opalr v1.4.1


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'Opal' Data Repository Client and 'DataSHIELD' Utils

Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.


Opal R

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Opal R Client


o <- opal.login('username', 'passwd', 'http://localhost:8080')
# Assign one variable to a R symbol
opal.assign(o, 'VAR1', 'datasource.table:VAR1')
opal.execute(o, 'summary(VAR1)')
# Assign some variables as a data.frame to a R symbol
opal.assign(o, 'TABLE', 'datasource.table', variables=list('VAR1','VAR2'))
opal.execute(o, 'summary(TABLE$VAR1)')
opal.execute(o, 'summary(TABLE$VAR2)')

DataSHIELD Client

See DSOpal.

Functions in opalr

Name Description
.handleError Handle error response
dsadmin.install_package Install a DataSHIELD package
.handleResponseLocation Default request response Location handler.
dsadmin.get_options Get the DataSHIELD options
dsadmin.get_method Get a DataSHIELD method
dsadmin.rm_option Remove a DataSHIELD option
dsadmin.get_methods Get DataSHIELD methods
dsadmin.rm_method Remove DataSHIELD method
.is.verbose Verbose option
.handleResponse Default request response handler.
.handleResponseOrCallback Process response with default handler or the provided one
.isContentEmpty Check if response content is empty.
dsadmin.set_package_methods Set DataSHIELD package methods
opal.as_md_table Array to Markdown
harmo.annotate Set variable annotation with a taxonomy term
opal.assign Data or expression assignment
dsadmin.rm_methods Remove DataSHIELD methods.
.newProgress Create a new progress instance with default settings.
dsadmin.set_method Set DataSHIELD method
.rmOpalSession Remove a Opal session (logout)
.opal.login Create the opal object
dsadmin.rm_package_methods Remove DataSHIELD package methods
opal.command_rm Remove an asynchronous command
opal.execute Execute a R script
.tickProgress Output the progress status if option "datashield.progress" is allows to.
opal.commands List the asynchronous commands
dsadmin.installed_package Check DataSHIELD package
.listToJson Simple transformation function of a list into a JSON object/array.
dsadmin.package_description Get DataSHIELD package description
harmo.table_get Get a Opal table as a tibble
harmo.dictionary_apply Apply the dictionary to a tibble
oadmin.install_package Install package
.tokenHeader Constructs the value for the X-Opal-Auth header
harmo.dictionary_update Update the dictionary of a Opal table
oadmin.installed_package Check package is installed
dsadmin.set_option Set DataSHIELD option
.rmRSession Remove a R session from Opal.
opal.execute.source Execute a R file script
opal.annotate Apply the annotations to a Opal table
opal.annotations Get the annotations of a Opal table
.select Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
harmo.table_save Save a local tibble as a Opal table
harmo.annotate.status Set variable annotation with Harmonization Status term
opal.login Opal login
oadmin.installed_packages List installed packages
.newSession Create a new R session in Opal.
oadmin.installed_devtools Check devtools package
opal.assign.data Data assignment
harmo.annotations List the annotations
oadmin.package_description Get package description
oadmin.remove_package Remove package
opal.file_download Download a file
opal.command Get an asynchronous command
opal.assign.script R script assignment
.url Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
dsadmin.remove_package Remove DataSHIELD package
dsadmin.package_descriptions Get DataSHIELD package descriptions
opal.assign.table Data assignment to a data.frame
opal.assign.table.tibble Data assignment to a tibble
opal.attribute_values Get a vector of values
.verbose Verbose flag
oadmin.install_devtools Install devtools package
opal.file_read Read a file
opal.command_result Get result of an asynchronous command
opal.datasources Get datasources
opal.file_rm Remove a file
opal.delete Generic REST resource deletion.
opal.report Opal report
opal.logout Logout from Opal(s)
opal.commands_rm Remove all asynchronous commands
opal.report_md Turn a R markdown file to html.
opal.tasks Get the tasks
oadmin.install_github Install a package form GitHub
opal.taxonomies Get taxonomies
opal.file_upload Upload a file
opal.file_write Write a file
opal.datasource Get a datasource
opal.resource Get a resource of a project
opal.assign.resource Resource assignment
opal.file_cp Copy a file
opal.file Get file content
opal.task_cancel Cancel a task
opal.resources Get the resource references of a project
opal.tables Get tables of a datasource
opal.file_ls List content of a folder
opal.task Get a task
opal.file_mv Move and/or rename a file
opal.file_mkdir Make a folder
opal.symbols List R symbols
opal.rm Remove a R symbol (deprecated)
opal.symbol_import Import a tibble
opal.variable Get a variable of a table
opal.table Get a table of a datasource
opal.post Generic REST resource creation.
opal.get Generic REST resource getter.
opal.load_package Load package
opal.task_wait Wait for a task to complete.
opal.projects Get projects
opal.symbol_rm Remove a R symbol
opal.put Generic REST resource update.
opal.variables Get variables of a table
opal.vocabularies Get the vocabularies of a taxonomy
opal.version_compare Compare
opal.vocabulary Get a taxonomy vocabulary
opal.project Get a project
opal.workspace_rm Remove a R workspace from a opal.
opal.symbol_save Save a tibble
opal.taxonomy Get a taxonomy
opal.workspaces Get the R workspaces from a opal.
opal.workspace_save Save the current session in a opal R workspace.
opal.terms Get the terms of a vocabulary
opal.valueset Get the values of an entity
opal.unload_package Unload package
.getContent Wrapper of httr::content()
.getSessions Get all R session in Opal.
.getPEMFilePath Extract absolute path to the pem file
.getRSessionId Extract R session Id from opal object, create a new R session if not found.
.extractJsonField Extract JSON
.authorizationHeader Constructs the value for the Authorization header
.extractOpalSessionId Extract opalsid from cookie data frame.
.deparse Turn expression into character strings.
.extractLabel Extract label for locale. If not found, fallback to undefined language label (if any).
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License GPL-3
URL https://www.obiba.org/ https://www.obiba.org/pages/products/opal/ https://doi.org/10.1093/ije/dyx180 http://www.datashield.ac.uk/
BugReports https://github.com/obiba/opalr
RoxygenNote 7.1.0
VignetteBuilder knitr
Encoding UTF-8
NeedsCompilation no
Packaged 2020-06-08 08:29:03 UTC; yannick
Repository CRAN
Date/Publication 2020-06-08 09:30:02 UTC

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