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dataminer: New workarounds to fix some broken behaviour.

This commit is contained in:
Andrea Dell'Amico 2017-09-19 14:44:35 +02:00
parent c0864e4e43
commit 7f91b5f36a
12 changed files with 309 additions and 1 deletions
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12
smartgears/dataminer_app/defaults/main.yml
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@ -34,3 +34,15 @@ dataminer_data_file_from_thredds: 'http://thredds.d4science.org/thredds/fileServ
# dev, prod, preprod
dataminer_infra_reference: dev
dataminer_properties_files:
- algorithms.properties
- clusterers.properties
- dynamictransducerers.properties
- evaluators.properties
- generators.properties
- modelers.properties
- models.properties
- nodealgorithms.properties
- transducerers.properties
- userperspective.properties

17
smartgears/dataminer_app/files/algorithms.properties Normal file
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@ -0,0 +1,17 @@
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
LWR=org.gcube.dataanalysis.executor.nodes.algorithms.LWR
BIONYM_BIODIV=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv
BIONYM=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer
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
CMSY=org.gcube.dataanalysis.executor.nodes.algorithms.CMSY
FAOMSY=org.gcube.dataanalysis.executor.nodes.algorithms.FAOMSY
ICCAT_VPA=org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA
FEED_FORWARD_NEURAL_NETWORK_CLOUD_REGRESSOR=org.gcube.data.analysis.algorithms.neuralnetworks.feedforward.FeedForwardNeuralNetworkCloudRegressor

4
smartgears/dataminer_app/files/clusterers.properties Normal file
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@ -0,0 +1,4 @@
DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan
LOF=org.gcube.dataanalysis.ecoengine.clustering.LOF
KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans
XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper

1
smartgears/dataminer_app/files/dynamictransducerers.properties Normal file
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@ -0,0 +1 @@
#org.gcube.dataanalysis.geo.wps.factory.DynamicWPSTransducerer

4
smartgears/dataminer_app/files/evaluators.properties Normal file
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@ -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

3
smartgears/dataminer_app/files/generators.properties Normal file
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@ -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

1
smartgears/dataminer_app/files/modelers.properties Normal file
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@ -0,0 +1 @@
HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler

3
smartgears/dataminer_app/files/models.properties Normal file
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@ -0,0 +1,3 @@
HSPEN=org.gcube.dataanalysis.ecoengine.models.ModelHSPEN
AQUAMAPSNN=org.gcube.dataanalysis.ecoengine.models.ModelAquamapsNN
FEED_FORWARD_ANN=org.gcube.dataanalysis.ecoengine.models.FeedForwardNN

16
smartgears/dataminer_app/files/nodealgorithms.properties Normal file
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@ -0,0 +1,16 @@
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
LWR=org.gcube.dataanalysis.executor.nodes.algorithms.LWR
BIONYM_BIODIV=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymBiodiv
BIONYM=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer
CMSY=org.gcube.dataanalysis.executor.nodes.algorithms.CMSY
FAOMSY=org.gcube.dataanalysis.executor.nodes.algorithms.FAOMSY
ICCAT_VPA=org.gcube.dataanalysis.executor.nodes.algorithms.ICCATVPA
FEED_FORWARD_NEURAL_NETWORK_CLOUD_REGRESSOR=org.gcube.data.analysis.algorithms.neuralnetworks.feedforward.FeedForwardNeuralNetworkCloudRegressor
AQUAMAPS_NATIVE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNN
AQUAMAPS_SUITABLE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNNSuitable

