Files in jbrzusto/motus-R-package
Operate a server to process data for http://motus.org
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Copse.R
R/RL.R
R/TS.R
R/archiveMessage.R
R/archivePath.R
R/as.list.motusMap.R
R/authenticate_user.R
R/claimJob.R
R/cleanTagRegistrations.R
R/cleanup.R
R/closeRecvSrc.R
R/commitMetadataHistory.R
R/createFilterTagsDB.R
R/createRecvTagDB.R
R/dataServer.R
R/dateStem.R
R/dbHumanizeTimestamps.R
R/dbInsertOrReplace.R
R/deleteFromMotus.R
R/deleteTestBatches.R
R/digestFile.R
R/dirSortedBy.R
R/dropBatchesFromTransfer.R
R/email.R
R/embroilHuman.R
R/enqueue.R
R/enqueueCommand.R
R/ensureMonoBN.R
R/ensureMotusTransferTables.R
R/ensureParamOverridesTable.R
R/ensureRecvDBTables.R
R/ensureServerDB.R
R/ensureServerDirs.R
R/ensureTagProjDB.R
R/error_from_app.R
R/exportGlobalTags.R
R/fixDOSfilenames.R
R/getDownloadURL.R
R/getFeeder.R
R/getFileAsBZ2.R
R/getFileAsText.R
R/getGlobalTagsView.R
R/getMap.R
R/getMotusDeviceID.R
R/getMotusMetaDB.R
R/getPGID.R
R/getParamOverrides.R
R/getProjDir.R
R/getProjectTags.R
R/getRecvDBPath.R
R/getRecvModel.R
R/getRecvSrc.R
R/getRecvType.R
R/getTagProjSrc.R
R/getYearProjSite.R
R/guessTagModel.R
R/hackError.R
R/handleExportData.R
R/handleExportPulses.R
R/handleFullRecvRerun.R
R/handleLogs.R
R/handleLtFiles.R
R/handleLtFindtags.R
R/handleNewFiles.R
R/handlePlotData.R
R/handleQueueArchives.R
R/handleRegisterTags.R
R/handleRerunReceiver.R
R/handleSGfiles.R
R/handleSGfindtags.R
R/handleSanityCheck.R
R/handleServerFiles.R
R/handleSyncReceiver.R
R/handleUnknownFiles.R
R/handleUnpackArchive.R
R/handleUploadFile.R
R/handleUploadProcessed.R
R/isTopJob.R
R/isTopJobDone.R
R/jobFail.R
R/jobHasFolder.R
R/jobLog.R
R/jobPath.R
R/jobProduced.R
R/lightWeightCopy.R
R/loadJobs.R
R/lockSymbol.R
R/loggingTry.R
R/ltDTAregex.R
R/ltDefaultFindTagsParams.R
R/ltFindTags.R
R/ltGetCodeset.R
R/ltMergeFiles.R
R/ltSyncDBtoRepo.R
R/makeQueuePath.R
R/makeReceiverPlot.R
R/makeTagProjDB.R
R/matchTags.R
R/motusAuthenticateUser.R
R/motusConstants.R
R/motusDeployTag.R
R/motusListProjects.R
R/motusListSensorDeps.R
R/motusListSensors.R
R/motusListSpecies.R
R/motusLoadSecrets.R
R/motusLog.R
R/motusQuery.R
R/motusQuickRegTag.R
R/motusRegisterReceiver.R
R/motusRegisterTag.R
R/motusReserveKeys.R
R/motusSaveSecrets.R
R/motusSearchTags.R
R/moveDirContents.R
R/moveFiles.R
R/moveFilesUniquely.R
R/moveJob.R
R/newJob.R
R/newSubJob.R
R/openMotusDB.R
R/parseFilenames.R
R/plotTagTimeline.R
R/postInstall.R
R/predictTagLifespan.R
R/processServer.R
R/productsDir.R
R/purgeFromMotus.R
R/pushToMotus.R
R/queueJob.R
R/queueKnownFiles.R
R/queueUnfinishedSubjobs.R
R/readDTA.R
R/realFile.R
R/refreshMotusMetaDBCache.R
R/regexPieces.R
R/registerProducts.R
R/repackageRecoverdSGdata.R
R/reparentJob.R
R/rerunUploadJob.R
R/retryJob.R
R/return_file_from_app.R
R/return_from_app.R
R/runningCount.R
R/safeFileRename.R
R/safeSQL.R
R/safeSQLiteConnect.R
R/safeSrcSQLite.R
R/safeSys.R
R/safe_arg.R
R/serverCommon.R
R/serverError.R
R/sgDefaultFindTagsParams.R
R/sgFilenameRegex.R
R/sgFindTags.R
R/sgMergeFiles.R
R/sgRawDataRegex.R
R/sgStreamToFile.R
R/sgSyncDBtoRepo.R
R/sgTimeAtBoot.R
R/splitToDF.R
R/sqliteToRDS.R
R/statusServer.R
R/statusServer2.R
R/subjobsInQueue.R
R/syncDBtoRepo.R
R/syncServer.R
R/tagview.R
R/testFile.R
R/textFileContents.R
R/toInbox.R
R/toTrash.R
R/topJob.R
R/trimCommonPath.R
R/updateMetadataForTags.R
