Package 'neurohcp'

Retrieve S3 Bucket List

Description

Lists the Buckets available with the Key/Secrete

Usage

bucketlist(region = "us-east-1", access_key = NULL, secret_key = NULL, ...)

Arguments

region	Region of S3 Bucket
access_key	Amazon S3 Access Key
secret_key	Amazon S3 Secret Key
...	arguments to pass to bucket_list_df

Value

List of Buckets

Examples

if (have_aws_key()){
bucketlist()
}

---

Download an entire directory from HCP

Description

Downloads a directory/folder from HCP database

Usage

download_hcp_dir(
  prefix,
  delimiter = "",
  outdir = tempfile(),
  verbose = TRUE,
  ...
)

download_fcp_dir(...)

download_openneuro_dir(...)

Arguments

prefix	Folder to download
delimiter	Delimiter for files
outdir	Output directory
verbose	Should diagnostic values be printed?
...	additional arguments to pass to hcp_list_files

Value

List of return from calling hcp_list_files, the output directory, and all destination files (not subsetted by those that did in fact download)

Examples

if (have_aws_key()) {
   prefix = "HCP/100307/release-notes"
   res = download_hcp_dir(prefix = prefix, verbose = FALSE)
}

---

Download HCP file

Description

Downloads a file from HCP S3 Bucket

Usage

download_hcp_file(
  path_to_file,
  destfile = NULL,
  verbose = TRUE,
  error = TRUE,
  ...
)

download_fcp_file(...)

download_openneuro_file(...)

Arguments

path_to_file	Path to file on HCP S3 Bucket
destfile	Destination filename
verbose	should progress be added to downloading?
error	Should the function error if the return was bad?
...	arguments to pass to hcp_aws_url

Value

Output filename that was downloaded

Examples

if (have_aws_key()){
path_to_file <- "HCP_900/100206/MNINonLinear/100206.164k_fs_LR.wb.spec"
download_hcp_file(path_to_file = path_to_file)
}

---

Get HCP file

Description

Wraps a make_aws_call to a GET statement to get the file

Usage

get_hcp_file(path_to_file = "/", ..., verbose = TRUE, verb = "GET")

head_hcp_file(...)

get_fcp_file(...)

head_fcp_file(...)

get_openneuro_file(...)

head_openneuro_file(...)

Arguments

path_to_file	Path to file on HCP S3 Bucket
...	arguments to pass to make_aws_call
verbose	Should the URL be printed?
verb	passed to VERB

Value

Result of GET

---

Scanning Information for HCP 1200 Data

Description

A data.frame with all the available scanning information for the HCP 1200 data.

Usage

hcp_1200_scanning_info

Format

An object of class tbl_df (inherits from tbl, data.frame) with 69615 rows and 18 columns.

---

Scanning Information for HCP 900 Data

Description

A data.frame with all the available scanning information for the HCP 900 data.

Usage

hcp_900_scanning_info

Format

An object of class tbl_df (inherits from tbl, data.frame) with 34406 rows and 18 columns.

---

Construct AWS S3 String

Description

Constructs url string for AWS S3 Bucket to pass in for HCP downloading

Usage

hcp_aws_url(
  path_to_file = "",
  bucket = "hcp-openaccess",
  region = "us-east-1",
  access_key = NULL,
  secret_key = NULL,
  lifetime_minutes = 20,
  query = NULL,
  verb = "GET",
  sign = TRUE
)

Arguments

path_to_file	Path to file on HCP S3 Bucket
bucket	Bucket to download from
region	Region of S3 Bucket
access_key	Amazon S3 Access Key
secret_key	Amazon S3 Secret Key
lifetime_minutes	Time that connection can be opened
query	additional query to add to url
verb	httr VERB to be used
sign	Should the url be signed?

Value

Character of the url to be passed to httr 'VERB's

Examples

if (have_aws_key()){
path_to_file <- "HCP_900/100206/MNINonLinear/100206.164k_fs_LR.wb.spec"
hcp_aws_url(path_to_file)
}

---

Get list of HCP Ids

Description

Returns list of IDs of folders in the HCP database

Usage

hcp_ids(group = c("HCP", "HCP_900", "HCP_1200", "HCP_Retest"))

Arguments

group

Group of IDs to return

Value

Character vector

Examples

if (have_aws_key()) {
head(hcp_ids("HCP"))
head(hcp_ids("HCP_900"))
}

---

List files from HCP bucket

Description

Lists a set of files from an HCP bucket for a specific sub-folder

Usage

hcp_list_files(prefix = "", delimiter = NULL, query = NULL, marker = NULL, ...)

fcp_list_files(prefix = "", delimiter = NULL, query = NULL, marker = NULL, ...)

openneuro_list_files(
  prefix = "",
  delimiter = NULL,
  query = NULL,
  marker = NULL,
  ...
)

hcp_list_dirs(prefix = "HCP/", ...)

fcp_list_dirs(prefix = "data/Projects/", ...)

openneuro_list_dirs(prefix = NULL, ...)

