Package: opalr 3.5.0

Yannick Marcon

opalr: '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.

Authors:Yannick Marcon [aut, cre], Amadou Gaye [ctb], OBiBa group [cph]

opalr_3.5.0.tar.gz
opalr_3.5.0.zip(r-4.5)opalr_3.5.0.zip(r-4.4)opalr_3.5.0.zip(r-4.3)
opalr_3.5.0.tgz(r-4.4-any)opalr_3.5.0.tgz(r-4.3-any)
opalr_3.5.0.tar.gz(r-4.5-noble)opalr_3.5.0.tar.gz(r-4.4-noble)
opalr_3.5.0.tgz(r-4.4-emscripten)opalr_3.5.0.tgz(r-4.3-emscripten)
opalr.pdf |opalr.html✨
opalr/json (API)

# Install 'opalr' in R:
install.packages('opalr', repos = c('https://obiba.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/obiba/opalr/issues

On CRAN:

7.88 score 3 stars 2 packages 177 scripts 904 downloads 201 exports 41 dependencies

Last updated 2 months agofrom:b5e6fa2e20. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winOKOct 18 2024
R-4.5-linuxOKOct 18 2024
R-4.4-winOKOct 18 2024
R-4.4-macOKOct 18 2024
R-4.3-winOKOct 18 2024
R-4.3-macOKOct 18 2024

Exports:dictionary.annotatedictionary.annotate.harmo_statusdictionary.annotationsdictionary.applydictionary.inspectdsadmin.activitydsadmin.activity_summarydsadmin.get_methoddsadmin.get_methodsdsadmin.get_optionsdsadmin.install_github_packagedsadmin.install_local_packagedsadmin.install_packagedsadmin.installed_packagedsadmin.logdsadmin.package_descriptiondsadmin.package_descriptionsdsadmin.permdsadmin.perm_adddsadmin.perm_deletedsadmin.profiledsadmin.profile_accessdsadmin.profile_createdsadmin.profile_deletedsadmin.profile_enabledsadmin.profile_existsdsadmin.profile_initdsadmin.profile_permdsadmin.profile_perm_adddsadmin.profile_perm_deletedsadmin.profile_rparserdsadmin.profilesdsadmin.publish_packagedsadmin.remove_packagedsadmin.rm_methoddsadmin.rm_methodsdsadmin.rm_optiondsadmin.rm_optionsdsadmin.rm_package_methodsdsadmin.set_methoddsadmin.set_optiondsadmin.set_package_methodsdsadmin.unpublish_packageoadmin.activityoadmin.activity_summaryoadmin.install_bioconductor_packageoadmin.install_cran_packageoadmin.install_devtoolsoadmin.install_github_packageoadmin.install_local_packageoadmin.install_packageoadmin.installed_devtoolsoadmin.installed_packageoadmin.installed_packagesoadmin.logoadmin.log_restoadmin.log_sqloadmin.package_descriptionoadmin.permoadmin.perm_addoadmin.perm_deleteoadmin.r_permoadmin.r_perm_addoadmin.r_perm_deleteoadmin.remove_packageoadmin.system_metricsoadmin.system_permoadmin.system_perm_addoadmin.system_perm_deleteoadmin.user_addoadmin.user_deleteoadmin.user_enableoadmin.user_existsoadmin.user_profile_deleteoadmin.user_profilesoadmin.user_reset_passwordoadmin.usersopal.annotateopal.annotationsopal.as_md_tableopal.assignopal.assign.dataopal.assign.resourceopal.assign.scriptopal.assign.tableopal.assign.table.tibbleopal.attribute_valuesopal.commandopal.command_resultopal.command_rmopal.commandsopal.commands_rmopal.datasourceopal.datasourcesopal.deleteopal.executeopal.execute.sourceopal.fileopal.file_cpopal.file_downloadopal.file_lsopal.file_mkdiropal.file_mkdir_tmpopal.file_mvopal.file_readopal.file_rmopal.file_unzipopal.file_uploadopal.file_writeopal.getopal.load_packageopal.loginopal.logoutopal.permsopal.postopal.profilesopal.projectopal.project_backupopal.project_commandopal.project_createopal.project_deleteopal.project_existsopal.project_permopal.project_perm_addopal.project_perm_deleteopal.project_restoreopal.projectsopal.projects_databasesopal.putopal.reportopal.resourceopal.resource_createopal.resource_deleteopal.resource_existsopal.resource_extension_createopal.resource_getopal.resource_permopal.resource_perm_addopal.resource_perm_deleteopal.resource_view_createopal.resource_view_reconnectopal.resourcesopal.resources_permopal.resources_perm_addopal.resources_perm_deleteopal.rmopal.sqlopal.sql_historyopal.symbol_importopal.symbol_rmopal.symbol_saveopal.symbolsopal.tableopal.table_createopal.table_deleteopal.table_dictionary_getopal.table_dictionary_updateopal.table_existsopal.table_exportopal.table_getopal.table_importopal.table_permopal.table_perm_addopal.table_perm_deleteopal.table_saveopal.table_truncateopal.table_view_createopal.table_view_updateopal.tablesopal.tables_permopal.tables_perm_addopal.tables_perm_deleteopal.taskopal.task_cancelopal.task_waitopal.tasksopal.taxonomiesopal.taxonomyopal.taxonomy_deleteopal.taxonomy_downloadopal.taxonomy_uploadopal.termsopal.tokenopal.token_datashield_createopal.token_deleteopal.token_r_createopal.token_renewopal.token_sql_createopal.tokensopal.unload_packageopal.valuesetopal.variableopal.variable_summaryopal.variablesopal.version_compareopal.vocabulariesopal.vocabularyopal.workspace_restoreopal.workspace_rmopal.workspace_saveopal.workspaces