R/updateTagDeployments.R
R/uploadServer.R
R/validateMotusTagDB.R
R/validate_request.R
R/wavFindTags.R
R/z%or%.R
R/z.onLoad.R
README.md
data/speciesTagModel.R
data/tagLifespanPars.rda
inst/doc/2018-May_issues.md
inst/doc/Makefile
inst/doc/beeper_product_format.md
inst/doc/data_flow.dot
inst/doc/data_flow.pdf
inst/doc/data_flow.svg
inst/doc/lotekTagLifespanByBatteryAndBI.csv
inst/doc/maintenance.md
inst/doc/modelLotekTagLifeSpan.Rmd
inst/doc/modelLotekTagLifeSpan.pdf
inst/doc/modelLotekTagLifeSpan.rda
inst/doc/motus_administrator_guide.md
inst/doc/motus_data_overview.md
inst/doc/motus_data_overview.pdf
inst/doc/motus_processing_overview.md
inst/doc/networked_receivers.md
inst/doc/rds_format.md
inst/doc/rds_format.txt
inst/doc/requirePrograms.md
inst/doc/sensorgnome_data_flow.dot
inst/doc/sensorgnome_data_flow.pdf
inst/doc/sensorgnome_data_flow.svg
inst/doc/servers.md
inst/doc/slow_queries.md
inst/doc/status_api.md
inst/doc/status_of_transition_to_new_server.md
inst/doc/tag_detection_imprecision.md
inst/doc/tags_view_graph.dot
inst/doc/tags_view_graph.pdf
inst/doc/uploads.md
inst/motusMetadataSchema.sql
inst/motusTransferTableSchema.sql
inst/receiverToMasterKeyMapSchema.sql
inst/root_overlay.md
inst/root_overlay/etc/apache2/sites-available/001-sgdata-ssl.conf
inst/root_overlay/etc/apache2/sites-available/002-sgdata-nossl.conf
inst/root_overlay/etc/apache2/sites-available/live-sensorgnome
inst/root_overlay/etc/cron.d/monthly_trash_dump
inst/root_overlay/etc/cron.d/refreshMotusMetaDB
inst/root_overlay/etc/cron.d/sqlite_daily_backup
inst/root_overlay/etc/rc.local
inst/root_overlay/etc/sysctl.d/local.conf
inst/scripts/backup_sqlite_db.sh
inst/scripts/boot_time_tasks.sh
inst/scripts/chown_sg_www-data.sh
inst/scripts/create_live_sqlite_database.sqlite
inst/scripts/debug.php
inst/scripts/decryptLotekDB.R
inst/scripts/hackError.R
inst/scripts/killAllMotusServers.sh
inst/scripts/killMotusDataServer.sh
inst/scripts/killMotusProcessServers.sh
inst/scripts/killMotusStatusServer.sh
inst/scripts/killMotusStatusServer2.sh
inst/scripts/killMotusSyncServer.sh
inst/scripts/lastError.R
inst/scripts/maintenance/README.TXT
inst/scripts/maintenance/buildFileRepo.R
inst/scripts/maintenance/checkSyncDBtoRepo.sh
inst/scripts/maintenance/clearTransferTables.R
inst/scripts/maintenance/ensureAllFiles.R
inst/scripts/maintenance/ensureAllFiles.sh
inst/scripts/maintenance/generate_projAmbig.R
inst/scripts/maintenance/humanize.R
inst/scripts/maintenance/makeDailyHierarchy.R
inst/scripts/maintenance/populate_products_table.R
inst/scripts/maintenance/post_install.sh
inst/scripts/maintenance/re-push-metadata_hash.R
inst/scripts/maintenance/register_failed_uploads.R
inst/scripts/maintenance/syncDBtoFiles.R
inst/scripts/maintenance/syncDBtoRepo.R
inst/scripts/maintenance/update_batchRuns_tagDepProjectID.R
inst/scripts/maintenance/update_hits_tagDepProjectID.R
inst/scripts/monthly_trash_dump.sh
inst/scripts/refreshMotusMetaDB.R
inst/scripts/rerunMotusServers.sh
inst/scripts/rerunReceiver.R
inst/scripts/rerunUploadJob.R
inst/scripts/retryJob.R
inst/scripts/rpack
inst/scripts/runAllMotusServers.sh
inst/scripts/runMotusDataServer.sh
inst/scripts/runMotusProcessServer.sh
inst/scripts/runMotusStatusServer.sh
inst/scripts/runMotusStatusServer2.sh
inst/scripts/runMotusSyncServer.sh
inst/scripts/runNewFiles.R
