Export resources from API endpoint tand write to csv file

importer/README.md

@@ -131,3 +131,11 @@ The coverage report `coverage.html` will be at the working directory
 - The script will check to see if every user has a keycloak uuid that has a Practitioner uuid that matches the one provided in the csv file
 - Note that if none of the Practitioner uuids match then all will be deleted
 - Set `cascade_delete` to True or False if you would like to automatically delete any linked resources. If you set it to False, and there are any linked resources, then the resources will NOT be deleted
+
+## 10. Export resources from API endpoint to CSV file
+- Run `python3  main.py --export_resources True --parameter _lastUpdated --value gt2023-08-01 --batch_size 20 --resource_type locations --log_level info`
+- `export_resources` can either be True or False, checks if it is True and exports the resources
+- The `parameter` is used as a filter for the resources "e.g _lastUpdated", and `value` is where you pass the actual parameter value "e.g gt2023-08-01" used to filter the resources
+- The `batch_size` is the number of resources handled/processed at a time
+- Specify the `resource_type` you want to export, different resource_types are exported to different csv_files
+- The csv_file containing the exported resources is labelled using the current time, to know when the resources were exported for example, csv/2024-02-21-12-21-export_Location.csv

importer/main.py

@@ -17,6 +17,7 @@
 
 global_access_token = ""
 
+
 # This function takes in a csv file
 # reads it and returns a list of strings/lines
 # It ignores the first line (assumes headers)
@@ -861,8 +862,75 @@ def clean_duplicates(users, cascade_delete):
                 logging.info("No Practitioners found")
 
 
+# Create a csv file and initialize the CSV writer
+def write_csv(data, resource_type, fieldnames):
+    logging.info("Writing to csv file")
+    current_time = datetime.now().strftime("%Y-%m-%d-%H-%M")
+    csv_file = f"csv/{current_time}-export_{resource_type}.csv"
+    with open(csv_file, 'w', newline='') as file:
+        csv_writer = csv.writer(file)
+        csv_writer.writerow(fieldnames)
+        csv_writer.writerows(data)
+
+
+# This function exports resources from the API to a csv file
+def export_resources_to_csv(resource_type, parameter, value, batch_size):
+    resource_type = get_valid_resource_type(resource_type)
+    resource_url = "/".join([config.fhir_base_url, resource_type])
+    if len(parameter) > 0:
+        resource_url = resource_url + "?" + parameter + "=" + value + "&_count=" + str(batch_size)
+    response = handle_request("GET", "", resource_url)
+    if response[1] == 200:
+        resources = json.loads(response[0])
+        data = []
+        if resource_type == "Location":
+            elements = ["name", "status", "id", "identifier", "parentName", "parentID", "type", "typeCode",
+                        "physicalType", "physicalTypeCode"]
+        elif resource_type == "Organization":
+            elements = ["name", "active", "id", "identifier", "alias"]
+        elif resource_type == "CareTeam":
+            elements = ["name", "status", "id", "identifier", " organizations", "participants"]
+        else:
+            elements = []
+        for x in resources["entry"]:
+            rl = []
+            for element in elements:
+                try:
+                    if element == "active":
+                        value = x["resource"]["active"]
+                    elif element == "identifier":
+                        value = x["resource"]["identifier"][0]["value"]
+                    elif element == "parentName":
+                        value = x["resource"]["partOf"]["display"]
+                    elif element == "parentID":
+                        value = x["resource"]["partOf"]["reference"]
+                    elif element == "type":
+                        value = x["resource"]["type"][0]["coding"][0]["display"]
+                    elif element == "typeCode":
+                        value = x["resource"]["type"][0]["coding"][0]["code"]
+                    elif element == "physicalType":
+                        value = x["resource"]["physicalType"]["coding"][0]["display"]
+                    elif element == "physicalTypeCode":
+                        value = x["resource"]["physicalType"]["coding"][0]["code"]
+                    elif element == "alias":
+                        value = x["resource"]["alias"][0]
+                    else:
+                        value = x["resource"][element]
+                except KeyError:
+                    value = ""
+                rl.append(value)
+            data.append(rl)
+        write_csv(data, resource_type, elements)
+    else:
+        logging.error(f"Failed to retrieve resource. Status code: {response[1]}")
+
+
 @click.command()
-@click.option("--csv_file", required=True)
+@click.option("--csv_file", required=False)
+@click.option("--export_resources", required=False)
+@click.option("--parameter", required=False)
+@click.option("--value", required=False)
+@click.option("--batch_size", required=False)
 @click.option("--access_token", required=False)
 @click.option("--resource_type", required=False)
 @click.option("--assign", required=False)
@@ -874,7 +942,10 @@ def clean_duplicates(users, cascade_delete):
     "--log_level", type=click.Choice(["DEBUG", "INFO", "ERROR"], case_sensitive=False)
 )
 def main(
-    csv_file, access_token, resource_type, assign, setup, group, roles_max, cascade_delete, log_level
+        csv_file, export_resources, parameter, value, batch_size, access_token, resource_type, assign, setup, group,
+        roles_max,
+        cascade_delete,
+        log_level
 ):
     if log_level == "DEBUG":
         logging.basicConfig(level=logging.DEBUG)
@@ -886,6 +957,13 @@ def main(
     start_time = datetime.now()
     logging.info("Start time: " + start_time.strftime("%H:%M:%S"))
 