Dependencies:askpassbitbit64clicliprcpp11crayoncurldplyrfansiforcatsgenericsgluehavenhmshttrjsonlitelabelledlifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

DataSHIELD Administration

Yannick Marcon

Rendered fromdatashield-admin.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2021-06-30
Started: 2021-06-30

Opal Files

Yannick Marcon

Rendered fromopal-files.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2021-06-30
Started: 2017-02-09

Opal Projects

Yannick Marcon

Rendered fromopal-projects.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2021-07-01
Started: 2019-02-05

Opal R Session

Yannick Marcon

Rendered fromopal-rsession.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2021-07-01
Started: 2019-02-05

Readme and manuals

Help Manual

Help pageTopics
Set variable annotation with a taxonomy termdictionary.annotate
Set variable annotation with Harmonization Status termdictionary.annotate.harmo_status
List the annotationsdictionary.annotations
Apply the dictionary to a tibbledictionary.apply
Inspect the dictionary of a tibbledictionary.inspect
Get DataSHIELD activitydsadmin.activity
Get DataSHIELD activity summarydsadmin.activity_summary
Get a DataSHIELD methoddsadmin.get_method
Get DataSHIELD methodsdsadmin.get_methods
Get the DataSHIELD optionsdsadmin.get_options
Install a DataSHIELD package from GitHubdsadmin.install_github_package
Install a DataSHIELD package from a local archive filedsadmin.install_local_package
Install a DataSHIELD packagedsadmin.install_package
Check DataSHIELD packagedsadmin.installed_package
Get DataSHIELD logsdsadmin.log
Get DataSHIELD package descriptiondsadmin.package_description
Get DataSHIELD package descriptionsdsadmin.package_descriptions
Get the DataSHIELD permissionsdsadmin.perm
Add or update a DataSHIELD permissiondsadmin.perm_add
Delete a DataSHIELD permissiondsadmin.perm_delete
Get a DataSHIELD profiledsadmin.profile
Restrict or open access to a DataSHIELD profiledsadmin.profile_access
Create a DataSHIELD profiledsadmin.profile_create
Delete a DataSHIELD profiledsadmin.profile_delete
Enable or disable a DataSHIELD profiledsadmin.profile_enable
Check a DataSHIELD profile existsdsadmin.profile_exists
Initialize a DataSHIELD profiledsadmin.profile_init
Get the permissions of a DataSHIELD profiledsadmin.profile_perm
Add or update a permission on a DataSHIELD profiledsadmin.profile_perm_add
Delete a permission from a DataSHIELD profiledsadmin.profile_perm_delete
Set or remove the R parser version of a DataSHIELD profiledsadmin.profile_rparser
Get DataSHIELD profilesdsadmin.profiles
Publish DataSHIELD package settingsdsadmin.publish_package
Remove DataSHIELD packagedsadmin.remove_package
Remove DataSHIELD methoddsadmin.rm_method
Remove DataSHIELD methods.dsadmin.rm_methods
Remove a DataSHIELD optiondsadmin.rm_option
Remove all DataSHIELD optionsdsadmin.rm_options
Remove DataSHIELD package methodsdsadmin.rm_package_methods
Set DataSHIELD methoddsadmin.set_method
Set DataSHIELD optiondsadmin.set_option
Set DataSHIELD package methodsdsadmin.set_package_methods
Unpublish DataSHIELD package settingsdsadmin.unpublish_package
Get R activityoadmin.activity
Get R activity summaryoadmin.activity_summary
Install a package from Bioconductoroadmin.install_bioconductor_package
Install a package from CRANoadmin.install_cran_package
Install devtools packageoadmin.install_devtools