Arguments

prefix	directory folder to list files. If "", then it will be the root path
delimiter	Delimiter to list files. For example ".mat", for ".mat"
query	Additional query arguments
marker	the marker to start the listing, needed for pagination of results
...	additional arguments passed to get_hcp_file

Value

List with the result of the GET command, the parsed result, and the content from the result.

Examples

if (have_aws_key()){
x = hcp_list_files(prefix = "HCP/100307/unprocessed/3T/Diffusion",
   delimiter="bval")
stopifnot(x$parsed_result$ListBucketResult$Name[[1]] == "hcp-openaccess")
t1_niis = hcp_list_files(prefix ="HCP/100307/T1w",
delimiter = ".nii.gz")
all_dirs = hcp_list_dirs("HCP/")
}

if (have_aws_key()){
  res = hcp_list_dirs("HCP/")
  projects = unlist(parse_list_files(res)$prefixes)
  projects = unname(projects)
  projects = unname(projects)
  head(projects)
  head(basename(projects))
  stopifnot("100307" %in% basename(projects))
}
if (have_aws_key()){
res = fcp_list_dirs()
projects = unlist(parse_list_files(res)$prefixes)
projects = unname(projects)
head(projects)
head(basename(projects))
stopifnot("ABIDE" %in% basename(projects))
}
res = openneuro_list_dirs()
projects = unlist(parse_list_files(res)$prefixes)
projects = unname(projects)
head(projects)
if (length(projects) > 0) {
head(basename(projects))
stopifnot("ds000002" %in% basename(projects))
}

---

Scanning Information for HCP Data

Description

A data.frame with all the available scanning information for the HCP data.

Usage

hcp_scanning_info

Format

An object of class tbl_df (inherits from tbl, data.frame) with 34406 rows and 18 columns.

---

Construct AWS S3 Call

Description

Constructs GET information string for AWS S3 Bucket

Usage

make_aws_call(
  path_to_file = "/",
  bucket = "hcp-openaccess",
  region = "us-east-1",
  access_key = NULL,
  secret_key = NULL,
  lifetime_minutes = 5,
  query = NULL,
  verb = "GET",
  sign = TRUE
)

Arguments

path_to_file	Path to file on HCP S3 Bucket
bucket	Bucket to download from
region	Region of S3 Bucket
access_key	Amazon S3 Access Key
secret_key	Amazon S3 Secret Key
lifetime_minutes	Time that connection can be opened
query	additional query to add to verb command
verb	httr VERB to be used
sign	Should the url be signed?

Value

Character of the url to be passed to httr 'VERB's

Examples

if (have_aws_key()){
path_to_file <- paste0(
   "HCP_900/100206/MNINonLinear/",
   "100206.164k_fs_LR.wb.spec")
result = make_aws_call(path_to_file)
# don't want this stuff printed because it has keys
result$headers$secret_key = NULL
result$headers$access_key = NULL
result$query$AWSAccessKeyId = NULL
result$query$Signature = NULL
result
}

---

Parse listed files from HCP bucket

Description

This parses the result from hcp_list_files and organizes the files into data.frames

Usage

parse_list_files(ret)

Arguments

ret	object with element parsed_result, usually from hcp_list_files

Value

List of 2 data.frames, the contents and the commonprefixes elements from the list

Examples

if (have_aws_key()){
   ret = hcp_list_files(prefix = "HCP/100307/unprocessed/3T/Diffusion")
   parsed = parse_list_files(ret)
   stopifnot(!is.null(parsed$contents))
 }

---

Set Amazon AWS Key

Description

Sets and returns the AWS keys. This will error if not all are specified.

Usage

set_aws_api_key(
  access_key = NULL,
  secret_key = NULL,
  default_region = "us-east-1",
  error = TRUE
)

have_aws_key()

Arguments

access_key	Amazon access key. If NULL then looks at the AWS_ACCESS_KEY_ID system variable.
secret_key	Amazon secret key. If NULL then looks at the AWS_SECRET_ACCESS_KEY system variable.
default_region	Amazon default region. If NULL then looks at the AWS_DEFAULT_REGION system variable.
error	Should this function error if things are not specified?

Value

List of access_key, secret_key, and default_region

---