def get_projects(token_info, include_stats, is_active=None):
validate_admin_access(token_info)
with Transaction() as t:
admin_repo = AdminRepo(t)
projects_list = admin_repo.get_projects(include_stats, is_active)
result = [x.to_api() for x in projects_list]
return jsonify(result), 200
def _set_up_and_query_projects(self, t, include_stats, is_active_val):
updated_dict = self._FULL_PROJECT_DICT.copy()
updated_dict[p.PROJ_NAME_KEY] = 'test_proj'
input = p.Project.from_dict(updated_dict)
admin_repo = AdminRepo(t)
# existing project 8 in test db
admin_repo.update_project(8, input)
set_up_sql = """
-- add some additional scans to project 8 so can test that
-- computed statistics based on latest scans are choosing all
-- (and only) the scans that they should:
-- add a scan w an earlier timestamp (though added into db
-- later) than existing one showing that this barcode USED TO
-- have a problem but no longer does.
insert into barcodes.barcode_scans
(barcode, scan_timestamp, sample_status)
VALUES ('000007640', '2012-11-01', 'no-registered-account');
-- add a second *sample-is-valid* scan for the same barcode
-- so can ensure that sample status count are distinct
insert into barcodes.barcode_scans
(barcode, scan_timestamp, sample_status)
VALUES ('000007640', '2012-12-01', 'sample-is-valid');
-- add two additional scans for a different barcode: a valid
-- scan followed by a problem scan, thus indicting this sample
-- currently has a problem.
insert into barcodes.barcode_scans
(barcode, scan_timestamp, sample_status)
VALUES ('000070796', '2020-07-01', 'sample-is-valid');
insert into barcodes.barcode_scans
(barcode, scan_timestamp, sample_status)
VALUES ('000070796', '2020-09-01', 'no-registered-account');
UPDATE barcodes.project SET is_active = FALSE
WHERE project_id = 2;
"""
with t.cursor() as cur:
cur.execute(set_up_sql)
output = admin_repo.get_projects(include_stats, is_active_val)
updated_dict["project_id"] = 8
computed_stats = \
{p.NUM_FULLY_RETURNED_KITS_KEY: 1,
p.NUM_KITS_KEY: 5,
p.NUM_KITS_W_PROBLEMS_KEY: 1,
'num_no_associated_source': 0,
'num_no_collection_info': 0,
'num_no_registered_account': 1,
'num_received_unknown_validity': 0,
'num_sample_is_valid': 4,
p.NUM_PARTIALLY_RETURNED_KITS_KEY: 2,
p.NUM_SAMPLES_KEY: 20,
p.NUM_SAMPLES_RECEIVED_KEY: 5,
p.NUM_UNIQUE_SOURCES_KEY: 4}
updated_dict[p.COMPUTED_STATS_KEY] = \
computed_stats if include_stats else {}
return updated_dict, output
def list_barcode_query_fields(token_info):
validate_admin_access(token_info)
# Generates a json array declaring the filters
# that can be used for barcode queries
# Will be parseable by jQuery QueryBuilder
# to allow a user to modify queries.
# Barcode queries can filter on:
# - project (categorical, any project in our db)
# - sample_status (categorical, fixed list)
# - sample_type (categorical, fixed list)
# See examples https://querybuilder.js.org/demo.html
# https://querybuilder.js.org/assets/demo-import-export.js
with Transaction() as t:
admin_repo = AdminRepo(t)
projects_list = admin_repo.get_projects(False)
projects_list.sort(key=lambda x: x.project_name)
filter_fields = []
filter_fields.append(
{
'id': 'project_id',
'label': 'Project',
'type': 'integer',
'input': 'select',
'values': {
x.project_id: x.project_name for x in projects_list
},
'operators': ['equal', 'not_equal']
}
)
filter_fields.append(
{
'id': 'sample_status',
'label': 'Sample Status',
'type': 'string',
'input': 'select',
'values': {
"sample-is-valid": "Sample Is Valid",
"no-associated-source": "No Associated Source",
"no-registered-account": "No Registered Account",
"no-collection-info": "No Collection Info",
"sample-has-inconsistencies": "Sample Has Inconsistencies",
"received-unknown-validity": "Received Unknown Validity"
},
'operators': ['equal', 'not_equal', 'is_null', 'is_not_null']
}
)
filter_fields.append(
{
'id': 'site_sampled',
'label': 'Sample Site',
'type': 'string',
'input': 'select',
'values': {
"Blood (skin prick)": "Blood (skin prick)",
"Saliva": "Saliva",
"Ear wax": "Ear wax",
"Forehead": "Forehead",
"Fur": "Fur",
"Hair": "Hair",
"Left hand": "Left hand",
"Left leg": "Left leg",
"Mouth": "Mouth",
"Nares": "Nares",
"Nasal mucus": "Nasal mucus",
"Right hand": "Right hand",
"Right leg": "Right leg",
"Stool": "Stool",
"Tears": "Tears",
"Torso": "Torso",
"Vaginal mucus": "Vaginal mucus"
},
'operators': ['equal', 'not_equal', 'is_null', 'is_not_null']
}
)
filter_fields.append(
{
# Note that this id string must match the
# latest scan timestamp in the exact
# barcode search query.
'id': 'scan_timestamp_latest',
'label': 'Last Scanned',
'type': 'date',
'description': "YYYY/MM/DD",
'default_value': "YYYY/MM/DD",
'validation': {
"format": "YYYY/MM/DD"
},
'operators': ['less_or_equal',
'greater_or_equal',
'is_null',
'is_not_null']
}
)
return jsonify(filter_fields), 200
