,
Amadou Gaye [ctb] ,
OBiBa group [cph]| Title: | 'Opal' Data Repository Client and 'DataSHIELD' Utils |
|---|---|
| Description: | 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] |
| Maintainer: | Yannick Marcon <[email protected]> |
| License: | GPL-3 |
| Version: | 3.5.0 |
| Built: | 2025-02-11 05:58:49 UTC |
| Source: | https://github.com/obiba/opalr |
Apply or remove an annotation from a set of variables.
dictionary.annotate( tibble, variables = NULL, taxonomy = "Mlstr_area", vocabulary, term )dictionary.annotate( tibble, variables = NULL, taxonomy = "Mlstr_area", vocabulary, term )
tibble |
Tibble to be annotated. |
variables |
A character vector of variable names to be annotated. If NULL or empty, all the columns of the tibble will be annotated. |
taxonomy |
The taxonomy to which the vocabulary belongs. If NULL, the annotation is a simple attribute (i.e. without a taxonomy reference). |
vocabulary |
The vocabulary to which the term belongs. |
term |
The term to apply. If NULL, the annotation will be deleted. |
The annotated tibble
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") cqx <- dictionary.annotate(cqx, variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"), taxonomy = "Mlstr_area", vocabulary = "Sociodemographic_economic_characteristics", term = "Education") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") cqx <- dictionary.annotate(cqx, variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"), taxonomy = "Mlstr_area", vocabulary = "Sociodemographic_economic_characteristics", term = "Education") opal.logout(o) ## End(Not run)
Apply or remove an harmonization status annotation from a set of variables. The harmonization status is described by the "status" vocabulary in the "Mlstr_harmo" taxonomy.
dictionary.annotate.harmo_status(tibble, variables = NULL, status)dictionary.annotate.harmo_status(tibble, variables = NULL, status)
tibble |
Tibble to be annotated. |
variables |
A character vector of variable names to be annotated. If NULL or empty, all the columns of the tibble will be annotated. |
status |
The harmonization status to apply: 'complete', 'undetermined', 'impossible' or 'na'. If NULL, the annotation will be deleted. |
The annotated tibble
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") cqx <- dictionary.annotate.harmo_status(cqx, variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"), status = "complete") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") cqx <- dictionary.annotate.harmo_status(cqx, variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"), status = "complete") opal.logout(o) ## End(Not run)
List the annotations of each of the variables.
dictionary.annotations( tibble, variables = NULL, taxonomy = NULL, vocabulary = NULL )dictionary.annotations( tibble, variables = NULL, taxonomy = NULL, vocabulary = NULL )
tibble |
Tibble to be annotated |
variables |
A character vector of variable names to be inspected. If NULL or empty, all the columns of the tibble will be inspected. |
taxonomy |
Filter by taxonomy name(s) (if provided). |
vocabulary |
Filter by vocabulary name(s) (if provided). |
A data frame in long format (one row per annotation).
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status") opal.logout(o) ## End(Not run)
Apply the dictionary described in a Opal Excel format as attributes of the tibble's columns.
dictionary.apply(tibble, variables, categories = NULL, merge = FALSE)dictionary.apply(tibble, variables, categories = NULL, merge = FALSE)
tibble |
Tibble to be decorated. |
variables |
A data frame with one row per variable (column name) and then one column per property/attribute. |
categories |
A data frame with one row per category (columns variable and name) and then column per property/attribute. |
merge |
Either append attributes to existing ones or replace them. Default is FALSE, for dictionary consistency. |
## Not run: data <- tibble::as_tibble(mtcars) variables <- tibble::tribble( ~name, ~valueType, ~`label:en`, ~`label:fr`, ~`Namespace::Name`, ~unit, ~repeatable, ~index, "mpg", "decimal", "Mpg label", "Mpg libellé", "Value1", "years", 0, 1, "cyl", "decimal", "Cyl label", "Cyl libellé", "Value2", "kg/m2", 0, 2, "disp", "decimal", "Disp label", "Disp libellé", NA, NA, 1, 3 ) categories <- tibble::tribble( ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`, "cyl", "4", 0, "Four", "Quatre", "cyl", "6", 0, "Six", "Six", "cyl", "8", 1, "Height", "Huit" ) data <- dictionary.apply(data, variables, categories) ## End(Not run)## Not run: data <- tibble::as_tibble(mtcars) variables <- tibble::tribble( ~name, ~valueType, ~`label:en`, ~`label:fr`, ~`Namespace::Name`, ~unit, ~repeatable, ~index, "mpg", "decimal", "Mpg label", "Mpg libellé", "Value1", "years", 0, 1, "cyl", "decimal", "Cyl label", "Cyl libellé", "Value2", "kg/m2", 0, 2, "disp", "decimal", "Disp label", "Disp libellé", NA, NA, 1, 3 ) categories <- tibble::tribble( ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`, "cyl", "4", 0, "Four", "Quatre", "cyl", "6", 0, "Six", "Six", "cyl", "8", 1, "Height", "Huit" ) data <- dictionary.apply(data, variables, categories) ## End(Not run)
Inspect the data dictionary, checking for inconsistencies. Error is raised when the identifiers column cannot be found.
dictionary.inspect(tibble, id.name = "id", warn = TRUE)dictionary.inspect(tibble, id.name = "id", warn = TRUE)
tibble |
Tibble to be inspected. |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. |
warn |
Print warning messages. Default is TRUE. |
TRUE if inspection is successful, FALSE otherwise.
## Not run: # prepare datasets of visits, several visits for one patient visits <- tibble::tribble( ~id, ~patient_id, ~sex, ~visit_date, 1, 1, "M", as.Date("2020-01-01"), 2, 2, "F", as.Date("2020-01-02"), 3, 3, "M", as.Date("2020-01-03"), 4, 3, "M", as.Date("2020-01-04")) o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org") # save visits dataset opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE) # get visit and make it a dataset of patients patients <- opal.table_get(o, "RSRC", "visits", id.name = "id") # set dataset IDs patients$visit_id <- patients$id patients$id <- patients$patient_id patients$patient_id <- NULL patients # save patients dataset, there should be a warning that some variables are not repeatable # while there are patients with multiple data lines opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE) opal.logout(o) ## End(Not run)## Not run: # prepare datasets of visits, several visits for one patient visits <- tibble::tribble( ~id, ~patient_id, ~sex, ~visit_date, 1, 1, "M", as.Date("2020-01-01"), 2, 2, "F", as.Date("2020-01-02"), 3, 3, "M", as.Date("2020-01-03"), 4, 3, "M", as.Date("2020-01-04")) o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org") # save visits dataset opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE) # get visit and make it a dataset of patients patients <- opal.table_get(o, "RSRC", "visits", id.name = "id") # set dataset IDs patients$visit_id <- patients$id patients$id <- patients$patient_id patients$patient_id <- NULL patients # save patients dataset, there should be a warning that some variables are not repeatable # while there are patients with multiple data lines opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE) opal.logout(o) ## End(Not run)
Get the recorded DataSHIELD session metrics.
dsadmin.activity( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )dsadmin.activity( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )
opal |
Opal connection object. |
user |
Optional user name. |
profile |
Optional profile name. |
from |
Optional start date. |
to |
Optional end date. |
df |
Return a data.frame (default is TRUE) |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics dsadmin.activity(o) # user and profile specific session metrics dsadmin.activity(o, user = 'dsuser', profile = 'default') # user sessions in a time range dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics dsadmin.activity(o) # user and profile specific session metrics dsadmin.activity(o, user = 'dsuser', profile = 'default') # user sessions in a time range dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)
Get the recorded DataSHIELD session metrics, grouped by profile and user.
dsadmin.activity_summary( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )dsadmin.activity_summary( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )
opal |
Opal connection object. |
user |
Optional user name. |
profile |
Optional profile name. |
from |
Optional start date. |
to |
Optional end date. |
df |
Return a data.frame (default is TRUE) |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics dsadmin.activity_summary(o) # user and profile specific session metrics dsadmin.activity_summary(o, user = 'dsuser', profile = 'default') # user sessions in a time range dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics dsadmin.activity_summary(o) # user and profile specific session metrics dsadmin.activity_summary(o, user = 'dsuser', profile = 'default') # user sessions in a time range dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)
Get a DataSHIELD method
dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
opal |
Opal object or list of opal objects. |
name |
Name of the method, as it is accessed by DataSHIELD users. |
type |
Type of the method: "aggregate" (default) or "assign" |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_method(o, 'class') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_method(o, 'class') opal.logout(o) ## End(Not run)
Get DataSHIELD methods
dsadmin.get_methods(opal, type = "aggregate", profile = NULL)dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
opal |
Opal object or list of opal objects. |
type |
Type of the method: "aggregate" (default) or "assign" |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_methods(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_methods(o) opal.logout(o) ## End(Not run)
Get the DataSHIELD options
dsadmin.get_options(opal, profile = NULL)dsadmin.get_options(opal, profile = NULL)
opal |
Opal object or list of opal objects. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_options(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.get_options(o) opal.logout(o) ## End(Not run)
Install a package from a DataSHIELD source repository on GitHub.
dsadmin.install_github_package( opal, pkg, username = "datashield", ref = "master", profile = NULL )dsadmin.install_github_package( opal, pkg, username = "datashield", ref = "master", profile = NULL )
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
username |
GitHub username/organization of the git repository. Default is 'datashield'. |
ref |
Desired git reference (could be a commit, tag, or branch name). Default is 'master'. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if installed
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge') opal.logout(o) ## End(Not run)
Install a package from a package archive file, resulting from the build of a server-side DataSHIELD package. This will upload the archive file and run its installation in the R server.
dsadmin.install_local_package(opal, path, profile = NULL)dsadmin.install_local_package(opal, path, profile = NULL)
opal |
Opal object or list of opal objects. |
path |
Path to the package archive, ending with . |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # install a pre-built local archive file dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz') # or build archive file from local package source (in current working folder) dsadmin.install_local_package(o, devtools::build()) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # install a pre-built local archive file dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz') # or build archive file from local package source (in current working folder) dsadmin.install_local_package(o, devtools::build()) opal.logout(o) ## End(Not run)
Install a package from DataSHIELD public package repository or (if Git reference and GitHub username is provided) from DataSHIELD source repository on GitHub.
dsadmin.install_package( opal, pkg, githubusername = NULL, ref = NULL, profile = NULL )dsadmin.install_package( opal, pkg, githubusername = NULL, ref = NULL, profile = NULL )
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
githubusername |
GitHub username of git repository. If NULL (default), try to install from DataSHIELD package repository. |
ref |
Desired git reference (could be a commit, tag, or branch name). If NULL (default), try to install from DataSHIELD package repository. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if installed
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.install_package(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.install_package(o, 'dsBase') opal.logout(o) ## End(Not run)
Check if a DataSHIELD package is installed.
dsadmin.installed_package(opal, pkg, profile = NULL)dsadmin.installed_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if installed
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.installed_package(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.installed_package(o, 'dsBase') opal.logout(o) ## End(Not run)
The DataSHIELD log is structured as follows:
dsadmin.log(opal, all = TRUE)dsadmin.log(opal, all = TRUE)
opal |
Opal connection object. |
all |
Get all or only latest log messages. |
Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.log(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.log(o) opal.logout(o) ## End(Not run)
Get DataSHIELD package description
dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
fields |
A character vector giving the fields to extract from each package's DESCRIPTION file in addition to the default ones, or NULL (default). Unavailable fields result in NA values. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_description(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_description(o, 'dsBase') opal.logout(o) ## End(Not run)
Get DataSHIELD package descriptions
dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
opal |
Opal object or list of opal objects. |
fields |
A character vector giving the fields to extract from each package's DESCRIPTION file in addition to the default ones, or NULL (default). Unavailable fields result in NA values. |
df |
Return a data.frame (default is TRUE) |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
The DataSHIELD package descriptions as a data.frame or a list
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_descriptions(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_descriptions(o) opal.logout(o) ## End(Not run)
Get the permissions that were applied to the DataSHIELD service.
dsadmin.perm(opal)dsadmin.perm(opal)
opal |
Opal connection object. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on the DataSHIELD service.
dsadmin.perm_add(opal, subject, type = "user", permission)dsadmin.perm_add(opal, subject, type = "user", permission)
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: use or administrate. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied to the DataSHIELD service. Silently returns when there is no such permission.
dsadmin.perm_delete(opal, subject, type = "user")dsadmin.perm_delete(opal, subject, type = "user")
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use') dsadmin.perm(o) dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Note that getting a specific DataSHIELD profile details is not allowed for regular DataSHIELD users when the profile has no restricted access. This function is for profiles editors only (system administrators or DataSHIELD administrators).
dsadmin.profile(opal, name)dsadmin.profile(opal, name)
opal |
Opal object. |
name |
Name of the profile. |
Other DataSHIELD profiles:
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile(o, name = 'default') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile(o, name = 'default') opal.logout(o) ## End(Not run)
When access is restricted, only users (or group of users) with this profile use permissions will be allowed to use this profile. When access is not restricted, all DataSHIELD users are allowed to use this profile. See also dsadmin.profile_perm.
dsadmin.profile_access(opal, name, restricted = TRUE)dsadmin.profile_access(opal, name, restricted = TRUE)
opal |
Opal object. |
name |
Name of the profile. |
restricted |
Default value is TRUE. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_access(o, name = 'survival', restricted = TRUE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_access(o, name = 'survival', restricted = TRUE) opal.logout(o) ## End(Not run)
The created DataSHIELD profile will not be enabled and no access restrictions is applied.
dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
opal |
Opal object. |
name |
Name of the profile. |
cluster |
Name of the R servers cluster to which the profile will be attached to. Default value is 'default'. |
rParser |
Version of the DataSHIELD R parser that applies to this profile. If not specified, the system's default one will be used. A valid version would be one of 'v1' or 'v2'. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') opal.logout(o) ## End(Not run)
Delete a DataSHIELD profile
dsadmin.profile_delete(opal, name)dsadmin.profile_delete(opal, name)
opal |
Opal object. |
name |
Name of the profile. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_delete(o, name = 'survival') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_delete(o, name = 'survival') opal.logout(o) ## End(Not run)
Enable or disable a DataSHIELD profile
dsadmin.profile_enable(opal, name, enabled = TRUE)dsadmin.profile_enable(opal, name, enabled = TRUE)
opal |
Opal object. |
name |
Name of the profile. |
enabled |
Default value is TRUE. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_enable(o, name = 'survival', enabled = TRUE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_enable(o, name = 'survival', enabled = TRUE) opal.logout(o) ## End(Not run)
Check a DataSHIELD profile exists
dsadmin.profile_exists(opal, name)dsadmin.profile_exists(opal, name)
opal |
Opal object. |
name |
Name of the profile. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') if (!dsadmin.profile_exists(o, name = 'survival')) dsadmin.profile_create(o, name = 'survival', cluster = 'demo') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') if (!dsadmin.profile_exists(o, name = 'survival')) dsadmin.profile_create(o, name = 'survival', cluster = 'demo') opal.logout(o) ## End(Not run)
Clean the DataSHIELD's profile settings from all methods and options (including custom ones). These settings are then repopulated with installed DataSHIELD R packages settings, optionaly filtered by the name. See also dsadmin.publish_package, dsadmin.set_package_methods or dsadmin.set_option.
dsadmin.profile_init(opal, name, packages = NULL)dsadmin.profile_init(opal, name, packages = NULL)
opal |
Opal object. |
name |
Name of the profile. |
packages |
A list DataSHIELD R package names |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival')) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival')) opal.logout(o) ## End(Not run)
Get the permissions of a DataSHIELD profile
dsadmin.profile_perm(opal, name)dsadmin.profile_perm(opal, name)
opal |
Opal connection object. |
name |
Profile name. |
A data.frame with columns: subject, type, permission
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
When adding/updating some permissions on a DataSHIELD profile, this profile is automatically set in restricted access mode.
dsadmin.profile_perm_add( opal, name, subject, type = "user", permission = "use" )dsadmin.profile_perm_add( opal, name, subject, type = "user", permission = "use" )
opal |
Opal connection object. |
name |
Profile. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: use. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied on a DataSHIELD profile. Silently returns when there is no such permission.
dsadmin.profile_perm_delete(opal, name, subject, type = "user")dsadmin.profile_perm_delete(opal, name, subject, type = "user")
opal |
Opal connection object. |
name |
Profile name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_rparser(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use') dsadmin.profile_perm(o, 'default') dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Set or remove the R parser version of a DataSHIELD profile
dsadmin.profile_rparser(opal, name, rParser = NULL)dsadmin.profile_rparser(opal, name, rParser = NULL)
opal |
Opal object. |
name |
Name of the profile. |
rParser |
Version of the DataSHIELD R parser that applies to this profile. If not specified, the system's default one will be used. A valid version would be one of 'v1' or 'v2'. |
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profiles()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') # apply R parser version v2 dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2') # apply system's default R parser version dsadmin.profile_rparser(o, name = 'survival') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.profile_create(o, name = 'survival', cluster = 'demo') # apply R parser version v2 dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2') # apply system's default R parser version dsadmin.profile_rparser(o, name = 'survival') opal.logout(o) ## End(Not run)
Get DataSHIELD profiles
dsadmin.profiles(opal, df = TRUE)dsadmin.profiles(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
The DataSHIELD profiles as a data.frame or a list
Other DataSHIELD profiles:
dsadmin.profile(),
dsadmin.profile_access(),
dsadmin.profile_create(),
dsadmin.profile_delete(),
dsadmin.profile_enable(),
dsadmin.profile_exists(),
dsadmin.profile_init(),
dsadmin.profile_perm(),
dsadmin.profile_perm_add(),
dsadmin.profile_perm_delete(),
dsadmin.profile_rparser()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_descriptions(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.package_descriptions(o) opal.logout(o) ## End(Not run)
Declare DataSHIELD aggregate/assign methods and options as defined by the package.
dsadmin.publish_package(opal, pkg, profile = NULL)dsadmin.publish_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if successfull
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.publish_package(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.publish_package(o, 'dsBase') opal.logout(o) ## End(Not run)
Remove a DataSHIELD package permanently.
dsadmin.remove_package(opal, pkg, profile = NULL)dsadmin.remove_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.remove_package(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.remove_package(o, 'dsBase') opal.logout(o) ## End(Not run)
Remove DataSHIELD method
dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
opal |
Opal object or list of opal objects. |
name |
Name of the method, as it is accessed by DataSHIELD users. |
type |
Type of the method: "aggregate" (default) or "assign" |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_method(o, 'foo') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_method(o, 'foo') opal.logout(o) ## End(Not run)
Remove DataSHIELD methods.
dsadmin.rm_methods(opal, type = NULL, profile = NULL)dsadmin.rm_methods(opal, type = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
type |
Type of the method: "aggregate" or "assign". Default is NULL (=all type of methods). |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_methods(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_methods(o) opal.logout(o) ## End(Not run)
Remove a DataSHIELD option
dsadmin.rm_option(opal, name, profile = NULL)dsadmin.rm_option(opal, name, profile = NULL)
opal |
Opal object or list of opal objects. |
name |
Name of the option |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_option(o, 'foo') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_option(o, 'foo') opal.logout(o) ## End(Not run)
Remove all DataSHIELD options
dsadmin.rm_options(opal, profile = NULL)dsadmin.rm_options(opal, profile = NULL)
opal |
Opal object or list of opal objects. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_options(o, 'foo') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_options(o, 'foo') opal.logout(o) ## End(Not run)
Remove DataSHIELD aggregate and assign methods defined by the package.
dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
type |
Type of the method: "aggregate" or "assign". Default is NULL (=all type of methods). |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_package_methods(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.rm_package_methods(o, 'dsBase') opal.logout(o) ## End(Not run)
Set DataSHIELD method
dsadmin.set_method( opal, name, func = NULL, path = NULL, type = "aggregate", profile = NULL )dsadmin.set_method( opal, name, func = NULL, path = NULL, type = "aggregate", profile = NULL )
opal |
Opal object or list of opal objects. |
name |
Name of the method, as it will be accessed by DataSHIELD users. |
func |
Function name or function code. |
path |
Path to the R file containing the script (mutually exclusive with func). |
type |
Type of the method: "aggregate" (default) or "assign" |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_option(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # as a package's function dsadmin.set_method(o, 'foo', func = 'base::mean') # as a custom function dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) }) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # as a package's function dsadmin.set_method(o, 'foo', func = 'base::mean') # as a custom function dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) }) opal.logout(o) ## End(Not run)
Set a DataSHIELD option (add or update).
dsadmin.set_option(opal, name, value, profile = NULL)dsadmin.set_option(opal, name, value, profile = NULL)
opal |
Opal object or list of opal objects. |
name |
Name of the option |
value |
Value of the option |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_package_methods(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.set_option(o, 'foo', 'bar') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.set_option(o, 'foo', 'bar') opal.logout(o) ## End(Not run)
Declare DataSHIELD aggregate and assign methods as defined by the package.
dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
type |
Type of the method: "aggregate" or "assign". Default is NULL (=all type of methods). |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if successfull
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.unpublish_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.set_package_methods(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.set_package_methods(o, 'dsBase') opal.logout(o) ## End(Not run)
Remove DataSHIELD aggregate/assign methods and options as defined by the package from the DataSHIELD configuration.
dsadmin.unpublish_package(opal, pkg, profile = NULL)dsadmin.unpublish_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The DataSHIELD profile name to which operation applies. See also dsadmin.profiles. |
TRUE if successfull
Other DataSHIELD functions:
dsadmin.get_method(),
dsadmin.get_methods(),
dsadmin.get_options(),
dsadmin.install_github_package(),
dsadmin.install_local_package(),
dsadmin.install_package(),
dsadmin.installed_package(),
dsadmin.package_description(),
dsadmin.package_descriptions(),
dsadmin.publish_package(),
dsadmin.remove_package(),
dsadmin.rm_method(),
dsadmin.rm_methods(),
dsadmin.rm_option(),
dsadmin.rm_options(),
dsadmin.rm_package_methods(),
dsadmin.set_method(),
dsadmin.set_option(),
dsadmin.set_package_methods()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.unpublish_package(o, 'dsBase') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dsadmin.unpublish_package(o, 'dsBase') opal.logout(o) ## End(Not run)
Get the recorded R session metrics.
oadmin.activity( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )oadmin.activity( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )
opal |
Opal connection object. |
user |
Optional user name. |
profile |
Optional profile name. |
from |
Optional start date. |
to |
Optional end date. |
df |
Return a data.frame (default is TRUE) |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics oadmin.activity(o) # user and profile specific session metrics oadmin.activity(o, user = 'dsuser', profile = 'default') # user sessions in a time range oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics oadmin.activity(o) # user and profile specific session metrics oadmin.activity(o, user = 'dsuser', profile = 'default') # user sessions in a time range oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)
Get the recorded R session metrics, grouped by profile and user.
oadmin.activity_summary( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )oadmin.activity_summary( opal, user = NULL, profile = NULL, from = NULL, to = NULL, df = TRUE )
opal |
Opal connection object. |
user |
Optional user name. |
profile |
Optional profile name. |
from |
Optional start date. |
to |
Optional end date. |
df |
Return a data.frame (default is TRUE) |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics oadmin.activity_summary(o) # user and profile specific session metrics oadmin.activity_summary(o, user = 'dsuser', profile = 'default') # user sessions in a time range oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # all sessions metrics oadmin.activity_summary(o) # user and profile specific session metrics oadmin.activity_summary(o, user = 'dsuser', profile = 'default') # user sessions in a time range oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01") opal.logout(o) ## End(Not run)
Install a package from a source repository on GitHub.
oadmin.install_bioconductor_package(opal, pkg, profile = NULL)oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_bioconductor_package(o, 'GWASTools') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_bioconductor_package(o, 'GWASTools') opal.logout(o) ## End(Not run)
Install a package from configured CRAN repositories.
oadmin.install_cran_package(opal, pkg, profile = NULL)oadmin.install_cran_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_cran_package(o, 'opalr', 'obiba') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_cran_package(o, 'opalr', 'obiba') opal.logout(o) ## End(Not run)
Install devtools package if not already available.
oadmin.install_devtools(opal, profile = NULL)oadmin.install_devtools(opal, profile = NULL)
opal |
Opal object or list of opal objects. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_devtools(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_devtools(o) opal.logout(o) ## End(Not run)
Install a package from a source repository on GitHub.
oadmin.install_github_package( opal, pkg, username = getOption("github.user"), ref = "master", profile = NULL )oadmin.install_github_package( opal, pkg, username = getOption("github.user"), ref = "master", profile = NULL )
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
username |
GitHub user or organization name. |
ref |
Desired git reference. Could be a commit, tag, or branch name. Defaults to "master". |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_github_package(o, 'opalr', 'obiba') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_github_package(o, 'opalr', 'obiba') opal.logout(o) ## End(Not run)
Install a package from a package archive file. This will upload the archive file and run its installation in the R server. The R server profile to which the operation applies is the one specified at login time.
oadmin.install_local_package(opal, path, profile = NULL)oadmin.install_local_package(opal, path, profile = NULL)
opal |
Opal object or list of opal objects. |
path |
Path to the package archive file. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # install a pre-built local archive file oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz') # or build archive file from local package source (in current working folder) oadmin.install_local_package(o, devtools::build()) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # install a pre-built local archive file oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz') # or build archive file from local package source (in current working folder) oadmin.install_local_package(o, devtools::build()) opal.logout(o) ## End(Not run)
Install package from CRAN repos. To install the latest version of a package, it has to be removed first.
oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
repos |
Character vector, the base URLs of the repositories to use. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
TRUE if successfully installed
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_package(o, 'xxx') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.install_package(o, 'xxx') opal.logout(o) ## End(Not run)
Check if devtools package is installed.
oadmin.installed_devtools(opal, profile = NULL)oadmin.installed_devtools(opal, profile = NULL)
opal |
Opal object or list of opal objects. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_devtools(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_devtools(o) opal.logout(o) ## End(Not run)
Check package is installed
oadmin.installed_package(opal, pkg, profile = NULL)oadmin.installed_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
TRUE if installed
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_packages(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_package(o, 'xxx') oadmin.installed_package(o, 'stats') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_package(o, 'xxx') oadmin.installed_package(o, 'stats') opal.logout(o) ## End(Not run)
Get the installed packages from all the R servers in the cluster described by the profile.
oadmin.installed_packages(opal, profile = NULL)oadmin.installed_packages(opal, profile = NULL)
opal |
Opal object. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
The result of the installed.packages() call
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.package_description(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_packages(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.installed_packages(o) opal.logout(o) ## End(Not run)
Get Opal main logs
oadmin.log(opal, all = TRUE)oadmin.log(opal, all = TRUE)
opal |
Opal connection object. |
all |
Get all or only latest log messages. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log(o) opal.logout(o) ## End(Not run)
Get Opal REST API logs
oadmin.log_rest(opal, all = TRUE)oadmin.log_rest(opal, all = TRUE)
opal |
Opal connection object. |
all |
Get all or only latest log messages. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log_rest(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log_rest(o) opal.logout(o) ## End(Not run)
Get Opal SQL API logs
oadmin.log_sql(opal, all = TRUE)oadmin.log_sql(opal, all = TRUE)
opal |
Opal connection object. |
all |
Get all or only latest log messages. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log_sql(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.log_sql(o) opal.logout(o) ## End(Not run)
Get package description
oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
fields |
A character vector giving the fields to extract from each package's DESCRIPTION file in addition to the default ones, or NULL (default). Unavailable fields result in NA values. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.remove_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.package_description(o, 'stats') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.package_description(o, 'stats') opal.logout(o) ## End(Not run)
Deprecated, use oadmin.r_perm.
