Lintin'

monarch-initiative · Sep 22, 2023 · 941d250 · 941d250
1 parent 025d56b
commit 941d250
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py
@@ -437,6 +437,7 @@ def iteratively_generate_extract(
     ):
         write_extraction(results, output, output_format)
 
+
 # TODO: combine this command with pubmed_annotate - they are converging
 @main.command()
 @template_option

diff --git a/src/ontogpt/engines/spires_engine.py b/src/ontogpt/engines/spires_engine.py
@@ -79,7 +79,7 @@ def extract_from_text(
                 logging.info(f"RAW TEXT: {raw_text}")
                 next_object = self.parse_completion_payload(
                     raw_text, cls, object=object  # type: ignore
-                )  
+                )
                 if extracted_object is None:
                     extracted_object = next_object
                 else:
@@ -96,7 +96,7 @@ def extract_from_text(
             logging.info(f"RAW TEXT: {raw_text}")
             extracted_object = self.parse_completion_payload(
                 raw_text, cls, object=object  # type: ignore
-            )  
+            )
         return ExtractionResult(
             input_text=text,
             raw_completion_output=raw_text,
@@ -516,13 +516,13 @@ def _parse_line_to_dict(
                 logging.debug(f"  RECURSING ON SLOT: {slot.name}, range={slot_range.name}")
                 vals = [
                     self._extract_from_text_to_dict(v, slot_range) for v in vals  # type: ignore
-                ]  
+                ]
             else:
                 for sep in [" - ", ":", "/", "*", "-"]:
                     if all([sep in v for v in vals]):
                         vals = [
                             dict(zip(slots_of_range, v.split(sep, 1))) for v in vals  # type: ignore
-                        ]  
+                        ]
                         for v in vals:
                             for k in v.keys():  # type: ignore
                                 v[k] = v[k].strip()  # type: ignore

diff --git a/src/ontogpt/evaluation/hpoa/eval_hpoa.py b/src/ontogpt/evaluation/hpoa/eval_hpoa.py
@@ -21,7 +21,7 @@
 DATABASE_DIR = Path(__file__).parent / "database"
 TEST_CASES_DIR = Path("tests").joinpath("input")
 TEST_HPOA_FILE = "test_sample.hpoa.tsv"
-NUM_TESTS = 3 # Note: each test requires input text; see provided test cases
+NUM_TESTS = 3  # Note: each test requires input text; see provided test cases
 
 DISEASE_ID = str
 TERM = str
@@ -182,7 +182,7 @@ def eval_against_pubs(self, num_tests=NUM_TESTS) -> EvaluationObjectSetHPOA:
         eos.training = []
         eos.predictions = []
         shuffle(eos.test)
-        for test_case in eos.test[0:num_tests-1]:
+        for test_case in eos.test[0 : num_tests - 1]:
             # text = self.disease_text(test_case.id)
             if len(test_case.publications) != 1:
                 raise ValueError(f"Expected 1 publication, got {len(test_case.publications)}")

diff --git a/src/ontogpt/io/yaml_wrapper.py b/src/ontogpt/io/yaml_wrapper.py
@@ -5,7 +5,6 @@
 
 import pydantic
 from ruamel.yaml import YAML, RoundTripRepresenter
-from ruamel.yaml.comments import CommentedMap
 
 # import yaml
 # from yaml import SafeDumper