inst/scripts/sqlite_daily_backup.sh
inst/scripts/updateAllProjectGlobalFiles.R
inst/scripts/www/data_server_unavailable.php
inst/scripts/www/fake_authenticate_user.php
inst/scripts/www/index.html
inst/scripts/www/index.php
inst/scripts/www/jquery-ui-1.12.1/AUTHORS.txt
inst/scripts/www/jquery-ui-1.12.1/LICENSE.txt
inst/scripts/www/jquery-ui-1.12.1/external/jquery/jquery.js
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_444444_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_555555_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_777620_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_777777_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_cc0000_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_ffffff_256x240.png
inst/scripts/www/jquery-ui-1.12.1/index.html
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.js
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.min.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.min.js
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.structure.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.structure.min.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.theme.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.theme.min.css
inst/scripts/www/jquery-ui-1.12.1/package.json
inst/scripts/www/jquery.mustache.min.js
inst/scripts/www/login.php
inst/scripts/www/mustache.min.js
inst/scripts/www/obsolete/status2.php
inst/scripts/www/robots.txt
inst/scripts/www/status.php
inst/scripts/www/status2.css
inst/scripts/www/status2.html
inst/scripts/www/status2.js
inst/scripts/www/status_message.html
man/Copse.Rd
man/MOTUS_API_ENTRY_POINTS.Rd
man/RL.Rd
man/Reval.Rd
man/TS.Rd
man/addToOrder.Rd
man/api_info.Rd
man/archiveMessage.Rd
man/archivePath.Rd
man/authenticate_user.Rd
man/batches_for_all.Rd
man/batches_for_receiver.Rd
man/batches_for_tag_project.Rd
man/beginsWith.Rd
man/cash-.motusMap.Rd
man/cash-.safeSQL.Rd
man/cash-set-.motusMap.Rd
man/childrenWhere.Copse.Rd
man/claimJob.Rd
man/cleanTagRegistrations.Rd
man/cleanup.Rd
man/closeRecvSrc.Rd
man/commitMetadataHistory.Rd
man/compressedFileDone.Rd
man/createFilterTagsDB.Rd
man/createRecvTagDB.Rd
man/dataServer.Rd
man/dateStem.Rd
man/dbHumanizeTimestamps.Rd
man/dbInsertOrReplace.Rd
man/deleteFromMotus.Rd
man/deleteTestBatches.Rd
man/deviceID_for_receiver.Rd
man/digestFile.Rd
man/dirSortedBy.Rd
man/dropBatchesFromTransfer.Rd
man/dumpJobDetails.Rd
man/email.Rd
man/embroilHuman.Rd
man/enqueue.Rd
man/enqueueCommand.Rd
man/ensureMonoBN.Rd
man/ensureMotusTransferTables.Rd
man/ensureParamOverridesTable.Rd
man/ensureRecvDBTables.Rd
man/ensureServerDB.Rd
man/ensureServerDirs.Rd
man/ensureTagProjDB.Rd
man/error_from_app.Rd
man/exportGlobalTags.Rd
man/files_from_recv_DB.Rd
man/files_from_repo.Rd
man/fixDOSfilenames.Rd
man/getDownloadURL.Rd
man/getFeeder.Rd
man/getFileAsBZ2.Rd
man/getFileAsText.Rd
man/getGlobalTagsView.Rd
man/getMap.Rd
man/getMotusDeviceID.Rd
man/getMotusMetaDB.Rd
man/getPGID.Rd
man/getParamOverrides.Rd
man/getProjDir.Rd
man/getProjectTags.Rd
man/getRecvDBPath.Rd
man/getRecvModel.Rd
man/getRecvSrc.Rd
man/getRecvType.Rd
man/getTagProjSrc.Rd
man/getYearProjSite.Rd
man/get_job_stackdump.Rd
man/get_receiver_info.Rd
man/gps_for_receiver.Rd
man/gps_for_tag_project.Rd
man/grapes-or-grapes.Rd
man/guessTagModel.Rd
man/hackError.Rd
man/handleExportData.Rd
man/handleExportPulses.Rd
