def test_searches_parsers_params_parser_get_must_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&files.file_type!=fastq&field=status&type=*')
p = ParamsParser(dummy_request)
assert p.get_must_filters() == [('type', 'Experiment'), ('type', 'File'),
('field', 'status')]
def test_searches_parsers_params_parser_get_field_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&field=status&type!=Item'
'&searchTerm=my+favorite+experiment&searchTerm=my+other+experiment')
p = ParamsParser(dummy_request)
assert p.get_field_filters() == [('field', 'status')]
def test_searches_parsers_params_parser_get_query_string(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=File&file_format%21=bigWig&file_type%21=bigBed+tss_peak'
'&file_format_type=bed3%2B')
p = ParamsParser(dummy_request)
assert dummy_request.environ['QUERY_STRING'] == p.get_query_string()
def test_searches_parsers_params_parser_get_wildcard_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'status=released&type=*&file_format%21=*'
'&file_type%21=bigBed+tss_peak&file_format_type=bed3%2B')
p = ParamsParser(dummy_request)
assert p.get_wildcard_filters() == [('type', '*'), ('file_format!', '*')]
def test_searches_parsers_params_parser_get_debug(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'frame=embedded&status!=submitted&type=File&sort=date_created&debug=true'
)
p = ParamsParser(dummy_request)
assert p.get_debug() == [('debug', 'true')]
def test_searches_parsers_params_parser_get_advanced_query_filters_empty(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&field=status&type!=Item')
p = ParamsParser(dummy_request)
assert p.get_advanced_query_filters() == []
def test_searches_parsers_params_parser_get_not_exists_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&files.file_type!=fastq'
'&field=status&type=*&file_size!=*')
p = ParamsParser(dummy_request)
assert p.get_not_exists_filters() == [('file_size!', '*')]
def test_searches_parsers_params_parser_get_key_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&status=archived&type!=Item&status!=released'
)
p = ParamsParser(dummy_request)
assert p.get_key_filters(key='status') == [('status', 'archived'),
('status!', 'released')]
def test_searches_parsers_params_parser_is_param(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&files.file_type=fastq&field=status')
p = ParamsParser(dummy_request)
assert p.is_param(key='type', value='File')
assert p.is_param(key='files.file_type', value='fastq')
assert not p.is_param(key='files.file_type', value='bam')
def test_searches_parsers_params_parser_param_remove_not_flag(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'frame=embedded&status!=submitted&type=File&sort=date_created')
p = ParamsParser(dummy_request)
assert p.remove_not_flag() == [('frame', 'embedded'),
('status', 'submitted'), ('type', 'File'),
('sort', 'date_created')]
def test_searches_parsers_params_parser_get_mode(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'frame=embedded&status!=submitted&mode=picker&type=File&sort=date_created'
)
p = ParamsParser(dummy_request)
assert p.get_mode() == [('mode', 'picker')]
assert p.param_values_to_list(params=p.get_mode())[0] == 'picker'
def test_searches_parsers_params_parser_get_filters_by_condition_value_status(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ[
'QUERY_STRING'] = 'type=Experiment&type=File&field=status'
p = ParamsParser(dummy_request)
assert p.get_filters_by_condition(
key_and_value_condition=lambda _, v: v == 'status') == [('field',
'status')]
def test_searches_parsers_params_parser_params_coerce_value_to_int_or_return_none(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'frame=embedded&status!=submitted&type=File&sort=date_created')
p = ParamsParser(dummy_request)
assert p.coerce_value_to_int_or_return_none('12') == 12
assert p.coerce_value_to_int_or_return_none(12) == 12
assert p.coerce_value_to_int_or_return_none('all') is None
def test_searches_parsers_params_parser_get_must_not_match_advanced_query_filters(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&field=status&type!=Item'
'&advancedQuery!=whatever')
p = ParamsParser(dummy_request)
assert p.get_must_not_match_advanced_query_filters() == [('advancedQuery!',
'whatever')]
def test_searches_parsers_params_parser_get_filters_by_condition_none(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ[
