def test_update_bad_field():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
# perform update
doc_id = '000000000000000000000002'
doc = search_by_id(doc_id)
new_doc_id, error_msg = update(doc_id, remove_doc=False, \
update_pairs={'bad_field':'val'}, \
new_meas_objects=[], \
meas_remove_indices=[] \
)
assert new_doc_id == None
# test that doc did not get transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == None
#test that currversion doc was not inserted
all_docs = query_for_all_docs()
for doc in all_docs:
assert 'bad_field' not in list(doc.keys())
def test_update_new_meas_objects_str_for_val_b():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
new_meas_objects = [{
'isotope': 'U-235',
'type': 'range',
'unit': 'g',
'value': ['a', 'b']
}]
doc_id = '000000000000000000000002'
orig_doc = search_by_id(doc_id)
new_doc_id, error_msg = update(doc_id,
remove_doc=False,
new_meas_objects=new_meas_objects)
assert new_doc_id == None
# test that doc got transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == None
# test no change to original doc
new_doc = search_by_id(doc_id)
assert len(new_doc['measurement']['results']) == len(
orig_doc['measurement']['results'])
def test_update_new_meas_objects():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
new_meas_objects = [{
'isotope': 'K-40',
'type': 'measurement',
'unit': 'g/cm',
'value': [0.2]
}, {
'isotope': 'U-235',
'type': 'range',
'unit': 'g',
'value': [0.3, 2.1]
}]
doc_id = '000000000000000000000002'
orig_doc = search_by_id(doc_id)
new_doc_id, error_msg = update(doc_id,
remove_doc=False,
new_meas_objects=new_meas_objects)
assert new_doc_id != None
new_doc_id = str(new_doc_id)
# test that doc got transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == orig_doc
# test new (current version) doc
new_doc = search_by_id(new_doc_id)
# test version num
orig_doc.pop('_version')
new_version = new_doc.pop('_version')
assert new_version == 2
# test parent id
orig_doc.pop('_id')
parent_id = new_doc.pop('_parent_id')
assert parent_id == doc_id
# test id once more
new_version_doc_id = str(new_doc.pop('_id'))
assert new_doc_id == new_version_doc_id
# test orig doc and curr version doc equality
len_orig_meas_results = len(orig_doc['measurement'].pop('results'))
assert new_doc['measurement'].pop(
'results')[len_orig_meas_results:] == new_meas_objects
assert orig_doc == new_doc
def test_update_remove_doc():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
# perform update
doc_id = '000000000000000000000002'
doc = search_by_id(doc_id) #, db_obj=db_obj)
new_doc_id, error_msg = update(doc_id, remove_doc=True) #, db_obj=db_obj)
assert new_doc_id == None
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert doc == oldversion_doc
def perform_update(doc_id, remove_doc, update_pairs, meas_remove_indices, meas_add_eles, db_obj, is_assay_request_update=False, is_assay_request_verify=False):
"""This function calls the dunetoolkit update function with the update fields and values parsed from the form data.
args:
* doc_id (str): the ID of the document to update, extracted from the form data.
* remove_doc (bool): whether to remove the entire document from the database (if True).
* update_pairs (dict): a set of (non-measurement results) fields and corresponding values to update in the document in the database.
* meas_remove_indices (list of int): the integer indices of measurement results objects to remove entirely from the measurement results field.
* meas_add_eles (list of dict): the new measurement results objects to add to the measurement results field.
* db_obj (pymongo.database.Database): a pymongo database object that, once a collection has been selected, can be used to query.
* is_assay_request_update (bool): whether the document to update is an assay (in the "assays" collection) or an assay request (in the "assay_requests" collection).
returns:
* bson.objectid.ObjectId. The ID of the document that was just updated (if successful).
* str. An error message (if an error happened).