oadmin.perm(opal)oadmin.perm(opal)
opal |
Opal connection object. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Deprecated, use oadmin.r_perm_add.
oadmin.perm_add(opal, subject, type = "user", permission)oadmin.perm_add(opal, subject, type = "user", permission)
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: use. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Deprecated, use oadmin.r_perm_delete.
oadmin.perm_delete(opal, subject, type = "user")oadmin.perm_delete(opal, subject, type = "user")
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Get the permissions that were applied to the R service.
oadmin.r_perm(opal)oadmin.r_perm(opal)
opal |
Opal connection object. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on the R service.
oadmin.r_perm_add(opal, subject, type = "user", permission = "use")oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: use. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied to the R service. Silently returns when there is no such permission.
oadmin.r_perm_delete(opal, subject, type = "user")oadmin.r_perm_delete(opal, subject, type = "user")
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use') oadmin.r_perm(o) oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Remove package permanently.
oadmin.remove_package(opal, pkg, profile = NULL)oadmin.remove_package(opal, pkg, profile = NULL)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
profile |
The R servers profile name to which operation applies. See also opal.profiles. |
Other administration functions:
oadmin.install_bioconductor_package(),
oadmin.install_cran_package(),
oadmin.install_devtools(),
oadmin.install_github_package(),
oadmin.install_local_package(),
oadmin.install_package(),
oadmin.installed_devtools(),
oadmin.installed_package(),
oadmin.installed_packages(),
oadmin.package_description()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.remove_package(o, 'xxx') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.remove_package(o, 'xxx') opal.logout(o) ## End(Not run)
Get some metrics about the Opal system status. The following information are returned: 'timestamp' (the EPOC time at which the metrics were collected), 'uptime' (the running time in millis), 'heapMemory' (the memory currently used), 'nonHeapMemory' (the memory that can be used), 'threads' (the current (count) and maximum (peak) numbers of threads), 'gcs' (the garbage collectors activity).
oadmin.system_metrics(opal)oadmin.system_metrics(opal)
opal |
Opal connection object. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_metrics(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_metrics(o) opal.logout(o) ## End(Not run)
Get the permissions that were applied to the whole system.
oadmin.system_perm(opal)oadmin.system_perm(opal)
opal |
Opal connection object. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on the whole system.
oadmin.system_perm_add(opal, subject, type = "user", permission)oadmin.system_perm_add(opal, subject, type = "user", permission)
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: project_add or administrate. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied to the whole system. Silently returns when there is no such permission.
oadmin.system_perm_delete(opal, subject, type = "user")oadmin.system_perm_delete(opal, subject, type = "user")
opal |
Opal connection object. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add') oadmin.system_perm(o) oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add a user in Opal internal users registry.
oadmin.user_add(opal, name, groups = NULL, password = NULL)oadmin.user_add(opal, name, groups = NULL, password = NULL)
opal |
Opal object. |
name |
User name |
groups |
User groups |
password |
User password. If not provided, a password will be generated and returned. |
Other user functions:
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) opal.logout(o) ## End(Not run)
Delete a user from Opal internal users registry. Fails silently if user does not exist.
oadmin.user_delete(opal, name)oadmin.user_delete(opal, name)
opal |
Opal object. |
name |
User name |
Other user functions:
oadmin.user_add(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_delete(o, "foo") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_delete(o, "foo") opal.logout(o) ## End(Not run)
Enable or disable a user from Opal internal users registry.
oadmin.user_enable(opal, name, enabled = TRUE)oadmin.user_enable(opal, name, enabled = TRUE)
opal |
Opal object. |
name |
User name |
enabled |
Logical to enable a user. |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_enable(o, "foo", enabled = FALSE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_enable(o, "foo", enabled = FALSE) opal.logout(o) ## End(Not run)
Check whether a user exists, either in the internal user registry (see oadmin.users) or as an external user that already logged in (see oadmin.user_profiles).
oadmin.user_exists(opal, name)oadmin.user_exists(opal, name)
opal |
Opal object. |
name |
User name |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') if (!oadmin.user_exists(o, "foo")) oadmin.user_add(o, "foo", password = "bar123") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') if (!oadmin.user_exists(o, "foo")) oadmin.user_add(o, "foo", password = "bar123") opal.logout(o) ## End(Not run)
Delete a user profile without deleting user if this one is defined in the Opal internal users registry. Fails silently if user profile does not exist. A user profile is the footprint of a user, created at first login. It keeps track of its activity, the realm from which he/she was authenticated, its groups at time of the last login and more.
oadmin.user_profile_delete(opal, name)oadmin.user_profile_delete(opal, name)
opal |
Opal object. |
name |
User name |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profiles(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_profile_delete(o, "foo") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_profile_delete(o, "foo") opal.logout(o) ## End(Not run)
When a user has logged in Opal, he/she has a profile representing its activity. The user can be defined in the Opal internal user registry, or in an external realm.
oadmin.user_profiles(opal, df = TRUE)oadmin.user_profiles(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_reset_password(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.user_profiles(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.user_profiles(o) opal.logout(o) ## End(Not run)
Reset the password of a user from Opal internal users registry.
oadmin.user_reset_password(opal, name, password = NULL)oadmin.user_reset_password(opal, name, password = NULL)
opal |
Opal object. |
name |
User name |
password |
User password. If not provided, a password will be generated and returned. |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.users()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_reset_password(o, "foo", password = "password1234") oadmin.user_rm(o, "foo") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM")) oadmin.user_reset_password(o, "foo", password = "password1234") oadmin.user_rm(o, "foo") opal.logout(o) ## End(Not run)
Get the users from the Opal internal users registry.
oadmin.users(opal, df = TRUE)oadmin.users(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other user functions:
oadmin.user_add(),
oadmin.user_delete(),
oadmin.user_enable(),
oadmin.user_exists(),
oadmin.user_profile_delete(),
oadmin.user_profiles(),
oadmin.user_reset_password()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.users(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') oadmin.users(o) opal.logout(o) ## End(Not run)
Set the provided annotations (as the one that can be retrieved from opal.annotations) to the table's data dictionary. Variables that do not exists in the table are ignored.
opal.annotate(opal, datasource, table, annotations)opal.annotate(opal, datasource, table, annotations)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
annotations |
A data frame of annotations, with the expected columns: 'variable' (variable name), 'taxonomy' (the taxonomy name), 'vocabulary' (the vocabulary name) and 'term' (the term value, if NULL of NA the annotation is removed). |
Other datasource functions:
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') annots <- opal.annotations(o, 'CPTP', 'Coreqx_final') opal.annotate(o, 'CPTP', 'Cag_coreqx', annots) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') annots <- opal.annotations(o, 'CPTP', 'Coreqx_final') opal.annotate(o, 'CPTP', 'Cag_coreqx', annots) opal.logout(o) ## End(Not run)
Directly retrieves from the table's data dictionary the variable annotations (attributes with a namespace).
opal.annotations(opal, datasource, table)opal.annotations(opal, datasource, table)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
A data frame in long format (one row per annotation).
Other datasource functions:
opal.annotate(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.annotations(o, 'CPTP', 'Coreqx_final') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.annotations(o, 'CPTP', 'Coreqx_final') opal.logout(o) ## End(Not run)
Helper function for turning an array into its Markdown representation.
opal.as_md_table( table, icons = TRUE, digits = getOption("digits"), col.names = colnames(table), align, caption = NULL )opal.as_md_table( table, icons = TRUE, digits = getOption("digits"), col.names = colnames(table), align, caption = NULL )
table |
An array, including a matrix or a data.frame. |
icons |
Turn logicals to icons (requires bootstrap style). Default is TRUE. |
digits |
The maximum number of digits for numeric columns (passed to round()); it can also be a vector of length ncol(table) to set the number of digits for individual columns. |
col.names |
A character vector of column names to be used in the table |
align |
The alignment of columns: a character vector consisting of 'l' (left), 'c' (center) and/or 'r' (right); by default, numeric columns are right-aligned, and other columns are left-aligned; if align = NULL, the default alignment is used. |
caption |
The table caption. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1')) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1')) opal.logout(o) ## End(Not run)
Assign a Opal table, or a R expression or a R object to a R symbol in the current R session.
opal.assign( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = NULL, updated.name = NULL, async = FALSE )opal.assign( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = NULL, updated.name = NULL, async = FALSE )
opal |
Opal object or list of opal objects. |
symbol |
Name of the R symbol. |
value |
The value to assign evaluated in the following order: a R expression, a function, a fully qualified name of a variable or a table in Opal or any other R object (data.frame, vector). |
variables |
List of variable names or Javascript expression that selects the variables of a table (ignored if value does not refere to a table). See javascript documentation: http://wiki.obiba.org/display/OPALDOC/Variable+Methods |
missings |
If TRUE, missing values will be pushed from Opal to R, default is FALSE. Ignored if value is an R expression. |
identifiers |
Name of the identifiers mapping to use when assigning entities to R (from Opal 2.0). |
id.name |
Add a vector with the given name representing the entity identifiers (from Opal 2.6). Default is NULL. |
updated.name |
Add a vector with the given name representing the creation and last update timestamps (from Opal 2.6). Default is NULL. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign.data(),
opal.assign.resource(),
opal.assign.script(),
opal.assign.table(),
opal.assign.table.tibble()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a list of variables from table CNSIM1 opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC")) # assign all the variables matching 'LAB' from table HOP of opal object o opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')") # assign a function and call it opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))})) opal.execute(o, "hello('Mr Bean')") # push an arbitrary data frame to the R server #opal.assign(o, "D", mtcars) # push an arbitrary vector to the R server #opal.assign(o, "C", mtcars$cyl) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a list of variables from table CNSIM1 opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC")) # assign all the variables matching 'LAB' from table HOP of opal object o opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')") # assign a function and call it opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))})) opal.execute(o, "hello('Mr Bean')") # push an arbitrary data frame to the R server #opal.assign(o, "D", mtcars) # push an arbitrary vector to the R server #opal.assign(o, "C", mtcars$cyl) opal.logout(o) ## End(Not run)
Assign a R object to a R symbol in the current R session.
opal.assign.data(opal, symbol, value, async = FALSE)opal.assign.data(opal, symbol, value, async = FALSE)
opal |
Opal object or list of opal objects. |
symbol |
Name of the R symbol. |
value |
The R object to assign (data.frame, vector). |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign(),
opal.assign.resource(),
opal.assign.script(),
opal.assign.table(),
opal.assign.table.tibble()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # push an arbitrary data frame to the R server opal.assign.data(o, "D", mtcars) # push an arbitrary vector to the R server opal.assign.data(o, "C", mtcars$cyl) # push a string opal.assign.data(o, "S", "Hello!") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # push an arbitrary data frame to the R server opal.assign.data(o, "D", mtcars) # push an arbitrary vector to the R server opal.assign.data(o, "C", mtcars$cyl) # push a string opal.assign.data(o, "S", "Hello!") opal.logout(o) ## End(Not run)
Assign a ResourceClient object to a R symbol in the current R session.
opal.assign.resource(opal, symbol, value, async = FALSE)opal.assign.resource(opal, symbol, value, async = FALSE)
opal |
Opal object or list of opal objects. |
symbol |
Name of the R symbol. |
value |
The fully qualified name of a resource in Opal. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign(),
opal.assign.data(),
opal.assign.script(),
opal.assign.table(),
opal.assign.table.tibble()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a resource and make some operation on it opal.assign.resource(o, "D", "datashield.cram1") opal.execute(o, "class(D)") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a resource and make some operation on it opal.assign.resource(o, "D", "datashield.cram1") opal.execute(o, "class(D)") opal.logout(o) ## End(Not run)
Assign a R script or expression to a R symbol in the current R session.
opal.assign.script(opal, symbol, value, async = FALSE)opal.assign.script(opal, symbol, value, async = FALSE)
opal |
Opal object or list of opal objects. |
symbol |
Name of the R symbol. |
value |
The R expression to assign. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign(),
opal.assign.data(),
opal.assign.resource(),
opal.assign.table(),
opal.assign.table.tibble()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a function and call it opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))})) opal.execute(o, "hello('Mr Bean')") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a function and call it opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))})) opal.execute(o, "hello('Mr Bean')") opal.logout(o) ## End(Not run)
Assign a Opal table to a data.frame identified by a R symbol in the current R session.