'QUERY_STRING'] = 'type=Experiment&type=File&field=status'
p = ParamsParser(dummy_request)
assert p.get_filters_by_condition() == [('type', 'Experiment'),
('type', 'File'),
('field', 'status')]
def test_searches_parsers_params_parser_get_advanced_query_filters(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&field=status&type!=Item'
'&advancedQuery=my+favorite+experiment&searchTerm=my+other+experiment'
'&searchTerm!=whatever')
p = ParamsParser(dummy_request)
assert p.get_advanced_query_filters() == [('advancedQuery',
'my favorite experiment')]
def test_searches_parsers_params_parser_get_keys_filters(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=File&file_format%21=bigWig&file_type%21=bigBed+tss_peak'
'&file_format_type=bed3%2B')
p = ParamsParser(dummy_request)
assert p.get_keys_filters(['type', 'file_format_type'
]) == [('type', 'File'),
('file_format_type', 'bed3+')]
assert p.get_keys_filters() == []
def test_searches_parsers_params_parser_get_filters_by_condition_contains_letter(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ[
'QUERY_STRING'] = 'type=Experiment&type=File&field=status'
p = ParamsParser(dummy_request)
assert p.get_filters_by_condition(
key_and_value_condition=lambda k, v: 't' in k and 'F' in v) == [
('type', 'File')
]
def test_searches_responses_fielded_response_is_request_from_embed(
dummy_request):
from snovault.elasticsearch.searches.responses import FieldedResponse
from snovault.elasticsearch.searches.parsers import ParamsParser
fr = FieldedResponse()
assert not fr._is_request_from_embed()
fr = FieldedResponse(_meta={'params_parser': ParamsParser(dummy_request)})
assert not fr._is_request_from_embed()
dummy_request.__parent__ = 'something'
fr = FieldedResponse(_meta={'params_parser': ParamsParser(dummy_request)})
assert fr._is_request_from_embed()
def test_searches_parsers_params_parser_param_values_to_list(dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'frame=embedded&status!=submitted&type=File&sort=date_created')
p = ParamsParser(dummy_request)
assert p.param_values_to_list() == [
'embedded',
'submitted',
'File',
'date_created',
]
def test_searches_parsers_params_parser_get_must_match_advanced_query_filters(
dummy_request):
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=Experiment&type=File&field=status&type!=Item'
'&advancedQuery=date_created:[01/01/2018 TO 01/02/2019]'
'&advancedQuery=@type:Experiment date_released:[2009-01-01 TO 2019-12-31]'
'&searchTerm=whatever')
p = ParamsParser(dummy_request)
assert p.get_must_match_advanced_query_filters() == [
('advancedQuery', 'date_created:[01/01/2018 TO 01/02/2019]'),
('advancedQuery',
'@type:Experiment date_released:[2009-01-01 TO 2019-12-31]')
]
def test_searchers_parsers_params_parser_split_filters_by_must_and_exists(
dummy_request):
from snovault.elasticsearch.searches.defaults import NOT_FILTERS
from snovault.elasticsearch.searches.parsers import ParamsParser
dummy_request.environ['QUERY_STRING'] = (
'type=*&status=released&status!=submitted&type=File&file_size=*'
'&file_format%21=bigWig&restricted!=*&no_file_available!=*&limit=all')
p = ParamsParser(dummy_request)
must, must_not, exists, not_exists = p.split_filters_by_must_and_exists(
params=p.get_not_keys_filters(not_keys=NOT_FILTERS) +
p.get_type_filters())
assert must == [('status', 'released'), ('type', 'File')]
assert must_not == [('status!', 'submitted'), ('file_format!', 'bigWig')]
assert exists == [('file_size', '*'), ('type', '*')]
assert not_exists == [('restricted!', '*'), ('no_file_available!', '*')]
def test_searches_responses_fielded_response_should_stream_response(
dummy_request):
from snovault.elasticsearch.searches.responses import FieldedResponse
from snovault.elasticsearch.searches.parsers import ParamsParser
fr = FieldedResponse()
assert not fr._should_stream_response()
fr = FieldedResponse(_meta={'params_parser': ParamsParser(dummy_request)})
assert not fr._should_stream_response()
fr.response = {'a': (x for x in [1, 2, 3])}
assert fr._should_stream_response()
dummy_request.__parent__ = 'something'
fr = FieldedResponse(_meta={'params_parser': ParamsParser(dummy_request)})
assert not fr._should_stream_response()
fr.response = {'a': (x for x in [1, 2, 3])}
assert not fr._should_stream_response()
def cart_search(context, request):
'''
Like search but takes cart params.
'''
# Note the order of rendering matters for some fields, e.g. AllResponseField and
# NotificationResponseField depend on results from CartSearchWithFacetsResponseField.
fr = FieldedResponse(_meta={'params_parser': ParamsParser(request)},
response_fields=[
TitleResponseField(title='Cart search'),
TypeResponseField(at_type=[SEARCH_TITLE]),
IDResponseField(),
ContextResponseField(),
CartSearchWithFacetsResponseField(
default_item_types=DEFAULT_ITEM_TYPES,
cart=CartWithElements(request),
),
AllResponseField(),
NotificationResponseField(),
CartFiltersResponseField(),
ClearFiltersResponseFieldWithCarts(),
ColumnsResponseField(),
SortResponseField(),
DebugQueryResponseField()
])
return fr.render()
def matrixv2_raw(context, request):
fr = FieldedResponse(_meta={'params_parser': ParamsParser(request)},
response_fields=[
RawMatrixWithAggsResponseField(
default_item_types=DEFAULT_ITEM_TYPES)
])
return fr.render()
def search(context, request):
# Note the order of rendering matters for some fields, e.g. AllResponseField and
# NotificationResponseField depend on results from BasicSearchWithFacetsResponseField.
fr = FieldedResponse(
_meta={
'params_parser': ParamsParser(request)
},
response_fields=[
TitleResponseField(
title=SEARCH_TITLE
),
TypeResponseField(
at_type=[SEARCH_TITLE]
),
IDResponseField(),
ContextResponseField(),
BasicSearchWithFacetsResponseField(
default_item_types=DEFAULT_ITEM_TYPES
),
AllResponseField(),
NotificationResponseField(),
FiltersResponseField(),
ClearFiltersResponseField(),
ColumnsResponseField(),
SortResponseField(),
DebugQueryResponseField()
]
)
return fr.render()
def audit(context, request):
fr = FieldedResponse(
_meta={
'params_parser': ParamsParser(request)
},
response_fields=[
TitleResponseField(
title=AUDIT_TITLE
),
TypeResponseField(
at_type=[AUDIT_TITLE]
),
IDResponseField(),
SearchBaseResponseField(),
ContextResponseField(),
AuditMatrixWithFacetsResponseField(
default_item_types=DEFAULT_ITEM_TYPES
),
NotificationResponseField(),
FiltersResponseField(),
TypeOnlyClearFiltersResponseField(),
DebugQueryResponseField()
]
)
return fr.render()
def test_searches_responses_fielded_generator_response_render(dummy_request):
from snovault.elasticsearch.searches.responses import FieldedGeneratorResponse
from snovault.elasticsearch.searches.responses import GeneratorResponse
from snovault.elasticsearch.searches.parsers import ParamsParser
from types import GeneratorType
from pyramid.response import Response
fgr = FieldedGeneratorResponse()
fgr.response = {'a': 1}
response = fgr.render()
assert isinstance(response, dict)
fgr.response = {'a': (x for x in [1, 2, 3])}
response = fgr.render()
assert isinstance(response, dict)
assert 'a' in response
assert isinstance(response['a'], GeneratorType)
assert list(response['a']) == [1, 2, 3]
dummy_request.__parent__ = 'something'
fgr = FieldedGeneratorResponse(
_meta={'params_parser': ParamsParser(dummy_request)})
fgr.response = {'a': (x for x in [1, 2, 3])}
response = fgr.render()
assert isinstance(response, dict)
assert 'a' in response
assert isinstance(response['a'], GeneratorType)
assert list(response['a']) == [1, 2, 3]
def searchv2_quick(context, request):
fr = FieldedResponse(
_meta={'params_parser': ParamsParser(request)},
response_fields=[
BasicSearchResponseField(default_item_types=DEFAULT_ITEM_TYPES)
])
return fr.render()
def summary(context, request):
fr = FieldedResponse(
_meta={
'params_parser': ParamsParser(request)
},
response_fields=[
TitleResponseField(
title=SUMMARY_TITLE
),
TypeResponseField(
at_type=[SUMMARY_TITLE]
),
IDResponseField(),
SearchBaseResponseField(),
ContextResponseField(),
BasicMatrixWithFacetsResponseField(
default_item_types=DEFAULT_ITEM_TYPES,
matrix_definition_name=SUMMARY_MATRIX
),
NotificationResponseField(),
FiltersResponseField(),
TypeOnlyClearFiltersResponseField(),
DebugQueryResponseField()
]
)
return fr.render()
