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Merge pull request #1 from ralmond/NoMongo
No mongo, Mongo pulled out of test suite, too.
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‎.gitignore‎

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*~
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#*#
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.#*
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#EAEngineMongo.R#
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.Rhistory

‎ChangeLog‎

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2020-04-03 Russell Almond <ralmond@Cherry>
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* R/EAEngine.R (BNEngine): Removed netDirectory field as this
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properly belongs in PnetWarehouse.
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2020-04-01 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (newSR): Added warning when replacing a student model.
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(getSR): Added code to generate ID in the NDB case.
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2020-03-31 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (getSR): Changed this protocol so it returns null
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if the record does not exist. This way we can test for existance
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if necessary.
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(saveSR): Added function to set the _id in no database version.
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* R/EngineGears.R (getRecordForUser): Moved building new record if
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null functionality to here.
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* R/StudentRec.R (saveSR): Make sure this always returns the recrod.
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2020-03-30 Russell Almond <ralmond@Cherry>
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* R/EngineGears.R (accumulateEvidence): Changed to use the
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updateRecord function.
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* R/StudentRec.R (updeateRecord): Added this function, as it
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seemed like burrying it in accumulateEvdience was a bad idea.
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* R/EAEngine.R (fetchNextEvidence, markEvidence): Added this as a formal
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function, so we could document it more clearly.
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2020-03-29 Russell Almond <ralmond@Cherry>
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* R/EngineGears.R (updateSM): Modified so that it checks both name
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and title.
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2020-03-25 Russell Almond <ralmond@Cherry>
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* R/EngineGears.R (loadManifest): Need to assign to
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eng$warehouseObj, not eng$warehouse() as latter does not have
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assignment method.
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* R/EAEngine.R: (eng$setManifest) Killed call to warehouse() in
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setManifest method, again, circular loading pattern.
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* R/EngineGears.R (loadManifest): Added test for zero row manifest
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to avoid circular loading.
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2020-03-21 Russell Almond <ralmond@Cherry>
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* R/EAEngineNDB.R (BNEngineNDB): Changed listeners to listenerSet.
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* R/EAEngineMongo.R (BNEngineMongo): Changed listeners to
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listenerSet.
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* R/EAEngine.R: Changed protocol so that ListenerSet is created
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before engine. This allows more flexibility in configurion
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(with/without database).
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2020-03-15 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (StudentRecordSet$recorddb): Make sure that "" is
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intepreted as no database.
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2020-03-02 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (unparseHist, parseHist): killing these functions
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as they are not being used.
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(unparseStats, stats2json, parseStats): Added flattening features
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which allows for either nested, or unested JSON.
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(strsplit2, unflattenNames): Auxiliary functions used in
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flattening and unflattening stat lists.
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2020-03-01 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (parseStudentRecord): Addes some as.characters to
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get rid of excessive listiness.
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2020-02-19 Russell Almond <ralmond@Cherry>
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* R/StudentRec.R (parseStudentRecord, as.jlist): History list is
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delicate, need to protect with serialization.
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* R/EngineGears.R (configStats): saveStats is an R6 method of
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eng. This needs to be moved onto the working branch.
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2020-02-15 Russell Almond <ralmond@Cherry>
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* R/EngineGears.R: Regular functions and S4 generics and methods
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moved to this file.
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* R/EAEngineNDB.R (BNEngineNDB): No database version of the EA
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engine.
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* R/EAEngineMongo.R (BNMongoEngine): Split off Mongo-dependent
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pieces.
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* R/EAEngine.R (BNEngine): Split the main engine up into a core
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engine and the peices that use Mongo, and a Mongo-free piece for
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the DataArcade link.
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2018-08-14 Rusell Almond <ralmond@Cherry>
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* DESCRIPTION (Depends): Renamed package EABN, as this version is

‎DESCRIPTION‎

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Package: EABN
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Version: 0.5-1
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Date: 2019/11/28
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Version: 0.5-2
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Date: 2020/02/15
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Title: Evidence Accumulation Bayes Net Engine
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Author: Russell Almond
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Maintainer: Russell Almond <ralmond@fsu.edu>
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Depends: R (>= 3.0), methods, mongolite, jsonlite, Peanut (>= 0.8), Proc4 (>= 0.3), futile.logger
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Description: Extracts observables from a sequence of events.
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License: Artistic-2.0
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URL: http://pluto.coe.fsu.edu/Proc4
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Collate: Evidence.R StudentRec.R EAEngine.R EAEngineMongo.R EngineGears.R
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Collate: Evidence.R StudentRec.R EAEngine.R EAEngineMongo.R EAEngineNDB.R EngineGears.R