185
smartgears/dataminer_app/files/transducerers.properties Normal file
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@ -0,0 +1,185 @@
HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter
ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution
BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer
BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTransducer
BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer
BIONYM_LOCAL=org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer
OCCURRENCES_DUPLICATES_DELETER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsDuplicatesDeleter
OCCURRENCES_MARINE_TERRESTRIAL=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth
HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer
PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints
MOST_OBSERVED_SPECIES=org.gcube.dataanalysis.trendylyzeralgorithms.AbsoluteSpeciesBarChartsAlgorithm
MOST_OBSERVED_TAXA=org.gcube.dataanalysis.trendylyzeralgorithms.TaxaObservationsBarChartAlgorithm
SPECIES_OBSERVATIONS_PER_AREA=org.gcube.dataanalysis.trendylyzeralgorithms.SpeciesObservationsAreaBarChart
SPECIES_OBSERVATIONS_TREND_PER_YEAR=org.gcube.dataanalysis.trendylyzeralgorithms.SpeciesObservationsPerYear
SPECIES_OBSERVATION_LME_AREA_PER_YEAR=org.gcube.dataanalysis.trendylyzeralgorithms.SpeciesObservationsPerLMEAreaPerYearLineChart
SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR=org.gcube.dataanalysis.trendylyzeralgorithms.SpeciesObservationsPerMEOWAreaPerYearLineChart
TAXONOMY_OBSERVATIONS_TREND_PER_YEAR=org.gcube.dataanalysis.trendylyzeralgorithms.TaxaObservationsPerYearLineChart
GETTABLEDETAILS=org.gcube.dataaccess.algorithms.drmalgorithms.GetTableDetails
LISTDBINFO=org.gcube.dataaccess.algorithms.drmalgorithms.ListDBInfo
LISTDBNAMES=org.gcube.dataaccess.algorithms.drmalgorithms.ListNames
LISTDBSCHEMA=org.gcube.dataaccess.algorithms.drmalgorithms.ListSchemas
LISTTABLES=org.gcube.dataaccess.algorithms.drmalgorithms.ListTables
RANDOMSAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.RandomSampleOnTable
SAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.SampleOnTable
SMARTSAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.SmartSampleOnTable
SUBMITQUERY=org.gcube.dataaccess.algorithms.drmalgorithms.SubmitQuery
XYEXTRACTOR=org.gcube.dataanalysis.geo.algorithms.XYExtraction
XYEXTRACTOR_TABLE=org.gcube.dataanalysis.geo.algorithms.XYExtractionTable
ZEXTRACTION=org.gcube.dataanalysis.geo.algorithms.ZExtraction
ZEXTRACTION_TABLE=org.gcube.dataanalysis.geo.algorithms.ZExtractionTable
TIMEEXTRACTION=org.gcube.dataanalysis.geo.algorithms.TimeExtraction
TIMEEXTRACTION_TABLE=org.gcube.dataanalysis.geo.algorithms.TimeExtractionTable
TIME_GEO_CHART=org.gcube.dataanalysis.geo.algorithms.TimeGeoChartProducer
TIME_SERIES_ANALYSIS=org.gcube.dataanalysis.ecoengine.transducers.TimeSeriesAnalysis
TIME_SERIES_CHARTS=org.gcube.dataanalysis.ecoengine.transducers.charts.TimeSeriesChartsTransducerer
KNITR_COMPILER=org.gcube.dataanalysis.executor.rscripts.KnitrCompiler
SGVM_INTERPOLATION=org.gcube.dataanalysis.executor.rscripts.SGVMS_Interpolation
MAX_ENT_NICHE_MODELLING=org.gcube.dataanalysis.geo.algorithms.MaxEnt4NicheModellingTransducer
SEADATANET_INTERPOLATOR=org.gcube.dataanalysis.seadatanet.SeaDataNetConnector
RASTER_DATA_PUBLISHER=org.gcube.dataanalysis.geo.algorithms.RasterDataPublisher
GEO_CHART=org.gcube.dataanalysis.geo.algorithms.StaticGeoChartProducer
ESRI_GRID_EXTRACTION=org.gcube.dataanalysis.geo.algorithms.ESRIGRIDExtraction
OCCURRENCE_ENRICHMENT=org.gcube.dataanalysis.geo.algorithms.OccurrenceEnrichment
POLYGONS_TO_MAP=org.gcube.dataanalysis.geo.algorithms.PolygonMapsCreator
SPECIES_MAP_FROM_CSQUARES=org.gcube.dataanalysis.geo.algorithms.SpeciesDistributionsMapsCreatorFromCsquares
SPECIES_MAP_FROM_POINTS=org.gcube.dataanalysis.geo.algorithms.SpeciesDistributionsMapsCreatorFromPoints
GENERIC_CHARTS=org.gcube.dataanalysis.ecoengine.transducers.charts.QuantitiesAttributesChartsTransducerer
POINTS_TO_MAP=org.gcube.dataanalysis.geo.algorithms.PointsMapsCreator
CSQUARES_TO_COORDINATES=org.gcube.dataanalysis.geo.vti.CSquare2Coordinates
CSQUARE_COLUMN_CREATOR=org.gcube.dataanalysis.geo.algorithms.CSquaresCreator
