diff --git a/data_management/lib/spectrack_connection.py b/data_management/lib/spectrack_connection.py index bcecf6a..4750563 100644 --- a/data_management/lib/spectrack_connection.py +++ b/data_management/lib/spectrack_connection.py @@ -94,7 +94,7 @@ def get_results(self, url: str, params: dict = {}): "There was a problem decoding the JSON from: " + url + " with params " - + params + + str(params), error ) return res_json diff --git a/data_management/services/spectrack.py b/data_management/services/spectrack.py index bd69db8..5b7e8ad 100644 --- a/data_management/services/spectrack.py +++ b/data_management/services/spectrack.py @@ -59,7 +59,9 @@ def convert_to_dmd_specimens(self, specimens: list): specimen["redcap_record_id"] is not None ): specimen_kit = self.get_specimen_kit(specimen["specimen_kit_id"]) - if "Biopsy Kit" in specimen_kit["kit_type_name"]: + if specimen["specimen_kit_id"] and "Biopsy Kit" in specimen_kit["kit_type_name"]: + print(specimen["sample_id"]) + print(specimen["redcap_record_id"]) biopsy = self.get_biopsy(specimen["redcap_record_id"]) site = biopsy["collecting_org"]["org_name"] disease_category = biopsy["disease_category"] @@ -71,6 +73,7 @@ def convert_to_dmd_specimens(self, specimens: list): biopsy_date = None sample_type = self.get_sample_type(specimen["sample_type_id"]) + kit_id = "N/A" if specimen['specimen_kit_id'] is None else specimen['specimen_kit_id'] dmd_specimen_tuple = ( specimen["id"], specimen["sample_id"], @@ -80,7 +83,7 @@ def convert_to_dmd_specimens(self, specimens: list): specimen["redcap_record_id"], specimen["level"], sample_type["sample_type_code"], - specimen["specimen_kit_id"], + kit_id, specimen_kit["kit_type_name"], specimen_kit["redcap_project_type"], site,