From 08b07e47e8b7b5bd10e3ff227adf483e9f87f368 Mon Sep 17 00:00:00 2001 From: Devon Joseph Leadman Date: Mon, 3 Jun 2024 13:20:46 -0400 Subject: [PATCH] merge fix --- .gitmodules | 4 ++-- RDAS_GFKG/prep_neo4j_data.py | 8 ++++++-- RDAS_PAKG/epi4GARD | 2 +- start_dev.py | 4 ++-- sysvars.py | 5 +++++ 5 files changed, 16 insertions(+), 7 deletions(-) diff --git a/.gitmodules b/.gitmodules index b7ae983..48d22a8 100755 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,6 @@ [submodule "RDAS_PAKG/epi4GARD"] path = RDAS_PAKG/epi4GARD - url = https://github.com/ncats/epi4GARD.git + url = git@github.com:ncats/epi4GARD.git [submodule "RDAS_PAKG/NaturalHistory4GARD"] path = RDAS_PAKG/NaturalHistory4GARD - url = https://github.com/ncats/NaturalHistory4GARD.git + url = git@github.com:ncats/NaturalHistory4GARD.git diff --git a/RDAS_GFKG/prep_neo4j_data.py b/RDAS_GFKG/prep_neo4j_data.py index e1bd1f8..284ac63 100755 --- a/RDAS_GFKG/prep_neo4j_data.py +++ b/RDAS_GFKG/prep_neo4j_data.py @@ -174,6 +174,12 @@ def run_normmap(): prj_files = sorted(prj_files) for idx, abs_file in enumerate(abs_files): + year = re.findall(r'\d+', abs_file)[0] + + if os.path.exists(data_raw(f'normmap/RePORTER_NORMMAP_{year}.csv')): + print(data_raw(f'normmap/RePORTER_NORMMAP_{year}.csv') + ' already exists... bypassing') + continue + prj_file = prj_files[idx] print(abs_file, ' -merged- ',prj_file) @@ -184,8 +190,6 @@ def run_normmap(): merged_df = pd.merge(tmp, tmp2, on=['APPLICATION_ID']) merged_df['APPLICATION_ID'] = merged_df['APPLICATION_ID'].astype(int) - year = re.findall(r'\d+', abs_file)[0] - merged_df.to_csv(data_raw(f'normmap/RePORTER_NORMMAP_{year}.csv'), index=False) diff --git a/RDAS_PAKG/epi4GARD b/RDAS_PAKG/epi4GARD index dac3f5c..5d6e097 160000 --- a/RDAS_PAKG/epi4GARD +++ b/RDAS_PAKG/epi4GARD @@ -1 +1 @@ -Subproject commit dac3f5ce0cfc5a62458cc9a6f8e463b76f574162 +Subproject commit 5d6e0975cd08aea9328c845514f36638d80e510f diff --git a/start_dev.py b/start_dev.py index 48c3e32..df04ae3 100644 --- a/start_dev.py +++ b/start_dev.py @@ -3,6 +3,7 @@ import sys workspace = os.path.dirname(os.path.abspath(__file__)) sys.path.append(workspace) +sys.path.append('/home/leadmandj/RDAS/') sys.path.append(os.getcwd()) print(sys.path) import sysvars @@ -13,8 +14,7 @@ import argparse from datetime import date,datetime from AlertCypher import AlertCypher -from gard.methods import get_node_counts -import ses_firebase +from RDAS_GARD.methods import get_node_counts import firebase_admin from firebase_admin import auth from firebase_admin import credentials diff --git a/sysvars.py b/sysvars.py index 43cc129..eee566a 100644 --- a/sysvars.py +++ b/sysvars.py @@ -14,6 +14,11 @@ base_path = '/home/{current_user}/{base_directory_name}/'.format(current_user=current_user, base_directory_name=base_directory_name) +# RDAS Team contacts for emails +contacts = [ + "leadmandj@nih.gov" +] + # Folder paths backup_path = '{base_path}backup/'.format(base_path=base_path) transfer_path = '{base_path}transfer/'.format(base_path=base_path)