Man pages for opalr
'Opal' Data Repository Client and 'DataSHIELD' Utils
| dictionary.annotate | Set variable annotation with a taxonomy term |
| dictionary.annotate.harmo_status | Set variable annotation with Harmonization Status term |
| dictionary.annotations | List the annotations |
| dictionary.apply | Apply the dictionary to a tibble |
| dictionary.inspect | Inspect the dictionary of a tibble |
| dot-aclsToDataFrame | Permsissions (ACLs) into a data frame. |
| dot-as.zeroOne | Turns a value into 0/1 numeric. |
| dot-authorizationHeader | Constructs the value for the Authorization header |
| dot-deparse | Turn expression into character strings. |
| dot-extractJsonField | Extract JSON |
| dot-extractLabel | Extract label for locale. If not found, fallback to undefined... |
| dot-extractOpalSessionId | Extract opalsid from cookie data frame. |
| dot-getContent | Wrapper of httr::content() |
| dot-getPEMFilePath | Extract absolute path to the pem file |
| dot-getRSessionId | Extract R session Id from opal object, create a new R session... |
| dot-getSessions | Get all R session in Opal. |
| dot-handleError | Handle error response |
| dot-handleResponse | Default request response handler. |
| dot-handleResponseLocation | Default request response Location handler. |
| dot-handleResponseOrCallback | Process response with default handler or the provided one |
| dot-isContentEmpty | Check if response content is empty. |
| dot-is.verbose | Verbose option |
| dot-listToJson | Simple transformation function of a list into a JSON... |
| dot-newProgress | Create a new progress instance with default settings. |
| dot-newSession | Create a new R session in Opal. |
| dot-opal.login | Create the opal object |
| dot-rmOpalSession | Remove a Opal session (logout) |
| dot-rmRSession | Remove a R session from Opal. |
| dot-select | Returns a list r such that r[[i]] == l[[i]][field] for all... |
| dot-tickProgress | Output the progress status if option "datashield.progress" is... |
| dot-tokenHeader | Constructs the value for the X-Opal-Auth header |
| dot-url | Utility method to build urls. Concatenates all arguments and... |
| dot-verbose | Verbose flag |
| dsadmin.activity | Get DataSHIELD activity |
| dsadmin.activity_summary | Get DataSHIELD activity summary |
| dsadmin.get_method | Get a DataSHIELD method |
| dsadmin.get_methods | Get DataSHIELD methods |
| dsadmin.get_options | Get the DataSHIELD options |
| dsadmin.installed_package | Check DataSHIELD package |
| dsadmin.install_github_package | Install a DataSHIELD package from GitHub |
| dsadmin.install_local_package | Install a DataSHIELD package from a local archive file |
| dsadmin.install_package | Install a DataSHIELD package |
| dsadmin.log | Get DataSHIELD logs |
| dsadmin.package_description | Get DataSHIELD package description |
| dsadmin.package_descriptions | Get DataSHIELD package descriptions |
| dsadmin.perm | Get the DataSHIELD permissions |
| dsadmin.perm_add | Add or update a DataSHIELD permission |
| dsadmin.perm_delete | Delete a DataSHIELD permission |
| dsadmin.profile | Get a DataSHIELD profile |
| dsadmin.profile_access | Restrict or open access to a DataSHIELD profile |
| dsadmin.profile_create | Create a DataSHIELD profile |
| dsadmin.profile_delete | Delete a DataSHIELD profile |
| dsadmin.profile_enable | Enable or disable a DataSHIELD profile |
| dsadmin.profile_exists | Check a DataSHIELD profile exists |
| dsadmin.profile_init | Initialize a DataSHIELD profile |
| dsadmin.profile_perm | Get the permissions of a DataSHIELD profile |
| dsadmin.profile_perm_add | Add or update a permission on a DataSHIELD profile |
| dsadmin.profile_perm_delete | Delete a permission from a DataSHIELD profile |
| dsadmin.profile_rparser | Set or remove the R parser version of a DataSHIELD profile |
| dsadmin.profiles | Get DataSHIELD profiles |
| dsadmin.publish_package | Publish DataSHIELD package settings |
| dsadmin.remove_package | Remove DataSHIELD package |
| dsadmin.rm_method | Remove DataSHIELD method |
| dsadmin.rm_methods | Remove DataSHIELD methods. |
| dsadmin.rm_option | Remove a DataSHIELD option |
| dsadmin.rm_options | Remove all DataSHIELD options |
| dsadmin.rm_package_methods | Remove DataSHIELD package methods |