opal.assign.table( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = NULL, updated.name = NULL, class = "data.frame", async = FALSE )opal.assign.table( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = NULL, updated.name = NULL, class = "data.frame", async = FALSE )
opal |
Opal object or list of opal objects. |
symbol |
Name of the R symbol. |
value |
The value to assign evaluated in the following order: a fully qualified name of a variable or a table in Opal. |
variables |
List of variable names or Javascript expression that selects the variables of a table (ignored if value does not refere to a table). See javascript documentation: http://wiki.obiba.org/display/OPALDOC/Variable+Methods |
missings |
If TRUE, missing values will be pushed from Opal to R, default is FALSE. |
identifiers |
Name of the identifiers mapping to use when assigning entities to R (from Opal 2.0). |
id.name |
Add a vector with the given name representing the entity identifiers (from Opal 2.6). Default is NULL. |
updated.name |
Deprecated. Add a vector with the given name representing the creation and last update timestamps (from Opal 2.6). Default is NULL. |
class |
The data frame class into which the table is written: can 'data.frame' (default) or 'tibble' (from Opal 2.6 to 2.13) or 'tibble.with.factors' (from Opal 2.14). |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign(),
opal.assign.data(),
opal.assign.resource(),
opal.assign.script(),
opal.assign.table.tibble()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a list of variables from table CNSIM1 opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC")) opal.execute(o, "colnames(D)") # assign a table CNSIM1 with a identifiers column opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id") opal.execute(o, "colnames(H)") # assign all the variables matching 'LAB' from table HOP of opal object o opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')") opal.execute(o, "colnames(D)") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a list of variables from table CNSIM1 opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC")) opal.execute(o, "colnames(D)") # assign a table CNSIM1 with a identifiers column opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id") opal.execute(o, "colnames(H)") # assign all the variables matching 'LAB' from table HOP of opal object o opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')") opal.execute(o, "colnames(D)") opal.logout(o) ## End(Not run)
Assign a Opal table to a tibble identified by a R symbol in the current R session.
opal.assign.table.tibble( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = "id", with.factors = FALSE, updated.name = NULL, async = FALSE )opal.assign.table.tibble( opal, symbol, value, variables = NULL, missings = FALSE, identifiers = NULL, id.name = "id", with.factors = FALSE, updated.name = NULL, async = FALSE )
opal |
Opal object. |
symbol |
Name of the R symbol. |
value |
The fully qualified name of a table in Opal. |
variables |
List of variable names or Javascript expression that selects the variables of a table (ignored if value does not refere to a table). See javascript documentation: http://wiki.obiba.org/display/OPALDOC/Variable+Methods |
missings |
If TRUE, missing values will be pushed from Opal to R, default is FALSE. |
identifiers |
Name of the identifiers mapping to use when assigning entities to R (from Opal 2.0). |
id.name |
Add a vector with the given name representing the entity identifiers (from Opal 2.6). Default is 'id'. |
with.factors |
If TRUE, the categorical variables will be assigned as factors (from Opal 2.14). Default is FALSE. |
updated.name |
Deprecated. Add a vector with the given name representing the creation and last update timestamps (from Opal 2.6 to 2.13). Default is NULL. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other assignment functions:
opal.assign(),
opal.assign.data(),
opal.assign.resource(),
opal.assign.script(),
opal.assign.table()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a table and make some operation on it opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1') opal.execute(o, "class(D)") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # assign a table and make some operation on it opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1') opal.execute(o, "class(D)") opal.logout(o) ## End(Not run)
Get a vector of attribute values (for each locale) matching the given attribute namespace and name. Vector is null if no such attribute is found.
opal.attribute_values(attributes, namespace = NULL, name = "label")opal.attribute_values(attributes, namespace = NULL, name = "label")
attributes |
A list of attributes, usually variable or category attributes. |
namespace |
Optional attribute namespace. |
name |
Required attribute name. |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.attribute_values(var$attributes) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.attribute_values(var$attributes) opal.logout(o) ## End(Not run)
Get an asynchronous R commands in the remote R session.
opal.command(opal, id, wait = FALSE)opal.command(opal, id, wait = FALSE)
opal |
Opal object. |
id |
R command ID. |
wait |
Wait for the command to complete. |
Other command functions:
opal.command_result(),
opal.command_rm(),
opal.commands(),
opal.commands_rm()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command(o, '1234') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command(o, '1234') opal.logout(o) ## End(Not run)
Get the result of an asynchronous R commands in the remote R session. The command is removed from the remote R session after this call.
opal.command_result(opal, id, wait = FALSE)opal.command_result(opal, id, wait = FALSE)
opal |
Opal object. |
id |
R command ID. |
wait |
Wait for the command to complete. |
Other command functions:
opal.command(),
opal.command_rm(),
opal.commands(),
opal.commands_rm()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command_result(o, '1234') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command_result(o, '1234') opal.logout(o) ## End(Not run)
Remove an asynchronous R commands in the remote R session.
opal.command_rm(opal, id)opal.command_rm(opal, id)
opal |
Opal object. |
id |
R command ID. |
Other command functions:
opal.command(),
opal.command_result(),
opal.commands(),
opal.commands_rm()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command_rm(o, '1234') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.command_rm(o, '1234') opal.logout(o) ## End(Not run)
Get the list of asynchronous R commands in the remote R session.
opal.commands(opal, df = TRUE)opal.commands(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other command functions:
opal.command(),
opal.command_result(),
opal.command_rm(),
opal.commands_rm()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.commands(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.commands(o) opal.logout(o) ## End(Not run)
Remove all asynchronous R commands in the remote R session.
opal.commands_rm(opal)opal.commands_rm(opal)
opal |
Opal object. |
Other command functions:
opal.command(),
opal.command_result(),
opal.command_rm(),
opal.commands()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.commands_rm(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.commands_rm(o) opal.logout(o) ## End(Not run)
Get a datasource
opal.datasource(opal, datasource)opal.datasource(opal, datasource)
opal |
Opal object. |
datasource |
Name of the datasource. |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.datasource(o, 'CNSIM') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.datasource(o, 'CNSIM') opal.logout(o) ## End(Not run)
Get datasources
opal.datasources(opal, df = TRUE)opal.datasources(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.datasources(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.datasources(o) opal.logout(o) ## End(Not run)
Generic REST resource deletion.
opal.delete(opal, ..., query = list(), callback = NULL)opal.delete(opal, ..., query = list(), callback = NULL)
opal |
Opal object. |
... |
Resource path segments. |
query |
Named list of query parameters. |
callback |
A callback function to handle the response object. |
Other REST functions:
opal.get(),
opal.post(),
opal.put()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.delete(o, 'some', 'resource') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.delete(o, 'some', 'resource') opal.logout(o) ## End(Not run)
Execute a R script in the remote R session.
opal.execute(opal, script, async = FALSE)opal.execute(opal, script, async = FALSE)
opal |
Opal object or list of opal objects. |
script |
R script to execute. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other execution functions:
opal.execute.source(),
opal.load_package(),
opal.unload_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.execute(o, "x <- 'foo'") opal.execute(o, "ls()") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.execute(o, "x <- 'foo'") opal.execute(o, "ls()") opal.logout(o) ## End(Not run)
Upload a R file script and execute it in the remote R session with source().
opal.execute.source(opal, path, async = FALSE)opal.execute.source(opal, path, async = FALSE)
opal |
Opal object or list of opal objects. |
path |
Path to the R file script to execute. |
async |
R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1). |
Other execution functions:
opal.execute(),
opal.load_package(),
opal.unload_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.execute.source(o, "myscript.R") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.execute.source(o, "myscript.R") opal.logout(o) ## End(Not run)
Get file content from the Opal file system.
opal.file(opal, path, key = NULL)opal.file(opal, path, key = NULL)
opal |
Opal object. |
path |
Path to the file in the Opal file system. |
key |
File encryption key: downloaded file will be a zip file with content encrypted (use 7zip to decrypt). |
Other file functions:
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.file(o, '/home/administrator/joins/join-src-3.csv') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.file(o, '/home/administrator/joins/join-src-3.csv') opal.logout(o) ## End(Not run)
Copy a file or a folder to another location in the Opal file system.
opal.file_cp(opal, source, destination)opal.file_cp(opal, source, destination)
opal |
Opal object. |
source |
Path to the file in the Opal file system. |
destination |
New path to the file in the Opal file system. |
Other file functions:
opal.file(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # copy a file to another folder opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables') # copy recursively a folder to another folder opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # copy a file to another folder opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables') # copy recursively a folder to another folder opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables') opal.logout(o) ## End(Not run)
Download a file or a folder from the Opal file system.
opal.file_download(opal, source, destination = NULL, key = NULL)opal.file_download(opal, source, destination = NULL, key = NULL)
opal |
Opal object. |
source |
Path to the file in the Opal file system. |
destination |
Path to the file to be written. If ommitted, file with same name in the working directory will be written. |
key |
File encryption key: downloaded file will be a zip file with content encrypted (use 7zip to decrypt). |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # download a file opal.file_download(o, '/home/administrator/joins/join-src-3.csv') # download a file encrypted by a key: resulting file is a zip with an encrypted content opal.file_download(o, '/home/administrator/export/some-data.csv', destination='some-data.zip', key='AZF57893FBDE') # download, create destination folder and rename file opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav') # download a folder opal.file_download(o, '/home/administrator/export', 'export.zip') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # download a file opal.file_download(o, '/home/administrator/joins/join-src-3.csv') # download a file encrypted by a key: resulting file is a zip with an encrypted content opal.file_download(o, '/home/administrator/export/some-data.csv', destination='some-data.zip', key='AZF57893FBDE') # download, create destination folder and rename file opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav') # download a folder opal.file_download(o, '/home/administrator/export', 'export.zip') opal.logout(o) ## End(Not run)
List content of a folder in the Opal file system.
opal.file_ls(opal, path)opal.file_ls(opal, path)
opal |
Opal object. |
path |
Path to the folder in the Opal file system. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # list content of a folder opal.file_ls(o, '/home/administrator') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # list content of a folder opal.file_ls(o, '/home/administrator') opal.logout(o) ## End(Not run)
Make a folder in the Opal file system. Use the parents parameter to ignore if it already exist and to create parent folders.
opal.file_mkdir(opal, path, parents = FALSE)opal.file_mkdir(opal, path, parents = FALSE)
opal |
Opal object. |
path |
Path to the new folder in the Opal file system. |
parents |
No error if existing, make parent directories as needed. Default is FALSE. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a folder opal.file_mkdir(o, '/home/administrator/test', parents = TRUE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a folder opal.file_mkdir(o, '/home/administrator/test', parents = TRUE) opal.logout(o) ## End(Not run)
Make a user personal temporary folder in the Opal file system (make sure it does not exists).
opal.file_mkdir_tmp(opal)opal.file_mkdir_tmp(opal)
opal |
Opal object. |
The path of the created folder.
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a folder path <- opal.file_mkdir_tmp(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a folder path <- opal.file_mkdir_tmp(o) opal.logout(o) ## End(Not run)
Move and/or rename a file or a folder in the Opal file system.
opal.file_mv(opal, source, destination)opal.file_mv(opal, source, destination)
opal |
Opal object. |
source |
Path to the file in the Opal file system. |
destination |
New path to the file in the Opal file system. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # move a file to another folder opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables') # rename a file opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv', '/home/administrator/export/some-data.csv') # move and rename a file opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv', '/home/userx/deliverables/some-data.csv') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # move a file to another folder opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables') # rename a file opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv', '/home/administrator/export/some-data.csv') # move and rename a file opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv', '/home/userx/deliverables/some-data.csv') opal.logout(o) ## End(Not run)
Read a file from the R session workspace into the Opal file system.
opal.file_read(opal, source, destination)opal.file_read(opal, source, destination)
opal |
Opal object. |
source |
Path to the file in the R session workspace (must exists). |
destination |
Path to the destination file or folder. Any required sub-folders will be created. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # read into folder opal.file_read(o,"DatabaseTest.sav", "/tmp") # read and rename opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav") # user home expansion opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # read into folder opal.file_read(o,"DatabaseTest.sav", "/tmp") # read and rename opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav") # user home expansion opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav") opal.logout(o) ## End(Not run)
Remove a file or a folder from the Opal file system.
opal.file_rm(opal, path)opal.file_rm(opal, path)
opal |
Opal object. |
path |
Path to the file in the Opal file system. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_unzip(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # remove a file opal.file_rm(o, '/home/administrator/export/some-data.csv') # remove recursively a folder opal.file_rm(o, '/home/administrator/export') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # remove a file opal.file_rm(o, '/home/administrator/export/some-data.csv') # remove recursively a folder opal.file_rm(o, '/home/administrator/export') opal.logout(o) ## End(Not run)
Unzip a zip archive file from the Opal file system.
opal.file_unzip(opal, source, destination, key = NULL)opal.file_unzip(opal, source, destination, key = NULL)
opal |
Opal object. |
source |
Path to the file in the Opal file system (must exist and have the ".zip" file extension). |
destination |
Path to the destination file or folder in the Opal file system. |
key |
Key to decrypt archive. |
The path of the extracted archive folder in the Opal file system.
