Man pages for jbrzusto/motusServer
Operate a server to process data for http://motus.org

addToOrderadd condition(s) to the order by clause
api_inforeturn information about the api
archiveMessageSave a handled email message in the appropriate place.
archivePathMove a file or folder to a new location, ensuring it has a...
authenticate_userauthenticate a user for a Rook request
batches_for_allget batches for any receiver
batches_for_receiverget batches for a receiver
batches_for_tag_projectget batches for a tag project
beginsWithdoes a string begin with another string
cash-.motusMapReturn the value of an item from a motusMap.
cash-.safeSQLsafeSQL method to provide read access to some internals
cash-set-.motusMapset an element in a motus map
childrenWhere.Copsefind children of Twig which satisfy a query
claimJobtry to accept a job for processing in a queue
cleanTagRegistrationsFix systematic problems with the tag registration database.
cleanupremove old processed data from a receiver database.
closeRecvSrcClose the src_sqlite for a receiver database.
commitMetadataHistorycommit any changes to the metadata history git repo
compressedFileDoneis a .gz file actually finished?
CopseCreate a copse, a persistent structure for holding R objects...
createFilterTagsDBcreate a tag database for use by the dta2sg function in the...
createRecvTagDBcreate a receiver tag database, for use by the sensorgnome...
dataServerserve http requests for tag detection data
dateStemGet the common portion of a range of dates.
dbHumanizeTimestampscreate a view of a table where timestamps are displayed in...
dbInsertOrReplaceSave records from a data frame into a db table, replacing...
deleteFromMotusdelete a set of detections from motus by adding records to...
deleteTestBatchesdelete one or more test batches from the master motus DB
deviceID_for_receiverget deviceIDs for receiver serial numbers
digestFilecalculate a digest of a file
dirSortedByGet listing of full paths to items in folder(s), sorted by...
dropBatchesFromTransferdelete a set of batches and all related data from the master...
dumpJobDetailsdump details of job j to res, as ith job listing
emailSend an email message.
embroilHumanSave a set of files we don't know how to deal with, and...
enqueueAdd a file or folder to the server queue.
enqueueCommandEnqueue a command that doesn't require a file or folder.
ensureMonoBNEnsure we have monotonic boot numbers for a receiver...
ensureMotusTransferTablesEnsure we have the mysql transfer tables for moving SG data...
ensureParamOverridesTablemake sure we have a valid parameterOverrides table
ensureRecvDBTablesmake sure a receiver database has the required tables; also,...
ensureServerDBensure we have created the server database
ensureServerDirsEnsure existence of a hierarchy of folders for running a...
ensureTagProjDBmake sure a tag project database has the required tables;...
error_from_appreturn an error from a Rook app
exportGlobalTagsexport a global tags view as an old-style globaltags .rds...
files_from_recv_DBreturn a dplyr::tbl of files from a receiver database
files_from_reporeturn a dplyr::tbl of files from the file repository for a...
fixDOSfilenamesCorrect DOS-style 8.3 filenames into (almost) their original...
getDownloadURLreturn the URL to the download site for a project
getFeederreturn a function which returns the next item from a folder.
getFileAsBZ2read a file and (re-) compress it into a bzip2-format raw...
getFileAsTextread a file as text, converting if necessary
getGlobalTagsViewget a view of tag detections with the same columns as the...
get_job_stackdumpreturn a URL to an .rds file stack dump for a job with errors
getMapAccess (maybe after creating) a persistent named list in a...
getMotusDeviceIDGet the motus device ID for a receiver, given its database.
getMotusMetaDBGet a safeSQL connection to the cached copy of the motus...
getParamOverridesGet the parameter overrides for a receiver and time or boot...
getPGIDreturn the process group ID for the R session
getProjDirGet the directory where files for a project are stored.
getProjectTagsreturn the tags registered for a project with motus
get_receiver_inforeturn information for a receiver
getRecvDBPathGet the path to a receiver database given its serial number.
getRecvModeldetermine the model from a receiver serial number
getRecvSrcGet the src_sqlite for a receiver database given its serial...
getRecvTypedetermine the receiverType from a serial number
getTagProjSrcGet the src_sqlite for a tag project database given its...
getUploadTokenGet a random token for inclusion in data transfer emails
getYearProjSiteGet project and site names, given a receiver serial number...
gps_for_receiverget all GPS fixes from a batch
gps_for_tag_projectget all GPS fixes from a batch "relevant to" detections of...
