler()
filter_handler.add_filters([lt_filter, gt_filter])
filter_handler.apply_filters(icat_query)
assert icat_query.conditions == {"id": ["< '10'", "> '5'"]}
def test_sort_filters(self):
limit_filter = PythonICATLimitFilter(10)
where_filter = PythonICATWhereFilter("id", 2, "eq")
test_handler = FilterOrderHandler()
test_handler.add_filters([limit_filter, where_filter])
test_handler.sort_filters()
assert test_handler.filters == [where_filter, limit_filter]
def test_apply_filters(self, icat_query):
where_filter = PythonICATWhereFilter("id", 2, "eq")
limit_filter = PythonICATLimitFilter(10)
test_handler = FilterOrderHandler()
test_handler.add_filters([where_filter, limit_filter])
test_handler.apply_filters(icat_query)
assert icat_query.conditions == {"id": "= '2'"} and icat_query.limit == (0, 10)
def test_direction_is_uppercase(self, icat_query):
"""Direction must be uppercase for Python ICAT to see the input as valid"""
test_filter = PythonICATOrderFilter("id", "asc")
filter_handler = FilterOrderHandler()
filter_handler.add_filter(test_filter)
assert test_filter.direction == "ASC"
filter_handler.clear_python_icat_order_filters()
def get_facility_cycles_for_instrument_count(instrument_id, filters):
"""
Given an instrument_id get the facility cycles count where the instrument has
investigations that occur within that cycle
:param filters: The filters to be applied to the query
:param instrument_id: The id of the instrument
:return: The count of the facility cycles
"""
with InstrumentFacilityCyclesCountQuery(instrument_id) as query:
filter_handler = FilterOrderHandler()
filter_handler.add_filters(filters)
filter_handler.apply_filters(query)
return query.get_count()
def get_filtered_row_count(table, filters):
"""
returns the count of the rows that match a given filter in a given table
:param table: the table to be checked
:param filters: the filters to be applied to the query
:return: int: the count of the rows
"""
log.info(" getting count for %s", table.__tablename__)
with CountQuery(table) as count_query:
filter_handler = FilterOrderHandler()
filter_handler.add_filters(filters)
filter_handler.apply_filters(count_query)
return count_query.get_count()
def get_investigations_for_instrument_in_facility_cycle(
instrument_id,
facility_cycle_id,
filters,
):
"""
Given an instrument id and facility cycle id, get investigations that use the given
instrument in the given cycle
:param filters: The filters to be applied to the query
:param instrument_id: The id of the instrument
:param facility_cycle_id: the ID of the facility cycle
:return: The investigations
"""
filter_handler = FilterOrderHandler()
with InstrumentFacilityCycleInvestigationsQuery(
instrument_id,
facility_cycle_id,
) as query:
return get_filtered_read_query_results(filter_handler, filters, query)
def get_investigations_for_instrument_in_facility_cycle_count(
instrument_id,
facility_cycle_id,
filters,
):
"""
Given an instrument id and facility cycle id, get the count of the investigations
that use the given instrument in the given cycle
:param filters: The filters to be applied to the query
:param instrument_id: The id of the instrument
:param facility_cycle_id: the ID of the facility cycle
:return: The investigations count
"""
with InstrumentFacilityCycleInvestigationsCountQuery(
instrument_id,
facility_cycle_id,
) as query:
filter_handler = FilterOrderHandler()
filter_handler.add_filters(filters)
filter_handler.apply_filters(query)
return query.get_count()
def test_remove_not_added_filter(self):
test_handler = FilterOrderHandler()
test_filter = PythonICATWhereFilter("id", 2, "eq")
with pytest.raises(ValueError):
test_handler.remove_filter(test_filter)