"""
new_doc_id, error_msg = update(doc_id, db_obj, remove_doc, update_pairs, meas_add_eles, meas_remove_indices, is_assay_request_update=is_assay_request_update, is_assay_request_verify=is_assay_request_verify)
return new_doc_id, error_msg
def test_update_meas_remove_indices():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
remove_indices = [0, 2] # list len is 3
doc_id = '000000000000000000000002'
orig_doc = search_by_id(doc_id, db_obj=db_obj)
new_doc_id, error_msg = update(doc_id,
remove_doc=False,
meas_remove_indices=remove_indices)
assert new_doc_id != None
new_doc_id = str(new_doc_id)
# test that doc got transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == orig_doc
# test new (current version) doc
new_doc = search_by_id(new_doc_id)
# test version num
orig_doc.pop('_version')
new_version = new_doc.pop('_version')
assert new_version == 2
# test parent id
orig_doc.pop('_id')
parent_id = new_doc.pop('_parent_id')
assert parent_id == doc_id
# test id once more
new_version_doc_id = str(new_doc.pop('_id'))
assert new_doc_id == new_version_doc_id
# test orig doc and curr version doc equality
orig_meas_results = orig_doc['measurement'].pop('results')
new_meas_results = new_doc['measurement'].pop('results')
assert len(new_meas_results) == 1
assert new_meas_results[0] == orig_meas_results[1]
assert orig_doc == new_doc
def test_update_nochange():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
# perform update
doc_id = '000000000000000000000002'
doc = search_by_id(doc_id) #, db_obj=db_obj)
new_doc_id, error_msg = update(doc_id, remove_doc=False, \
update_pairs={}, \
new_meas_objects=[], \
meas_remove_indices=[] \
)
assert new_doc_id != None
assert type(new_doc_id) is ObjectId
new_doc_id = str(new_doc_id)
# test value in oldversion database
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert doc == oldversion_doc
# test currversion doc
currversion_doc = search_by_id(new_doc_id) #, db_obj=db_obj)
# test version num
doc.pop('_version')
new_version = currversion_doc.pop('_version')
assert new_version == 2
# test parent id
doc.pop('_id')
parent_id = currversion_doc.pop('_parent_id')
assert parent_id == doc_id
# test id once more
new_version_doc_id = str(currversion_doc.pop('_id'))
assert new_doc_id == new_version_doc_id
# test orig doc and curr version doc equality
assert doc == currversion_doc
def test_update_meas_remove_indices_bad_idx():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
remove_indices = [4] # list len is 3
doc_id = '000000000000000000000002'
orig_doc = search_by_id(doc_id)
new_doc_id, error_msg = update(doc_id,
remove_doc=False,
meas_remove_indices=remove_indices)
assert new_doc_id == None
# test that doc did not get transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == None
# test no change to original doc
new_doc = search_by_id(doc_id)
assert len(new_doc['measurement']['results']) == len(
orig_doc['measurement']['results'])
def test_update_all():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
update_pairs = {
'grouping': 'new test value',
'data_source.input.contact': '*****@*****.**',
'measurement.results.0.unit': 'g',
'measurement.date': ['2020-10-21']
}
new_meas_objects = [{
'isotope': 'K-40',
'type': 'measurement',
'unit': 'g/cm',
'value': [0.2]
}, {
'isotope': 'U-235',
'type': 'range',
'unit': 'g',
'value': [0.3, 2.1]
}]
remove_indices = [1, 2]
doc_id = '000000000000000000000002'
orig_doc = search_by_id(doc_id)
new_doc_id, error_msg = update(doc_id,
remove_doc=False,
update_pairs=update_pairs,
new_meas_objects=new_meas_objects,
meas_remove_indices=remove_indices)
assert new_doc_id != None
new_doc_id = str(new_doc_id)
# test that doc got transferred
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert oldversion_doc == orig_doc
# test new (current version) doc
new_doc = search_by_id(new_doc_id)
# test version num
orig_doc.pop('_version')
new_version = new_doc.pop('_version')
assert new_version == 2
# test parent id
orig_doc.pop('_id')
parent_id = new_doc.pop('_parent_id')
assert parent_id == doc_id
# test id once more
new_version_doc_id = str(new_doc.pop('_id'))
assert new_doc_id == new_version_doc_id
# correct the date values to be datetime objects now, not strings
for update_key in ['measurement.date', 'data_source.input.date']:
if update_key in list(update_pairs.keys()):
for i in range(len(update_pairs[update_key])):
update_pairs[update_key][i] = convert_str_to_date(
update_pairs[update_key][i])
# test orig doc and curr version doc equality
for update_key in update_pairs:
new_val = update_pairs[update_key]
key_parts = update_key.split('.')
