Merge pull request #17 from smart-on-fhir/mikix/custom-config

feat: support secondary config files with --config

chart_review/cli.py

@@ -3,7 +3,7 @@
 import argparse
 import sys
 
-from chart_review import cohort
+from chart_review import cohort, config
 from chart_review.commands.accuracy import accuracy
 
 
@@ -18,8 +18,14 @@ def add_project_args(parser: argparse.ArgumentParser) -> None:
     parser.add_argument(
         "--project-dir",
         default=".",
-        help="Directory holding project files, "
-        "like config.yaml and labelstudio-export.json (default: current dir)",
+        metavar="DIR",
+        help=(
+            "Directory holding project files, "
+            "like labelstudio-export.json (default: current dir)"
+        ),
+    )
+    parser.add_argument(
+        "--config", "-c", metavar="PATH", help="Config file (default: [project-dir]/config.yaml)"
     )
 
 
@@ -49,7 +55,8 @@ def add_accuracy_subparser(subparsers) -> None:
 
 
 def run_accuracy(args: argparse.Namespace) -> None:
-    reader = cohort.CohortReader(args.project_dir)
+    proj_config = config.ProjectConfig(args.project_dir, config_path=args.config)
+    reader = cohort.CohortReader(proj_config)
     accuracy(reader, args.truth_annotator, args.annotator)
 
 

chart_review/cohort.py

@@ -11,36 +11,24 @@
 
 
 class CohortReader:
-    def __init__(self, project_dir: str):
+    def __init__(self, proj_config: config.ProjectConfig):
         """
-        :param project_dir: str like /opt/labelstudio/study_name
+        :param proj_config: parsed project configuration
         """
-        self.project_dir = project_dir
-        self.config = config.ProjectConfig(project_dir)
-        self.labelstudio_json = self.path(
-            "labelstudio-export.json"
-        )  # TODO: refactor labelstudio.py
+        self.config = proj_config
+        self.project_dir = self.config.project_dir
+        self.labelstudio_json = self.config.path("labelstudio-export.json")
         self.annotator = self.config.annotators
         self.note_range = self.config.note_ranges
         self.class_labels = self.config.class_labels
-        self.annotations = None
+        self.annotations = simplify.simplify_full(self.labelstudio_json, self.annotator)
 
         saved = common.read_json(self.labelstudio_json)
-        if isinstance(saved, list):
-            self.annotations = simplify.simplify_full(self.labelstudio_json, self.annotator)
-        else:
-            # TODO: int keys cant be saved in JSON, compatability hack use instead LabelStudio.py
-            compat = dict()
-            compat["files"] = saved["files"]
-            compat["annotations"] = dict()
-            for k in saved["annotations"].keys():
-                compat["annotations"][int(k)] = saved["annotations"][k]
-            self.annotations = compat
 
         # Load external annotations (i.e. from NLP tags or ICD10 codes)
         for name, value in self.config.external_annotations.items():
             self.annotations = external.merge_external(
-                self.annotations, saved, project_dir, name, value
+                self.annotations, saved, self.project_dir, name, value
             )
 
         # Detect note ranges if they were not defined in the project config
@@ -67,9 +55,6 @@ def __init__(self, project_dir: str):
                     continue
             self.ignored_notes.add(ls_id)
 
-    def path(self, filename):
-        return os.path.join(self.project_dir, filename)
-
     def calc_term_freq(self, annotator) -> dict:
         """
         Calculate Term Frequency of highlighted mentions.

chart_review/config.py

@@ -2,7 +2,7 @@
 import os
 import re
 import sys
-from typing import Iterable, Union
+from typing import Iterable, Optional, Union
 
 import yaml
 
@@ -13,22 +13,12 @@ class ProjectConfig:
     _NUMBER_REGEX = re.compile(r"\d+")
     _RANGE_REGEX = re.compile(r"\d+-\d+")
 
-    def __init__(self, project_dir: str):
+    def __init__(self, project_dir: str, config_path: Optional[str] = None):
         """
         :param project_dir: str like /opt/labelstudio/study_name
         """
-        self._data = None
-
-        for filename in ("config.yaml", "config.json"):
-            try:
-                path = os.path.join(project_dir, filename)
-                with open(path, "r", encoding="utf8") as f:
-                    self._data = yaml.safe_load(f)
-            except FileNotFoundError:
-                continue
-
-        if self._data is None:
-            raise FileNotFoundError(f"No config.yaml or config.json file found in {project_dir}")
+        self.project_dir = project_dir
+        self._data = self._load_config(config_path)
 
         # ** Annotators **
         # Internally, we're often dealing with numeric ID as the primary annotator identifier,
@@ -57,6 +47,26 @@ def __init__(self, project_dir: str):
                 value = {value}
             self.implied_labels[key] = set(value)
 
+    def path(self, filename: str) -> str:
+        return os.path.join(self.project_dir, filename)
+
+    @staticmethod
+    def _read_yaml(path) -> dict:
+        with open(path, encoding="utf8") as f:
+            return yaml.safe_load(f)
+
+    def _load_config(self, config_path: Optional[str]) -> dict:
+        if config_path is None:
+            # Support config.json in case folks prefer that
+            try:
+                return self._read_yaml(self.path("config.json"))
+            except FileNotFoundError:
+                return self._read_yaml(self.path("config.yaml"))
+
+        # Don't resolve config_path relative to the project dir, because
+        # this will have come from the command line and will resolve relative to `pwd`.
+        return self._read_yaml(config_path)
+
     def _parse_note_range(self, value: Union[str, int, list[Union[str, int]]]) -> Iterable[int]:
         if isinstance(value, list):
             return list(itertools.chain.from_iterable(self._parse_note_range(v) for v in value))

tests/test_cli.py

@@ -94,3 +94,18 @@ def test_ignored_ids(self):
             self.assertEqual(0, accuracy_json["FN"])
             self.assertEqual(2, accuracy_json["TN"])
             self.assertEqual(0, accuracy_json["FP"])
+
+    def test_custom_config(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            shutil.copy(f"{DATA_DIR}/cold/labelstudio-export.json", tmpdir)
+            cli.main_cli(
+                [
+                    "accuracy",
+                    "--project-dir",
+                    tmpdir,
+                    "-c",
+                    f"{DATA_DIR}/cold/config.yaml",
+                    "jane",
+                    "john",
+                ]
+            )  # just confirm it doesn't error out

tests/test_external.py

@@ -5,7 +5,7 @@
 import tempfile
 import unittest
 
-from chart_review import cohort
+from chart_review import cohort, config
 
 DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
 
@@ -20,7 +20,7 @@ def setUp(self):
     def test_basic_read(self):
         with tempfile.TemporaryDirectory() as tmpdir:
             shutil.copytree(f"{DATA_DIR}/external", tmpdir, dirs_exist_ok=True)
-            reader = cohort.CohortReader(tmpdir)
+            reader = cohort.CohortReader(config.ProjectConfig(tmpdir))
 
             self.assertEqual(
                 {