diff --git a/cfg/ALog.properties b/cfg/ALog.properties new file mode 100644 index 0000000..6c46474 --- /dev/null +++ b/cfg/ALog.properties @@ -0,0 +1,25 @@ +#### Use two appenders, one to log to console, another to log to a file +log4j.rootCategory= R + +#### Second appender writes to a file +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Threshold=trace +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n + +log4j.logger.AnalysisLogger=R, stdout +log4j.appender.R=org.apache.log4j.RollingFileAppender +log4j.appender.R.Threshold=trace +log4j.appender.R.File=./Analysis.log +log4j.appender.R.MaxFileSize=50000KB +log4j.appender.R.MaxBackupIndex=2 +log4j.appender.R.layout=org.apache.log4j.PatternLayout +log4j.appender.R.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n + +#### Third appender writes to a file +log4j.logger.org.hibernate=H +log4j.appender.H=org.apache.log4j.AsyncAppender +log4j.appender.H.Threshold=OFF +log4j.appender.H.layout=org.apache.log4j.PatternLayout +log4j.appender.H.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n + diff --git a/cfg/DestinationDBHibernate.cfg.xml b/cfg/DestinationDBHibernate.cfg.xml new file mode 100644 index 0000000..61a9ac8 --- /dev/null +++ b/cfg/DestinationDBHibernate.cfg.xml @@ -0,0 +1,18 @@ + + + + org.postgresql.Driver + org.hibernate.connection.C3P0ConnectionProvider + jdbc:postgresql://localhost/testdb + gcube + d4science2 + + org.hibernate.dialect.PostgreSQLDialect + org.hibernate.transaction.JDBCTransactionFactory + 0 + 1 + 0 + 1 + thread + + \ No newline at end of file diff --git a/cfg/algorithms.properties b/cfg/algorithms.properties new file mode 100644 index 0000000..9fcf228 --- /dev/null +++ b/cfg/algorithms.properties @@ -0,0 +1,7 @@ +AQUAMAPS_SUITABLE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable +AQUAMAPS_NATIVE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative +AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative2050 +AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable2050 +AQUAMAPS_NATIVE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNN +AQUAMAPS_SUITABLE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNNSuitable +FEED_FORWARD_A_N_N_DISTRIBUTION=org.gcube.dataanalysis.ecoengine.spatialdistributions.FeedForwardNeuralNetworkDistribution \ No newline at end of file diff --git a/cfg/clusterers.properties b/cfg/clusterers.properties new file mode 100644 index 0000000..c2801e9 --- /dev/null +++ b/cfg/clusterers.properties @@ -0,0 +1,3 @@ +DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan +KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans +XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper \ No newline at end of file diff --git a/cfg/evaluators.properties b/cfg/evaluators.properties new file mode 100644 index 0000000..9d7a554 --- /dev/null +++ b/cfg/evaluators.properties @@ -0,0 +1,4 @@ +MAPS_COMPARISON=org.gcube.dataanalysis.geo.algorithms.MapsComparator +DISCREPANCY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis +QUALITY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DistributionQualityAnalysis +HRS=org.gcube.dataanalysis.ecoengine.evaluation.HabitatRepresentativeness \ No newline at end of file diff --git a/cfg/generators.properties b/cfg/generators.properties new file mode 100644 index 0000000..90eaa34 --- /dev/null +++ b/cfg/generators.properties @@ -0,0 +1,3 @@ +LOCAL_WITH_DATABASE=org.gcube.dataanalysis.ecoengine.processing.LocalSplitGenerator +SIMPLE_LOCAL=org.gcube.dataanalysis.ecoengine.processing.LocalSimpleSplitGenerator +D4SCIENCE=org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing diff --git a/cfg/modelers.properties b/cfg/modelers.properties new file mode 100644 index 0000000..d5c652e --- /dev/null +++ b/cfg/modelers.properties @@ -0,0 +1 @@ +HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler \ No newline at end of file diff --git a/cfg/models.properties b/cfg/models.properties new file mode 100644 index 0000000..479b406 --- /dev/null +++ b/cfg/models.properties @@ -0,0 +1,4 @@ +HSPEN=org.gcube.dataanalysis.ecoengine.models.ModelHSPEN +AQUAMAPSNN=org.gcube.dataanalysis.ecoengine.models.ModelAquamapsNN +FEED_FORWARD_ANN=org.gcube.dataanalysis.ecoengine.models.FeedForwardNN +FEED_FORWARD_ANN_FILE=org.gcube.dataanalysis.ecoengine.models.testing.FeedForwardNNFile \ No newline at end of file diff --git a/cfg/nodealgorithms.properties b/cfg/nodealgorithms.properties new file mode 100644 index 0000000..6e43c89 --- /dev/null +++ b/cfg/nodealgorithms.properties @@ -0,0 +1,7 @@ +AQUAMAPS_SUITABLE=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitableNode +AQUAMAPS_NATIVE=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNativeNode +AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsNative2050Node +AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.executor.nodes.algorithms.AquamapsSuitable2050Node +OCCURRENCES_MERGER=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode +OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceIntersectionNode +OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceSubtractionNode \ No newline at end of file diff --git a/cfg/operators.xml b/cfg/operators.xml new file mode 100644 index 0000000..93b465c --- /dev/null +++ b/cfg/operators.xml @@ -0,0 +1,2620 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/cfg/transducerers.properties b/cfg/transducerers.properties new file mode 100644 index 0000000..9a89163 --- /dev/null +++ b/cfg/transducerers.properties @@ -0,0 +1,14 @@ +ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution +BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTransducer +BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer +BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer +HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer +HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter +HSPEN_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HspenFilter +OCCURRENCES_MERGER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger +OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsIntersector +OCCURRENCES_MARINE_TERRESTRIAL=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth +OCCURRENCES_DUPLICATES_DELETER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsDuplicatesDeleter +OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsSubtraction +PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints +FIN_TAXA_MATCH=org.gcube.dataanalysis.fin.taxamatch.TaxaMatchTransducer \ No newline at end of file diff --git a/cfg/userperspective.properties b/cfg/userperspective.properties new file mode 100644 index 0000000..d015260 --- /dev/null +++ b/cfg/userperspective.properties @@ -0,0 +1,13 @@ +ANOMALIES_DETECTION=DBSCAN,KMEANS,XMEANS +CLASSIFICATION=FEED_FORWARD_A_N_N_DISTRIBUTION +CLIMATE=BIOCLIMATE_HSPEC,BIOCLIMATE_HCAF,BIOCLIMATE_HSPEN,HCAF_INTERPOLATION +CORRELATION_ANALYSIS=HRS +DATA_CLUSTERING=DBSCAN,KMEANS,XMEANS +FILTERING=HCAF_FILTER,HSPEN_FILTER +FUNCTION_SIMULATION=FEED_FORWARD_A_N_N_DISTRIBUTION +OCCURRENCES=ABSENCE_CELLS_FROM_AQUAMAPS,PRESENCE_CELLS_GENERATION,OCCURRENCES_MERGER,OCCURRENCES_INTERSECTOR,OCCURRENCES_MARINE_TERRESTRIAL,OCCURRENCES_DUPLICATES_DELETER,OCCURRENCES_SUBTRACTION +PERFORMANCES_EVALUATION=QUALITY_ANALYSIS,DISCREPANCY_ANALYSIS +SPECIES_SIMULATION=AQUAMAPS_SUITABLE,AQUAMAPS_NATIVE,AQUAMAPS_NATIVE_2050,AQUAMAPS_SUITABLE_2050,AQUAMAPS_NATIVE_NEURALNETWORK,AQUAMAPS_SUITABLE_NEURALNETWORK +TRAINING=HSPEN,AQUAMAPSNN,FEED_FORWARD_ANN +TIME_SERIES=HCAF_INTERPOLATION +TAXA=FIN_TAXA_MATCH \ No newline at end of file