Merge branch 'main' into add-structure-map-tooling

importer/csv/locations/locations_full.csv

@@ -1,4 +1,4 @@
-name,status,method,version,id,parentName,parentID,type,physicalType
-City1,active,update,1,ba787982-b973-4bd5-854e-eacbe161e297,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,jurisdiction,jurisdiction
-Building1,active,update,1,0a04f1c2-de2a-4869-bab2-763d017e5316,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,building,building
-City2,active,create,1,,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,jurisdiction,jurisdiction
+name,status,method,id,parentName,parentID,type,physicalType
+City1,active,update,ba787982-b973-4bd5-854e-eacbe161e297,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,jurisdiction,jurisdiction
+Building1,active,update,0a04f1c2-de2a-4869-bab2-763d017e5316,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,building,building
+City2,active,create,,test location-1,18fcbc2e-4240-4a84-a270-7a444523d7b6,jurisdiction,jurisdiction

importer/main.py

@@ -193,27 +193,33 @@ def create_user_resources(user_id, user):
 
 # custom extras for organizations
 def organization_extras(resource, payload_string):
+    _, active, *_, alias = resource
     try:
-        if resource[5]:
-            payload_string = payload_string.replace("$alias", resource[5])
+        if alias:
+            payload_string = payload_string.replace("$alias", alias)
+        else:
+            obj = json.loads(payload_string)
+            del obj["resource"]["alias"]
+            payload_string = json.dumps(obj, indent=4)
     except IndexError:
         obj = json.loads(payload_string)
         del obj["resource"]["alias"]
         payload_string = json.dumps(obj, indent=4)
 
     try:
-        payload_string = payload_string.replace("$active", resource[1])
+        payload_string = payload_string.replace("$active", active)
     except IndexError:
         payload_string = payload_string.replace("$active", "true")
     return payload_string
 
 
 # custom extras for locations
 def location_extras(resource, payload_string):
+    name, *_, parentName, parentID, type, physicalType = resource
     try:
-        if resource[4]:
-            payload_string = payload_string.replace("$parentName", resource[4]).replace(
-                "$parentID", resource[5]
+        if parentName:
+            payload_string = payload_string.replace("$parentName", parentName).replace(
+                "$parentID", parentID
             )
         else:
             obj = json.loads(payload_string)
@@ -225,16 +231,16 @@ def location_extras(resource, payload_string):
         payload_string = json.dumps(obj, indent=4)
 
     try:
-        if resource[7] == "building":
+        if type == "building":
             payload_string = payload_string.replace("$t_code", "bu").replace(
                 "$t_display", "Building"
             )
-        elif resource[7] == "jurisdiction":
+        elif type == "jurisdiction":
             payload_string = payload_string.replace("$t_code", "jdn").replace(
                 "$t_display", "Jurisdiction"
             )
         else:
-            logging.error("Unsupported location type provided for " + resource[0])
+            logging.error("Unsupported location type provided for " + name)
             obj = json.loads(payload_string)
             del obj["resource"]["type"]
             payload_string = json.dumps(obj, indent=4)
@@ -244,16 +250,18 @@ def location_extras(resource, payload_string):
         payload_string = json.dumps(obj, indent=4)
 
     try:
-        if resource[8] == "building":
+        if physicalType == "building":
             payload_string = payload_string.replace("$pt_code", "bu").replace(
                 "$pt_display", "Building"
             )
-        elif resource[8] == "jurisdiction":
+        elif physicalType == "jurisdiction":
             payload_string = payload_string.replace("$pt_code", "jdn").replace(
                 "$pt_display", "Jurisdiction"
             )
         else:
-            logging.error("Unsupported location physical type provided for " + resource[0])
+            logging.error(
+                "Unsupported location physical type provided for " + name
+            )
             obj = json.loads(payload_string)
             del obj["resource"]["type"]
             payload_string = json.dumps(obj, indent=4)
@@ -274,15 +282,16 @@ def care_team_extras(
     elements = []
     elements2 = []
 
