R.Panel-methods.R Maven / Gradle / Ivy
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#' PanelClient methods
#' @include AllClasses.R
#' @include AllGenerics.R
#' @include commons.R
#' @description This function implements the OpenCGA calls for managing Disease Panels.
#' The following table summarises the available *actions* for this client:
#'
#' | endpointName | Endpoint WS | parameters accepted |
#' | -- | :-- | --: |
#' | updateAcl | /{apiVersion}/panels/acl/{members}/update | study, members[*], action[*], body[*] |
#' | create | /{apiVersion}/panels/create | include, exclude, study, includeResult, body |
#' | distinct | /{apiVersion}/panels/distinct | study, id, uuid, name, internalStatus, disorders, variants, genes, source, regions, categories, tags, deleted, status, creationDate, modificationDate, acl, release, snapshot, field[*] |
#' | importPanels | /{apiVersion}/panels/import | study, jobId, jobDependsOn, jobDescription, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body |
#' | search | /{apiVersion}/panels/search | include, exclude, limit, skip, count, study, id, uuid, name, internalStatus, disorders, variants, genes, source, regions, categories, tags, deleted, status, creationDate, modificationDate, acl, release, snapshot |
#' | acl | /{apiVersion}/panels/{panels}/acl | panels[*], study, member, silent |
#' | delete | /{apiVersion}/panels/{panels}/delete | study, panels[*] |
#' | info | /{apiVersion}/panels/{panels}/info | include, exclude, panels[*], study, version, deleted |
#' | update | /{apiVersion}/panels/{panels}/update | include, exclude, study, panels[*], includeResult, body |
#'
#' @md
#' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation
#' \url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}
#' [*]: Required parameter
#' @export
setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) {
switch(endpointName,
#' @section Endpoint /{apiVersion}/panels/acl/{members}/update:
#' Update the set of permissions granted for the member.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param members Comma separated list of user or group ids.
#' @param action Action to be performed [ADD, SET, REMOVE or RESET]. Allowed values: ['SET ADD REMOVE RESET']
#' @param data JSON containing the parameters to update the permissions.
updateAcl=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory="acl",
subcategoryId=members, action="update", params=params, httpMethod="POST", as.queryParam=c("action"),
...),
#' @section Endpoint /{apiVersion}/panels/create:
#' Create a panel.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data Panel parameters.
create=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory=NULL, subcategoryId=NULL,
action="create", params=params, httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/distinct:
#' Panel distinct method.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of panel UUIDs up to a maximum of 100.
#' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param internalStatus Filter by internal status.
#' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param source Comma separated list of source ids or names.
#' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param deleted Boolean to retrieve deleted entries.
#' @param status Filter by status.
#' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
#' @param release Release when it was created.
#' @param snapshot Snapshot value (Latest version of the entry in the specified release).
#' @param field Comma separated list of fields for which to obtain the distinct values.
distinct=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory=NULL,
subcategoryId=NULL, action="distinct", params=params, httpMethod="GET", as.queryParam=c("field"), ...),
#' @section Endpoint /{apiVersion}/panels/import:
#' Import panels.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobDescription Job description.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Panel parameters.
importPanels=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory=NULL,
subcategoryId=NULL, action="import", params=params, httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/search:
#' Panel search.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of panel UUIDs up to a maximum of 100.
#' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param internalStatus Filter by internal status.
#' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param source Comma separated list of source ids or names.
#' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param deleted Boolean to retrieve deleted entries.
#' @param status Filter by status.
#' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. .
#' @param release Release when it was created.
#' @param snapshot Snapshot value (Latest version of the entry in the specified release).
search=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=NULL, subcategory=NULL, subcategoryId=NULL,
action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/{panels}/acl:
#' Returns the acl of the panels. If member is provided, it will only return the acl for the member.
#' @param panels Comma separated list of panel IDs up to a maximum of 100.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param member User or group id.
#' @param silent Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries looked for cannot be shown for whichever reason.
acl=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=panels, subcategory=NULL, subcategoryId=NULL,
action="acl", params=params, httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/{panels}/delete:
#' Delete existing panels.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param panels Comma separated list of panel ids.
delete=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=panels, subcategory=NULL,
subcategoryId=NULL, action="delete", params=params, httpMethod="DELETE", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/{panels}/info:
#' Panel info.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param panels Comma separated list of panel IDs up to a maximum of 100.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param version Comma separated list of panel versions. 'all' to get all the panel versions. Not supported if multiple panel ids are provided.
#' @param deleted Boolean to retrieve deleted panels.
info=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=panels, subcategory=NULL, subcategoryId=NULL,
action="info", params=params, httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/panels/{panels}/update:
#' Update panel attributes.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param panels Comma separated list of panel ids.
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data Panel parameters.
update=fetchOpenCGA(object=OpencgaR, category="panels", categoryId=panels, subcategory=NULL,
subcategoryId=NULL, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
)
})