| dsadmin.set_method | Set DataSHIELD method |
| dsadmin.set_option | Set DataSHIELD option |
| dsadmin.set_package_methods | Set DataSHIELD package methods |
| dsadmin.unpublish_package | Unpublish DataSHIELD package settings |
| oadmin.activity | Get R activity |
| oadmin.activity_summary | Get R activity summary |
| oadmin.install_bioconductor_package | Install a package from Bioconductor |
| oadmin.install_cran_package | Install a package from CRAN |
| oadmin.install_devtools | Install devtools package |
| oadmin.installed_devtools | Check devtools package |
| oadmin.installed_package | Check package is installed |
| oadmin.installed_packages | List installed packages |
| oadmin.install_github_package | Install a package from GitHub |
| oadmin.install_local_package | Install a package from a local archive file |
| oadmin.install_package | Install CRAN package |
| oadmin.log | Get Opal main logs |
| oadmin.log_rest | Get Opal REST API logs |
| oadmin.log_sql | Get Opal SQL API logs |
| oadmin.package_description | Get package description |
| oadmin.perm | Get the R permissions (deprecated) |
| oadmin.perm_add | Add or update a R permission (deprecated) |
| oadmin.perm_delete | Delete a R permission (deprecated) |
| oadmin.remove_package | Remove package |
| oadmin.r_perm | Get the R permissions |
| oadmin.r_perm_add | Add or update a R permission |
| oadmin.r_perm_delete | Delete a R permission |
| oadmin.system_metrics | Get system metrics |
| oadmin.system_perm | Get the System permissions |
| oadmin.system_perm_add | Add or update a System permission |
| oadmin.system_perm_delete | Delete a System permission |
| oadmin.user_add | Add a user |
| oadmin.user_delete | Delete a user |
| oadmin.user_enable | Enable a user |
| oadmin.user_exists | Check user exists |
| oadmin.user_profile_delete | Delete a user profile |
| oadmin.user_profiles | Get user profiles |
| oadmin.user_reset_password | Reset user password |
| oadmin.users | Get the users |
| opal.annotate | Apply the annotations to a Opal table |
| opal.annotations | Get the annotations of a Opal table |
| opal.as_md_table | Array to Markdown |
| opal.assign | Data or expression assignment |
| opal.assign.data | Data assignment |
| opal.assign.resource | Resource assignment |
| opal.assign.script | R script assignment |
| 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 attribute values |
| opal.command | Get an asynchronous command |
| opal.command_result | Get result of an asynchronous command |
| opal.command_rm | Remove an asynchronous command |
| opal.commands | List the asynchronous commands |
| opal.commands_rm | Remove all asynchronous commands |
| opal.datasource | Get a datasource |
| opal.datasources | Get datasources |
| opal.delete | Generic REST resource deletion. |
| opal.execute | Execute a R script |
| opal.execute.source | Execute a R file script |
| opal.file | Get file content |
| opal.file_cp | Copy a file |
| opal.file_download | Download a file |
| opal.file_ls | List content of a folder |
| opal.file_mkdir | Make a folder |
| opal.file_mkdir_tmp | Make a temporary folder |
| opal.file_mv | Move and/or rename a file |
| opal.file_read | Read a file |
| opal.file_rm | Remove a file |
| opal.file_unzip | Unzip a zip archive file |
| opal.file_upload | Upload a file or a folder |
| opal.file_write | Write a file |
| opal.get | Generic REST resource getter. |
| opal.load_package | Load package |
| opal.login | Opal login |
| opal.logout | Logout from Opal(s) |
| opal.perms | Get the permissions of a subject |
| opal.post | Generic REST resource creation. |
| opal.profiles | List R profiles |
| opal.project | Get a project |
| opal.project_backup | Backup a project |
| opal.project_command | Get project task |
| opal.project_create | Create a project |
| opal.project_delete | Delete a project |
| opal.project_exists | Check a project exists |
| opal.project_perm | Get the permissions on a project |
| opal.project_perm_add | Add or update a permission on a project |
| opal.project_perm_delete | Delete a permission from a project |
| opal.project_restore | Restore a project |
| opal.projects | Get projects |
| opal.projects_databases | Get projects databases |
| opal.put | Generic REST resource update. |
| opal.report | Opal report |
| opal.report_md | Turn a R markdown file to html. |
| opal.resource | Get a resource reference of a project |
| opal.resource_create | Create a resource reference in a project |
| opal.resource_delete | Delete a resource reference |
| opal.resource_exists | Check a resource reference exists |
| opal.resource_extension_create | Create an extended resource reference in a project |
| opal.resource_get | Get the resource object of a project |
| opal.resource_perm | Get the permissions on a resource |
| opal.resource_perm_add | Add or update a permission on a resource |
| opal.resource_perm_delete | Delete a permission from a resource |
| opal.resources | Get the resource references of a project |
| opal.resources_perm | Get the permissions on any resource |
| opal.resources_perm_add | Add or update a permission on any resource |
| opal.resources_perm_delete | Delete a permission from any resource |
| opal.resource_view_create | Create an Opal view over a resource reference |
| opal.resource_view_reconnect | Reconnect an Opal view to its underlying resource |
| opal.rm | Remove a R symbol (deprecated) |
| opalr-package | opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils |
| opal.sql | Execute a SQL query on tables |
| opal.sql_history | SQL query execution history |
| opal.symbol_import | Import a tibble |
| opal.symbol_rm | Remove a R symbol |
| opal.symbols | List R symbols |
| opal.symbol_save | Save a tibble |
| opal.table | Get a table of a datasource |
| opal.table_create | Create an Opal table or view |
| opal.table_delete | Delete a Opal table |
| opal.table_dictionary_get | Get the dictionary of a Opal table |
| opal.table_dictionary_update | Update the dictionary of a Opal table |
| opal.table_exists | Check a Opal table exists |
| opal.table_export | Export a table as a file |
| opal.table_get | Get a Opal table as a tibble |
| opal.table_import | Import a file as table |
| opal.table_perm | Get the permissions on a table |
| opal.table_perm_add | Add or update a permission on a table |
| opal.table_perm_delete | Delete a permission from a table |
| opal.tables | Get tables of a datasource |
| opal.table_save | Save a local tibble as a Opal table |
| opal.tables_perm | Get the permissions on any table of a project |
| opal.tables_perm_add | Add or update a permission on any table of a project |
| opal.tables_perm_delete | Delete a permission from any table of a project |
| opal.table_truncate | Truncate a Opal table |
| opal.table_view_create | Create an Opal view over tables |
| opal.table_view_update | Update the table references and the entity filter of an Opal... |
| opal.task | Get a task |
| opal.task_cancel | Cancel a task |
| opal.tasks | Get the tasks |
| opal.task_wait | Wait for a task to complete. |
| opal.taxonomies | Get taxonomies |
| opal.taxonomy | Get a taxonomy |
| opal.taxonomy_delete | Delete a taxonomy |
| opal.taxonomy_download | Download a taxonomy file |
| opal.taxonomy_upload | Upload a taxonomy file |
| opal.terms | Get the terms of a vocabulary |
| opal.token | Get a personal access token |
| opal.token_datashield_create | Create a personal access token for Datashield usage |
| opal.token_delete | Delete a personal access token |
| opal.token_r_create | Create a personal access token for R usage |
| opal.token_renew | Renew an inactive personal access token |
| opal.tokens | Get the personal access tokens |
| opal.token_sql_create | Create a personal access token for SQL usage |
| opal.unload_package | Unload package |
| opal.valueset | Get the values of an entity |
| opal.variable | Get a variable of a table |
| opal.variables | Get variables of a table |
| opal.variable_summary | Get summary statistics of a variable of a table |
| opal.version_compare | Compare |
| opal.vocabularies | Get the vocabularies of a taxonomy |
| opal.vocabulary | Get a taxonomy vocabulary |
| opal.workspace_restore | Restore a R workspace from a opal. |
| opal.workspace_rm | Remove a R workspace from a opal. |
| opal.workspaces | Get the R workspaces from a opal. |
| opal.workspace_save | Save the current session in a opal R workspace. |
