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Merged
merged 6 commits into from
Jul 20, 2017
Merged

Add dataexplorer tests #847

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739f226
add unit tests for POST /api/dataexplorer/search
ambrussimon Jul 10, 2017
e6d1d00
add tests for all dataexplorer handler methods
ambrussimon Jul 11, 2017
3cffeda
rebase and fix dataexplorer tests for follow-up changes
ambrussimon Jul 12, 2017
00a1b03
add tests for /dataexplorer/search/fields/aggregate (typeahead)
ambrussimon Jul 12, 2017
6b7d681
subclass TransportError in test to fix ci failure
ambrussimon Jul 12, 2017
bd67b59
remove non-reachable try / add todo
ambrussimon Jul 20, 2017
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70 changes: 49 additions & 21 deletions api/handlers/dataexplorerhandler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,52 @@
}


SOURCE_COMMON = [
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Thanks for cleaning this up 👍

"group._id",
"group.label",
"permissions.*",
"project._id",
"project.archived",
"project.label",
"session._id",
"session.archived",
"session.created",
"session.label",
"session.timestamp",
"subject.code",
]

SOURCE = {
"file": SOURCE_COMMON + [
"acquisition._id",
"acquisition.archived",
"acquisition.label",
"analysis._id",
"analysis.label",
"file.created",
"file.measurements",
"file.name",
"file.size",
"file.type",
],
"session": SOURCE_COMMON,
"acquisition": SOURCE_COMMON + [
"acquisition._id",
"acquisition.archived",
"acquisition.created",
"acquisition.label",
"acquisition.timestamp",
],
"analysis": SOURCE_COMMON + [
"analysis._id",
"analysis.created",
"analysis.label",
"analysis.parent",
"analysis.user",
],
}


class DataExplorerHandler(base.RequestHandler):
# pylint: disable=broad-except

Expand Down Expand Up @@ -308,6 +354,7 @@ def aggregate_field_values(self):
}
}
if not filters:
# TODO add non-user auth support (#865)
body['query']['bool'].pop('filter')
if search_string is None:
body['query']['bool']['must'] = MATCH_ALL
Expand Down Expand Up @@ -370,11 +417,6 @@ def get_facets(self):
def search_fields(self):
field_query = self.request.json_body.get('field')

try:
field_query = str(field_query)
except ValueError:
self.abort(400, 'Must specify string for field query')

es_query = {
"size": 15,
"query": {
Expand Down Expand Up @@ -415,15 +457,6 @@ def _construct_query(self, return_type, search_string, filters, size=100):
if return_type == 'file':
return self._construct_file_query(search_string, filters, size)

source = [ "permissions.*", "session._id", "session.label", "session.created", "session.timestamp",
"subject.code", "project.label", "group.label", "group._id", "project._id", "session.archived", "project.archived" ]

if return_type == 'acquisition':
source.extend(["acquisition._id", "acquisition.label", "acquisition.created", "acquisition.timestamp", "acquisition.archived"])

if return_type == 'analysis':
source.extend(["analysis._id", "analysis.label", "analysis.created", "analysis.parent", "analysis.user"])

query = {
"size": 0,
"query": {
Expand Down Expand Up @@ -452,7 +485,7 @@ def _construct_query(self, return_type, search_string, filters, size=100):
"aggs": {
"by_top_hit": {
"top_hits": {
"_source": source,
"_source": SOURCE[return_type],
"size": 1
}
}
Expand All @@ -475,14 +508,9 @@ def _construct_query(self, return_type, search_string, filters, size=100):
return query

def _construct_file_query(self, search_string, filters, size=100):
source = [ "permissions.*", "session._id", "session.label", "session.created",
"session.timestamp", "subject.code", "project.label", "group.label", "acquisition.label",
"acquisition._id", "group._id", "project._id", "analysis._id", "analysis.label",
"session.archived", "acquisition.archived", "project.archived" ]
source.extend(["file.name", "file.created", "file.type", "file.measurements", "file.size", "parent"])
query = {
"size": size,
"_source": source,
"_source": SOURCE['file'],
"query": {
"bool": {
"must": {
Expand Down
18 changes: 15 additions & 3 deletions test/unit_tests/python/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,19 +42,31 @@ def log_db(app):
return api.config.log_db


@pytest.fixture(scope='session')
def es(app):
"""Return Elasticsearch mock (MagickMock instance)"""
return api.config.es


@pytest.yield_fixture(scope='session')
def app():
"""Return api instance that uses mocked os.environ and MongoClient"""
env_patch = mock.patch.dict(
os.environ, {'SCITRAN_CORE_DRONE_SECRET': SCITRAN_CORE_DRONE_SECRET}, clear=True)
"""Return api instance that uses mocked os.environ, ElasticSearch and MongoClient"""
test_env = {
'SCITRAN_CORE_DRONE_SECRET': SCITRAN_CORE_DRONE_SECRET,
'TERM': 'xterm', # enable terminal features - useful for pdb sessions
}
env_patch = mock.patch.dict(os.environ, test_env, clear=True)
env_patch.start()
es_patch = mock.patch('elasticsearch.Elasticsearch')
es_patch.start()
mongo_patch = mock.patch('pymongo.MongoClient', new=mongomock.MongoClient)
mongo_patch.start()
# NOTE db and log_db is created at import time in api.config
# reloading the module is needed to use the mocked MongoClient
reload(api.config)
yield api.web.start.app_factory()
mongo_patch.stop()
es_patch.stop()
env_patch.stop()


Expand Down
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