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Phil Snyder philerooski

  • Seattle, WA
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View parse_healthkit_metadata.R
library(tidyverse)
library(synapser)
library(optparse)
JSON_REGEX <- '\'"""{.*}"""\''
#' Read command line arguments
read_args <- function() {
parser <- OptionParser(description = paste(
"Take a folder on Synapse containing health kit data which may or may not",
View get_bridge_uploads.py
import bridgeclient # https://github.com/larssono/bridgeclient
import functools
def get_bridge_client(email, password, study):
bridge = bridgeclient.bridgeConnector(email, password, study=study)
return bridge
"""
View reduce_features.py
import synapseclient
import argparse
import pandas
import json
import os
DUMMY_ARG = "dummy" # A 'None' like string we can pass to boto
View tremorModule.R
# Entry function to extract tremor features
######################
# Load Libraries
######################
library(optparse)
library(data.table)
library(plyr)
library(tidyverse)
View walkingModule.R
library("synapseClient")
synapseLogin()
library("plyr")
library("dplyr")
library("ggplot2")
library("jsonlite")
library("parallel")
library("tidyr")
library("lubridate")
View submit_jobs.py
import synapseclient
import pandas
import argparse
import boto3
import os
import json
import uuid
AWS_BATCH_ARRAY_SIZE_LIMIT = 10000
View curate_mpower.R
rm(list=ls())
options(stringsAsFactors = F)
library(synapser)
library(tidyverse)
library(lubridate)
fetch_and_prep <- function() {
mpower_f <- synGet("syn21213531") #"syn11488492")
mpower <- read_tsv(mpower_f$path)
now <- lubridate::now()
View change_sharing_scope.R
library(synapser)
library(tidyverse)
PROJECT_ID <- "syn12030321"
UDALL_USERS <- "syn18691020"
AT_HOME_PD_USERS <- "syn16786935"
get_users <- function(user_table_id) {
user_table <- as_tibble(synTableQuery(paste(
View compute_md5.py
"""
Compute MD5 hashes of files in a local directory or in an S3 bucket.
Outputs a CSV file with columns `path` and `md5`.
When computing MD5 hashes of objects in an S3 bucket, `path` corresponds
to the S3 URI.
"""
import multiprocessing as mp
import boto3 as boto
import pandas as pd
@philerooski
philerooski / exportMD5.py
Last active Apr 22, 2019
Update Healthcode to MD5 hash table for JourneyPro, Presence, ElevateMS
View exportMD5.py
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'}