added timing to functions

db/scripts/main.py

@@ -1,6 +1,6 @@
 import reader as rd
 from uploader import catlas_extention, base_setup, bulk_extention
-from utils import print_update
+from utils import print_update, time_function
 from querier import run_queries
 import os
 import pandas as pd
@@ -12,19 +12,21 @@
 os.environ["_DEFAULT_CREDENTIALS_PATH"] = "../../config.yml"
 os.environ["_DEV_MAX_REL"] = str(10000)
 os.environ["_NEO4J_IMPORT_PATH"] = "/usr/local/bin/neo4j/import/"
-os.environ["_FUNCTION_TIME_PATH"] = "../source/misc/function_times.tsv"
+os.environ["_FUNCTION_TIME_PATH"] = "../source/timing/function_times.tsv"
 
-os.environ["_TIME_FUNCTIONS"] = str(False)
+os.environ["_TIME_FUNCTIONS"] = str(True)
 os.environ["_SILENT"] = str(False)
 os.environ["_PRODUCTION"] = str(True)
 os.environ["_UPDATE_NEO4J"] = str(True)
 
 
+@time_function
 def read_experiment_files(genes_annotated_mouse):
     data = rd.read(reformat=True, genes_annotated_mouse=genes_annotated_mouse, mode=0)
     return data
 
 
+@time_function
 def read_string_files(
     complete_mouse: pd.DataFrame,
     proteins_mouse: pd.DataFrame,
@@ -41,21 +43,25 @@ def read_string_files(
     return data
 
 
+@time_function
 def read_ensembl_files():
     data = rd.read(mode=2)
     return data
 
 
+@time_function
 def read_functional_files():
     data = rd.read(mode=3)
     return data
 
 
+@time_function
 def read_catlas_files(or_nodes: pd.DataFrame, distance: pd.DataFrame):
     data = rd.read(or_nodes=or_nodes, distance=distance, mode=4)
     return data
 
 
+@time_function
 def upload_workflow():
     (
         complete_mouse,

db/scripts/read/read_functional.py

@@ -103,10 +103,8 @@ def _reformat_ft_overlap_human(df: pd.DataFrame):
 
 
 def _reformat_terms_mouse(df: pd.DataFrame):
-    df = df.drop(columns=["Unnamed: 0"])
     return df
 
 
 def _reformat_terms_human(df: pd.DataFrame):
-    df = df.drop(columns=["Unnamed: 0"])
     return df

db/scripts/reader.py

@@ -8,7 +8,6 @@
 from read.read_catlas import parse_catlas
 
 
-@time_function
 def read(
     dir_path: str = None,
     reformat: bool = True,

db/scripts/upload/upload_catlas.py

@@ -2,11 +2,12 @@
 import numpy as np
 from neo4j import Driver
 from upload.upload_experiment import create_correlation, create_context, create_motif
-from utils import execute_query, print_update
+from utils import execute_query, print_update, time_function
 
 __CATLAS__STUDY = {"name": "Catlas, Whole Mouse Brain", "source": "catlas.org/wholemousebrain/"}
 
 
+@time_function
 def create_source(cell_info: pd.DataFrame, species: str, driver: Driver):
     print_update(update_type="Node Creation", text="Study, (Sub-/Subsub-)Celltype and Source", color="blue")
     _, nuclei_counts, celltype, subtype, subsubtype = (