Install a package from GitHuboadmin.install_github_package
Install a package from a local archive fileoadmin.install_local_package
Install CRAN packageoadmin.install_package
Check devtools packageoadmin.installed_devtools
Check package is installedoadmin.installed_package
List installed packagesoadmin.installed_packages
Get Opal main logsoadmin.log
Get Opal REST API logsoadmin.log_rest
Get Opal SQL API logsoadmin.log_sql
Get package descriptionoadmin.package_description
Get the R permissions (deprecated)oadmin.perm
Add or update a R permission (deprecated)oadmin.perm_add
Delete a R permission (deprecated)oadmin.perm_delete
Get the R permissionsoadmin.r_perm
Add or update a R permissionoadmin.r_perm_add
Delete a R permissionoadmin.r_perm_delete
Remove packageoadmin.remove_package
Get system metricsoadmin.system_metrics
Get the System permissionsoadmin.system_perm
Add or update a System permissionoadmin.system_perm_add
Delete a System permissionoadmin.system_perm_delete
Add a useroadmin.user_add
Delete a useroadmin.user_delete
Enable a useroadmin.user_enable
Check user existsoadmin.user_exists
Delete a user profileoadmin.user_profile_delete
Get user profilesoadmin.user_profiles
Reset user passwordoadmin.user_reset_password
Get the usersoadmin.users
Apply the annotations to a Opal tableopal.annotate
Get the annotations of a Opal tableopal.annotations
Array to Markdownopal.as_md_table
Data or expression assignmentopal.assign
Data assignmentopal.assign.data
Resource assignmentopal.assign.resource
R script assignmentopal.assign.script
Data assignment to a data.frameopal.assign.table
Data assignment to a tibbleopal.assign.table.tibble
Get a vector of attribute valuesopal.attribute_values
Get an asynchronous commandopal.command
Get result of an asynchronous commandopal.command_result
Remove an asynchronous commandopal.command_rm
List the asynchronous commandsopal.commands
Remove all asynchronous commandsopal.commands_rm
Get a datasourceopal.datasource
Get datasourcesopal.datasources
Generic REST resource deletion.opal.delete
Execute a R scriptopal.execute
Execute a R file scriptopal.execute.source
Get file contentopal.file
Copy a fileopal.file_cp
Download a fileopal.file_download
List content of a folderopal.file_ls
Make a folderopal.file_mkdir
Make a temporary folderopal.file_mkdir_tmp
Move and/or rename a fileopal.file_mv
Read a fileopal.file_read
Remove a fileopal.file_rm
Unzip a zip archive fileopal.file_unzip
Upload a file or a folderopal.file_upload
Write a fileopal.file_write
Generic REST resource getter.opal.get
Load packageopal.load_package
Opal loginopal.login
Logout from Opal(s)opal.logout
Get the permissions of a subjectopal.perms
Generic REST resource creation.opal.post
List R profilesopal.profiles
Get a projectopal.project
Backup a projectopal.project_backup
Get project taskopal.project_command
Create a projectopal.project_create
Delete a projectopal.project_delete
Check a project existsopal.project_exists
Get the permissions on a projectopal.project_perm
Add or update a permission on a projectopal.project_perm_add
Delete a permission from a projectopal.project_perm_delete
Restore a projectopal.project_restore
Get projectsopal.projects
Get projects databasesopal.projects_databases
Generic REST resource update.opal.put
Opal reportopal.report
Get a resource reference of a projectopal.resource
Create a resource reference in a projectopal.resource_create