+    *_, organizations, participants = resource
     if load_type == "min":
         try:
-            if resource[5]:
-                elements = resource[5].split("|")
+            if organizations:
+                elements = organizations.split("|")
         except IndexError:
             pass
         try:
-            if resource[6]:
-                elements2 = resource[6].split("|")
+            if participants:
+                elements2 = participants.split("|")
         except IndexError:
             pass
     elif load_type == "full":
@@ -351,11 +360,12 @@ def care_team_extras(
 def extract_matches(resource_list):
     teamMap = {}
     for resource in resource_list:
-        if resource[1].strip() and resource[3].strip():
-            if resource[1] not in teamMap.keys():
-                teamMap[resource[1]] = [resource[3] + ":" + resource[2]]
+        group_name, group_id, item_name, item_id = resource
+        if group_id.strip() and item_id.strip():
+            if group_id not in teamMap.keys():
+                teamMap[group_id] = [item_id + ":" + item_name]
             else:
-                teamMap[resource[1]].append(resource[3] + ":" + resource[2])
+                teamMap[group_id].append(item_id + ":" + item_name)
         else:
             logging.error("Missing required id: Skipping " + str(resource))
     return teamMap
@@ -459,16 +469,16 @@ def build_org_affiliation(resources, resource_list):
 # This function is used to Capitalize the 'resource_type'
 # and remove the 's' at the end, a version suitable with the API
 def get_valid_resource_type(resource_type):
-    logging.info("Modify the string resource_type")
+    logging.debug("Modify the string resource_type")
     modified_resource_type = resource_type[0].upper() + resource_type[1:-1]
     return modified_resource_type
 
 
 # This function gets the current resource version from the API
 def get_resource_version(resource_id, resource_type):
-    logging.info("Getting resource version")
+    logging.debug("Getting resource version")
     modified_resource_type = get_valid_resource_type(resource_type)
-    resource_url = config.fhir_base_url + "/" + modified_resource_type + "/" + resource_id
+    resource_url = "/".join([config.fhir_base_url, modified_resource_type, resource_id])
     response = handle_request("GET", "", resource_url)
     json_response = json.loads(response[0])
     return json_response["meta"]["versionId"]
@@ -484,45 +494,46 @@ def build_payload(resource_type, resources, resource_payload_file):
         payload_string = json_file.read()
 
     for resource in resources:
+        name, status, method, id, *_ = resource
         try:
-            if resource[2] == "create":
-                if len(resource[4].strip()) > 0:
+            if method == "create":
+                if len(id.strip()) > 0:
                     # use the provided id
-                    unique_uuid = resource[4].strip()
-                    identifier_uuid = resource[4] if resource[5] == "" else resource[5]
+                    unique_uuid = id.strip()
+                    identifier_uuid = id.strip()
                 else:
                     # generate a new uuid
-                    unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, resource[0]))
+                    unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, name))
                     identifier_uuid = unique_uuid
-            elif resource[2] == "update":
-                if len(resource[4].strip()) > 0:
+            elif method == "update":
+                if len(id.strip()) > 0:
                     # use the provided id
-                    unique_uuid = resource[4].strip()
-                    identifier_uuid = resource[4] if resource[5] == "" else resource[5]
+                    unique_uuid = id.strip()
+                    identifier_uuid = id.strip()
                 else:
                     # generate a new uuid
-                    unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, resource[0]))
+                    unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, name))
                     identifier_uuid = unique_uuid
         except IndexError:
             # default if method is not provided
-            unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, resource[0]))
+            unique_uuid = str(uuid.uuid5(uuid.NAMESPACE_DNS, name))
             identifier_uuid = unique_uuid
 
         # ps = payload_string
         ps = (
-            payload_string.replace("$name", resource[0])
+            payload_string.replace("$name", name)
             .replace("$unique_uuid", unique_uuid)
             .replace("$identifier_uuid", identifier_uuid)
         )
 
         try:
-            ps = ps.replace("$status", resource[1])
+            ps = ps.replace("$status", status)
         except IndexError:
             ps = ps.replace("$status", "active")
 
         # Get resource versions from API
         try:
-            version = get_resource_version(resource[3], resource_type)
+            version = get_resource_version(id, resource_type)
             ps = ps.replace("$version", version)
         except Exception:
             ps = ps.replace("$version", "1")
@@ -764,11 +775,10 @@ def delete_resource(resource_type, resource_id, cascade):
     else:
         cascade = ""
 
-    r = handle_request(
-        "DELETE",
-        "",
-        config.fhir_base_url + "/" + resource_type + "/" + resource_id + cascade,
+    resource_url = "/".join(
+        [config.fhir_base_url, resource_type, resource_id + cascade]
     )
+    r = handle_request("DELETE", "", resource_url)
     logging.info(r.text)
 
 

importer/requirements.txt

@@ -5,3 +5,4 @@ requests-oauthlib==1.3.1
 urllib3==2.0.3
 backoff==2.2.1
 pytest==7.4.2
+jsonschema==4.21.1