man.fileClient-OpencgaR-method.Rd Maven / Gradle / Ivy
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/File-methods.R
\name{fileClient,OpencgaR-method}
\alias{fileClient,OpencgaR-method}
\title{FileClient methods}
\usage{
\S4method{fileClient}{OpencgaR}(
OpencgaR,
folder,
members,
file,
annotationSet,
files,
endpointName,
params = NULL,
...
)
}
\arguments{
\item{folder}{Folder id or name. Paths must be separated by : instead of /.}
\item{members}{Comma separated list of user or group ids.}
\item{file}{File uuid, id, or name.}
\item{annotationSet}{AnnotationSet ID to be updated.}
\item{files}{Comma separated list of file ids, names or paths. Paths must be separated by : instead of /.}
\item{creationYear}{Creation year.}
\item{creationMonth}{Creation month (JANUARY, FEBRUARY...).}
\item{creationDay}{Creation day.}
\item{creationDayOfWeek}{Creation day of week (MONDAY, TUESDAY...).}
\item{software}{Software.}
\item{experiment}{Experiment.}
\item{numSamples}{Number of samples.}
\item{numRelatedFiles}{Number of related files.}
\item{default}{Calculate default stats.}
\item{variableSetId}{Variable set ID or name.}
\item{annotationSetId}{Annotation set id. If not provided, variableSetId will be used.}
\item{field}{Field for which to obtain the distinct values.}
\item{jobDependsOn}{Comma separated list of existing job IDs the job will depend on.}
\item{jobDescription}{Job description.}
\item{jobTags}{Job tags.}
\item{id}{Comma separated list of file IDs up to a maximum of 100.}
\item{uuid}{Comma separated list file UUIDs up to a maximum of 100.}
\item{name}{Comma separated list of file names.}
\item{path}{Comma separated list of paths.}
\item{uri}{Comma separated list of uris.}
\item{type}{File type, either FILE or DIRECTORY.}
\item{format}{Comma separated Format values. For existing Formats see files/formats.}
\item{external}{Boolean field indicating whether to filter by external or non external files.}
\item{status}{Filter by status.}
\item{internalStatus}{Filter by internal status.}
\item{internalVariantIndexStatus}{Filter by internal variant index status.}
\item{softwareName}{Software name.}
\item{directory}{Directory under which we want to look for files or folders.}
\item{creationDate}{Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.}
\item{modificationDate}{Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.}
\item{tags}{Tags.}
\item{size}{File size.}
\item{sampleIds}{Comma separated list sample IDs or UUIDs up to a maximum of 100.}
\item{jobId}{Job ID that created the file(s) or folder(s).}
\item{annotation}{Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.}
\item{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. .}
\item{release}{Release when it was created.}
\item{filename}{File name to overwrite the input fileName.}
\item{fileFormat}{File format.}
\item{bioformat}{File bioformat.}
\item{checksum}{Expected MD5 file checksum.}
\item{relativeFilePath}{Path within catalog where the file will be located (default: root folder).}
\item{description}{description.}
\item{parents}{Create the parent directories if they do not exist.}
\item{member}{User or group id.}
\item{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.}
\item{skipTrash}{Skip trash and delete the files/folders from disk directly (CANNOT BE RECOVERED).}
\item{flattenAnnotations}{Flatten the annotations?.}
\item{deleted}{Boolean to retrieve deleted files.}
\item{sampleIdsAction}{Action to be performed if the array of samples is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{annotationSetsAction}{Action to be performed if the array of annotationSets is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{relatedFilesAction}{Action to be performed if the array of relatedFiles is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{tagsAction}{Action to be performed if the array of tags is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{action}{Action to be performed: ADD to add new annotations; REPLACE to replace the value of an already existing annotation; SET to set the new list of annotations removing any possible old annotations; REMOVE to remove some annotations; RESET to set some annotations to the default value configured in the corresponding variables of the VariableSet if any. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{data}{Json containing the map of annotations when the action is ADD, SET or REPLACE, a json with only the key 'remove' containing the comma separated variables to be removed as a value when the action is REMOVE or a json with only the key 'reset' containing the comma separated variables that will be set to the default value when the action is RESET.}
\item{pattern}{String pattern.}
\item{ignoreCase}{Flag to perform a case insensitive search.}
\item{maxCount}{Stop reading a file after 'n' matching lines. 0 means no limit.}
\item{offset}{Starting byte from which the file will be read.}
\item{lines}{Maximum number of lines to be returned up to a maximum of 1000.}
\item{limit}{Number of results to be returned.}
\item{skip}{Number of results to skip.}
\item{count}{Get the total number of results matching the query. Deactivated by default.}
\item{include}{Fields included in the response, whole JSON path must be provided.}
\item{exclude}{Fields excluded in the response, whole JSON path must be provided.}
\item{study}{Study [\link{user@}project:]study where study and project can be either the ID or UUID.}
\item{maxDepth}{Maximum depth to get files from.}
}
\description{
This function implements the OpenCGA calls for managing Files.