Delete a resource referenceopal.resource_delete
Check a resource reference existsopal.resource_exists
Create an extended resource reference in a projectopal.resource_extension_create
Get the resource object of a projectopal.resource_get
Get the permissions on a resourceopal.resource_perm
Add or update a permission on a resourceopal.resource_perm_add
Delete a permission from a resourceopal.resource_perm_delete
Create an Opal view over a resource referenceopal.resource_view_create
Reconnect an Opal view to its underlying resourceopal.resource_view_reconnect
Get the resource references of a projectopal.resources
Get the permissions on any resourceopal.resources_perm
Add or update a permission on any resourceopal.resources_perm_add
Delete a permission from any resourceopal.resources_perm_delete
Remove a R symbol (deprecated)opal.rm
Execute a SQL query on tablesopal.sql
SQL query execution historyopal.sql_history
Import a tibbleopal.symbol_import
Remove a R symbolopal.symbol_rm
Save a tibbleopal.symbol_save
List R symbolsopal.symbols
Get a table of a datasourceopal.table
Create an Opal table or viewopal.table_create
Delete a Opal tableopal.table_delete
Get the dictionary of a Opal tableopal.table_dictionary_get
Update the dictionary of a Opal tableopal.table_dictionary_update
Check a Opal table existsopal.table_exists
Export a table as a fileopal.table_export
Get a Opal table as a tibbleopal.table_get
Import a file as tableopal.table_import
Get the permissions on a tableopal.table_perm
Add or update a permission on a tableopal.table_perm_add
Delete a permission from a tableopal.table_perm_delete
Save a local tibble as a Opal tableopal.table_save
Truncate a Opal tableopal.table_truncate
Create an Opal view over tablesopal.table_view_create
Update the table references and the entity filter of an Opal viewopal.table_view_update
Get tables of a datasourceopal.tables
Get the permissions on any table of a projectopal.tables_perm
Add or update a permission on any table of a projectopal.tables_perm_add
Delete a permission from any table of a projectopal.tables_perm_delete
Get a taskopal.task
Cancel a taskopal.task_cancel
Wait for a task to complete.opal.task_wait
Get the tasksopal.tasks
Get taxonomiesopal.taxonomies
Get a taxonomyopal.taxonomy
Delete a taxonomyopal.taxonomy_delete
Download a taxonomy fileopal.taxonomy_download
Upload a taxonomy fileopal.taxonomy_upload
Get the terms of a vocabularyopal.terms
Get a personal access tokenopal.token
Create a personal access token for Datashield usageopal.token_datashield_create
Delete a personal access tokenopal.token_delete
Create a personal access token for R usageopal.token_r_create
Renew an inactive personal access tokenopal.token_renew
Create a personal access token for SQL usageopal.token_sql_create
Get the personal access tokensopal.tokens
Unload packageopal.unload_package
Get the values of an entityopal.valueset
Get a variable of a tableopal.variable
Get summary statistics of a variable of a tableopal.variable_summary
Get variables of a tableopal.variables
Compareopal.version_compare
Get the vocabularies of a taxonomyopal.vocabularies
Get a taxonomy vocabularyopal.vocabulary
Restore a R workspace from a opal.opal.workspace_restore
Remove a R workspace from a opal.opal.workspace_rm
Save the current session in a opal R workspace.opal.workspace_save
Get the R workspaces from a opal.opal.workspaces