if len(key_parts) == 1:
orig_doc.pop(key_parts[0])
assert new_doc.pop(key_parts[0]) == new_val
elif len(key_parts) == 2:
orig_doc[key_parts[0]].pop(key_parts[1])
assert new_doc[key_parts[0]].pop(key_parts[1]) == new_val
elif len(key_parts) == 3:
orig_doc[key_parts[0]][key_parts[1]].pop(key_parts[2])
assert new_doc[key_parts[0]][key_parts[1]].pop(
key_parts[2]) == new_val
elif len(key_parts) == 4:
try:
key_parts_2 = int(key_parts[2])
except:
key_parts_2 = key_parts[2]
orig_doc[key_parts[0]][key_parts[1]][key_parts_2].pop(key_parts[3])
assert new_doc[key_parts[0]][key_parts[1]][key_parts_2].pop(
key_parts[3]) == new_val
else:
assert 0 == 1
orig_meas = orig_doc['measurement'].pop('results')
meas_eles = new_doc['measurement'].pop('results')
for new_meas in new_meas_objects:
assert new_meas in meas_eles
for removed_meas in [orig_meas[1], orig_meas[2]]:
assert removed_meas not in meas_eles
assert orig_doc == new_doc
def test_update_update_pairs_update_twice():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
# PERFORM AND TEST FIRST UPDATE
u1_doc_id = '000000000000000000000002'
u1_doc = search_by_id(u1_doc_id)
u1_update_pairs = {
'grouping': 'new test value',
'data_source.input.contact': '*****@*****.**',
'measurement.results.0.unit': 'g',
'measurement.date': ['2020-10-21']
}
u1_new_doc_id, u1_error_msg = update(u1_doc_id, remove_doc=False, \
update_pairs=u1_update_pairs, \
new_meas_objects=[], \
meas_remove_indices=[] \
)
assert u1_new_doc_id != None
u1_new_doc_id = str(u1_new_doc_id)
# test value in oldversion database
u1_oldversion_doc = search_by_id(u1_doc_id, coll_type='old_versions')
assert (u1_doc == u1_oldversion_doc)
# test new (current version) doc
u1_new_doc = search_by_id(u1_new_doc_id)
# test version num
u1_doc.pop('_version')
u1_new_version = u1_new_doc.pop('_version')
assert u1_new_version == 2
# test parent id
u1_doc.pop('_id')
u1_parent_id = u1_new_doc.pop('_parent_id')
assert u1_parent_id == u1_doc_id
# test id once more
u1_new_version_doc_id = str(u1_new_doc.pop('_id'))
assert u1_new_doc_id == u1_new_version_doc_id
# test orig doc and curr version doc equality
u1_doc.pop('grouping')
u1_doc['data_source']['input'].pop('contact')
u1_doc['measurement']['results'][0].pop('unit')
u1_doc['measurement'].pop('date')
assert u1_new_doc.pop('grouping') == 'new test value'
assert u1_new_doc['data_source']['input'].pop(
'contact') == '*****@*****.**'
assert u1_new_doc['measurement']['results'][0].pop('unit') == 'g'
assert u1_new_doc['measurement'].pop('date') == [
datetime.datetime(2020, 10, 21)
]
assert u1_doc == u1_new_doc
# PERFORM AND TEST SECOND UPDATE
u2_doc_id = u1_new_version_doc_id
u2_doc = search_by_id(u2_doc_id)
u2_update_pairs = {'grouping': 'test value two'}
u2_new_doc_id, u2_error_msg = update(u2_doc_id,
remove_doc=False,
update_pairs=u2_update_pairs)
assert u2_new_doc_id != None
u2_new_doc_id = str(u2_new_doc_id)
u2_oldversion_doc = search_by_id(u2_doc_id, coll_type='old_versions')
assert u2_doc == u2_oldversion_doc
u2_new_doc = search_by_id(u2_new_doc_id)
u2_doc.pop('_version')
u2_new_version = u2_new_doc.pop('_version')
assert u2_new_version == 3
u2_doc.pop('_id')
u2_parent_id = u2_new_doc.pop('_parent_id')