‎NAMESPACE‎

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importFrom("mongolite","mongo")
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importFrom("jsonlite", "toJSON", "fromJSON","base64_enc","base64_dec")
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export(StudentRecord, sm, stats, evidence, "evidence<-",
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export(StudentRecord, sm, "sm<-", stats, evidence, "evidence<-",
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statNames, histNames, stat,
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history, parseStudentRecord,parseStats,stats2json,unparseStats,
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fetchSM, unpackSM, markEvidence, getSR, saveSR, newSR,
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parseHist, unparseHist)
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exportClasses(StudentRecord)
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history, parseStudentRecord, parseStats, stats2json, unparseStats,
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fetchSM, unpackSM, updateRecord,
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StudentRecordSet, getSR, saveSR, newSR, clearSRs)
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exportClasses(StudentRecord,StudentRecordSet)
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exportMethods(evidence, "evidence<-",
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sm, stats, app, uid, context, timestamp, mess,
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as.jlist, toString, show, statNames, histNames, stat,
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exportClasses(EvidenceSet)
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exportMethods(seqno, "seqno<-")
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exportClass(BNMongoEngine)
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export(BNMongoEngine, loadManifest, setupDefaultSR,
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exportClass(BNEngine,BNEngineMongo)
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export(BNEngine,BNEngineMongo, loadManifest, setupDefaultSR,
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logEvidence, accumulateEvidence, configStats, updateStats,
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announceStats, baselineHist, updateHist, getRecordForUser,
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handleEvidence, mainLoop, updateSM)
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exportMethods(notifyListeners)
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handleEvidence, mainLoop, updateSM, fetchNextEvidence, markProcessed)
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exportMethods(notifyListeners,fetchNextEvidence,markProcessed)
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exportClass(BNSQLEngine)
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export(BNSQLEngine)
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exportClass(BNEngineNDB)
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export(BNEngineNDB)
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‎R/EAEngine.R‎

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setClassUnion("NullRecordSet",c("StudentRecordSet","NULL"))
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setClassUnion("NullListenerSet",c("ListenerSet","NULL"))
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BNEngine <-
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setRefClass("BNEngine",
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c(
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app = "character",
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session="Psession",
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srs = "NullRecordSet",
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profModel = "character",
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listenerSet="ListenerSet",
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listenerSet="NullListenerSet",
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statistics="list",
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histNodes="character",
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warehouseObj="PnetWarehouse",
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fetchStats = function() {
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stop("Abstract method.")
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},
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saveStats = function(statmat) {
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saveStats = function(stats) {
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stop("Abstract method.")
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},
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evidenceSets = function() {
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setProcessed= function (mess) {
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mess@processed <- TRUE
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saveRec(mess,evidenceSets())
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mess
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},
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setError= function (mess,e) {
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markAsError(mess,evidenceSets(),e)
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mess
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},
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fetchNextEvidence = function() {
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stop("Abstract Method")
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warehouseObj
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},
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setManifest = function(manifest) {
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warehouse() # Initialize Warehouse
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WarehouseManifest(warehouseObj) <<- manifest
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if (nrow(manifest) > 0L) {
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## warehouse() # Warehouse is now pre-installed.
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WarehouseManifest(warehouseObj) <<- manifest
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}
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},
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fetchManifest = function() {
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stop("Abstract method.")
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},
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saveManifest = function(manifest) {
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saveManifest = function(manif) {
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stop("Abstract method.")
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},
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isActivated = function() {
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## key="Name")
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BNEngine <- function(app="default",warehouse,listeners=list(),
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username="",password="",host="localhost",
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port="",dbname="EARecords",processN=Inf,
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P4dbname="Proc4", waittime=.25, profModel=character(),
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BNEngine <- function(app="default",session,listenerSet=NULL,
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waittime=.25, profModel=character(),
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...) {
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stop("BNEngine now abstract, use BNMongoEngine or BNSQLEngine.")
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}
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## Listener notification.
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setMethod("notifyListeners","BNEngine",
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function(sender,mess) {
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sender$listenerSet$notifyListeners(mess)
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if (!is.null(sender$listenerSet))
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sender$listenerSet$notifyListeners(mess)
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})
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setGeneric("fetchNextEvidence",
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function (eng) standardGeneric("fetchNextEvidence"))
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setMethod("fetchNextEvidence","BNEngine",
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function(eng) eng$fetchNextEvidence())
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setGeneric("markProcessed",
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function(eng,eve) standardGeneric("markProcessed"))
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setMethod("markProcessed","BNEngine",
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function(eng,eve) eng$setProcessed(eve))
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