annotator modules added by passing config val

.gitignore

@@ -1,7 +1,6 @@
 # Git ignore bioler plate from https://github.com/github/gitignore/blob/master/Python.gitignore
 .secret-env
-Merge-helm/
-Merge-Dug-Architecture.md
+.vscode/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

dags/roger/config/__init__.py

@@ -88,6 +88,7 @@ class BulkLoaderConfig(DictLike):
 
 @dataclass
 class AnnotationConfig(DictLike):
+    annotator_type: str = "annotator_monarch"
     annotator: str = "https://api.monarchinitiative.org/api/nlp/annotate/entities?min_length=4&longest_only=false&include_abbreviation=false&include_acronym=false&include_numbers=false&content="
     normalizer: str = "https://nodenormalization-sri.renci.org/get_normalized_nodes?curie="
     synonym_service: str = "https://onto.renci.org/synonyms/"
@@ -195,6 +196,7 @@ def to_dug_conf(self) -> DugConfig:
             redis_port=self.redisgraph.port,
             nboost_host=self.elasticsearch.nboost_host,
             preprocessor=self.annotation.preprocessor,
+            annotator_type=self.annotation.annotator_type,
             annotator={
                 'url': self.annotation.annotator,
             },

dags/roger/core/bulkload.py

@@ -42,6 +42,11 @@ def tables_up_to_date (self):
             targets=glob.glob (storage.bulk_path ("nodes/**.csv")) + \
             glob.glob (storage.bulk_path ("edges/**.csv")))
 
+    def create (self):
+        """Used in the CLI on args.create_bulk"""
+        self.create_nodes_csv_file()
+        self.create_edges_csv_file()
+
     def create_nodes_csv_file(self):
         if self.tables_up_to_date ():
             log.info ("up to date.")

dags/roger/pipelines/base.py

@@ -14,11 +14,12 @@
 
 import requests
 
-from dug.core import get_parser, get_plugin_manager, DugConcept
-from dug.core.annotate import DugAnnotator, ConceptExpander
+from dug.core import get_parser, get_annotator, get_plugin_manager, DugConcept
+from dug.core.concept_expander import ConceptExpander
 from dug.core.crawler import Crawler
 from dug.core.factory import DugFactory
 from dug.core.parsers import Parser, DugElement
+from dug.core.annotators import Annotator
 from dug.core.async_search import Search
 from dug.core.index import Index
 
@@ -130,8 +131,9 @@ def __init__(self, config: RogerConfig, to_string=True):
             log.addHandler(self.string_handler)
         self.s3_utils = S3Utils(self.config.s3_config)
 
-        self.annotator: DugAnnotator = self.factory.build_annotator()
-
+        self.annotator: Annotator = get_annotator(
+            dug_plugin_manager.hook, self.get_annotator_name(dug_conf)
+        )
         self.tranqlizer: ConceptExpander = self.factory.build_tranqlizer()
 
         graph_name = self.config["redisgraph"]["graph"]
@@ -195,6 +197,13 @@ def get_parser_name(self):
         can also be overriden.
         """
         return getattr(self, 'parser_name', self.pipeline_name)
+
+    def get_annotator_name(dug_conf):
+        """
+        Access method for annotator_name
+        Defaults to annotator_monarch unless specified using annotation.annotator_type in the configuration file.
+        """
+        return getattr(dug_conf, "annotator_type", "annotator_monarch")
 
     def annotate_files(self, parsable_files, output_data_path=None):
         """

requirements.txt

@@ -5,7 +5,8 @@ flatten-dict
 redisgraph-bulk-loader==0.12.3
 pytest
 PyYAML
-git+https://github.com/helxplatform/dug@dug-merge
+# git+https://github.com/helxplatform/dug@dug-merge # Version used by mbacon for dev
+git+https://github.com/helxplatform/dug@329-annotator-modules # Version used for annotator modules
 orjson
 kg-utils==0.0.6
 bmt==1.1.0