philerooski

from __future__ import division, print_function
import synapseclient as sc
import pandas as pd
import numpy as np
import argparse
import LDopaScorer


TRAINING_TABLE = 'syn10495809'
TESTING_TABLE = 'syn10701954'

philerooski

import bridgeclient
import hashlib
import pandas as pd
import synapseclient as sc
import argparse

SYNAPSE_TABLES = {
        'journey-pro': 'syn11439373',
        'elevate-ms': 'syn11439398',
        'lilly-presence': 'syn11445782'}

philerooski

Mounting an EFS Instance From an External Account

Only First time:

1. Send Thaneer your AWS account ID and he will add you to the trusted entities for the IAM role that he has created.
2. If you don't have one already, create an IAM user. Permissions aren't relevant since you will be switching roles as soon as you sign in as the IAM user, but you may want to omit any permissions so that you don't accidentally create an instance before switching roles.

Every time

1. When you are signed in as an IAM user under your root account, go to this link, enter a display name, (pick your favorite color), and click "Switch Role" https://signin.aws.amazon.com/switchrole?roleName=mPowerEFSRole&account=389689814525

philerooski

AWS Batch Tips and Tricks

Working with AWS Batch works roughly like this:

​ Compute Environments > Job Queues ⊥ Job Definitions > Jobs

Meaning compute environments and job queues are configured independently of job definitions and jobs — though if you're going to create a job, you're going to need a job definition, and if you're going to create a job queue, it's going to need a compute environment to run within.

Job Definitions > Jobs

philerooski

title	output	date
JourneyPRO - on-going summary	html_document html_notebook pdf_document default default default	`r format(Sys.time(), '%d %B, %Y')`

philerooski

#' SF12v2 questionnaire scoring
library(synapseClient)
synapseLogin()
healthSurveyId <- "syn10278768"
healthSurvey <- synTableQuery(paste("select * from", healthSurveyId))@values
questionCols <- names(healthSurvey)[12:23]
sf <- healthSurvey[c("recordId", "healthCode", "dataGroups", questionCols)] %>% 
    filter(dataGroups %in% c("beta_thalassemia", "myelodysplastic_syndrome", "myelofibrosis")) %>% na.omit()

sf12v2 <- function( X = NULL ) {

philerooski

import synapseclient as sc
import matplotlib.pyplot as plt
import pandas as pd
import argparse

def read_args():
    parser = argparse.ArgumentParser(description='Plot camera vs oximeter readings.')
    parser.add_argument('medianData')
    return parser.parse_args()