Added python script to transform the tsv file into csv file with corresponding table name

Author: Tanzira

src/ontology/ak-ontology.Makefile

@@ -20,6 +20,7 @@ exports/CL.tsv: imports/CL_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/CL.tsv CellOntology
 
 exports/DOID.tsv: imports/DOID_import.owl | exports/
 	$(ROBOT) extract \
@@ -30,6 +31,7 @@ exports/DOID.tsv: imports/DOID_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/DOID.tsv TODO
 
 exports/PATO.tsv: imports/PATO_import.owl | exports/
 	$(ROBOT) extract \
@@ -40,6 +42,7 @@ exports/PATO.tsv: imports/PATO_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/PATO.tsv TODO
 
 exports/UO.tsv: imports/UO_import.owl | exports/
 	$(ROBOT) extract \
@@ -50,6 +53,7 @@ exports/UO.tsv: imports/UO_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/UO.tsv TODO
 
 exports/UBERON.tsv: imports/UBERON_import.owl | exports/
 	$(ROBOT) extract \
@@ -60,6 +64,7 @@ exports/UBERON.tsv: imports/UBERON_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/UBERON.tsv TODO
 
 exports/OBI.tsv: imports/OBI_import.owl | exports/
 	$(ROBOT) extract \
@@ -70,6 +75,7 @@ exports/OBI.tsv: imports/OBI_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/OBI.tsv BiomedicalInvestigations
 
 exports/MRO.tsv: imports/MRO_import.owl | exports/
 	$(ROBOT) extract \
@@ -80,6 +86,7 @@ exports/MRO.tsv: imports/MRO_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/MRO.tsv TODO
 
 exports/NCBITaxon.tsv: imports/NCBITaxon_import.owl | exports/
 	$(ROBOT) extract \
@@ -90,3 +97,4 @@ exports/NCBITaxon.tsv: imports/NCBITaxon_import.owl | exports/
 	--header 'ID|Label|SubClassOf [ID]' \
 	--sort ID \
 	--export $@
+	python3 ../scripts/ontology_table_transform.py exports/NCBITaxon.tsv TODO

src/scripts/ontology_table_transform.py

@@ -0,0 +1,37 @@
+import pandas as pd
+import os
+import sys
+
+file_dir = 'ak-ontology/src/ontology/exports'
+save_file_dir = "/ak_data/ak-data-load/ontology"
+
+# filename to be that needs to be converted from tsv to csv
+filename = f'{sys.argv[1]}'
+table_name = sys.argv[2]
+# filename for the csv file Which should be the Table name in the database
+ontology_term_filename = f'{table_name}.csv'
+term_parents_filename = f'{table_name}_parent.csv'
+print("====================================================================================")
+print(f'Now processing: {filename} for {table_name} and {table_name}_parent table.')
+tsv_path = os.path.join(file_dir, filename)
+df = pd.read_csv(tsv_path, sep = '\t', dtype=str)
+#set column names based on the keys of the table
+df.columns = ["term_id", "term_label", "parent_term_id"]
+df["parent_term_id"] = df["parent_term_id"].fillna(df["term_id"])
+# get only ontology terms and their label
+ontology_term = df[["term_id", "term_label"]]
+# put multiple parents into its own row
+df["parent_term_id"] = df["parent_term_id"].str.split("|")
+term_parents = df.explode("parent_term_id").reset_index(drop=True)
+# get only ontology terms and their parent
+term_parents = term_parents[["term_id", "parent_term_id"]]
+term_parents.rename(columns={"term_id": f"{table_name}_term_id"}, inplace=True)
+print(term_parents.head())
+#save these csv file in ak directory
+ontology_term.to_csv(f'{save_file_dir}/{ontology_term_filename}',index = False)
+term_parents.to_csv(f'{save_file_dir}/{term_parents_filename}',index = False)
+
+print(f"Done creating {ontology_term_filename} and {term_parents_filename} file.")
+print("====================================================================================")
+
+