man/handleFullRecvRerun.Rd
man/handleLogs.Rd
man/handleLtFiles.Rd
man/handleLtFindtags.Rd
man/handleNewFiles.Rd
man/handlePlotData.Rd
man/handleQueueArchives.Rd
man/handleRegisterTags.Rd
man/handleRerunReceiver.Rd
man/handleSGfiles.Rd
man/handleSGfindtags.Rd
man/handleSanityCheck.Rd
man/handleServerFiles.Rd
man/handleSyncReceiver.Rd
man/handleUnknownFiles.Rd
man/handleUnpackArchive.Rd
man/handleUploadFile.Rd
man/handleUploadProcessed.Rd
man/hits_for_receiver.Rd
man/hits_for_tag_project.Rd
man/infimum.Rd
man/isTopJob.Rd
man/isTopJobDone.Rd
man/jobFail.Rd
man/jobHasFolder.Rd
man/jobLog.Rd
man/jobPath.Rd
man/jobProduced.Rd
man/lightWeightCopy.Rd
man/list_jobs.Rd
man/list_receiver_files.Rd
man/loadJobs.Rd
man/lockSymbol.Rd
man/loggingTry.Rd
man/ltDTAregex.Rd
man/ltDefaultFindTagsParams.Rd
man/ltFindTags.Rd
man/ltGetCodeset.Rd
man/ltMergeFiles.Rd
man/ltSyncDBtoRepo.Rd
man/makeQueuePath.Rd
man/makeReceiverPlot.Rd
man/makeTagProjDB.Rd
man/makeWhere.Rd
man/matchTags.Rd
man/maybeRetireJob.Rd
man/metadata_for_receivers.Rd
man/metadata_for_tags.Rd
man/motusAuthenticateUser.Rd
man/motusDeployTag.Rd
man/motusListProjects.Rd
man/motusListSensorDeps.Rd
man/motusListSensors.Rd
man/motusListSpecies.Rd
man/motusLoadSecrets.Rd
man/motusLog.Rd
man/motusQuery.Rd
man/motusQuickRegTag.Rd
man/motusRegisterReceiver.Rd
man/motusRegisterTag.Rd
man/motusReserveKeys.Rd
man/motusSaveSecrets.Rd
man/motusSearchTags.Rd
man/moveDirContents.Rd
man/moveFiles.Rd
man/moveFilesUniquely.Rd
man/moveJob.Rd
man/names.motusMap.Rd
man/newJob.Rd
man/newSubJob.Rd
man/openMotusDB.Rd
man/parseFilenames.Rd
man/plotTagTimeline.Rd
man/postInstall.Rd
man/predictTagLifespan.Rd
man/print.safeSQL.Rd
man/processServer.Rd
man/productsDir.Rd
man/project_ambiguities_for_tag_project.Rd
man/pulse_counts_for_receiver.Rd
man/purgeFromMotus.Rd
man/pushToMotus.Rd
man/queueJob.Rd
man/queueKnownFiles.Rd
man/queueUnfinishedSubjobs.Rd
man/readDTA.Rd
man/realFile.Rd
man/receivers_for_project.Rd
man/refreshMotusMetaDBCache.Rd
man/regexPieces.Rd
man/registerProducts.Rd
man/repackageRecoveredSGdata.Rd
man/reparentJob.Rd
man/rerunUploadJob.Rd
man/retryJob.Rd
man/return_from_app.Rd
man/runningCount.Rd
man/runs_for_receiver.Rd
man/runs_for_tag_project.Rd
man/safeFileRename.Rd
man/safeSQL.Rd
man/safeSQLiteConnect.Rd
man/safeSrcSQLite.Rd
man/safeSys.Rd
man/safe_arg.Rd
man/serializeNoHeader.Rd
man/serno_collision_rules.Rd
man/serverCommon.Rd
man/serverError.Rd
man/setParent.Copse.Rd
man/sgDefaultFindTagsParams.Rd
man/sgFilenameRegex.Rd
man/sgFindTags.Rd
man/sgMergeFiles.Rd
man/sgRawDataRegex.Rd
man/sgStreamToFile.Rd
man/sgSyncDBtoRepo.Rd
man/sgTimeAtBoot.Rd
man/size_of_update_for_receiver.Rd
man/size_of_update_for_tag_project.Rd
man/splitToDF.Rd
man/sqliteCloneIntoDB.Rd
man/sqliteToRDS.Rd
man/statusServer.Rd
man/statusServer2.Rd
man/status_api_info.Rd
man/sub-sub-.motusMap.Rd
man/sub-subset-.motusMap.Rd
man/subjobsInQueue.Rd
man/subset-.Copse.Rd
man/syncDBtoRepo.Rd
man/syncServer.Rd
man/tags_for_ambiguities.Rd
man/tagview.Rd
man/testFile.Rd
man/textFileContents.Rd
man/toInbox.Rd
man/toTrash.Rd
man/topJob.Rd
man/trimCommonPath.Rd
man/uncompressedSize.Rd
man/updateMetadataForTags.Rd
man/updateTagDeployments.Rd
man/uploadServer.Rd
man/validateMotusTagDB.Rd
man/validate_request.Rd
man/wavFindTags.Rd
src/Makefile
src/Sqlite_Compression_Extension.c
tests/testthat.R