assert u2_parent_id == u2_doc_id
u2_new_doc.pop('_id')
u2_doc.pop('grouping')
assert u2_new_doc.pop('grouping') == 'test value two'
def test_update_update_pairs_all():
os.environ[
'TOOLKIT_CONFIG_NAME'] = '../dunetoolkit/toolkit_config_test.json'
# set up database to be updated
teardown_db_for_test()
db_obj = set_up_db_for_test()
# perform update
doc_id = '000000000000000000000002'
doc = search_by_id(doc_id)
update_pairs = {
'grouping': 'new test value',
'sample.name': 'testing sample name',
'sample.description': 'test descrip',
'sample.source': 'example src',
'sample.id': '123456test',
'sample.owner.name': 'test',
'sample.owner.contact': '*****@*****.**',
'measurement.results.0.isotope': 'K-40',
'measurement.results.0.type': 'range',
'measurement.results.0.unit': 'g',
'measurement.results.0.value': [10.3, 12.9],
'measurement.practitioner.name': 'tester',
'measurement.practitioner.contact': '*****@*****.**',
'measurement.technique': 'test',
'measurement.institution': 'test place',
'measurement.date': ['2020-10-21'],
'measurement.description': 'test descrip',
'measurement.requestor.name': 'test requestor',
'measurement.requestor.contact': '*****@*****.**',
'data_source.reference': 'testing',
'data_source.input.name': 'testing',
'data_source.input.contact': '*****@*****.**',
'data_source.input.date': ['2010/18/02', '2020-10-21'],
'data_source.input.notes': 'test test test',
}
new_doc_id, error_msg = update(doc_id, remove_doc=False, \
update_pairs=update_pairs, \
new_meas_objects=[], \
meas_remove_indices=[] \
)
assert new_doc_id != None
new_doc_id = str(new_doc_id)
# test value in oldversion database
oldversion_doc = search_by_id(doc_id, coll_type='old_versions')
assert (doc == oldversion_doc)
# test currversion doc
currversion_doc = search_by_id(new_doc_id)
# test version num
doc.pop('_version')
new_version = currversion_doc.pop('_version')
assert new_version == 2
# test parent id
doc.pop('_id')
parent_id = currversion_doc.pop('_parent_id')
assert parent_id == doc_id
# test id once more
new_version_doc_id = str(currversion_doc.pop('_id'))
assert new_doc_id == new_version_doc_id
# correct the date values to be datetime objects now, not strings
for update_key in ['measurement.date', 'data_source.input.date']:
for i in range(len(update_pairs[update_key])):
update_pairs[update_key][i] = convert_str_to_date(
update_pairs[update_key][i])
# test orig doc and curr version doc equality
for update_key in update_pairs:
new_val = update_pairs[update_key]
key_parts = update_key.split('.')
if len(key_parts) == 1:
doc.pop(key_parts[0])
assert currversion_doc.pop(key_parts[0]) == new_val
elif len(key_parts) == 2:
doc[key_parts[0]].pop(key_parts[1])
assert currversion_doc[key_parts[0]].pop(key_parts[1]) == new_val
elif len(key_parts) == 3:
doc[key_parts[0]][key_parts[1]].pop(key_parts[2])
assert currversion_doc[key_parts[0]][key_parts[1]].pop(
key_parts[2]) == new_val
elif len(key_parts) == 4:
try:
key_parts_2 = int(key_parts[2])
except:
key_parts_2 = key_parts[2]
doc[key_parts[0]][key_parts[1]][key_parts_2].pop(key_parts[3])
assert currversion_doc[key_parts[0]][
key_parts[1]][key_parts_2].pop(key_parts[3]) == new_val
else:
assert 0 == 1