| addToOrder | add condition(s) to the order by clause |
| api_info | return information about the api |
| archiveMessage | Save a handled email message in the appropriate place. |
| archivePath | Move a file or folder to a new location, ensuring it has a... |
| authenticate_user | authenticate a user for a Rook request |
| batches_for_all | get batches for any receiver |
| batches_for_receiver | get batches for a receiver |
| batches_for_tag_project | get batches for a tag project |
| beginsWith | does a string begin with another string |
| cash-.motusMap | Return the value of an item from a motusMap. |
| cash-.safeSQL | safeSQL method to provide read access to some internals |
| cash-set-.motusMap | set an element in a motus map |
| childrenWhere.Copse | find children of Twig which satisfy a query |
| claimJob | try to accept a job for processing in a queue |
| cleanTagRegistrations | Fix systematic problems with the tag registration database. |
| cleanup | remove old processed data from a receiver database. |
| closeRecvSrc | Close the src_sqlite for a receiver database. |
| commitMetadataHistory | commit any changes to the metadata history git repo |
| compressedFileDone | is a .gz file actually finished? |
| Copse | Create a copse, a persistent structure for holding R objects... |
| createFilterTagsDB | create a tag database for use by the dta2sg function in the... |
| createRecvTagDB | create a receiver tag database, for use by the sensorgnome... |
| dataServer | serve http requests for tag detection data |
| dateStem | Get the common portion of a range of dates. |
| dbHumanizeTimestamps | create a view of a table where timestamps are displayed in... |
| dbInsertOrReplace | Save records from a data frame into a db table, replacing... |
| deleteFromMotus | delete a set of detections from motus by adding records to... |
| deleteTestBatches | delete one or more test batches from the master motus DB |
| deviceID_for_receiver | get deviceIDs for receiver serial numbers |
| digestFile | calculate a digest of a file |
| dirSortedBy | Get listing of full paths to items in folder(s), sorted by... |
| dropBatchesFromTransfer | delete a set of batches and all related data from the master... |
| dumpJobDetails | dump details of job j to res, as ith job listing |
| email | Send an email message. |
| embroilHuman | Save a set of files we don't know how to deal with, and... |
| enqueue | Add a file or folder to the server queue. |
| enqueueCommand | Enqueue a command that doesn't require a file or folder. |
| ensureMonoBN | Ensure we have monotonic boot numbers for a receiver... |
| ensureMotusTransferTables | Ensure we have the mysql transfer tables for moving SG data... |
| ensureParamOverridesTable | make sure we have a valid parameterOverrides table |
| ensureRecvDBTables | make sure a receiver database has the required tables; also,... |
| ensureServerDB | ensure we have created the server database |
| ensureServerDirs | Ensure existence of a hierarchy of folders for running a... |
| ensureTagProjDB | make sure a tag project database has the required tables;... |
| error_from_app | return an error from a Rook app |
| exportGlobalTags | export a global tags view as an old-style globaltags .rds... |
| files_from_recv_DB | return a dplyr::tbl of files from a receiver database |
| files_from_repo | return a dplyr::tbl of files from the file repository for a... |
| fixDOSfilenames | Correct DOS-style 8.3 filenames into (almost) their original... |
| getDownloadURL | return the URL to the download site for a project |
| getFeeder | return a function which returns the next item from a folder. |
| getFileAsBZ2 | read a file and (re-) compress it into a bzip2-format raw... |
| getFileAsText | read a file as text, converting if necessary |
| getGlobalTagsView | get a view of tag detections with the same columns as the... |
| get_job_stackdump | return a URL to an .rds file stack dump for a job with errors |
| getMap | Access (maybe after creating) a persistent named list in a... |
| getMotusDeviceID | Get the motus device ID for a receiver, given its database. |
| getMotusMetaDB | Get a safeSQL connection to the cached copy of the motus... |
| getParamOverrides | Get the parameter overrides for a receiver and time or boot... |
| getPGID | return the process group ID for the R session |
| getProjDir | Get the directory where files for a project are stored. |
| getProjectTags | return the tags registered for a project with motus |
| get_receiver_info | return information for a receiver |
| getRecvDBPath | Get the path to a receiver database given its serial number. |
| getRecvModel | determine the model from a receiver serial number |
| getRecvSrc | Get the src_sqlite for a receiver database given its serial... |
| getRecvType | determine the receiverType from a serial number |
| getTagProjSrc | Get the src_sqlite for a tag project database given its... |
| getYearProjSite | Get project and site names, given a receiver serial number... |
| gps_for_receiver | get all GPS fixes from a batch |
| gps_for_tag_project | get all GPS fixes from a batch "relevant to" detections of... |
| grapes-or-grapes | perl/javascript style "or" |
| guessTagModel | guess the model of a tag used by the speciesID |
