fix assets/ installation

Dockerfile

@@ -17,7 +17,7 @@ ENV USE_MSSQL=${USE_MSSQL}
 ARG USE_OTEL=false
 ENV USE_OTEL=${USE_OTEL}
 # Set default log config
-ARG LOG_CONFIG=/code/assets/production_log_config.json
+ARG LOG_CONFIG=assets/production_log_config.json
 ENV LOG_CONFIG=${LOG_CONFIG}
 
 # Updgrade system packages and install curl
@@ -53,7 +53,6 @@ RUN if [ "$USE_OTEL" = "true" ]; then \
 # Copy over the rest of the code
 COPY ./src /code/src
 COPY ./docs /code/docs
-COPY ./assets /code/assets
 COPY README.md /code/README.md
 
 EXPOSE ${PORT}

compose.yml

@@ -43,7 +43,6 @@ services:
       opentelemetry-instrument --service_name recordlinker
       uvicorn recordlinker.main:app --app-dir src
       --host 0 --port 8080
-      --log-config src/recordlinker/log_config.yml
     depends_on:
       db:
         condition: service_healthy

pyproject.toml

@@ -62,6 +62,9 @@ prod = [
 [tool.setuptools]
 package-dir = {"" = "src"}
 
+[tool.setuptools.package-data]
+recordlinker = ["assets/*"]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 namespaces = false

src/recordlinker/config.py

@@ -1,10 +1,11 @@
-import json
 import logging.config
 import typing
 
 import pydantic
 import pydantic_settings
 
+from recordlinker.utils import path as utils
+
 
 class ConfigurationError(Exception):
     """
@@ -99,8 +100,7 @@ def configure_logging(self) -> None:
         if self.log_config:
             # Load logging config from the provided file
             try:
-                with open(self.log_config, "r") as fobj:
-                    config = json.loads(fobj.read())
+                config = utils.read_json(self.log_config)
             except Exception as exc:
                 msg = f"Error loading log configuration: {self.log_config}"
                 raise ConfigurationError(msg) from exc

src/recordlinker/models/algorithm.py

@@ -6,10 +6,10 @@
 from sqlalchemy import schema
 from sqlalchemy import types as sqltypes
 
-from recordlinker import utils
 from recordlinker.config import ConfigurationError
 from recordlinker.config import settings
 from recordlinker.utils import functools as func_utils
+from recordlinker.utils import path as path_utils
 
 from .base import Base
 
@@ -143,7 +143,7 @@ def create_initial_algorithms(target, connection, **kw) -> typing.List[Algorithm
     """
     if settings.initial_algorithms:
         try:
-            data = utils.read_json(settings.initial_algorithms)
+            data = path_utils.read_json(settings.initial_algorithms)
         except Exception as exc:
             raise ConfigurationError("Error loading initial algorithms") from exc
         if not any(algo.get("is_default") for algo in data):

src/recordlinker/utils/__init__.py

@@ -1,27 +0,0 @@
-import json
-import pathlib
-
-
-def project_root() -> pathlib.Path:
-    """
-    Returns the path to the project root directory.
-    """
-    cwd = pathlib.Path(__file__).resolve()
-    root = cwd
-
-    # FIXME: this only works when in the git project root and will fail if we install the
-    # package into the site-packages
-    while not (root / "pyproject.toml").exists():
-        if root.parent == root:
-            raise FileNotFoundError("Project root with 'pyproject.toml' not found.")
-        root = root.parent
-    return root
-
-
-def read_json(*filepaths: str) -> dict:
-    """
-    Loads a JSON file.
-    """
-    filename = pathlib.Path(project_root(), *filepaths)
-    with open(filename, "r") as fobj:
-        return json.load(fobj)

src/recordlinker/utils/path.py

@@ -0,0 +1,25 @@
+import json
+import pathlib
+
+
+def project_root() -> pathlib.Path:
+    """
+    Returns the path to the project root directory.
+    """
+    root = pathlib.Path(__file__).resolve()
+    while root.name != "recordlinker":
+        if root.parent == root:
+            raise FileNotFoundError("recordlinker project root not found.")
+        root = root.parent
+    return root
+
+
+def read_json(path: str) -> dict:
+    """
+    Loads a JSON file.
+    """
+    if not pathlib.Path(path).is_absolute():
+        # if path is relative, append to the project root
+        path = str(pathlib.Path(project_root(), path))
+    with open(path, "r") as fobj:
+        return json.load(fobj)

tests/unit/conftest.py

@@ -8,9 +8,10 @@
 from recordlinker import database
 from recordlinker import main
 from recordlinker import models
+from recordlinker.utils import path as utils
 