The following table summarises the available \emph{actions} for this client:\tabular{llr}{
endpointName \tab Endpoint WS \tab parameters accepted \cr
updateAcl \tab /{apiVersion}/files/acl/{members}/update \tab study, members\link{*}, action\link{*}, body\link{*} \cr
aggregationStats \tab /{apiVersion}/files/aggregationStats \tab study, name, type, format, bioformat, creationYear, creationMonth, creationDay, creationDayOfWeek, status, release, external, size, software, experiment, numSamples, numRelatedFiles, annotation, default, field \cr
loadAnnotationSets \tab /{apiVersion}/files/annotationSets/load \tab study, variableSetId\link{*}, path\link{*}, parents, annotationSetId, body \cr
bioformats \tab /{apiVersion}/files/bioformats \tab \cr
create \tab /{apiVersion}/files/create \tab study, parents, body\link{*} \cr
distinct \tab /{apiVersion}/files/distinct \tab study, id, uuid, name, path, uri, type, bioformat, format, external, status, internalStatus, internalVariantIndexStatus, softwareName, directory, creationDate, modificationDate, description, tags, size, sampleIds, jobId, annotation, acl, deleted, release, field\link{*} \cr
fetch \tab /{apiVersion}/files/fetch \tab jobId, jobDescription, jobDependsOn, jobTags, study, body\link{*} \cr
formats \tab /{apiVersion}/files/formats \tab \cr
link \tab /{apiVersion}/files/link \tab study, parents, body\link{*} \cr
runLink \tab /{apiVersion}/files/link/run \tab study, jobId, jobDependsOn, jobDescription, jobTags, body\link{*} \cr
runPostlink \tab /{apiVersion}/files/postlink/run \tab study, jobId, jobDependsOn, jobDescription, jobTags, body\link{*} \cr
search \tab /{apiVersion}/files/search \tab include, exclude, limit, skip, count, flattenAnnotations, study, id, uuid, name, path, uri, type, bioformat, format, external, status, internalStatus, internalVariantIndexStatus, softwareName, directory, creationDate, modificationDate, description, tags, size, sampleIds, jobId, annotation, acl, deleted, release \cr
upload \tab /{apiVersion}/files/upload \tab file, filename, fileFormat, bioformat, checksum, study, relativeFilePath, description, parents \cr
acl \tab /{apiVersion}/files/{files}/acl \tab files\link{*}, study, member, silent \cr
delete \tab /{apiVersion}/files/{files}/delete \tab study, files\link{*}, skipTrash \cr
info \tab /{apiVersion}/files/{files}/info \tab include, exclude, flattenAnnotations, files\link{*}, study, deleted \cr
unlink \tab /{apiVersion}/files/{files}/unlink \tab study, files\link{*} \cr
update \tab /{apiVersion}/files/{files}/update \tab include, exclude, files\link{*}, study, sampleIdsAction, annotationSetsAction, relatedFilesAction, tagsAction, body\link{*} \cr
updateAnnotationSetsAnnotations \tab /{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update \tab file\link{*}, study, annotationSet\link{*}, action, body \cr
download \tab /{apiVersion}/files/{file}/download \tab file\link{*}, study \cr
grep \tab /{apiVersion}/files/{file}/grep \tab file\link{*}, study, pattern, ignoreCase, maxCount \cr
head \tab /{apiVersion}/files/{file}/head \tab file\link{*}, study, offset, lines \cr
image \tab /{apiVersion}/files/{file}/image \tab file\link{*}, study \cr
refresh \tab /{apiVersion}/files/{file}/refresh \tab file\link{*}, study \cr
tail \tab /{apiVersion}/files/{file}/tail \tab file\link{*}, study, lines \cr
list \tab /{apiVersion}/files/{folder}/list \tab include, exclude, limit, skip, count, folder\link{*}, study \cr
tree \tab /{apiVersion}/files/{folder}/tree \tab include, exclude, folder\link{*}, study, maxDepth \cr
}
}
\section{Endpoint /{apiVersion}/files/acl/{members}/update}{
Update the set of permissions granted for the member.
