pnnl_dms_utils: Utilities for interacting with PNNL DMS

In PNNL-Comp-Mass-Spec/PNNL.DMS.utils: Tools for accessing PNNL's Data Management System

Utilities for interacting with PNNL DMS

Description

Fetches results of different data analysis tools. Not useful outside of PNNL unless connected through VPN. Works on windows out of the box. To make it work on Mac/Linux FreeTDS needs to be installed. Mac/Linux functionality is not well tested.

• get_dms_job_records(): returns job records given variety keyword patterns

• get_tool_output_files_for_job_number(): returns the output of the tool given tool name and file pattern

• get_output_folder_for_job_and_tool(): returns the path given job id and tool name

• get_AScore_results(): returns Ascore results given data package number

• get_job_records_by_dataset_package(): returns job records given data package number

• get_results_for_multiple_jobs(): returns concatenated results given job numbers

• get_results_for_multiple_jobs.dt(): returns results as concatenated data.table given job numbers

• get_results_for_single_job(): returns results given job number

• get_results_for_single_job.dt(): returns results as data.table given job number

• get_datasets_by_data_package(): returns table with datasets info

• download_datasets_by_data_package(): downloads datasets into provided location

Usage

tool2suffix

is_PNNL_DMS_connection_successful()

get_dms_job_records(
  jobs = NULL,
  datasetPttrn = "",
  experimentPttrn = "",
  toolPttrn = "",
  parPttrn = "",
  settingsPttrn = "",
  fastaPttrn = "",
  proteinOptionsPttrn = "",
  instrumentPttrn = ""
)

get_tool_output_files_for_job_number(
  jobNumber,
  toolName = NULL,
  fileNamePttrn,
  mostRecent = TRUE
)

get_output_folder_for_job_and_tool(jobNumber, toolName, mostRecent = TRUE)

get_job_records_by_dataset_package(data_package_num)

get_datasets_by_data_package(data_package_num)

download_datasets_by_data_package(
  data_package_num,
  copy_to = ".",
  fileNamePttrn = ".raw",
  ncores = 2
)

get_results_for_multiple_jobs(jobRecords)

get_results_for_multiple_jobs.dt(jobRecords, expected_multiple_files = FALSE)

get_results_for_single_job(pathToFile, fileNamePttrn)

get_url_from_dir_and_file(dir, file_name_segment)

get_results_for_single_job.dt(
  pathToFile,
  fileNamePttrn,
  expected_multiple_files = FALSE
)

path_to_FASTA_used_by_DMS(data_package_num, organism_db = NULL)

Arguments

jobs	(integer) DMS job ID
datasetPttrn
experimentPttrn
toolPttrn
parPttrn
settingsPttrn
fastaPttrn
proteinOptionsPttrn
instrumentPttrn
jobNumber
toolName
fileNamePttrn
mostRecent	(logical) only most recent or all output files
data_package_num	(integer) data package ID number.
copy_to	folder path to copy files into
ncores	number of cores to use in cluster
jobRecords
expected_multiple_files	do we expect multiple files for a single job or not. Default is FALSE.
pathToFile
dir
file_name_segment
organism_db	(character) FASTA file. This is the same as the Organism DB column. No need to specify this if there is only one FASTA file associated with the jobs.

Format

An object of class list of length 8.

Examples

if (is_PNNL_DMS_connection_successful()) {
  get_output_folder_for_job_and_tool(863951, "DTA_Refinery")
}

PNNL-Comp-Mass-Spec/PNNL.DMS.utils documentation built on Jan. 20, 2025, 9:10 a.m.