 
-def load_json_asset(*paths: str) -> dict | list:
+def load_test_json_asset(*paths: str) -> dict | list:
     """
     Loads a JSON file from the testing 'assets' directory.
     """
@@ -45,14 +46,14 @@ def client():
 @functools.lru_cache
 @pytest.fixture
 def basic_algorithm():
-    for algo in load_json_asset("initial_algorithms.json"):
+    for algo in utils.read_json("assets/initial_algorithms.json"):
         if algo["label"] == "dibbs-basic":
             return models.Algorithm.from_dict(**algo)
 
 
 @functools.lru_cache
 @pytest.fixture
 def enhanced_algorithm():
-    for algo in load_json_asset("initial_algorithms.json"):
+    for algo in utils.read_json("assets/initial_algorithms.json"):
         if algo["label"] == "dibbs-enhanced":
             return models.Algorithm.from_dict(**algo)

tests/unit/hl7/test_fhir.py

@@ -7,7 +7,7 @@
 
 import copy
 
-from conftest import load_json_asset
+from conftest import load_test_json_asset
 
 from recordlinker.hl7 import fhir
 
@@ -20,105 +20,91 @@ def test_fhir_record_to_pii_record():
             {
                 "value": "1234567890",
                 "type": {
-                    "coding": [{
-                        "code": "MR",
-                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
-                        "display": "Medical record number"
-                    }]
+                    "coding": [
+                        {
+                            "code": "MR",
+                            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                            "display": "Medical record number",
+                        }
+                    ]
                 },
             },
             {
-                "system" : "http://hl7.org/fhir/sid/us-ssn",
-                "value" : "111223333",
-                "type" : {
-                    "coding" : [{
-                        "system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
-                        "code" : "SS"
-                    }]
+                "system": "http://hl7.org/fhir/sid/us-ssn",
+                "value": "111223333",
+                "type": {
+                    "coding": [
+                        {"system": "http://terminology.hl7.org/CodeSystem/v2-0203", "code": "SS"}
+                    ]
                 },
             },
-              {
+            {
                 "use": "official",
                 "type": {
                     "text": "Driver's License",
                     "coding": [
                         {
-                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
-                        "code": "DL",
-                        "display": "Driver's License"
+                            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                            "code": "DL",
+                            "display": "Driver's License",
                         }
                     ],
                 },
-                    "system": "urn:oid:2.16.840.1.113883.3.19.3.1.8",
-                    "value": "D1234567",
-                    "assigner": {
+                "system": "urn:oid:2.16.840.1.113883.3.19.3.1.8",
+                "value": "D1234567",
+                "assigner": {
                     "display": "State DMV",
-                    "identifier": {
-                        "system": "urn:oid:2.16.840.1.113883.19.3.1.1", 
-                        "value": "CA"
-                    }
-                }
-            }
-        ],
-        "name": [
-            {
-                "family": "Shepard",
-                "given": [
-                "John"
-                ],
-                "use": "official"
-            }
+                    "identifier": {"system": "urn:oid:2.16.840.1.113883.19.3.1.1", "value": "CA"},
+                },
+            },
         ],
+        "name": [{"family": "Shepard", "given": ["John"], "use": "official"}],
         "birthDate": "2053-11-07",
         "gender": "male",
         "address": [
-        {
-            "line": [
-            "1234 Silversun Strip"
-            ],
-            "buildingNumber": "1234",
-            "city": "Boston",
-            "state": "Massachusetts",
-            "postalCode": "99999",
-            "district": "county",
-            "use": "home"
-        }
-        ],
-        "telecom": [
             {
+                "line": ["1234 Silversun Strip"],
+                "buildingNumber": "1234",
+                "city": "Boston",
+                "state": "Massachusetts",
+                "postalCode": "99999",
+                "district": "county",
                 "use": "home",
-                "system": "phone",
-                "value": "123-456-7890"
             }
         ],
-        "extension" : [
+        "telecom": [{"use": "home", "system": "phone", "value": "123-456-7890"}],
+        "extension": [
             {
-                "url" : "http://hl7.org/fhir/StructureDefinition/individual-genderIdentity",
-                "extension" : [{
-                    "url" : "value",
-                    "valueCodeableConcept" : {
-                        "coding" : [{
-                            "system" : "http://snomed.info/sct",
-                            "code" : "446141000124107",
-                            "display" : "Identifies as female gender (finding)"
-                        }]
+                "url": "http://hl7.org/fhir/StructureDefinition/individual-genderIdentity",
+                "extension": [
+                    {
+                        "url": "value",
+                        "valueCodeableConcept": {
+                            "coding": [
+                                {
+                                    "system": "http://snomed.info/sct",
+                                    "code": "446141000124107",
+                                    "display": "Identifies as female gender (finding)",
+                                }
+                            ]
+                        },
                     }
-                }]
+                ],
             },
             {
-                "url" : "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+                "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
                 "extension": [
                     {
-                        "url" : "ombCategory",
-                        "valueCoding" : {
-                            "system" : "urn:oid:2.16.840.1.113883.6.238",
-                            "code" : "2106-3",
-                            "display" : "White"
-                        }
+                        "url": "ombCategory",
+                        "valueCoding": {
+                            "system": "urn:oid:2.16.840.1.113883.6.238",
+                            "code": "2106-3",
+                            "display": "White",
+                        },
                     }
-                ]
-            }
-        ]
+                ],
+            },
+        ],
     }
 