| hackError | examine the calling environments of a failed job |
| handleExportData | push newly generated data to motus transfer tables |
| handleExportPulses | create an interim .sqlite file with tables of pulses and... |
| handleFullRecvRerun | fully re-run all raw data files from a receiver |
| handleLogs | Save a folder of linux system log files from a sensorgnome. |
| handleLtFiles | handle a folder of Lotek .DTA files |
| handleLtFindtags | run the tag finder on all files from a Lotek receiver |
| handleNewFiles | handle a new batch of files |
| handlePlotData | plot data from a receiver |
| handleQueueArchives | Queue a new sub-job for each archive in a folder. |
| handleRegisterTags | handle a batch of tag registrations |
| handleRerunReceiver | re-run data from a receiver |
| handleSanityCheck | Do basic sanity checks on all files (recursively0 in a... |
| handleServerFiles | handle a folder of files from the server |
| handleSGfiles | handle a folder of files from one or more sensorgnomes |
| handleSGfindtags | handle the job of running the tag finder on one sensorgnome... |
| handleSyncReceiver | sync from an attached receiver, processing any new data |
| handleUnknownFiles | handle a set of files of unknown type |
| handleUnpackArchive | Try unpack a compressed archive into its job folder. |
| handleUploadFile | handle an uploaded file |
| handleUploadProcessed | handler for completion of processing of an uploaded file |
| hits_for_receiver | get all hits from a batch for a receiver |
| hits_for_tag_project | get hits by tag project from a batch |
| infimum | get the greatest lower bound of each number in one set from... |
| isTopJob | is this a top-level job? |
| isTopJobDone | Check whether the top job of which a job is a subjob is done;... |
| jobFail | mark a job as failed |
| jobHasFolder | does a job have a folder in the filesystem? |
| jobLog | Add a message to the log for a job. Log messages are saved... |
| jobPath | get the filesystem path for a job |
| jobProduced | report and maybe record what a job produced |
| lightWeightCopy | Make a light-weight recursive copy of a folder. |
| list_jobs | return a list of jobs, sorted by user-selected criteria |
| list_receiver_files | return a list of files for a receiver |
| loadJobs | Load and maybe enqueue unfinished jobs from the server... |
| lockSymbol | Try to lock or unlock a symbol, preventing any other... |
| loggingTry | Try evaluate expression, logging the call stack in case of an... |
| ltDefaultFindTagsParams | default list of parameters for the tag finder for Lotek data |
| ltDTAregex | A PCRE-style regular expression for matching interesting... |
| ltFindTags | find tags in a Lotek receiver dataset |
| ltGetCodeset | Return the database of canonical parameters for a Lotek... |
| ltMergeFiles | Merge a batch of Lotek .DTA files with an existing database. |
| ltSyncDBtoRepo | Make sure all files stored internally in a Lotek receiver DB... |
| makeQueuePath | Create a filename or folder for the motus processing queue. |
| makeReceiverPlot | make a plot of tag detections and status of antennas |
| makeTagProjDB | create an sqlite database of all detections of tags from a... |
| makeWhere | add condition(s) to the where clause; strip any leading... |
| matchTags | find which tags match registered tags |
| maybeRetireJob | if a job is done and none of its subjobs are left in the... |
| metadata_for_receivers | get metadata for receivers |
| metadata_for_tags | get metadata for tags |
| MOTUS_API_ENTRY_POINTS | Constants for the motusServer package. |
| motusAuthenticateUser | authenticate a user with motus.org |
| motusDeployTag | register a tag deployment with motus |
| motusListProjects | return a list of all motus projects |
| motusListSensorDeps | return a list motus sensor deployments for a project |
| motusListSensors | return a list of all motus sensors |
| motusListSpecies | return a list of species IDs for the given codes or names |
| motusLoadSecrets | load secrets for motus web API |
| motusLog | Record messages to the motus main log. |
| motusQuery | Send a query to the motus API |
| motusQuickRegTag | Quickly register a tag with motus |
| motusRegisterReceiver | register a receiver with motus (admin only) |
| motusRegisterTag | register a tag with motus |
| motusReserveKeys | Reserve a block of consecutive primary keys in a motus... |
| motusSaveSecrets | save secrets for motus web API in default location |
| motusSearchTags | return a list of all motus tags |
| moveDirContents | Move the contents of a directory to another directory. |
| moveFiles | Move files/folders to a folder |
| moveFilesUniquely | Move files to a single folder, renaming new files in cases of... |
| moveJob | move a top job to a new folder |
| names.motusMap | get the key values of a map table in a database |
| newJob | create and enqueue a new job |
| newSubJob | create and enqueue a new subjob of an existing job |
| openMotusDB | Return a src_mysql attached to the motus mysql database. |
| parseFilenames | parse sensorgnome filenames into components |
| plotTagTimeline | plot a timeline of all deployed tags |
| postInstall | code to run after installing a new version of this package. |
| predictTagLifespan | predict the lifespan of specified tag model and burst... |