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_upload(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # unzip path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # unzip path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator") opal.logout(o) ## End(Not run)
Upload a file or a folder into the Opal file system. Creates the destination folder (and parents) when necessary. Hidden files and folders (with name starting with dot) can be excluded.
opal.file_upload(opal, source, destination, all.files = TRUE)opal.file_upload(opal, source, destination, all.files = TRUE)
opal |
Opal object. |
source |
Path to the file in the local file system. |
destination |
Path of the destination folder in the Opal file system. Folder (and parents) will be created if missing. |
all.files |
When FALSE, upload only visible files (following Unix-style visibility, that is files whose name does not start with a dot). Default is TRUE. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_write()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # upload a file opal.file_upload(o, 'some_data.csv', '/home/administrator') # upload a folder opal.file_upload(o, 'some_data', '/home/administrator') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # upload a file opal.file_upload(o, 'some_data.csv', '/home/administrator') # upload a folder opal.file_upload(o, 'some_data', '/home/administrator') opal.logout(o) ## End(Not run)
Write a file from the Opal file system into the R session workspace.
opal.file_write(opal, source, destination = NULL)opal.file_write(opal, source, destination = NULL)
opal |
Opal object. |
source |
Path to the file in the Opal file system (must exists and be accessible for the user). |
destination |
Path to the destination file, relative to the R session workspace. Any required sub-folders will be created. If ommitted, file with same name will be written. |
Other file functions:
opal.file(),
opal.file_cp(),
opal.file_download(),
opal.file_ls(),
opal.file_mkdir(),
opal.file_mkdir_tmp(),
opal.file_mv(),
opal.file_read(),
opal.file_rm(),
opal.file_unzip(),
opal.file_upload()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # user home expansion opal.file_write(o, "~/spss/DatabaseTest.sav") # rename file opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav") # create sub-folder opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # user home expansion opal.file_write(o, "~/spss/DatabaseTest.sav") # rename file opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav") # create sub-folder opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav") opal.logout(o) ## End(Not run)
Generic REST resource getter.
opal.get( opal, ..., query = list(), acceptType = "application/json", outFile = NULL, callback = NULL )opal.get( opal, ..., query = list(), acceptType = "application/json", outFile = NULL, callback = NULL )
opal |
Opal object. |
... |
Resource path segments. |
query |
Named list of query parameters. |
acceptType |
The type of the body content. Default is 'application/json', i.e. a serialized R object or an error message. |
outFile |
Write response body to file. Ignored if NULL (default). |
callback |
A callback function to handle the response object. |
Other REST functions:
opal.delete(),
opal.post(),
opal.put()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.get(o, 'project', 'CNSIM') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.get(o, 'project', 'CNSIM') opal.logout(o) ## End(Not run)
Load package in the remote R session.
opal.load_package(opal, pkg)opal.load_package(opal, pkg)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
Other execution functions:
opal.execute(),
opal.execute.source(),
opal.unload_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.load_package(o, 'stats') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.load_package(o, 'stats') opal.logout(o) ## End(Not run)
Log in Opal(s). Different login strategies are possible: (1) by providing username/password, or (2) by providing username/password and a one-time password code (TOPT) when user has activated two-factor authentication, or (3) by providing a personal access token (PAT), or (4) by providing a key pair in PEM format.
opal.login( username = getOption("opal.username"), password = getOption("opal.password"), token = getOption("opal.token"), url = getOption("opal.url"), opts = getOption("opal.opts", list()), profile = getOption("opal.profile"), restore = NULL )opal.login( username = getOption("opal.username"), password = getOption("opal.password"), token = getOption("opal.token"), url = getOption("opal.url"), opts = getOption("opal.opts", list()), profile = getOption("opal.profile"), restore = NULL )
username |
User name in opal(s). Can be provided by "opal.username" option. |
password |
User password in opal(s). Can be provided by "opal.password" option. |
token |
Personal access token (since opal 2.15). Only effective if the username or the password is NULL or empty. Can be provided by "opal.token" option. |
url |
Opal url or list of opal urls. Can be provided by "opal.url" option. Secure http (https) connection is required. |
opts |
Curl options as described by httr (call httr::httr_options() for details). Can be provided by "opal.opts" option. |
profile |
R server profile name. This will drive the R server in which a R session will be created. If no remote R session is needed (because Opal specific operations are done), this parameter does not need to be provided. Otherwise, if missing, the default R server profile will be applied ('default'). See also opal.profiles. |
restore |
Workspace ID to be restored (see also opal.logout) |
A opal object or a list of opal objects.
Other connection functions:
opal.logout(),
opal.profiles()
## Not run: #### The below examples illustrate the different ways to login in opal #### # explicite username/password login o <- opal.login(username = 'administrator', password = 'password', url = 'https://opal-demo.obiba.org') opal.logout(o) # explicite personal access token login o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke', url = 'https://opal-demo.obiba.org') opal.logout(o) # login using options and user credentials options(opal.username = 'administrator', opal.password = 'password', opal.url = 'https://opal-demo.obiba.org') o <- opal.login() opal.logout(o) # login using options and personal access token options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke', opal.url = 'https://opal-demo.obiba.org') o <- opal.login() opal.logout(o) # login using ssl key pair options(opal.opts = list( sslcert = 'my-publickey.pem', sslkey = 'my-privatekey.pem')) o <- opal.login(url = 'https://opal-demo.obiba.org') opal.logout(o) # login with a R server profile o <- opal.login(username = 'administrator', password = 'password', url = 'https://opal-demo.obiba.org', profile = 'default') opal.logout(o) ## End(Not run)## Not run: #### The below examples illustrate the different ways to login in opal #### # explicite username/password login o <- opal.login(username = 'administrator', password = 'password', url = 'https://opal-demo.obiba.org') opal.logout(o) # explicite personal access token login o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke', url = 'https://opal-demo.obiba.org') opal.logout(o) # login using options and user credentials options(opal.username = 'administrator', opal.password = 'password', opal.url = 'https://opal-demo.obiba.org') o <- opal.login() opal.logout(o) # login using options and personal access token options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke', opal.url = 'https://opal-demo.obiba.org') o <- opal.login() opal.logout(o) # login using ssl key pair options(opal.opts = list( sslcert = 'my-publickey.pem', sslkey = 'my-privatekey.pem')) o <- opal.login(url = 'https://opal-demo.obiba.org') opal.logout(o) # login with a R server profile o <- opal.login(username = 'administrator', password = 'password', url = 'https://opal-demo.obiba.org', profile = 'default') opal.logout(o) ## End(Not run)
Clear the R sessions and logout from Opal(s).
opal.logout(opal, save = FALSE)opal.logout(opal, save = FALSE)
opal |
Opal object or a list of opals. |
save |
Save the workspace with given identifier (default value is FALSE, current session ID if TRUE). |
Other connection functions:
opal.login(),
opal.profiles()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.logout(o) ## End(Not run)
Get the permissions of a subject. If the subject is a user, the permissions of the groups to which the user belongs are also added to the result.
opal.perms(opal, subject, type = "user")opal.perms(opal, subject, type = "user")
opal |
Opal connection object. |
subject |
A subject identifier: user or group name. |
type |
The type of subject: user (default) or group. |
A data.frame with columns: subject, type, target (path to the opal object to which the permission applies), target_type and perm (the permission name)
Other table functions:
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.perms(o, 'andrei') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.perms(o, 'andrei') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Generic REST resource creation.
opal.post( opal, ..., query = list(), body = "", contentType = "application/x-rscript", acceptType = "application/json", outFile = NULL, callback = NULL )opal.post( opal, ..., query = list(), body = "", contentType = "application/x-rscript", acceptType = "application/json", outFile = NULL, callback = NULL )
opal |
Opal object. |
... |
Resource path segments. |
query |
Named list of query parameters. |
body |
The body of the request. |
contentType |
The type of the body content. Default is 'application/x-rscript'. |
acceptType |
The type of the body content. Default is 'application/json', i.e. a serialized R object or an error message. |
outFile |
Write response body to file. Ignored if NULL (default). |
callback |
A callback function to handle the response object. |
Other REST functions:
opal.delete(),
opal.get(),
opal.put()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.post(o, 'some', 'resources', body = '{"some":"value"}') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.post(o, 'some', 'resources', body = '{"some":"value"}') opal.logout(o) ## End(Not run)
Each R profile corresponds one R servers cluster name. These profiles names can be provided when login (see opal.login) and on some package administration operations.
opal.profiles(opal, df = TRUE)opal.profiles(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
The R profiles as a data.frame or a list
Other connection functions:
opal.login(),
opal.logout()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.profiles(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.profiles(o) opal.logout(o) ## End(Not run)
Get a project
opal.project(opal, project)opal.project(opal, project)
opal |
Opal object. |
project |
Name of the project |
Other project functions:
opal.project_create(),
opal.project_delete(),
opal.project_exists(),
opal.projects(),
opal.projects_databases()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project(o, 'datashield') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project(o, 'datashield') opal.logout(o) ## End(Not run)
The project backup task has a limited scope: tables (dictionary and data export), views (either as a logical table or as an exported table), resources, files and report templates. Other project elements that are not part of the backup: user and group permissions, view change history, table analysis, report executions etc.
opal.project_backup( opal, project, archive, viewsAsTables = FALSE, override = TRUE, wait = TRUE )opal.project_backup( opal, project, archive, viewsAsTables = FALSE, override = TRUE, wait = TRUE )
opal |
Opal object. |
project |
Name of the project. |
archive |
Archive directory path in the Opal file system. If folder (and parents) does not exist, it will be created. |
viewsAsTables |
Treat views as tables, i.e. export data instead of keeping derivation scripts. Default is FALSE. |
override |
Overwrite an existing backup folder. Default is TRUE. |
wait |
Wait for backup task completion. Default is TRUE. |
The project command ID if wait parameter is FALSE. See opal.project_command to retrieve asynchronous command state.
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE') opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE') opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip') opal.logout(o) ## End(Not run)
Get the project's task command object.
opal.project_command(opal, project, id)opal.project_command(opal, project, id)
opal |
Opal object. |
project |
Name of the project. |
id |
The project command ID. |
The command state object.
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE) opal.project_command(opal, 'GREENSPACE', id) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE) opal.project_command(opal, 'GREENSPACE', id) opal.logout(o) ## End(Not run)
Create a project
opal.project_create( opal, project, database = NULL, title = NULL, description = NULL, tags = NULL, exportFolder = NULL )opal.project_create( opal, project, database = NULL, title = NULL, description = NULL, tags = NULL, exportFolder = NULL )
opal |
Opal object. |
project |
Name of the project |
database |
The database name (as declared in Opal) to be used to store project's data. If not provided, the project can have views and resources but no raw tables. If the the value is a logical and is TRUE, the default database will be selected or the first one if there is no default. |
title |
The title of the project (optional). |
description |
The description of the project (optional). |
tags |
A list of tag names (optional). |
exportFolder |
The default location of the exported data files in the Opal file system (optional). |
Other project functions:
opal.project(),
opal.project_delete(),
opal.project_exists(),
opal.projects(),
opal.projects_databases()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with named database opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test')) # with default database opal.project_create(o, 'test_default_db', database = TRUE) # no database, for views and resources only opal.project_create(o, 'test_no_db') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with named database opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test')) # with default database opal.project_create(o, 'test_default_db', database = TRUE) # no database, for views and resources only opal.project_create(o, 'test_no_db') opal.logout(o) ## End(Not run)
Delete a project and every data what could have been associated to it.
opal.project_delete(opal, project, archive = FALSE, silent = TRUE)opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
opal |
Opal object. |
project |
Name of the project |
archive |
Logical that is TRUE if the complete removal of the project is requested. |
silent |
Warn if project does not exist, default is TRUE. |
Other project functions:
opal.project(),
opal.project_create(),
opal.project_exists(),
opal.projects(),
opal.projects_databases()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_delete(o, 'test') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_delete(o, 'test') opal.logout(o) ## End(Not run)
Check whether a project already exists (and is visible by the requesting user).
opal.project_exists(opal, project)opal.project_exists(opal, project)
opal |
Opal object. |
project |
Name of the project |
A logical
Other project functions:
opal.project(),
opal.project_create(),
opal.project_delete(),
opal.projects(),
opal.projects_databases()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_exists(o, 'test') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_exists(o, 'test') opal.logout(o) ## End(Not run)
Get the permissions that were applied on a project.
opal.project_perm(opal, project)opal.project_perm(opal, project)
opal |
Opal connection object. |
project |
Project name. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on a project.
opal.project_perm_add( opal, project, subject, type = "user", permission = "administrate" )opal.project_perm_add( opal, project, subject, type = "user", permission = "administrate" )
opal |
Opal connection object. |
project |
Project name where the table will be located. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: administrate. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied on a project. Silently returns when there is no such permission.
opal.project_perm_delete(opal, project, subject, type = "user")opal.project_perm_delete(opal, project, subject, type = "user")
opal |
Opal connection object. |
project |
Project name where the table will be located. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.project_perm(o, 'CNSIM') opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Restore the data of a project from a backup archive file to be found on the Opal file system. The destination project must exist and can have a name different from the original one (beware that this could break views). Default behavior is to stop when an item to restore already exist (override can be forced).
opal.project_restore( opal, project, archive, key = NULL, override = TRUE, wait = TRUE )opal.project_restore( opal, project, archive, key = NULL, override = TRUE, wait = TRUE )
opal |
Opal object. |
project |
Name of the project. |
archive |
Archive directory or zip file path in the Opal file system. |
key |
Archive zip file password (if applies). |
override |
Overwrite existing items (table, view, resource, report). Project files override is not checked. Default is TRUE. |
wait |
Wait for restore task completion. Default is TRUE. |
The project command ID if wait parameter is FALSE. See opal.project_command to retrieve asynchronous command state.
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # create the project to restore, with the default database (to store tables) opal.project_create(o, 'GREENSPACE2', database = TRUE) # upload backup zip and launch restore task opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator') opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # create the project to restore, with the default database (to store tables) opal.project_create(o, 'GREENSPACE2', database = TRUE) # upload backup zip and launch restore task opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator') opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip') opal.logout(o) ## End(Not run)
Get projects
opal.projects(opal, df = TRUE)opal.projects(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other project functions:
opal.project(),
opal.project_create(),
opal.project_delete(),
opal.project_exists(),
opal.projects_databases()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.projects(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.projects(o) opal.logout(o) ## End(Not run)
When creating a project for storing data, it is required to name the database to be associated.
opal.projects_databases(opal)opal.projects_databases(opal)
opal |
Opal object. |
A character vector of databases names.