     pii_record = fhir.fhir_record_to_pii_record(fhir_record)
@@ -142,8 +128,9 @@ def test_fhir_record_to_pii_record():
     assert pii_record.drivers_license.authority == "CA"
     assert pii_record.drivers_license.value == "D1234567"
 
+
 def test_add_person_resource():
-    bundle = load_json_asset("patient_bundle.json")
+    bundle = load_test_json_asset("patient_bundle.json")
     raw_bundle = copy.deepcopy(bundle)
     patient_id = "TEST_PATIENT_ID"
     person_id = "TEST_PERSON_ID"
@@ -158,4 +145,3 @@ def test_add_person_resource():
     # Assert the added element is the person_resource bundle
     assert returned_bundle.get("entry")[-1].get("resource").get("resourceType") == "Person"
     assert returned_bundle.get("entry")[-1].get("request").get("url") == "Person/TEST_PERSON_ID"
-

tests/unit/linking/test_link.py

@@ -10,7 +10,7 @@
 import uuid
 
 import pytest
-from conftest import load_json_asset
+from conftest import load_test_json_asset
 
 from recordlinker import models
 from recordlinker import schemas
@@ -105,7 +105,7 @@ class TestLinkRecordAgainstMpi:
     # TODO: Add test case for last name O'Neil
     @pytest.fixture
     def patients(self):
-        bundle = load_json_asset("simple_patient_bundle_to_link_with_mpi.json")
+        bundle = load_test_json_asset("simple_patient_bundle_to_link_with_mpi.json")
         patients = []
         patients: list[schemas.PIIRecord] = []
         for entry in bundle["entry"]:
@@ -170,4 +170,4 @@ def test_enhanced_match_three(self, session, enhanced_algorithm, patients: list[
         # in second pass name blocks on different cluster and address matches it,
         #  finds greatest strength match and correctly assigns to larger cluster
         assert matches == [False, True, False, True, False, False, True]
-        assert sorted(list(mapped_patients.values())) == [1, 1, 1, 4]
+        assert sorted(list(mapped_patients.values())) == [1, 1, 1, 4]