Annotation Configuration file with versioning details, and leftover a…

…nnotation unit refactor (#164) * Fixed typo * fixed typo * Added version fields in configuration file * Updating Annotations configuration with Versioning Details (#152) * Added HPO date as version_type * Added HPO and Ensembl version details * added alliance genome versioning * Updated Annotation Configuration with versioning types and corresponding attributes * Rebased from main branch. Also deleted annotation-logging branch
uab-cgds-worthey · Mar 22, 2024 · de8626b · de8626b
1 parent 0f27285
commit de8626b
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Showing 5 changed files with 166 additions and 72 deletions.
diff --git a/backend/src/core/annotation.py b/backend/src/core/annotation.py
@@ -3,7 +3,6 @@
 import logging
 import queue
 
-# from .annotation_logging import annotation_log_label, annotation_unit_string
 from .annotation_task import AnnotationTaskFactory
 from ..models.analysis import Analysis
 from ..repository.annotation_config_collection import AnnotationConfigCollection

diff --git a/backend/src/core/annotation_logging.py b/backend/src/core/annotation_logging.py
diff --git a/backend/src/repository/annotation_config_collection.py b/backend/src/repository/annotation_config_collection.py
@@ -1,5 +1,5 @@
 """
-Manges the annotation configuration of various genomic units according to the
+Manages the annotation configuration of various genomic units according to the
 type of Genomic Unit.
 """
 

diff --git a/backend/tests/unit/core/test_annotation_task.py b/backend/tests/unit/core/test_annotation_task.py
@@ -31,7 +31,7 @@ def test_annotation_task_create_http_task(hgvs_variant_genomic_unit, transcript_
 
 
 def test_annotate_forge_gene_linkout_dataset(forge_annotation_task_gene):
-    """Verifies that the NCBI linkout dataset is structed as expected"""
+    """Verifies that the NCBI linkout dataset is structured as expected"""
     actual_annotation = forge_annotation_task_gene.annotate()
     assert "NCBI_linkout" in actual_annotation
     assert actual_annotation['NCBI_linkout'] == 'https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=45614'