grapes-or-grapesperl/javascript style "or"
guessTagModelguess the model of a tag used by the speciesID
hackErrorexamine the calling environments of a failed job
handleExportDatapush newly generated data to motus transfer tables
handleExportPulsescreate an interim .sqlite file with tables of pulses and...
handleFullRecvRerunfully re-run all raw data files from a receiver
handleLogsSave a folder of linux system log files from a sensorgnome.
handleLtFileshandle a folder of Lotek .DTA files
handleLtFindtagsrun the tag finder on all files from a Lotek receiver
handleNewFileshandle a new batch of files
handlePlotDataplot data from a receiver
handleQueueArchivesQueue a new sub-job for each archive in a folder.
handleRegisterTagshandle a batch of tag registrations
handleRerunReceiverre-run data from a receiver
handleSanityCheckDo basic sanity checks on all files (recursively0 in a...
handleServerFileshandle a folder of files from the server
handleSGfileshandle a folder of files from one or more sensorgnomes
handleSGfindtagshandle the job of running the tag finder on one sensorgnome...
handleSyncReceiversync from an attached receiver, processing any new data
handleUnknownFileshandle a set of files of unknown type
handleUnpackArchiveTry unpack a compressed archive into its job folder.
handleUploadFilehandle an uploaded file
handleUploadProcessedhandler for completion of processing of an uploaded file
hits_for_receiverget all hits from a batch for a receiver
hits_for_tag_projectget hits by tag project from a batch
infimumget the greatest lower bound of each number in one set from...
isTopJobis this a top-level job?
isTopJobDoneCheck whether the top job of which a job is a subjob is done;...
jobFailmark a job as failed
jobHasFolderdoes a job have a folder in the filesystem?
jobLogAdd a message to the log for a job. Log messages are saved...
jobPathget the filesystem path for a job
jobProducedreport and maybe record what a job produced
lightWeightCopyMake a light-weight recursive copy of a folder.
list_jobsreturn a list of jobs, sorted by user-selected criteria
list_receiver_filesreturn a list of files for a receiver
loadJobsLoad and maybe enqueue unfinished jobs from the server...
lockSymbolTry to lock or unlock a symbol, preventing any other...
loggingTryTry evaluate expression, logging the call stack in case of an...
ltDefaultFindTagsParamsdefault list of parameters for the tag finder for Lotek data
ltDTAregexA PCRE-style regular expression for matching interesting...
ltFindTagsfind tags in a Lotek receiver dataset
ltGetCodesetReturn the database of canonical parameters for a Lotek...
ltMergeFilesMerge a batch of Lotek .DTA files with an existing database.
ltSyncDBtoRepoMake sure all files stored internally in a Lotek receiver DB...
makeQueuePathCreate a filename or folder for the motus processing queue.
makeReceiverPlotmake a plot of tag detections and status of antennas
makeTagProjDBcreate an sqlite database of all detections of tags from a...
makeWhereadd condition(s) to the where clause; strip any leading...
matchTagsfind which tags match registered tags
maybeRetireJobif a job is done and none of its subjobs are left in the...
metadata_for_receiversget metadata for receivers
metadata_for_tagsget metadata for tags
MOTUS_API_ENTRY_POINTSConstants for the motusServer package.
motusAuthenticateUserauthenticate a user with motus.org
motusDeployTagregister a tag deployment with motus
motusListProjectsreturn a list of all motus projects
motusListSensorDepsreturn a list motus sensor deployments for a project
motusListSensorsreturn a list of all motus sensors
motusListSpeciesreturn a list of species IDs for the given codes or names
motusLoadSecretsload secrets for motus web API
motusLogRecord messages to the motus main log.
motusQuerySend a query to the motus API
motusQuickRegTagQuickly register a tag with motus
motusRegisterReceiverregister a receiver with motus (admin only)
motusRegisterTagregister a tag with motus
motusReserveKeysReserve a block of consecutive primary keys in a motus...
motusSaveSecretssave secrets for motus web API in default location
motusSearchTagsreturn a list of all motus tags
moveDirContentsMove the contents of a directory to another directory.
moveFilesMove files/folders to a folder
moveFilesUniquelyMove files to a single folder, renaming new files in cases of...
moveJobmove a top job to a new folder
names.motusMapget the key values of a map table in a database
newJobcreate and enqueue a new job
newSubJobcreate and enqueue a new subjob of an existing job
openMotusDBReturn a src_mysql attached to the motus mysql database.
parseFilenamesparse sensorgnome filenames into components
plotTagTimelineplot a timeline of all deployed tags
postInstallcode to run after installing a new version of this package.
