Merge pull request #701 from kids-first/add-datatypes

Add new single cell datatypes

Author: awarkow

kf_lib_data_ingest/common/constants.py

@@ -111,6 +111,13 @@ class DATA_TYPE:
         ISOFORM_EXPRESSION = "Isoform Expression"
         SOMATIC_COPY_NUMBER_VARIATIONS = "Somatic Copy Number Variations"
         SOMATIC_STRUCTURAL_VARIATIONS = "Somatic Structural Variations"
+        # single cell data types
+        QC_METRICS = "QC Metrics"
+        SPLICE_JUNCTION = "Splice Junction"
+        EXPRESSION_COUNTS = "Expression Counts"
+        STAR_SINGLE_CELL_COUNTS = "STAR Single Cell Counts"
+        STAR_CELL_RANGER_COUNTS = "STAR Cell Ranger Counts"
+        SINGLE_CELL_QC_METRICS = "Single Cell QC Metrics"
 
     class FORMAT:
         BAI = "bai"

kf_lib_data_ingest/templates/my_ingest_package/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Ingest Package Config """
+"""Ingest Package Config"""
 
 # The list of entities that will be loaded into the target service. These
 # should be class_name values of your target API config's target entity

kf_lib_data_ingest/validation/values.py

@@ -167,6 +167,12 @@ def inner(x):
         constants.GENOMIC_FILE.DATA_TYPE.UNALIGNED_READS,
         constants.GENOMIC_FILE.DATA_TYPE.VARIANT_CALLS,
         constants.GENOMIC_FILE.DATA_TYPE.VARIANT_CALLS_INDEX,
+        constants.GENOMIC_FILE.DATA_TYPE.QC_METRICS,
+        constants.GENOMIC_FILE.DATA_TYPE.SPLICE_JUNCTION,
+        constants.GENOMIC_FILE.DATA_TYPE.EXPRESSION_COUNTS,
+        constants.GENOMIC_FILE.DATA_TYPE.STAR_SINGLE_CELL_COUNTS,
+        constants.GENOMIC_FILE.DATA_TYPE.STAR_CELL_RANGER_COUNTS,
+        constants.GENOMIC_FILE.DATA_TYPE.SINGLE_CELL_QC_METRICS,
     },
     CONCEPT.GENOMIC_FILE.SIZE: check_non_negative,
     # INVESTIGATOR

tests/data/SD_ME0WME0W/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Ingest Package Config """
+"""Ingest Package Config"""
 
 from kf_lib_data_ingest.common.concept_schema import CONCEPT
 

tests/data/kfid_study/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Dataset Ingest Config """
+"""Dataset Ingest Config"""
 
 # The list of entities that will be loaded into the target service
 target_service_entities = [

tests/data/sample_registration/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Ingest Package Config """
+"""Ingest Package Config"""
 
 # The list of entities that will be loaded into the target service
 target_service_entities = ["sample" "biospecimen", "sample_relationship"]

tests/data/simple_study/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Dataset Ingest Config """
+"""Dataset Ingest Config"""
 
 from kf_lib_data_ingest.common.concept_schema import CONCEPT
 

tests/data/test_boyd_study/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Ingest Package Config """
+"""Ingest Package Config"""
 
 # The list of entities that will be loaded into the target service
 target_service_entities = [

tests/data/test_study/ingest_package_config.py

@@ -1,4 +1,4 @@
-""" Ingest Package Config """
+"""Ingest Package Config"""
 
 from kf_lib_data_ingest.common.concept_schema import CONCEPT