fix bigbio imports

pdr.py

@@ -28,6 +28,8 @@ import datasets
 from .bigbiohub import kb_features
 from .bigbiohub import BigBioConfig
 from .bigbiohub import Tasks
+from .bigbiohub import parse_brat_file
+from .bigbiohub import brat_parse_to_bigbio_kb
 
 _LANGUAGES = ['English']
 _PUBMED = True
@@ -198,21 +200,21 @@ class PDRDataset(datasets.GeneratorBasedBuilder):
 
                 if self.config.subset_id == "pdr_annotator1":
                     # Provide annotations of annotator 1
-                    example = parsing.parse_brat_file(file, [".ann"])
-                    example = parsing.brat_parse_to_bigbio_kb(example)
+                    example = parse_brat_file(file, [".ann"])
+                    example = brat_parse_to_bigbio_kb(example)
 
                 elif self.config.subset_id == "pdr_annotator2":
                     # Provide annotations of annotator 2
-                    example = parsing.parse_brat_file(file, [".ann2"])
-                    example = parsing.brat_parse_to_bigbio_kb(example)
+                    example = parse_brat_file(file, [".ann2"])
+                    example = brat_parse_to_bigbio_kb(example)
 
                 elif self.config.subset_id == "pdr":
                     # Provide merged version of annotator 1 and 2
-                    annotator1 = parsing.parse_brat_file(file, [".ann"])
-                    annotator1 = parsing.brat_parse_to_bigbio_kb(annotator1)
+                    annotator1 = parse_brat_file(file, [".ann"])
+                    annotator1 = brat_parse_to_bigbio_kb(annotator1)
 
-                    annotator2 = parsing.parse_brat_file(file, [".ann2"])
-                    annotator2 = parsing.brat_parse_to_bigbio_kb(annotator2)
+                    annotator2 = parse_brat_file(file, [".ann2"])
+                    annotator2 = brat_parse_to_bigbio_kb(annotator2)
 
                     example = self._merge_annotations_by_intersection(
                         file, annotator1, annotator2
@@ -229,11 +231,11 @@ class PDRDataset(datasets.GeneratorBasedBuilder):
                 if not str(file).endswith(".txt"):
                     continue
 
-                annotator1 = parsing.parse_brat_file(file, [".ann"])
-                annotator1 = parsing.brat_parse_to_bigbio_kb(annotator1)
+                annotator1 = parse_brat_file(file, [".ann"])
+                annotator1 = brat_parse_to_bigbio_kb(annotator1)
 
-                annotator2 = parsing.parse_brat_file(file, [".ann2"])
-                annotator2 = parsing.brat_parse_to_bigbio_kb(annotator2)
+                annotator2 = parse_brat_file(file, [".ann2"])
+                annotator2 = brat_parse_to_bigbio_kb(annotator2)
 
                 merged_annotation = self._merge_annotations_by_intersection(
                     file, annotator1, annotator2