Merge pull request #190 from kids-first/custom-search-parameters

✨ Add patient us-core-race and us-core-ethnicity search params

smilecdr/search_parameters/SearchParameter-us-core-ethnicity.json

@@ -0,0 +1,60 @@
+{
+  "resourceType": "SearchParameter",
+  "id": "us-core-ethnicity",
+  "url": "http://hl7.org/fhir/us/core/SearchParameter/us-core-ethnicity",
+  "version": "7.0.0",
+  "name": "USCoreEthnicity",
+  "status": "active",
+  "date": "2022-04-14",
+  "publisher": "HL7 International / Cross-Group Projects",
+  "contact": [
+    {
+      "name": "HL7 International / Cross-Group Projects",
+      "telecom": [
+        {
+          "system": "url",
+          "value": "http://www.hl7.org/Special/committees/cgp"
+        },
+        {
+          "system": "email",
+          "value": "[email protected]"
+        }
+      ]
+    }
+  ],
+  "description": "Returns patients with an ethnicity extension matching the specified code.",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "urn:iso:std:iso:3166",
+          "code": "US"
+        }
+      ]
+    }
+  ],
+  "code": "ethnicity",
+  "base": ["Patient"],
+  "type": "token",
+  "expression": "Patient.extension.where(url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity').extension.value.code",
+  "xpathUsage": "normal",
+  "multipleOr": true,
+  "_multipleOr": {
+    "extension": [
+      {
+        "url": "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation",
+        "valueCode": "MAY"
+      }
+    ]
+  },
+  "multipleAnd": true,
+  "_multipleAnd": {
+    "extension": [
+      {
+        "url": "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation",
+        "valueCode": "MAY"
+      }
+    ]
+  }
+}
+

smilecdr/search_parameters/SearchParameter-us-core-race.json

@@ -0,0 +1,60 @@
+{
+  "resourceType": "SearchParameter",
+  "id": "us-core-race",
+  "url": "http://hl7.org/fhir/us/core/SearchParameter/us-core-race",
+  "version": "7.0.0",
+  "name": "USCoreRace",
+  "status": "active",
+  "date": "2022-04-14",
+  "publisher": "HL7 International / Cross-Group Projects",
+  "contact": [
+    {
+      "name": "HL7 International / Cross-Group Projects",
+      "telecom": [
+        {
+          "system": "url",
+          "value": "http://www.hl7.org/Special/committees/cgp"
+        },
+        {
+          "system": "email",
+          "value": "[email protected]"
+        }
+      ]
+    }
+  ],
+  "description": "Returns patients with a race extension matching the specified code.",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "urn:iso:std:iso:3166",
+          "code": "US"
+        }
+      ]
+    }
+  ],
+  "code": "race",
+  "base": ["Patient"],
+  "type": "token",
+  "expression": "Patient.extension.where(url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race').extension.value.code",
+  "xpathUsage": "normal",
+  "multipleOr": true,
+  "_multipleOr": {
+    "extension": [
+      {
+        "url": "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation",
+        "valueCode": "MAY"
+      }
+    ]
+  },
+  "multipleAnd": true,
+  "_multipleAnd": {
+    "extension": [
+      {
+        "url": "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation",
+        "valueCode": "MAY"
+      }
+    ]
+  }
+}
+

src/bin/load_search_parameters.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+import os
+import argparse
+from pprint import pprint
+
+from requests.auth import HTTPBasicAuth
+
+from src.config import (
+    SEARCH_PARAMETER_DIR,
+    REINDEX_PAYLOAD,
+    BASE_URL,
+    REINDEX_ENDPOINT,
+    FHIR_APP_ADMIN,
+    FHIR_APP_ADMIN_PW
+)
+from src.misc import (
+    read_json,
+    send_request
+)
+
+
+def upsert_search_parameters(
+    client_id, client_secret, search_parameter_dir=SEARCH_PARAMETER_DIR
+):
+    """
+    Read search parameters from file, then upsert them in server
+    Last, reindex the resources so that SearchParameters take effect
+    """
+    print("Loading search parameters")
+
+    for fn in os.listdir(search_parameter_dir):
+        if not fn.endswith(".json"):
+            continue
+        filepath = os.path.join(search_parameter_dir, fn)
+        search_param = read_json(filepath)
+
+        # Load search parameter
+        id_ = search_param["id"]
+        endpoint = "/".join(
+            part.strip("/") for part in [BASE_URL, "SearchParameter", id_]
+        )
+        resp = send_request(
+            "put",
+            endpoint,
+            json=search_param,
+            auth=HTTPBasicAuth(client_id, client_secret),
+        )
+        print(
+            f"PUT {endpoint}"
+        )
+
+    # Start reindexing operation
+    endpoint = f"{BASE_URL}/$reindex"
+    resp = send_request(
+        "post",
+        endpoint,
+        json=REINDEX_PAYLOAD,
+        auth=HTTPBasicAuth(client_id, client_secret),
+    )
+    pprint(resp.json())
+
+
+def cli():
+    """
+    CLI for running this script
+    """
+    parser = argparse.ArgumentParser(
+        description='Load SearchParameters in FHIR server'
+    )
+    parser.add_argument(
+        "--client_id",
+        default=FHIR_APP_ADMIN,
+        help="Admin ID to authenticate with FHIR server",
+    )
+    parser.add_argument(
+        "--client_secret",
+        default=FHIR_APP_ADMIN_PW,
+        help="Admin secret to authenticate with FHIR server",
+    )
+    parser.add_argument(
+        "--search_parameter_dir",
+        default=SEARCH_PARAMETER_DIR,
+        help="Path to dir with SearchParameters",
+    )
+    args = parser.parse_args()
+
+    upsert_search_parameters(
+        args.client_id, args.client_secret, args.search_parameter_dir
+    )
+
+    print("✅ Load SearchParameters complete")
+
+
+if __name__ == "__main__":
+    cli()

