Type: Package
Title: Interact with BioUML Server
Version: 1.11
Date: 2021-08-10
Description: Functions for connecting to BioUML server, querying BioUML repository and launching BioUML analyses.
Maintainer: Ivan Yevshin <ivan@dote.ru>
License: GPL-2
Depends: RCurl, RJSONIO
NeedsCompilation: no
Packaged: 2021-08-10 06:29:20 UTC; ivan
Author: Ivan Yevshin [aut, cre], Tagir Valeev [aut]
Repository: CRAN
Date/Publication: 2021-08-10 09:00:02 UTC

Run BioUML analysis

Description

Run BioUML analysis optionaly tracking progress

Usage

biouml.analysis(analysisName, parameters=list(), wait=T, verbose=T)

Arguments

analysisName

name of BioUML analysis to run, use biouml.analysis.list to get the list of possible values

parameters

list of parameters to BioUML analysis, use biouml.analysis.parameters to get the list of parameters

wait

whether to wait for analysis completion or return immediately

verbose

print messages and progress from BioUML analysis, only meaningful if wait is TRUE

Value

Job id that can be passed to biouml.job.info and biouml.job.wait

List available BioUML analyses

Description

biouml.analysis.list fetches list of available analyses from current BioUML server

Usage

biouml.analysis.list()

Value

A data frame (data.frame) with two column 'Group' and 'Name'.

Get BioUML analysis parameters

Description

Get BioUML analysis parameters names and description

Usage

biouml.analysis.parameters(analysisName)

Arguments

analysisName

name of BioUML analysis, , use biouml.analysis.list to get the list of possible values

Value

A data frame (data.frame) with row.names corresponding to parameter names and one column 'description' with parameter description

Export data from BioUML

Description

biouml.export exports data from BioUML server to local file in given format

Usage

biouml.export(path, exporter="Tab-separated text (*.txt)",
                     exporter.params=list(), target.file="biouml.out")

Arguments

path

path in BioUML repository

exporter

character string specifying format, biouml.exporters provides possible values

exporter.params

list of parameters to exporter

target.file

a character string naming a file to export to

Value

None (invisible NULL).

Get BioUML export parameters

Description

Get BioUML export parameters

Usage

biouml.export.parameters(path, exporter)

Arguments

path

path to data element in BioUML repository to export

exporter

name of BioUML exporter, use biouml.exporters to get the list of possible values

Value

A data frame (data.frame) with row.names corresponding to parameter names and one column 'description' with parameter description

List BioUML exporters

Description

biouml.exporters fetches the list of exporters from BioUML server, these exporters can be used in biouml.export function

Usage

biouml.exporters()

Value

Character vector of BioUML exporters.

Fetch BioUML table

Description

biouml.get fetches table data from BioUML server

Usage

biouml.get(path)

Arguments

path

Path to table in BioUML repository

Value

A data frame (data.frame) representation of BioUML table from path.

Examples

## Not run: 
## fetch table from public BioUML server
biouml.login("https://ict.biouml.org")
x <- biouml.get("data/Examples/Optimization/Data/Experiments/exp_data_1")
head(x)
biouml.logout()

## End(Not run)

Import file to BioUML

Description

biouml.import imports file to BioUML repository

Usage

biouml.import(file, parentPath, importer, importer.params=list())

Arguments

file

The name of file to import

parentPath

Path to folder in BioUML repository

importer

character string specifying format, biouml.importers provides list of posible values

importer.params

list of parameters to exporter

Value

Resulting path in BioUML repository

Get BioUML import parameters

Description

Get BioUML import parameters

Usage

biouml.import.parameters(path, importer)

Arguments

path

path to data element in BioUML repository to import

importer

name of BioUML importer, use biouml.importers to get the list of possible values

Value

A data frame (data.frame) with row.names corresponding to parameter names and one column 'description' with parameter description

List BioUML importers

Description

biouml.importers fetches the list of importers from BioUML server, these importers can be used in biouml.import function

Usage

biouml.importers()

Value

Character vector of BioUML importers.

Fetch BioUML job info

Description

biouml.job.info fetches info about BioUML job

Usage

biouml.job.info(jobID)

Arguments

jobID

ID of job usually returned from biouml.analysis

Value

A list with following entries

status

job status, one of 'CREATED','RUNNING', 'PAUSED', 'COMPLETED', 'TERMINATED_BY_REQUEST', 'TERMINATED_BY_ERROR'

results

a list of resulting paths in BioUML repository

values

character vector of messages from job

percent

percent complete

Wait for job completion

Description

biouml.job.wait waits for BioUML job completion

Usage

biouml.job.wait(jobID, verbose=T)

Arguments

jobID

ID of job usually returned from biouml.analysis

verbose

print messages and progress from BioUML job

Value

A list with following entries

status

job status, one of 'CREATED','RUNNING', 'PAUSED', 'COMPLETED', 'TERMINATED_BY_REQUEST', 'TERMINATED_BY_ERROR'

results

a list of resulting paths in BioUML repository

values

character vector of messages from job

percent

percent complete

Login to BioUML server

Description

Login to BioUML server. The connection will be saved in global options under name biouml_connection for future reuse.

Usage

biouml.login(url='http://localhost:8080/biouml', user='', pass='')

Arguments

url

URL of running biouml server

user

BioUML user, empty string for anonymous login

pass

password

Value

Invisible connection to BioUML server, connection is a list with following items:

user

the name of user used for connection

pass

password in plain text

url

URL of biouml server

sessionId

session id returned by BioUML server

Examples

## Not run: 
## connect to public BioUML server at https://ict.biouml.org
biouml.login("https://ict.biouml.org")
getOption("biouml_connection")
biouml.logout()

## End(Not run)

Logout from BioUML server

Description

Logouts from BioUML server

Usage

biouml.logout()

List data elements by path

Description

biouml.ls lists children data elements by path in BioUML repository

Usage

biouml.ls(path, extended=F)

Arguments

path

Path to data collection in BioUML repository

extended

whether to return additional attributes for each children

Value

If extended is FALSE a character vector with child names, otherwise a data frame (data.frame) with row.names corresponding to child names and columns hasChildren and type.

Examples

## Not run: 
## list databases available in public BioUML server
biouml.login("https://ict.biouml.org")
biouml.ls("databases")
biouml.logout()

## End(Not run)

Put data.frame to BioUML repository

Description

biouml.put stores data.frame in BioUML repository

Usage

biouml.put(path, value)

Arguments

path

Path in BioUML repository

value

data.frame to store

Examples

## Not run: 
## put data.frame into BioUML repository
x <- data.frame(A=1:10,B=LETTERS[1:10])
biouml.login("https://ict.biouml.org")
biouml.put("data/Collaboration/Demo/Data/Rtest/test_df", x)
biouml.logout()

## End(Not run)

Run BioUML workflow

Description

Run BioUML workflow optionaly tracking progress

Usage

biouml.workflow(path, parameters=list(), wait=T, verbose=T)

Arguments

path

path to BioUML workflow

parameters

list of parameters to BioUML workflow

wait

whether to wait for workflow completion or return immediately

verbose

print messages and progress from BioUML workflow, only meaningful if wait is TRUE

Value

Job id that can be passed to biouml.job.info and biouml.job.wait