+    logging.info("Starting export...")
+    if export_resources == "True":
+        logging.info("Exporting " + resource_type)
+        export_resources_to_csv(resource_type, parameter, value, batch_size)
+        logging.info("Successfully written to csv")
+        exit()
+
     # set access token
     if access_token:
         global global_access_token
@@ -974,5 +1052,6 @@ def main(
     total_time = end_time - start_time
     logging.info("Total time: " + str(total_time.total_seconds()) + " seconds")
 
+
 if __name__ == "__main__":
     main()

importer/test_main.py

@@ -1,13 +1,16 @@
 import json
 import unittest
+from datetime import datetime
 from jsonschema import validate
 from mock import patch
 from main import (
     read_csv,
+    write_csv,
     build_payload,
     build_org_affiliation,
     extract_matches,
     create_user_resources,
+    export_resources_to_csv,
 )
 
 
@@ -18,6 +21,23 @@ def test_read_csv(self):
         self.assertIsInstance(records, list)
         self.assertEqual(len(records), 3)
 
+    def test_write_csv(self):
+        self.test_data = [
+            ["e2e-mom", "True", "caffe509-ae56-4d42-945e-7b4c161723d1", "d93ae7c3-73c0-43d1-9046-425a3466ecec",
+             "handy"],
+            ["e2e-skate", "True", "2d4feac9-9ab5-4585-9b33-e5abd14ceb0f", "58605ed8-7217-4bf3-8122-229b6f47fa64",
+             "foolish"
+             ]
+        ]
+        self.test_resource_type = "test_organization"
+        self.test_fieldnames = ["name", "active", "id", "identifier", "alias"]
+        write_csv(self.test_data, self.test_resource_type, self.test_fieldnames)
+        self.assertIsInstance(self.test_data, list)
+        self.assertEqual(len(self.test_data), 2)
+        current_time = datetime.now().strftime("%Y-%m-%d-%H-%M")
+        expected_csv_file_path = f"csv/{current_time}-export_{self.test_resource_type}.csv"
+        self.assertTrue(expected_csv_file_path, "CSV file created in expected location")
+
     @patch("main.get_resource")
     def test_build_payload_organizations(self, mock_get_resource):
         mock_get_resource.return_value = "1"
@@ -390,6 +410,38 @@ def test_update_resource_with_non_existing_id_fails(self, mock_get_resource):
             "Trying to update a Non-existent resource", str(raised_error.exception)
         )
 
+    @patch("main.handle_request")
+    @patch("main.write_csv")
+    def test_export_resources_to_csv(self, mock_write_csv, mock_handle_request):
+        mock_response_data = {
+            "entry": [
+                {
+                    "resource": {
+                        "name": "City1",
+                        "status": "active",
+                        "id": "ba787982-b973-4bd5-854e-eacbe161e297",
+                        "identifier": [{"value": "ba787 982-b973-4bd5-854e-eacbe161e297"}],
+                        "partOf": {"display": "test location-1", "reference": "Location/18fcbc2e-4240-4a84-a270"
+                                                                              "-7a444523d7b6"},
+                        "type": [{"coding": [{"display": "Jurisdiction", "code": "jdn"}]}],
+                        "physicalType": {"coding": [{"display": "Jurisdiction", "code": "jdn"}]},
+                    }
+                }
+            ]
+        }
+        mock_handle_request.return_value = (json.dumps(mock_response_data), 200)
+        test_data = [
+            ['City1', 'active', 'ba787982-b973-4bd5-854e-eacbe161e297', 'ba787 982-b973-4bd5-854e-eacbe161e297',
+             'test location-1', 'Location/18fcbc2e-4240-4a84-a270-7a444523d7b6', 'Jurisdiction', 'jdn',
+             'Jurisdiction', 'jdn']]
+
+        test_elements = ["name", "status", "id", "identifier", "parentName", "parentID", "type", "typeCode",
+                         "physicalType", "physicalTypeCode"]
+        export_resources_to_csv("locations", "parameter", "value", 10)
+        resource_type = "Location"
+
+        mock_write_csv.assert_called_once_with(test_data, resource_type, test_elements)
+
 
 if __name__ == "__main__":
     unittest.main()