Another pass at transform

Knowledge-Graph-Hub · Jul 22, 2024 · f61eed5 · f61eed5
1 parent d671b84
commit f61eed5
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/Makefile b/Makefile
@@ -73,7 +73,7 @@ download:
 
 .PHONY: run
 run: download
-	$(RUN) ingest sevilleja_transform
+	$(RUN) ingest transform
 	$(RUN) python scripts/generate-report.py
 
 

diff --git a/...estoration_ingests/sevilleja_transform.py → src/restoration_ingests/transform.py b/...estoration_ingests/sevilleja_transform.py → src/restoration_ingests/transform.py
@@ -3,26 +3,26 @@
 from biolink_model.datamodel.pydanticmodel_v2 import *  # Replace * with any necessary data classes from the Biolink Model
 from koza.cli_utils import get_koza_app
 
-koza_app = get_koza_app("data_source, ex. alliance, flybase, or hpoa._type_of_ingest, ex. gene, disease_to_phenotype, or disease_associations.")
+koza_app = get_koza_app("sevilleja_transform")
 
 while (row := koza_app.get_row()) is not None:
     # Code to transform each row of data
     # For more information, see https://koza.monarchinitiative.org/Ingests/transform
     entity_a = Entity(
-        id=f"XMPL:00000{row['example_column_1'].split('_')[-1]}",
-        name=row["example_column_1"],
+        id=f"plot:{row['Plot']}",
+        name=row['Plot'],
         category=["biolink:Entity"],
     )
     entity_b = Entity(
-        id=f"XMPL:00000{row['example_column_2'].split('_')[-1]}",
-        name=row["example_column_2"],
+        id=f"treat:{row['treat']}",
+        name=row['treat'],
         category=["biolink:Entity"],
     )
     association = Association(
         id=str(uuid.uuid1()),
-        subject=row["example_column_1"],
-        predicate=row["example_column_3"],
-        object=row["example_column_2"],
+        subject=row['Plot'],
+        predicate="plot_received_treatment",
+        object=row['treat'],
         subject_category="SUBJ",
         object_category="OBJ",
         category=["biolink:Association"],

diff --git a/...toration_ingests/sevilleja_transform.yaml → src/restoration_ingests/transform.yaml b/...toration_ingests/sevilleja_transform.yaml → src/restoration_ingests/transform.yaml
@@ -1,11 +1,11 @@
 # Config file for transforming data from a source
 # See additional/optional config parameters at https://koza.monarchinitiative.org/Ingests/source_config/
 
-name: "Sevilleja_et_al_2022"
+name: "sevilleja_transform"
 metadata: "./src/restoration_ingests/metadata.yaml"
 format: "csv"
 files:
-  - "./data/DATA-antsVeg_4years.csv"
+  - "DATA-antsVeg_4years.csv"
 #################################################################################################
 ### file_archive is typically optional, but required if:                                      ###
 ###    1. files is not provided                                                               ###