- Created by Nacho Medina, last modified by Marta Bleda on Nov 16, 2017
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Overview
The OpenCGA R Client has been implemented following the Bioconductor guidelines for package development which promote high-quality, well documented and interoperable software. The client provides a user-friendly interface to work with OpenCGA REST Web Services through R.
Client Library
The R package can be downloaded from XXXX and the source code can be found in https://github.com/opencb/opencga/tree/develop/opencga-client/src/main/R. The methods and classes implemented have been designed following the S4 interface as recommended by Bioconductor. Class definitions are stored in R/AllClasses.R. Currently, there is only one class defined containing the OpenCGA connection details which is extensively used by all methods in the package. A set of methods have been implemented to deal with the connectivity and login to the REST host. These methods are stored in R/OpencgaR-methods.R. Connection to the host is done in two steps using the functions initOpencgaR and opencgaLogin for defining the connection details and loging in, respectively.
# Initialise connection con <- initOpencgaR(host = "http://localhost:8080/opencga/", version = "v1") # Log in con <- opencgaLogin(opencga = con, userid = "user", passwd = "pass")
The package implements at least one function for each available resource (user, project, study, etc.) which are defined in R/AllGeneric.R. Currently, the following functions are available:
# User userClient(OpencgaR, user, action, params=NULL) userConfigClient(OpencgaR, user, name, action, params=NULL) userFilterClient(OpencgaR, user, name, action, params=NULL) # Project projectClient(OpencgaR, project, action, params=NULL) # Study studyClient(OpencgaR, study, action, params=NULL) studyGroupClient(OpencgaR, study, group=NULL, action, params=NULL) studyAclClient(OpencgaR, study, memberId, action, params=NULL) studyVariablesetClient(OpencgaR, variableSet, action, params=NULL) studyVariablesetFieldClient(OpencgaR, variableSet, action, params=NULL) # File fileClient(OpencgaR, f, action, params=NULL) fileAclClient(OpencgaR, f, memberId, action, params=NULL) # Job jobClient(OpencgaR, jobId, action, params=NULL) jobAclClient(OpencgaR, jobId, memberId, action, params=NULL) # Family familyClient(OpencgaR, family, action, params=NULL) familyAnnotationsetClient(OpencgaR, family, annotationsetName, action, params=NULL) familyAclClient(OpencgaR, memberIds, action, params=NULL) # Individual individualClient(OpencgaR, individual, action, params=NULL) individualAnnotationsetClient(OpencgaR, individual, annotationsetName, action, params=NULL) individualAclClient(OpencgaR, memberIds, action, params=NULL) # Sample sampleClient(OpencgaR, sample, action, params=NULL) sampleAnnotationsetClient(OpencgaR, sample, annotationsetName, action, params=NULL) sampleAclClient(OpencgaR, memberIds, action, params=NULL) # Cohort cohortClient(OpencgaR, cohort, action, params=NULL) cohortAnnotationsetClient(OpencgaR, cohort, annotationsetName, action, params=NULL) cohortAclClient(OpencgaR, memberIds, action, params=NULL) # Clinical clinicalClient(OpencgaR, clinicalAnalysis, action, params=NULL) # Meta metaClient(OpencgaR, action, params=NULL) # Ananlysis analysisVariantClient(OpencgaR, action, params=NULL)
Every method belonging to each resource takes the mandatory parameters individually and calls to the corresponding web service using the correct HTTP method (GET or POST). All functions require an OpencgaR connection object (as described in the initialisation and login step). The action parameter expects a character string specifying what information we want to obtain (the endpoint, as described here). Any additional query and body parameters (params) should be specified in the params field as a list(). For example, if we want to get the information about two samples ("sample1" and "sample2") excluding the attributes and stats fields, we could do it as follows:
# Create params list
params <- list(exclude="attributes,stats")
# Get information
sampleClient(OpencgaR=con,
sample=c("sample1","sample2"),
action="info",
params=params)
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