predictTagLifespanpredict the lifespan of specified tag model and burst...
print.safeSQLsafeSQL method for printing
processServerprocess batches of files from the queue
productsDirget the directory for products for a receiver
project_ambiguities_for_tag_projectget project ambiguity groups for a given project
pulse_counts_for_receiverget pulse counts from a batch
purgeFromMotusDelete all data for this receiver from ths motus transfer...
pushToMotusPush any new tag detections to the motus master database.
queueJobenqueue a job and maybe verify the path to its folder
queueKnownFilesQueue any files of known type from a folder.
queueUnfinishedSubjobsLoad unfinished jobs from server database and enqueue them.
readDTAread a lotek .DTA file
realFilefollow any symlinks, returning the path to a normal file or...
receivers_for_projectget receivers for a project
refreshMotusMetaDBCacheRefresh our cache of the motus database of metadata for tags,...
regexPiecesExtract named items from strings according to a regular...
registerProductsregister product files for a receiver
repackageRecoveredSGdatarepackage recovered data into hourly files with appropriate...
reparentJobmove a subjob to a new parent job
rerunUploadJobRerun an upload job, after some external error condition has...
retryJobRetry a job, after some external error condition has been...
return_from_appreturn an object from a Rook app
Revalevaluate portions of an expression enclosed in 'R( )',...
RLreload a function in a package from its source folder
runningCountrunning count of occurences for each unique value in a vector
runs_for_receiverget all runs from a batch for a receiver
runs_for_tag_projectget runs by tag project from a batch
safe_argExtract an argument from a list ensuring SQL-safety
safeFileRenamerename files, even across filesystems
safeSQLReturn a function that safely performs sql queries on a...
safeSQLiteConnectopen a 'safe' connection to an sqlite database
safeSrcSQLiteopen a dplyr::src to an sqlite database, without the locking...
safeSysCall an external program safely, return its output and...
serializeNoHeaderserialize an object to a raw vector, without the "RDS" file...
serno_collision_rulesget, create, or delete rules for resolving receiver serial...
serverCommoncommon code required by all XXXServer() functions
serverErrorHandle an error for the motus server.
setParent.Copseset the parent (and stump) of Twig(s)
sgDefaultFindTagsParamsdefault list of parameters for the tag finder
sgFilenameRegexRegular expression for parsing data filenames from a...
sgFindTagsfind tags in an SG stream
sgMergeFilesMerge a batch of raw SG files with their receiver...
sgRawDataRegexRegular expression for parsing line from raw data file.
sgStreamToFileSend a stream of raw data to a file
sgSyncDBtoRepoMake sure all files stored internally in a Sensorgnome...
sgTimeAtBootGet start times for boot sessions for a sensorgnome.
size_of_update_for_receiverget count of update items for a receiver
size_of_update_for_tag_projectget count of update items for a tag project
splitToDFRead a data.frame from a character vector according to a...
sqliteCloneIntoDBclone an sqlite table schema (including indexes) from the...
sqliteToRDSExport the results of an sqlite query directly into an .rds...
status_api_inforeturn information about the status api
statusServerreply to http requests for information on the processing...
statusServer2reply to http requests for information on the processing...
subjobsInQueuereturn a vector of subjobs of the given topjob which are in...
subset-.CopseTo support syntactic sugar like Jobs[! done &&...
sub-sub-.motusMapReturn the value of an item from a motusMap.
sub-subset-.motusMapset an element in a motus map
syncDBtoRepoMake sure all files stored internally in a receiver DB are...
syncServerwatch for attached receivers and sync files from them
tags_for_ambiguitiesget motus tagIDs for ambiguity IDs
tagviewcreate a tbl of tag detections with all metadata.
testFileTest files for validity.
textFileContentsreturn the contents of a text file as a character scalar, or...
toInboxMove a message to the inbox, from where the emailServer will...
topJobreturn the top-level job for which the given job is a subjob
toTrashsend files to the trash folder for eventual deletion
trimCommonPathRemove any common leading path from a set of paths.
TSbless a numeric vector with "timestamp" class
uncompressedSizeget size of uncompressed .gz file from 4-byte footer
updateMetadataForTagsupdate metadata for a set of tags
updateTagDeploymentsPull any new or modified tag deployment records from motus
uploadServerwatch for and enqueue uploaded files
validateMotusTagDBPerform sanity checks on the motus tag database, reporting...
validate_requestvalidate an API request by looking up its token
wavFindTagsdetect tags in a .wav audio file
jbrzusto/motusServer documentation built on Nov. 4, 2018, 9:49 p.m.