Other project functions:
opal.project(),
opal.project_create(),
opal.project_delete(),
opal.project_exists(),
opal.projects()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.projects_databases(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.projects_databases(o) opal.logout(o) ## End(Not run)
Generic REST resource update.
opal.put( opal, ..., query = list(), body = "", contentType = "application/x-rscript", callback = NULL )opal.put( opal, ..., query = list(), body = "", contentType = "application/x-rscript", callback = NULL )
opal |
Opal object. |
... |
Resource path segments. |
query |
Named list of query parameters. |
body |
The body of the request. |
contentType |
The type of the body content. |
callback |
A callback function to handle the response object. |
Other REST functions:
opal.delete(),
opal.get(),
opal.post()
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}') opal.logout(o) ## End(Not run)
Helper function for generating reports.
opal.report( input, output = NULL, progress = FALSE, verbose = FALSE, boot_style = NULL )opal.report( input, output = NULL, progress = FALSE, verbose = FALSE, boot_style = NULL )
input |
Path to the R markdown report file |
output |
Directory path where to ouput the html report file. Default is the current working directory. |
progress |
Knitr progress option |
verbose |
Knitr verbose option |
boot_style |
Deprecated, directives can be integrated in the YAML header of the R markdown document. |
## Not run: opal.report('input.Rmd', 'report', progress=TRUE) ## End(Not run)## Not run: opal.report('input.Rmd', 'report', progress=TRUE) ## End(Not run)
Get a resource reference of a project
opal.resource(opal, project, resource)opal.resource(opal, project, resource)
opal |
Opal object. |
project |
Name of the project. |
resource |
Name of the resource in the project. |
Other resource functions:
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource(o, 'RSRC', 'CNSIM1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource(o, 'RSRC', 'CNSIM1') opal.logout(o) ## End(Not run)
Create a resource reference in a project
opal.resource_create( opal, project, name, url, description = NULL, format = NULL, package = NULL, identity = NULL, secret = NULL )opal.resource_create( opal, project, name, url, description = NULL, format = NULL, package = NULL, identity = NULL, secret = NULL )
opal |
Opal object. |
project |
Name of the project. |
name |
Name of the resource in the project. |
url |
The URL of the resource. |
description |
The description of the resource (optional). |
format |
The format of the data described by the resource (optional). |
package |
The R package to be loaded prior to the assignment of the resource (optional). |
identity |
The identity key or username to be used when accessing the resource (optional). |
secret |
The secret key or password to be used when accessing the resource (optional). |
Other resource functions:
opal.resource(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_create(o, 'RSRC', 'CNSIM4', url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip', format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_create(o, 'RSRC', 'CNSIM4', url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip', format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq') opal.logout(o) ## End(Not run)
Removes the reference to a resource. The targeted resource remains untouched.
opal.resource_delete(opal, project, resource, silent = TRUE)opal.resource_delete(opal, project, resource, silent = TRUE)
opal |
Opal connection object. |
project |
Project name where the resource is located. |
resource |
Resource name to be deleted. |
silent |
Warn if resource does not exist, default is TRUE. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_delete(o, "RSRC", "CNSIM4") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_delete(o, "RSRC", "CNSIM4") opal.logout(o) ## End(Not run)
Check whether a resource already exists in the project (and is visible by the requesting user).
opal.resource_exists(opal, project, resource)opal.resource_exists(opal, project, resource)
opal |
Opal object. |
project |
Name of the project. |
resource |
Name of the resource in the project. |
A logical
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_exists(o, 'RSRC', 'CNSIM1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_exists(o, 'RSRC', 'CNSIM1') opal.logout(o) ## End(Not run)
Create an extended resource reference in a project
opal.resource_extension_create( opal, project, name, provider, factory, parameters, description = NULL, credentials = NULL )opal.resource_extension_create( opal, project, name, provider, factory, parameters, description = NULL, credentials = NULL )
opal |
Opal object. |
project |
Name of the project. |
name |
Name of the resource in the project. |
provider |
Name of the R package in which the resource is defined. |
factory |
Name of the JS function that turns parameters and credentials into a resource object. |
parameters |
A named list of the resource parameters. |
description |
The description of the resource (optional). |
credentials |
A named list of the resource credentials (optional). |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g', provider = 'dsOmics', factory = 'ga4gh-htsget', parameters = list( host = 'https://htsget.ga4gh.org', sample = '1000genomes.phase1.chr1', reference = '1', start = '1', end = '100000', format = 'GA4GHVCF' ) ) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g', provider = 'dsOmics', factory = 'ga4gh-htsget', parameters = list( host = 'https://htsget.ga4gh.org', sample = '1000genomes.phase1.chr1', reference = '1', start = '1', end = '100000', format = 'GA4GHVCF' ) ) opal.logout(o) ## End(Not run)
Get the resource object of a project
opal.resource_get(opal, project, resource)opal.resource_get(opal, project, resource)
opal |
Opal object. |
project |
Name of the project. |
resource |
Name of the resource in the project. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') res <- opal.resource_get(o, 'RSRC', 'CNSIM1') # then interpret locally the resource object (load the appropriate R packages) library(resourcer) # coerce to a data.frame as.data.frame(res) # or get the resource client object for low-level interactions rescli <- resourcer::newResourceClient(res) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') res <- opal.resource_get(o, 'RSRC', 'CNSIM1') # then interpret locally the resource object (load the appropriate R packages) library(resourcer) # coerce to a data.frame as.data.frame(res) # or get the resource client object for low-level interactions rescli <- resourcer::newResourceClient(res) opal.logout(o) ## End(Not run)
Get the permissions that were applied on a resource.
opal.resource_perm(opal, project, resource)opal.resource_perm(opal, project, resource)
opal |
Opal connection object. |
project |
The project name. |
resource |
The resource name. |
A data.frame with columns: subject, type, permission
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on a resource
opal.resource_perm_add( opal, project, resource, subject, type = "user", permission )opal.resource_perm_add( opal, project, resource, subject, type = "user", permission )
opal |
Opal connection object. |
project |
The project name. |
resource |
The resource name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: view, administrate. The 'view' permission is suitable for DataSHIELD operations. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied on a resource. Silently returns when there is no such permission.
opal.resource_perm_delete(opal, project, resource, subject, type = "user")opal.resource_perm_delete(opal, project, resource, subject, type = "user")
opal |
Opal connection object. |
project |
The project name. |
resource |
The resource name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resource_perm(o, 'CNSIM', 'CNSIM1') opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Create an Opal view if a table with same name does not already exist. The resource reference is required.The dictionary of the created view will be discovered at initialization time. Use opal.table_dictionary_update to apply a dictionary.
opal.resource_view_create( opal, project, table, resource, type = "Participant", idColumn = NULL, profile = NULL )opal.resource_view_create( opal, project, table, resource, type = "Participant", idColumn = NULL, profile = NULL )
opal |
Opal connection object. |
project |
Project name where the view will be located. |
table |
View name to be created. |
resource |
Fully qualified resource name. |
type |
Entity type, default is "Participant". |
idColumn |
Name of the column which contains the entity identifiers. If not specified, the first column will be used. |
profile |
R server profile to use for establishing the connection with the resource. If not specifed, the profile will guessed based on the resource definition. |
Other table functions:
opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view over a resource opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1") opal.resource_view_create(o, "CNSIM", "FEMALE_2439", resource = "RSRC.FEMALE_2439", idColumn = "Name") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view over a resource opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1") opal.resource_view_create(o, "CNSIM", "FEMALE_2439", resource = "RSRC.FEMALE_2439", idColumn = "Name") opal.logout(o) ## End(Not run)
A view over a resource handles a connection to this resource. When the resource changes (data update, broken connection etc.), the connection to this resource can be re-initialized.
opal.resource_view_reconnect(opal, project, table)opal.resource_view_reconnect(opal, project, table)
opal |
Opal connection object. |
project |
Project name where the view is located. |
table |
View name to be reconnected. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view over a resource opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1") # re-initialize the view's connection to the resource opal.resource_view_reconnect(o, "CNSIM", "CNSIM4") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view over a resource opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1") # re-initialize the view's connection to the resource opal.resource_view_reconnect(o, "CNSIM", "CNSIM4") opal.logout(o) ## End(Not run)
Get the resource references of a project
opal.resources(opal, project, df = TRUE)opal.resources(opal, project, df = TRUE)
opal |
Opal object. |
project |
Name of the project. |
df |
Return a data.frame (default is TRUE) |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources_perm(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources(o, 'RSRC') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources(o, 'RSRC') opal.logout(o) ## End(Not run)
Get the permissions that were applied globally on the project's resources.
opal.resources_perm(opal, project)opal.resources_perm(opal, project)
opal |
Opal connection object. |
project |
The project name. |
A data.frame with columns: subject, type, permission
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm_add(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM') opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM') opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a global permission on the project's resources
opal.resources_perm_add(opal, project, subject, type = "user", permission)opal.resources_perm_add(opal, project, subject, type = "user", permission)
opal |
Opal connection object. |
project |
The project name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: view, administrate. The 'view' permission is suitable for DataSHIELD operations. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_delete()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM') opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM') opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied globally on the project's resources. Silently returns when there is no such permission.
opal.resources_perm_delete(opal, project, subject, type = "user")opal.resources_perm_delete(opal, project, subject, type = "user")
opal |
Opal connection object. |
project |
The project name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
Other resource functions:
opal.resource(),
opal.resource_create(),
opal.resource_delete(),
opal.resource_exists(),
opal.resource_extension_create(),
opal.resource_get(),
opal.resource_perm(),
opal.resource_perm_add(),
opal.resource_perm_delete(),
opal.resources(),
opal.resources_perm(),
opal.resources_perm_add()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM', 'CNSIM1') opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.resources_perm(o, 'CNSIM', 'CNSIM1') opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Remove a symbol from the current R session. Deprecated: see opal.symbol_rm function instead.
opal.rm(opal, symbol)opal.rm(opal, symbol)
opal |
Opal object. |
symbol |
Name of the R symbol. |
Other symbol functions:
opal.symbol_import(),
opal.symbol_rm(),
opal.symbol_save(),
opal.symbols()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.rm(o, 'D') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.rm(o, 'D') opal.logout(o) ## End(Not run)
The SQL query can apply to raw tables and/or views and require the permission to view the values of these tables. When all tables belong to a project, it is possible to simplify the SQL query by providing the project name parameter. Otherwise the fully qualified table names ('<project>.<table>') must be specified in the FROM statements.
opal.sql(opal, query, project = NULL, id.name = "_id")opal.sql(opal, query, project = NULL, id.name = "_id")
opal |
Opal connection object. |
query |
The SQL query statement. |
project |
Project name where the table(s) are located. If not provided, the SQL query must refer to the full table name(s) (use backquotes to escape, see examples). |
id.name |
The name of the column representing the entity identifiers. Default is '_id'. |
The lists of columns and rows, as a data.frame.
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with project context opal.sql(o, 'select avg(LAB_HDL) as HDL_AVG, GENDER from CNSIM1 where LAB_HDL is not null group by GENDER', 'CNSIM') # without project context opal.sql(o, 'select avg(LAB_HDL) as HDL_AVG, GENDER from `CNSIM.CNSIM1` where LAB_HDL is not null group by GENDER') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with project context opal.sql(o, 'select avg(LAB_HDL) as HDL_AVG, GENDER from CNSIM1 where LAB_HDL is not null group by GENDER', 'CNSIM') # without project context opal.sql(o, 'select avg(LAB_HDL) as HDL_AVG, GENDER from `CNSIM.CNSIM1` where LAB_HDL is not null group by GENDER') opal.logout(o) ## End(Not run)
Getting the SQL execution is for being able to re-execute a previously submitted own SQL query (regular users) and for auditing users SQL activity (administrators only).
opal.sql_history( opal, project = NULL, offset = 0, limit = 100, user = NULL, df = TRUE )opal.sql_history( opal, project = NULL, offset = 0, limit = 100, user = NULL, df = TRUE )
opal |
Opal connection object. |
project |
Project name used as the SQL execution context, to filter. If not specified, history from any context is returned. If NA is specified, the history of SQL executions without context is returned. Default is NULL. |
offset |
Number of history items to skip. Default is 0 (note that the items are ordered by most recent first). |
limit |
Maximum number of history items to return. Default is 100. |
user |
Filter by user name, only administrators can retrieve SQL history of other users. If NA is specified, the SQL execution history of all users will be retrieved. Default is the current user name. |
df |
Result is a data.frame or a list of raw data. |
A data frame.
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with project context opal.sql_history(o, 'CNSIM') # without project context opal.sql_history(o, NA) # with or without project context opal.sql_history(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # with project context opal.sql_history(o, 'CNSIM') # without project context opal.sql_history(o, NA) # with or without project context opal.sql_history(o) opal.logout(o) ## End(Not run)
Import a tibble identified by the symbol as a table in Opal. This operation creates an importation task in Opal that can be followed (see tasks related functions).
opal.symbol_import( opal, symbol, project, identifiers = NULL, policy = "required", id.name = "id", type = "Participant", wait = TRUE )opal.symbol_import( opal, symbol, project, identifiers = NULL, policy = "required", id.name = "id", type = "Participant", wait = TRUE )
opal |
Opal object. |
symbol |
Name of the R symbol representing a tibble. |
project |
Name of the project into which the data are to be imported. |
identifiers |
Name of the identifiers mapping to use when assigning entities to Opal. |
policy |
Identifiers policy: 'required' (each identifiers must be mapped prior importation (default)), 'ignore' (ignore unknown identifiers) and 'generate' (generate a system identifier for each unknown identifier). |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. |
type |
Entity type (what the data are about). Default is 'Participant'. |
wait |
Wait for import task completion. Default is TRUE. |
Other symbol functions:
opal.rm(),
opal.symbol_rm(),
opal.symbol_save(),
opal.symbols()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_import(o, 'D', 'test') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_import(o, 'D', 'test') opal.logout(o) ## End(Not run)
Remove a symbol from the remote R session.
opal.symbol_rm(opal, symbol)opal.symbol_rm(opal, symbol)
opal |
Opal object. |
symbol |
Name of the R symbol. |
Other symbol functions:
opal.rm(),
opal.symbol_import(),
opal.symbol_save(),
opal.symbols()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_rm(o, 'D') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_rm(o, 'D') opal.logout(o) ## End(Not run)
Save a tibble identified by symbol as a file of format SAS, SPSS, Stata, CSV or TSV in the remote R session working directory.
opal.symbol_save(opal, symbol, destination)opal.symbol_save(opal, symbol, destination)
opal |
Opal object. |
symbol |
Name of the R symbol representing a tibble. |
destination |
The path of the file in the R session workspace. Supported file extensions are: .sav (SPSS), .zsav (compressed SPSS), .sas7bdat (SAS), .xpt (SAS Transport), .dta (Stata), .csv (comma separated values), .tsv (tab separated values). |
Other symbol functions:
opal.rm(),
opal.symbol_import(),
opal.symbol_rm(),
opal.symbols()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_save(o, 'D', 'test.sav') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbol_save(o, 'D', 'test.sav') opal.logout(o) ## End(Not run)
Get the R symbols available in the remote R session.
opal.symbols(opal)opal.symbols(opal)
opal |
Opal object. |
Other symbol functions:
opal.rm(),
opal.symbol_import(),
opal.symbol_rm(),
opal.symbol_save()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbols(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.symbols(o) opal.logout(o) ## End(Not run)
Get a table of a datasource
opal.table(opal, datasource, table, counts = FALSE)opal.table(opal, datasource, table, counts = FALSE)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
counts |
Flag to get the number of variables and entities (default is FALSE). |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table(o, 'CNSIM', 'CNSIM1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table(o, 'CNSIM', 'CNSIM1') opal.logout(o) ## End(Not run)
Create an Opal table if it does not already exist. If a list of table references are provided, the table will be a view. The table/view created will have no dictionary, use opal.table_dictionary_update to apply a dictionary.
opal.table_create(opal, project, table, type = "Participant", tables = NULL)opal.table_create(opal, project, table, type = "Participant", tables = NULL)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Table name to be created |
type |
Entity type, default is "Participant". Ignored if some table references are provided. |
tables |
List of the fully qualified table names that are referred by the view. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a raw table opal.table_create(o, "CNSIM", "CNSIM4") # make a view opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a raw table opal.table_create(o, "CNSIM", "CNSIM4") # make a view opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) opal.logout(o) ## End(Not run)
Removes both values and data dictionary of a table, or remove the table's logic if the table is a view. Fails if the table does not exist. See also opal.table_truncate.
opal.table_delete(opal, project, table, silent = TRUE)opal.table_delete(opal, project, table, silent = TRUE)
opal |
Opal connection object. |
project |
Project name where the table is located. |
table |
Table name to be deleted. |
silent |
Warn if table does not exist, default is TRUE. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_delete(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_delete(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)
Get the dictionary of a Opal table in a format that can be re-applied with opal.table_dictionary_update.
opal.table_dictionary_get(opal, project, table)opal.table_dictionary_get(opal, project, table)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Table name. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)
Directly update the dictionary of a Opal table with the provided dictionary.
opal.table_dictionary_update( opal, project, table, variables, categories = NULL )opal.table_dictionary_update( opal, project, table, variables, categories = NULL )
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Destination table name. |
variables |
A data frame with one row per variable (column name) and then one column per property/attribute (Opal Excel format). |
categories |
A data frame with one row per category (columns variable and name) and then column per property/attribute (Opal Excel format). If there are no categories, this parameter is optional. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') variables <- tibble::tribble( ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index, "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1, "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2, "disp", "decimal", "Disp label", NA, NA, 1, 3 ) categories <- tibble::tribble( ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`, "cyl", "4", 0, "Four", "Quatre", "cyl", "6", 0, "Six", "Six", "cyl", "8", 1, "Height", "Huit" ) opal.table_dictionary_update(o, "test", "mtcars", variables, categories) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') variables <- tibble::tribble( ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index, "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1, "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2, "disp", "decimal", "Disp label", NA, NA, 1, 3 ) categories <- tibble::tribble( ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`, "cyl", "4", 0, "Four", "Quatre", "cyl", "6", 0, "Six", "Six", "cyl", "8", 1, "Height", "Huit" ) opal.table_dictionary_update(o, "test", "mtcars", variables, categories) opal.logout(o) ## End(Not run)
Check whether a Opal table exists (and is visible). Optionally check whether the table is a raw table or a view.
opal.table_exists(opal, project, table, view = NA)opal.table_exists(opal, project, table, view = NA)
opal |
Opal connection object. |
project |
Project name where the table is located. |
table |
Table name. |
view |
Logical to perform an additional check whether the table is a view (TRUE) or a raw table (FALSE). If NULL or NA, the table can be indifferently a view or a raw table. Default is NA. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # check table exists opal.table_exists(o, "CNSIM", "CNSIM1") # check table exists AND is a NOT a view opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE) # check table exists AND is a view opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # check table exists opal.table_exists(o, "CNSIM", "CNSIM1") # check table exists AND is a NOT a view opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE) # check table exists AND is a view opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE) opal.logout(o) ## End(Not run)
Export a table as file in the specified format. The file destination is in the Opal server file system. See opal.file_download to download the file locally. See also opal.table_get to get directly the table as an R object.
opal.table_export( opal, project, table, file, identifiers = NULL, id.name = "id", wait = TRUE )opal.table_export( opal, project, table, file, identifiers = NULL, id.name = "id", wait = TRUE )
opal |
Opal connection object. |
project |
Project name where the table is located. |
table |
Table name to export. |
file |
Destination file in the Opal file system. The expected file extensions are: rds (RDS), sav (SPSS), zsav (SPSS compressed), sas7bdat (SAS), xpt (SAS Transport), dta (Stata).RDS (serialized single R object) is to be read by base::readRDS(), while other formats are supported by the haven R package. |
identifiers |
Name of the identifiers mapping to use when exporting entities from Opal. |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. |
wait |
Wait for import task completion. Default is TRUE. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_export(o, "CNSIM", "CNSIM1", file = "/home/administrator/cnsim1.sav") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_export(o, "CNSIM", "CNSIM1", file = "/home/administrator/cnsim1.sav") opal.logout(o) ## End(Not run)
Shortcut function to assign a Opal table to a tibble in the R server-side session and then retrieve it into the R client-side session. Requires to have the permission to see the individual values of the table and to perform R assignments.
opal.table_get( opal, project, table, id.name = "id", variables = NULL, missings = TRUE )opal.table_get( opal, project, table, id.name = "id", variables = NULL, missings = TRUE )
opal |
Opal connection object. |
project |
Project name where the table is located. |
table |
Table name from which the tibble should be extracted. |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. Requires Opal 4.0+. |
variables |
(Deprecated) List of variable names or Javascript expression that selects the variables of a table (ignored if value does not refer to a table). See javascript documentation: http://wiki.obiba.org/display/OPALDOC/Variable+Methods |
missings |
(Deprecated) Include the missing values (default is TRUE). |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") opal.logout(o) ## End(Not run)
Import a file as a table in Opal. The file formats supported are: RDS (.rds), SPSS (.sav), SPSS compressed (.zsav), SAS (.sas7bdat), SAS Transport (.xpt), Stata (.dta). The RDS format is a serialized single R object (expected to be of tibble class), that can be obtained using base::saveRDS(). The other file formats are the ones supported by the haven R package. This operation creates an importation task in Opal that can be followed (see tasks related functions).
opal.table_import( opal, file, project, table, identifiers = NULL, policy = "required", id.name = "id", type = "Participant", wait = TRUE )opal.table_import( opal, file, project, table, identifiers = NULL, policy = "required", id.name = "id", type = "Participant", wait = TRUE )
opal |
Opal object. |
file |
Path in Opal to the file that will be read as a tibble. |
project |
Name of the project into which the data are to be imported. |
table |
Destination table name. |
identifiers |
Name of the identifiers mapping to use when assigning entities to Opal. |
policy |
Identifiers policy: 'required' (each identifiers must be mapped prior importation (default)), 'ignore' (ignore unknown identifiers) and 'generate' (generate a system identifier for each unknown identifier). |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. |
type |
Entity type (what the data are about). Default is 'Participant'. |
wait |
Wait for import task completion. Default is TRUE. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable') opal.logout(o) ## End(Not run)
Get the permissions that were applied on a table.
opal.table_perm(opal, project, table)opal.table_perm(opal, project, table)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Destination table name. |
A data.frame with columns: subject, type, permission
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on a table.
opal.table_perm_add(opal, project, table, subject, type = "user", permission)opal.table_perm_add(opal, project, table, subject, type = "user", permission)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Destination table name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: view, view-values, edit, edit-values, administrate. The 'view' permission is suitable for DataSHIELD operations. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied on a table. Silently returns when there is no such permission.
opal.table_perm_delete(opal, project, table, subject, type = "user")opal.table_perm_delete(opal, project, table, subject, type = "user")
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Destination table name. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view') opal.table_perm(o, 'CNSIM', 'CNSIM1') opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Upload a local tibble to the R server side through Opal, assign this tibble to the provided symbol name and import it as a table into a Opal project.
opal.table_save( opal, tibble, project, table, overwrite = TRUE, force = FALSE, identifiers = NULL, policy = "required", id.name = "id", type = "Participant" )opal.table_save( opal, tibble, project, table, overwrite = TRUE, force = FALSE, identifiers = NULL, policy = "required", id.name = "id", type = "Participant" )
opal |
Opal connection object. |
tibble |
The tibble object to be imported. |
project |
Project name where the table will be located. |
table |
Destination table name. |
overwrite |
If the destination table already exists, it will be replaced (deleted, re-created with associated permissions reinstated and then imported). Otherwise the table will be updated (data dictionaries merge may conflict). Default is TRUE. See also opal.table_truncate function. |
force |
If the destination already exists, stop with an informative message if this flag is FALSE (default). |
identifiers |
Name of the identifiers mapping to use when assigning entities to Opal. |
policy |
Identifiers policy: 'required' (each identifiers must be mapped prior importation (default)), ignore' (ignore unknown identifiers) and 'generate' (generate a system identifier for each unknown identifier). |
id.name |
The name of the column representing the entity identifiers. Default is 'id'. |
type |
Entity type (what the data are about). Default is 'Participant' |
An invisible logical indicating whether the destination table exists.
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_truncate(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") # do some (meta)data transformations, then save in opal's database opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE) # or overwrite data only (keep original data dictionary) opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') cqx <- opal.table_get(o, "CPTP", "Cag_coreqx") # do some (meta)data transformations, then save in opal's database opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE) # or overwrite data only (keep original data dictionary) opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE) opal.logout(o) ## End(Not run)
Removes the values of a table and keep the dictionary untouched. Fails if the table does not exist or is a view. See also opal.table_delete.
opal.table_truncate(opal, project, table)opal.table_truncate(opal, project, table)
opal |
Opal connection object. |
project |
Project name where the table is located. |
table |
Table name to be truncated. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_view_create(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_truncate(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.table_truncate(o, "CNSIM", "CNSIM1") opal.logout(o) ## End(Not run)
Create an Opal view if a table with same name does not already exist. The view created will have no dictionary, use opal.table_dictionary_update to apply a dictionary.
opal.table_view_create(opal, project, table, tables, type = "Participant")opal.table_view_create(opal, project, table, tables, type = "Participant")
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Table name to be created |
tables |
List of the fully qualified table names that are referred by the view. |
type |
Entity type, default is "Participant". Ignored if some table references are provided. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_update()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view opal.table_view_create(o, "CNSIM", "CNSIM123", c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view opal.table_view_create(o, "CNSIM", "CNSIM123", c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) opal.logout(o) ## End(Not run)
Update the table references and/or the entity filter of an existing Opal view. The view dictionary will NOT be modified (use opal.table_dictionary_update to apply a dictionary).
opal.table_view_update(opal, project, table, tables = NULL, where = NULL)opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
table |
Table name to be created. |
tables |
List of the fully qualified table names that are referred by the view. Not modified when NULL (default). |
where |
The entity filter script. Not modified when NULL (default). To remove the filter, set an empty string. |
Other table functions:
opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
opal.table_dictionary_get(),
opal.table_dictionary_update(),
opal.table_exists(),
opal.table_export(),
opal.table_get(),
opal.table_import(),
opal.table_perm(),
opal.table_perm_add(),
opal.table_perm_delete(),
opal.table_save(),
opal.table_truncate(),
opal.table_view_create()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view opal.table_view_create(o, "CNSIM", "CNSIM123", c("CNSIM.CNSIM1")) # update the table references opal.table_view_update(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) # update the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)") # remove the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", where = "") # update both the table references and the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"), where = "$('LAB_TSC').ge(5)") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # make a view opal.table_view_create(o, "CNSIM", "CNSIM123", c("CNSIM.CNSIM1")) # update the table references opal.table_view_update(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3")) # update the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)") # remove the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", where = "") # update both the table references and the entity filter opal.table_view_update(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"), where = "$('LAB_TSC').ge(5)") opal.logout(o) ## End(Not run)
Get tables of a datasource
opal.tables(opal, datasource, counts = FALSE, df = TRUE)opal.tables(opal, datasource, counts = FALSE, df = TRUE)
opal |
Opal object. |
datasource |
Name of the datasource. |
counts |
Flag to get the number of variables and entities (default is FALSE). |
df |
Return a data.frame (default is TRUE) |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.valueset(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables(o, 'CNSIM') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables(o, 'CNSIM') opal.logout(o) ## End(Not run)
Get the permissions that were applied on any table of a project.
opal.tables_perm(opal, project)opal.tables_perm(opal, project)
opal |
Opal connection object. |
project |
Project name. |
A data.frame with columns: subject, type, permission
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Add or update a permission on any table of a project.
opal.tables_perm_add(opal, project, subject, type = "user", permission)opal.tables_perm_add(opal, project, subject, type = "user", permission)
opal |
Opal connection object. |
project |
Project name where the table will be located. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
permission |
The permission to apply: view-values, add, or administrate. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Delete a permission that was applied on any table of a project. Silently returns when there is no such permission.
opal.tables_perm_delete(opal, project, subject, type = "user")opal.tables_perm_delete(opal, project, subject, type = "user")
opal |
Opal connection object. |
project |
Project name where the table will be located. |
subject |
A vector of subject identifiers: user names or group names (depending on the type). |
type |
The type of subject: user (default) or group. |
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate') opal.tables_perm(o, 'CNSIM') opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user') opal.logout(o) ## End(Not run)
Get the details of a specific task.
opal.task(opal, id)opal.task(opal, id)
opal |
Opal object. |
id |
Task identifier. |
Other task functions:
opal.task_cancel(),
opal.task_wait(),
opal.tasks()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task(o, '1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task(o, '1') opal.logout(o) ## End(Not run)
Tries to cancel a task.
opal.task_cancel(opal, id)opal.task_cancel(opal, id)
opal |
Opal object. |
id |
Task identifier. |
Other task functions:
opal.task(),
opal.task_wait(),
opal.tasks()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task_cancel(o, '1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task_cancel(o, '1') opal.logout(o) ## End(Not run)
The task completion is defined by its status: *SUCCEEDED*, *FAILED* or *CANCELED*.
opal.task_wait(opal, id, max = NULL)opal.task_wait(opal, id, max = NULL)
opal |
Opal object. |
id |
Task identifier. |
max |
Maximum time (in seconds) to wait for the task completion. Default is NULL (no maximum). |
Other task functions:
opal.task(),
opal.task_cancel(),
opal.tasks()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task_wait(o, '1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.task_wait(o, '1') opal.logout(o) ## End(Not run)
Get all the tasks with their status at the time of the request.
opal.tasks(opal, df = TRUE)opal.tasks(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other task functions:
opal.task(),
opal.task_cancel(),
opal.task_wait()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tasks(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tasks(o) opal.logout(o) ## End(Not run)
Get all taxonomies. A taxonomy describes the annotations that can be applied to the variables. Taxonomies also drive the variables search interface.
opal.taxonomies(opal, locale = "en", df = TRUE)opal.taxonomies(opal, locale = "en", df = TRUE)
opal |
Opal object. |
locale |
The language for labels (default is "en"). |
df |
Return a data.frame (default is TRUE) |
Other taxonomy functions:
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomies(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomies(o) opal.logout(o) ## End(Not run)
Get a specific taxonomy details.
opal.taxonomy(opal, taxonomy)opal.taxonomy(opal, taxonomy)
opal |
Opal object. |
taxonomy |
Name of the taxonomy. |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy(o, 'Mlstr_area') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy(o, 'Mlstr_area') opal.logout(o) ## End(Not run)
Delete a taxonomy, without failing if the taxonomy does not exist.
opal.taxonomy_delete(opal, taxonomy)opal.taxonomy_delete(opal, taxonomy)
opal |
Opal object. |
taxonomy |
Name of the taxonomy. |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_delete(o, 'Mlstr_area') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_delete(o, 'Mlstr_area') opal.logout(o) ## End(Not run)
Download a taxonomy stored in a file in YAML format.
opal.taxonomy_download(opal, taxonomy, destination = NULL)opal.taxonomy_download(opal, taxonomy, destination = NULL)
opal |
Opal object. |
taxonomy |
Name of the taxonomy. |
destination |
Path to the taxonomy YAML file. If not provided, the downloaded file will have the taxonomy name with the '.yml' extension and will be located in the working directory. |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml') opal.logout(o) ## End(Not run)
Upload a taxonomy stored in a local file in YAML format. This operation will fail if the taxonomy already exists, see opal.taxonomy_delete.
opal.taxonomy_upload(opal, path)opal.taxonomy_upload(opal, path)
opal |
Opal object. |
path |
Path to the taxonomy YAML file. |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.terms(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_upload(o, '~/some/dir/taxo.yml') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.taxonomy_upload(o, '~/some/dir/taxo.yml') opal.logout(o) ## End(Not run)
Get all the terms of a vocabulary. The term describes the value of a variable annotation.
opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
opal |
Opal object. |
taxonomy |
Name of the taxonomy |
vocabulary |
Name of the vocabulary in the taxonomy |
locale |
The language for labels (default is "en"). |
df |
Return a data.frame (default is TRUE) |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.vocabularies(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours') opal.logout(o) ## End(Not run)
Get a personal access token details. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token(opal, name)opal.token(opal, name)
opal |
Opal object. |
name |
Name of the token |
Other token functions:
opal.token_datashield_create(),
opal.token_delete(),
opal.token_r_create(),
opal.token_renew(),
opal.token_sql_create(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token(o, 'sql-1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token(o, 'sql-1') opal.logout(o) ## End(Not run)
Create a personal access token for Datashield usage. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token_datashield_create(opal, name, projects = NULL)opal.token_datashield_create(opal, name, projects = NULL)
opal |
Opal object. |
name |
Name of the token |
projects |
Vector of project names, to which the token applies. Default is NULL (all projects). |
The token value.
Other token functions:
opal.token(),
opal.token_delete(),
opal.token_r_create(),
opal.token_renew(),
opal.token_sql_create(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_datashield_create(o, 'ds-1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_datashield_create(o, 'ds-1') opal.logout(o) ## End(Not run)
Delete a personal access token permanently. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token_delete(opal, name)opal.token_delete(opal, name)
opal |
Opal object. |
name |
Name of the token |
Other token functions:
opal.token(),
opal.token_datashield_create(),
opal.token_r_create(),
opal.token_renew(),
opal.token_sql_create(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token_delete(o, 'sql-1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token_delete(o, 'sql-1') opal.logout(o) ## End(Not run)
Create a personal access token for R (server) usage. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token_r_create( opal, name, projects = NULL, access = NULL, commands = c("export") )opal.token_r_create( opal, name, projects = NULL, access = NULL, commands = c("export") )
opal |
Opal object. |
name |
Name of the token |
projects |
Vector of project names, to which the token applies. Default is NULL (all projects). |
access |
Data access level: 'READ' (read-only) or 'READ_NO_VALUES' (read-only, without access to individual-level data) or NULL (default). |
commands |
Task commands that can launched on a project: 'import' and/or 'export'. Default is 'export' (use NULL for no task commands). |
The token value.
Other token functions:
opal.token(),
opal.token_datashield_create(),
opal.token_delete(),
opal.token_renew(),
opal.token_sql_create(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export') opal.logout(o) ## End(Not run)
Renew an inactive personal access token after it has been marked as being inactive. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token_renew(opal, name)opal.token_renew(opal, name)
opal |
Opal object. |
name |
Name of the token |
Other token functions:
opal.token(),
opal.token_datashield_create(),
opal.token_delete(),
opal.token_r_create(),
opal.token_sql_create(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token_renew(o, 'sql-1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.token_renew(o, 'sql-1') opal.logout(o) ## End(Not run)
Create a personal access token for SQL usage. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.token_sql_create(opal, name, projects = NULL)opal.token_sql_create(opal, name, projects = NULL)
opal |
Opal object. |
name |
Name of the token |
projects |
Vector of project names, to which the token applies. Default is NULL (all projects). |
The token value.
Other token functions:
opal.token(),
opal.token_datashield_create(),
opal.token_delete(),
opal.token_r_create(),
opal.token_renew(),
opal.tokens()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_sql_create(o, 'sql-1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') token <- opal.token_sql_create(o, 'sql-1') opal.logout(o) ## End(Not run)
Get the list of personal access tokens. Like for the other token functions, this operation requires the user to authenticate with username/password credentials.
opal.tokens(opal, df = TRUE)opal.tokens(opal, df = TRUE)
opal |
Opal object. |
df |
Return a data.frame (default is TRUE) |
Other token functions:
opal.token(),
opal.token_datashield_create(),
opal.token_delete(),
opal.token_r_create(),
opal.token_renew(),
opal.token_sql_create()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tokens(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.tokens(o) opal.logout(o) ## End(Not run)
Unload package from the remote R session.
opal.unload_package(opal, pkg)opal.unload_package(opal, pkg)
opal |
Opal object or list of opal objects. |
pkg |
Package name. |
Other execution functions:
opal.execute(),
opal.execute.source(),
opal.load_package()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.unload_package(o, 'stats') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.unload_package(o, 'stats') opal.logout(o) ## End(Not run)
Get the values of an entity in a table.
opal.valueset(opal, datasource, table, identifier)opal.valueset(opal, datasource, table, identifier)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
identifier |
Entity identifier. |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.variable(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362') opal.logout(o) ## End(Not run)
Get a variable of a table
opal.variable(opal, datasource, table, variable)opal.variable(opal, datasource, table, variable)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
variable |
Name of the variable in the table. |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable_summary(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.logout(o) ## End(Not run)
Get summary statistics of a variable of a table
opal.variable_summary( opal, datasource, table, variable, cached = TRUE, nature = NULL )opal.variable_summary( opal, datasource, table, variable, cached = TRUE, nature = NULL )
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
variable |
Name of the variable in the table. |
cached |
Get cached summary if exists. When FALSE, the cached summary is evicted and replaced by the newly calculated one. Default is TRUE. |
nature |
Force summary nature, independently from the variable. Possible values are: CATEGORICAL, CONTINUOUS, TEMPORAL, GEO, BINARY, UNDETERMINED. |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variables()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER') opal.logout(o) ## End(Not run)
Get variables of a table
opal.variables(opal, datasource, table, locale = "en", df = TRUE)opal.variables(opal, datasource, table, locale = "en", df = TRUE)
opal |
Opal object. |
datasource |
Name of the datasource. |
table |
Name of the table in the datasource. |
locale |
The language for labels (default is "en"). |
df |
Return a data.frame (default is TRUE) |
Other datasource functions:
opal.annotate(),
opal.annotations(),
opal.attribute_values(),
opal.datasource(),
opal.datasources(),
opal.table(),
opal.tables(),
opal.valueset(),
opal.variable(),
opal.variable_summary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variables(o, 'CNSIM', 'CNSIM1') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.variables(o, 'CNSIM', 'CNSIM1') opal.logout(o) ## End(Not run)
Compare Opal version with the provided one. Note that a request must have been done in order to have a non-null Opal version.
opal.version_compare(opal, version)opal.version_compare(opal, version)
opal |
Opal object. |
version |
The semantic version string to be compared. |
>0 if Opal version is more recent, 0 if equals, <0 otherwise.
## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.version_compare(o, "2.6.0") opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org') opal.version_compare(o, "2.6.0") opal.logout(o) ## End(Not run)
Get all the vocabularies of a taxonomy. A vocabulary describes the possible values of variable annotations.
opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
opal |
Opal object. |
taxonomy |
Name of the taxonomy |
locale |
The language for labels (default is "en"). |
df |
Return a data.frame (default is TRUE) |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabulary()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.vocabularies(o, 'Mlstr_area') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.vocabularies(o, 'Mlstr_area') opal.logout(o) ## End(Not run)
Get a specific vocabulary details.
opal.vocabulary(opal, taxonomy, vocabulary)opal.vocabulary(opal, taxonomy, vocabulary)
opal |
Opal object. |
taxonomy |
Name of the taxonomy |
vocabulary |
Name of the vocabulary in the taxonomy |
Other taxonomy functions:
opal.taxonomies(),
opal.taxonomy(),
opal.taxonomy_delete(),
opal.taxonomy_download(),
opal.taxonomy_upload(),
opal.terms(),
opal.vocabularies()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours') opal.logout(o) ## End(Not run)
Restore a R workspace from a opal.
opal.workspace_restore(opal, ws)opal.workspace_restore(opal, ws)
opal |
Opal object. |
ws |
The workspace name |
Other workspace functions:
opal.workspace_rm(),
opal.workspace_save(),
opal.workspaces()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspace_restore(o, 'test') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspace_restore(o, 'test') opal.logout(o) ## End(Not run)
Remove a R workspace from a opal.
opal.workspace_rm(opal, ws, user = NULL)opal.workspace_rm(opal, ws, user = NULL)
opal |
Opal object. |
ws |
The workspace name |
user |
The user name associated to the worskpace. If not provided, the current user is applied. |
Other workspace functions:
opal.workspace_restore(),
opal.workspace_save(),
opal.workspaces()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspace_rm(o, 'test') opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspace_rm(o, 'test') opal.logout(o) ## End(Not run)
Save the current session in a opal R workspace.
opal.workspace_save(opal, save = TRUE)opal.workspace_save(opal, save = TRUE)
opal |
Opal object. |
save |
Save the workspace with given identifier (default is TRUE, current session ID if TRUE). |
The workspace ID (invisible)
Other workspace functions:
opal.workspace_restore(),
opal.workspace_rm(),
opal.workspaces()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # provide a workspace ID opal.workspace_save(o, 'test') # or use default one id <- opal.workspace_save(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') # provide a workspace ID opal.workspace_save(o, 'test') # or use default one id <- opal.workspace_save(o) opal.logout(o) ## End(Not run)
Get the R workspaces from a opal.
opal.workspaces(opal)opal.workspaces(opal)
opal |
Opal object. |
Other workspace functions:
opal.workspace_restore(),
opal.workspace_rm(),
opal.workspace_save()
## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspaces(o) opal.logout(o) ## End(Not run)## Not run: o <- opal.login('administrator','password', url='https://opal-demo.obiba.org') opal.workspaces(o) opal.logout(o) ## End(Not run)