#' CREATED: 2022-01-18
#' MODIFIED: 2022-05-13
#' PURPOSE: Update the Menu setting in Application Settings
#' STATUS: stable
#' PACKAGES: rd3tools, dotenv, os, json
#' COMMENTS: NA
#'////////////////////////////////////////////////////////////////////////////
from rd3.api.molgenis import Molgenis
from dotenv import load_dotenv
from os import environ
import json
# set vars and init sessions for both Molgenis instances
load_dotenv()
rd3_acc = Molgenis(url=environ['MOLGENIS_ACC_HOST'])
rd3_prod = Molgenis(url=environ['MOLGENIS_PROD_HOST'])
rd3_prod.login(username=environ['MOLGENIS_PROD_USR'],
password=environ['MOLGENIS_PROD_PWD'])
rd3_acc.login(username=environ['MOLGENIS_ACC_USR'],
password=environ['MOLGENIS_ACC_PWD'])
# read contents of the menu config file
with open('rd3/molgenis_menu.json', 'r') as file:
menu = file.read()
file.close()
# parse json and stringify
molgenisMenuJson = json.loads(menu)
from datatable import dt, f, count, as_type, fread, rbind, by
from dotenv import load_dotenv
from os import environ
from datetime import datetime
# import pandas as pd
import re
# set vars
load_dotenv()
currentReleaseType = 'patch' # or 'release'
currentFreeze = 'freeze1' # 'freeze2'
currentPatch = 'patch3' # 'patch1'
# host=environ['MOLGENIS_PROD_HOST']
host = environ['MOLGENIS_ACC_HOST']
rd3 = Molgenis(url=host)
rd3.login(username=environ['MOLGENIS_ACC_USR'],
password=environ['MOLGENIS_ACC_PWD'])
# build entity IDs and paths based on current freeze and patch
paths = buildRd3Paths(freeze=currentFreeze,
patch=currentPatch,
baseFilePath=environ['CLUSTER_BASE'])
# def __unpack__phenotypicfeatures(phenotypicFeatures):
# """Unpack Phenotypic Features
# Extract `phenotypicFeatures` and separate into observed and unobserved
# phenotypic codes
# @param phenotypicFeatures : output from data['phenopacket']['phenotypicFeatures']
# @return a dictionary with observed and unobserved phenotype codes
# """
# ~ 0 ~
# Fetch Metadata for all releases
# init database connection
statusMsg('Connecting to RD3....')
load_dotenv()
# rd3=Molgenis(url=environ['MOLGENIS_ACC_HOST'])
# rd3.login(
# username=environ['MOLGENIS_ACC_USR'],
# password=environ['MOLGENIS_ACC_PWD']
# )
rd3=Molgenis(url=environ['MOLGENIS_PROD_HOST'])
rd3.login(
username=environ['MOLGENIS_PROD_USR'],
password=environ['MOLGENIS_PROD_PWD']
)
# SET RELEASES
# If new releases are added to RD3, add package identifier to the list below.
# Since the aim of the table is to be able to identify subjects that are
# lacking genetic data, it is best to separate novelomics releases from
# regular freezes, and then merge the two arrays
regularReleases=[
'freeze1',
'freeze2',