| print.safeSQL | safeSQL method for printing |
| processServer | process batches of files from the queue |
| productsDir | get the directory for products for a receiver |
| project_ambiguities_for_tag_project | get project ambiguity groups for a given project |
| pulse_counts_for_receiver | get pulse counts from a batch |
| purgeFromMotus | Delete all data for this receiver from ths motus transfer... |
| pushToMotus | Push any new tag detections to the motus master database. |
| queueJob | enqueue a job and maybe verify the path to its folder |
| queueKnownFiles | Queue any files of known type from a folder. |
| queueUnfinishedSubjobs | Load unfinished jobs from server database and enqueue them. |
| readDTA | read a lotek .DTA file |
| realFile | follow any symlinks, returning the path to a normal file or... |
| receivers_for_project | get receivers for a project |
| refreshMotusMetaDBCache | Refresh our cache of the motus database of metadata for tags,... |
| regexPieces | Extract named items from strings according to a regular... |
| registerProducts | register product files for a receiver |
| repackageRecoveredSGdata | repackage recovered data into hourly files with appropriate... |
| reparentJob | move a subjob to a new parent job |
| rerunUploadJob | Rerun an upload job, after some external error condition has... |
| retryJob | Retry a job, after some external error condition has been... |
| return_from_app | return an object from a Rook app |
| Reval | evaluate portions of an expression enclosed in 'R( )',... |
| RL | reload a function in a package from its source folder |
| runningCount | running count of occurences for each unique value in a vector |
| runs_for_receiver | get all runs from a batch for a receiver |
| runs_for_tag_project | get runs by tag project from a batch |
| safe_arg | Extract an argument from a list ensuring SQL-safety |
| safeFileRename | rename files, even across filesystems |
| safeSQL | Return a function that safely performs sql queries on a... |
| safeSQLiteConnect | open a 'safe' connection to an sqlite database |
| safeSrcSQLite | open a dplyr::src to an sqlite database, without the locking... |
| safeSys | Call an external program safely, return its output and... |
| serializeNoHeader | serialize an object to a raw vector, without the "RDS" file... |
| serno_collision_rules | get, create, or delete rules for resolving receiver serial... |
| serverCommon | common code required by all XXXServer() functions |
| serverError | Handle an error for the motus server. |
| setParent.Copse | set the parent (and stump) of Twig(s) |
| sgDefaultFindTagsParams | default list of parameters for the tag finder |
| sgFilenameRegex | Regular expression for parsing data filenames from a... |
| sgFindTags | find tags in an SG stream |
| sgMergeFiles | Merge a batch of raw SG files with their receiver... |
| sgRawDataRegex | Regular expression for parsing line from raw data file. |
| sgStreamToFile | Send a stream of raw data to a file |
| sgSyncDBtoRepo | Make sure all files stored internally in a Sensorgnome... |
| sgTimeAtBoot | Get start times for boot sessions for a sensorgnome. |
| size_of_update_for_receiver | get count of update items for a receiver |
| size_of_update_for_tag_project | get count of update items for a tag project |
| splitToDF | Read a data.frame from a character vector according to a... |
| sqliteCloneIntoDB | clone an sqlite table schema (including indexes) from the... |
| sqliteToRDS | Export the results of an sqlite query directly into an .rds... |
| status_api_info | return information about the status api |
| statusServer | reply to http requests for information on the processing... |
| statusServer2 | reply to http requests for information on the processing... |
| subjobsInQueue | return a vector of subjobs of the given topjob which are in... |
| subset-.Copse | To support syntactic sugar like Jobs[! done &&... |
| sub-sub-.motusMap | Return the value of an item from a motusMap. |
| sub-subset-.motusMap | set an element in a motus map |
| syncDBtoRepo | Make sure all files stored internally in a receiver DB are... |
| syncServer | watch for attached receivers and sync files from them |
| tags_for_ambiguities | get motus tagIDs for ambiguity IDs |
| tagview | create a tbl of tag detections with all metadata. |
| testFile | Test files for validity. |
| textFileContents | return the contents of a text file as a character scalar, or... |
| toInbox | Move a message to the inbox, from where the emailServer will... |
| topJob | return the top-level job for which the given job is a subjob |
| toTrash | send files to the trash folder for eventual deletion |
| trimCommonPath | Remove any common leading path from a set of paths. |
| TS | bless a numeric vector with "timestamp" class |
| uncompressedSize | get size of uncompressed .gz file from 4-byte footer |
| updateMetadataForTags | update metadata for a set of tags |
| updateTagDeployments | Pull any new or modified tag deployment records from motus |
| uploadServer | watch for and enqueue uploaded files |
| validateMotusTagDB | Perform sanity checks on the motus tag database, reporting... |
| validate_request | validate an API request by looking up its token |
| wavFindTags | detect tags in a .wav audio file |