}
\section{Endpoint /{apiVersion}/files/aggregationStats}{
Fetch catalog file stats.
}
\section{Endpoint /{apiVersion}/files/annotationSets/load}{
Load annotation sets from a TSV file.
}
\section{Endpoint /{apiVersion}/files/bioformats}{
List of accepted file bioformats.
}
\section{Endpoint /{apiVersion}/files/create}{
Create file or folder.
}
\section{Endpoint /{apiVersion}/files/distinct}{
File distinct method.
}
\section{Endpoint /{apiVersion}/files/fetch}{
Download an external file to catalog and register it.
}
\section{Endpoint /{apiVersion}/files/formats}{
List of accepted file formats.
}
\section{Endpoint /{apiVersion}/files/link}{
Link an external file into catalog.
}
\section{Endpoint /{apiVersion}/files/link/run}{
Link an external file into catalog asynchronously.
}
\section{Endpoint /{apiVersion}/files/postlink/run}{
Associate non-registered samples for files with high volumes of samples.
}
\section{Endpoint /{apiVersion}/files/search}{
File search method.
}
\section{Endpoint /{apiVersion}/files/upload}{
Resource to upload a file by chunks.
}
\section{Endpoint /{apiVersion}/files/{files}/acl}{
Return the acl defined for the file or folder. If member is provided, it will only return the acl for the member.
}
\section{Endpoint /{apiVersion}/files/{files}/delete}{
Delete existing files and folders.
}
\section{Endpoint /{apiVersion}/files/{files}/info}{
File info.
}
\section{Endpoint /{apiVersion}/files/{files}/unlink}{
Unlink linked files and folders.
}
\section{Endpoint /{apiVersion}/files/{files}/update}{
Update some file attributes.
}
\section{Endpoint /{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update}{
Update annotations from an annotationSet.
}
\section{Endpoint /{apiVersion}/files/{file}/download}{
Download file.
}
\section{Endpoint /{apiVersion}/files/{file}/grep}{
Filter lines of the file containing the pattern.
}
\section{Endpoint /{apiVersion}/files/{file}/head}{
Show the first lines of a file (up to a limit).
}
\section{Endpoint /{apiVersion}/files/{file}/image}{
Obtain the base64 content of an image.
}
\section{Endpoint /{apiVersion}/files/{file}/refresh}{
Refresh metadata from the selected file or folder. Return updated files.
}
\section{Endpoint /{apiVersion}/files/{file}/tail}{
Show the last lines of a file (up to a limit).
}
\section{Endpoint /{apiVersion}/files/{folder}/list}{
List all the files inside the folder.
}
\section{Endpoint /{apiVersion}/files/{folder}/tree}{
Obtain a tree view of the files and folders within a folder.
}
\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/}
\link{*}: Required parameter
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy