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Commit 3ffb4dab authored by Megan Henning's avatar Megan Henning
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Reorganize code pieces in de

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api/api.py
+ 1
− 1
View file @ 3ffb4dab
...@@ -103,7 +103,7 @@ endpoints = [ ...@@ -103,7 +103,7 @@ endpoints = [
route('/dataexplorer/search', DataExplorerHandler, h='search', m=['POST']), route('/dataexplorer/search', DataExplorerHandler, h='search', m=['POST']),
route('/dataexplorer/facets', DataExplorerHandler, h='get_facets', m=['POST']), route('/dataexplorer/facets', DataExplorerHandler, h='get_facets', m=['POST']),
route('/dataexplorer/search/fields', DataExplorerHandler, h='search_fields', m=['POST']), route('/dataexplorer/search/fields', DataExplorerHandler, h='search_fields', m=['POST']),
route('/dataexplorer/search/fields/aggregate', DataExplorerHandler, h='custom_field_values', m=['POST']), route('/dataexplorer/search/fields/aggregate', DataExplorerHandler, h='aggregate_field_values', m=['POST']),
route('/dataexplorer/index/fields', DataExplorerHandler, h='index_field_names', m=['POST']), route('/dataexplorer/index/fields', DataExplorerHandler, h='index_field_names', m=['POST']),
# Users # Users
......
api/handlers/dataexplorerhandler.py
+ 124
− 132
View file @ 3ffb4dab
...@@ -9,6 +9,78 @@ from ..auth import require_login, require_superuser ...@@ -9,6 +9,78 @@ from ..auth import require_login, require_superuser
log = config.log log = config.log
"""
EXAMPLE_SESSION_QUERY = {
"size": 0,
"query": {
"match": {
"_all": "test'"
}
},
"aggs": {
"by_session": {
"terms": {
"field": "session._id",
"size": 100
},
"aggs": {
"by_top_hit": {
"top_hits": {
"size": 1
}
}
}
}
}
}
EXAMPLE_ACQUISITION_QUERY = {
"size": 0,
"query": {
"match": {
"_all": "megan'"
}
},
"aggs": {
"by_session": {
"terms": {
"field": "acquisition._id",
"size": 100
},
"aggs": {
"by_top_hit": {
"top_hits": {
"size": 1
}
}
}
}
}
}
EXAMPLE_FILE_QUERY = {
"size": 100,
"query": {
"bool": {
"must": {
"match": {
"_all": "brain"
}
},
"filter": {
"bool" : {
"must" : [
{ "term" : {"file.type" : "dicom"}},
{ "term" : {"container_type" : "file"}}
]
}
}
}
}
}
"""
ANALYSIS = { ANALYSIS = {
"analyzer": { "analyzer": {
"my_analyzer": { "my_analyzer": {
...@@ -150,75 +222,6 @@ FACET_QUERY = { ...@@ -150,75 +222,6 @@ FACET_QUERY = {
} }
} }
EXAMPLE_SESSION_QUERY = {
"size": 0,
"query": {
"match": {
"_all": "test'"
}
},
"aggs": {
"by_session": {
"terms": {
"field": "session._id",
"size": 100
},
"aggs": {
"by_top_hit": {
"top_hits": {
"size": 1
}
}
}
}
}
}
EXAMPLE_ACQUISITION_QUERY = {
"size": 0,
"query": {
"match": {
"_all": "megan'"
}
},
"aggs": {
"by_session": {
"terms": {
"field": "acquisition._id",
"size": 100
},
"aggs": {
"by_top_hit": {
"top_hits": {
"size": 1
}
}
}
}
}
}
EXAMPLE_FILE_QUERY = {
"size": 100,
"query": {
"bool": {
"must": {
"match": {
"_all": "brain"
}
},
"filter": {
"bool" : {
"must" : [
{ "term" : {"file.type" : "dicom"}},
{ "term" : {"container_type" : "file"}}
]
}
}
}
}
}
class DataExplorerHandler(base.RequestHandler): class DataExplorerHandler(base.RequestHandler):
# pylint: disable=broad-except # pylint: disable=broad-except
...@@ -230,7 +233,7 @@ class DataExplorerHandler(base.RequestHandler): ...@@ -230,7 +233,7 @@ class DataExplorerHandler(base.RequestHandler):
try: try:
request = self.request.json_body request = self.request.json_body
except KeyError: except (ValueError):
if request_type == 'search': if request_type == 'search':
self.abort(400, 'Must specify return type') self.abort(400, 'Must specify return type')
return None, None, None return None, None, None
...@@ -265,85 +268,74 @@ class DataExplorerHandler(base.RequestHandler): ...@@ -265,85 +268,74 @@ class DataExplorerHandler(base.RequestHandler):
return return_type, modified_filters, search_string return return_type, modified_filters, search_string
@require_login @require_login
def custom_field_values(self): def aggregate_field_values(self):
""" """
Return list of type ahead values for a key given a value Return list of type ahead values for a key given a value
that the user has already started to type in for the value of that the user has already started to type in for the value of
a custom string field or a set of statistics if the field type is a custom string field or a set of statistics if the field type is
a number. a number.
""" """
try:
custom_field = self.request.json_body['field_name'] field_name = self.request.json_body['field_name']
except (KeyError, ValueError):
self.abort(400, 'Field name is required')
filters = [{'term': {'permissions._id': self.uid}}] filters = [{'term': {'permissions._id': self.uid}}]
field = config.es.indices.get_field_mapping(custom_field, try:
index='data_explorer', field = config.es.get(index='data_explorer_fields', id=field_name, doc_type='flywheel_field')
doc_type='flywheel')['data_explorer']['mappings']['flywheel'][custom_field] except TransportError as e:
field_type = self._get_field_type(field['mapping'][custom_field.split('.')[-1]]['type']) log.warning(e)
self.abort(404, 'Could not find mapping for field {}.'.format(field_name))
field_type = field['_source']['type']
search_string = self.request.json_body.get('search_string', None)
# If the field type is a string, return a list of type-ahead values # If the field type is a string, return a list of type-ahead values
if field_type == 'string': body = {
user_value = self.request.json_body['value'] "size": 0,
body = { "query": {
"size": 0, "bool": {
"query": { "must" : {
"bool": { "match" : { field_name : search_string}
"must" : { },
"match" : { custom_field : user_value} "filter" : filters
},
"filter" : filters
}
},
"aggs" : {
"results" : {
"terms" : {
"field" : custom_field + ".raw",
"size" : 15
}
}
} }
} }
}
if not filters:
body['query']['bool'].pop('filter')
if search_string is None:
body['query']['bool']['must'] = MATCH_ALL
if not filters: if field_type in ['string', 'boolean']:
body['query']['bool'].pop('filter') body['aggs'] = {
"results" : {
aggs = config.es.search( "terms" : {
index='data_explorer', "field" : field_name + ".raw",
doc_type='flywheel', "size" : 15
body=body }
)['aggregations']['results']['buckets'] }
aggs = [bucket['key'] for bucket in aggs] }
return {'type_aheads': aggs}
# If it is a number (int, date, or some other type), return various statistics on the values of the field # If it is a number (int, date, or some other type), return various statistics on the values of the field
else: elif field_type in ['integer', 'float', 'date']:
body = { body['aggs'] = {
"size": 0, "results" : {
"query": { "stats" : {
"bool": { "field" : field_name
"must" : {
"match_all" : {}
},
"filter" : filters
}
},
"aggs" : {
"results" : {
"stats" : {
"field" : custom_field
}
} }
} }
} }
if not filters: else:
body['query']['bool'].pop('filter') self.abort(400, 'Aggregations are only allowed on string, integer, float, data and boolean fields.')
aggs = config.es.search( aggs = config.es.search(
index='data_explorer', index='data_explorer',
doc_type='flywheel', doc_type='flywheel',
body=body body=body
)['aggregations']['results'] )['aggregations']['results']
return aggs return aggs
@require_login @require_login
def get_facets(self): def get_facets(self):
......
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