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 |
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'} |
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