src/config/__init__.py

@@ -5,6 +5,7 @@
 ROOT_DIR = os.path.dirname(os.path.dirname(os.path.dirname((__file__))))
 DATA_DIR = os.path.join(ROOT_DIR, "data", "resources")
 SEED_USERS_FILEPATH = os.path.join(ROOT_DIR, "smilecdr/settings", "users.json")
+SEARCH_PARAMETER_DIR = os.path.join(ROOT_DIR, "smilecdr/search_parameters")
 
 DOTENV_PATH = find_dotenv()
 if DOTENV_PATH:
@@ -17,6 +18,7 @@
 FHIR_APP_ADMIN_PW = os.environ.get("FHIR_APP_ADMIN_PW")
 FHIR_TEST_USER_PW = os.environ.get("FHIR_TEST_USER_PW")
 USER_MGMNT_ENDPOINT = os.environ.get("USER_MGMNT_ENDPOINT")
+REINDEX_ENDPOINT = os.environ.get("REINDEX_ENDPOINT")
 KEYCLOAK_PROXY_URL = os.environ.get(
     "KEYCLOAK_PROXY_URL", "http://localhost:8081/keycloak-proxy"
 )
@@ -25,3 +27,11 @@
 KEYCLOAK_READ_CLIENT_ID = os.environ.get("KEYCLOAK_READ_CLIENT_ID")
 KEYCLOAK_READ_CLIENT_SECRET = os.environ.get("KEYCLOAK_READ_CLIENT_SECRET")
 KEYCLOAK_ISSUER = os.environ.get("KEYCLOAK_ISSUER")
+
+REINDEX_PAYLOAD= {
+  "resourceType": "Parameters",
+  "parameter": [ {
+    "name": "url",
+    "valueString": "Patient?"
+  }]
+}

src/misc.py

@@ -1,11 +1,12 @@
+"""
+Miscellaneous utility functions
+"""
 import time
+import json
+from pprint import pformat
 
 import requests
 
-from src.config import (
-    BASE_URL,
-)
-
 
 def elapsed_time_hms(start_time):
     """
@@ -15,3 +16,72 @@ def elapsed_time_hms(start_time):
     return time.strftime('%H:%M:%S', time.gmtime(elapsed))
 
 
+def send_request(method, *args, ignore_status_codes=None, **kwargs):
+    """Send http request. Raise exception on status_code >= 300
+
+    :param method: name of the requests method to call
+    :type method: str
+    :raises: requests.Exception.HTTPError
+    :returns: requests Response object
+    :rtype: requests.Response
+    """
+    if isinstance(ignore_status_codes, str):
+        ignore_status_codes = [ignore_status_codes]
+
+    # NOTE: Set timeout so requests don't hang
+    # See https://requests.readthedocs.io/en/latest/user/advanced/#timeouts
+    if not kwargs.get("timeout"):
+        # connect timeout, read timeout
+        kwargs["timeout"] = (3, 60)
+    else:
+        print(
+            f"⌚️ Applying user timeout: {kwargs['timeout']} (connect, read)"
+            " seconds to request"
+        )
+
+    requests_op = getattr(requests, method.lower())
+    status_code = 0
+    try:
+        resp = requests_op(*args, **kwargs)
+        status_code = resp.status_code
+        resp.raise_for_status()
+    except requests.exceptions.HTTPError as e:
+        if ignore_status_codes and (status_code in ignore_status_codes):
+            pass
+        else:
+            body = ""
+            try:
+                body = pformat(resp.json())
+            except:
+                body = resp.text
+
+            msg = (
+                f"❌ Problem sending {method} request to server\n"
+                f"{str(e)}\n"
+                f"args: {args}\n"
+                f"kwargs: {pformat(kwargs)}\n"
+                f"{body}\n"
+            )
+            print(msg)
+            raise e
+
+    return resp
+
+
+def read_json(filepath, default=None):
+    """
+    Read JSON file into Python dict. If default is not None and the file
+    does not exist, then return default.
+
+    :param filepath: path to JSON file
+    :type filepath: str
+    :param default: default return value if file not found, defaults to None
+    :type default: any, optional
+    :returns: your data
+    :rtype: dict
+    """
+    if (default is not None) and (not os.path.isfile(filepath)):
+        return default
+
+    with open(filepath, "r") as json_file:
+        return json.load(json_file)