FAO_OCEAN_AREA_COLUMN_CREATOR=org.gcube.dataanalysis.geo.algorithms.FAOOceanAreaCreator
FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT=org.gcube.dataanalysis.geo.algorithms.FAOOceanAreaCreatorQuadrant
GRID_CWP_TO_COORDINATES=org.gcube.dataanalysis.geo.vti.GridCWP2Coordinates
EGIP_ENERGY_AGGREGATED_DISTRIBUTION=org.gcube.dataanalysis.geothermal.EnergyHistogramAggregated
EGIP_ENERGY_COUNTRY_DISTRIBUTION=org.gcube.dataanalysis.geothermal.EnergyHistogramPerCountry
EGIP_ENERGY_TRENDS=org.gcube.dataanalysis.geothermal.EnergyTrends
EGIP_ENERGY_YEAR_DISTRIBUTION=org.gcube.dataanalysis.geothermal.EnergyHistogramPerYear
ESTIMATE_FISHING_ACTIVITY=org.gcube.dataanalysis.geo.vti.EstimateFishingActivity
ESTIMATE_MONTHLY_FISHING_EFFORT=org.gcube.dataanalysis.geo.vti.EstimateMonthlyFishingEffort
WEB_APP_PUBLISHER=org.gcube.dataanalysis.executor.nodes.transducers.WebApplicationPublisher
SHAPEFILE_PUBLISHER=org.gcube.dataanalysis.geo.algorithms.ShapefilePublisher
GENERIC_WORKER=org.gcube.dataanalysis.executor.job.management.GenericWorker
ABSENCE_GENERATION_FROM_OBIS=org.gcube.dataanalysis.executor.rscripts.AbsencegenerationfromOBIS
ECOPATH_WITH_ECOSIM=org.gcube.dataanalysis.ewe.SimpleEwE
ENSEMBLE_MODEL=org.gcube.dataanalysis.ensemble.EnsembleAlgorithm
ICHTHYOP_MODEL_ONE_BY_ONE=org.gcube.dataanalysis.executor.rscripts.Ichthyopmodelonebyone
STEP_3___VPA_ICCAT_BFT_E_PROJECTION=org.gcube.dataanalysis.executor.rscripts.STEP3VPAICCATBFTEProjection
CCAMLR_EXPORTER_TOOL=org.gcube.dataanalysis.executor.rscripts.CCAMLRExporterTool
STEP_2__VPA_ICCAT_BFT_E_VISUALISATION=org.gcube.dataanalysis.executor.rscripts.STEP2VPAICCATBFTEVISUALISATION
ICHTHYOP_MODEL_MULTIPLE_RUNS=org.gcube.dataanalysis.executor.rscripts.Ichthyopmodelmultipleruns
PARALLELIZED_STEP1_VPA_ICCAT_BFT_E_RETROS=org.gcube.dataanalysis.executor.rscripts.parallelizedSTEP1VPAICCATBFTERetros
STEP_4_VPA_ICCAT_BFT_E_REPORT=org.gcube.dataanalysis.executor.rscripts.Step4VpaIccatBftEReport
TUNA_ATLAS_DATA_ACCESS=org.gcube.dataanalysis.executor.rscripts.TunaAtlasDataAccess
FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED=org.fao.fi.dataanalysis.spread.SpatialReallocationSimplifiedAlgorithm
FIGIS_SPATIAL_REALLOCATION_GENERIC=org.fao.fi.dataanalysis.spread.SpatialReallocationGenericAlgorithm
FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED_TABLE=org.fao.fi.dataanalysis.spread.SpatialReallocationSimplifiedTableAlgorithm
FIGIS_SDMX_DATA_CONVERTER=org.fao.fi.dataanalysis.stats.SDMXDataConverter
CATCHES_BY_SPECIES=org.gcube.dataanalysis.executor.rscripts.Catchesbyspecies
CATCHES_BY_FLAGS=org.gcube.dataanalysis.executor.rscripts.Catchesbyflags
MAKE_ICHTHYOP_NETCDF_CF_COMPLIANT=org.gcube.dataanalysis.executor.rscripts.MakeichthyopnetCDFCFcompliant
ICHTHYOP_NETCDF_OUTPUT_TO_SHAPEFILE=org.gcube.dataanalysis.executor.rscripts.IchthyopnetCDFoutputtoshapefile
GENETICALGORITHM=org.gcube.dataanalysis.executor.rscripts.GeneticAlgorithm
GLOBAL_CATCHES=org.gcube.dataanalysis.executor.rscripts.Globalcatches
MPA_INTERSECT_V2=org.gcube.dataanalysis.executor.rscripts.MPAIntersectv2
QUICK_RANK_TRAIN=it.cnr.isti.hpc.quickrank.qrtrain.QuickRankTrain
QUICK_RANK_TRAIN_NO_VALIDATION=it.cnr.isti.hpc.quickrank.qrtrainnovalid.QuickRankTrainNoValidation
QUICK_RANK_TEST=it.cnr.isti.hpc.quickrank.qrtest.QuickRankTest
STAT_VAL=org.gcube.dataanalysis.executor.rscripts.statval
TUNA_ATLAS_INDICATOR_1__SPECIES_BY_OCEAN_=org.gcube.dataanalysis.executor.rscripts.TunaAtlasIndicator1SpeciesByOcean
SIMULFISHKPIS=org.gcube.dataanalysis.executor.rscripts.SimulFishKPIs
READWFS=org.gcube.dataanalysis.executor.rscripts.ReadWFS
PROJECTIONS_REPORT_VPA_ICCAT_BFT_E=org.gcube.dataanalysis.executor.rscripts.ProjectionsreportVPAICCATBFTE
WHOLE_STEPS_VPA_ICCAT_BFT_E=org.gcube.dataanalysis.executor.rscripts.WholeStepsVPAICCATBFTE
CATCHES_BY_TYPE_OF_SCHOOL=org.gcube.dataanalysis.executor.rscripts.Catchesbytypeofschool
CATCHES_BY_GEAR_SIMPLIFIED_VERSION=org.gcube.dataanalysis.executor.rscripts.Catchesbygearsimplifiedversion
CATCHES_BY_FLAGS_SIMPLIFIED_VERSION=org.gcube.dataanalysis.executor.rscripts.Catchesbyflagssimplifiedversion
CATCHES_BY_SPECIES_SIMPLIFIED_VERSION=org.gcube.dataanalysis.executor.rscripts.Catchesbyspeciessimplifiedversion
CATCHES_BY_GEARS=org.gcube.dataanalysis.executor.rscripts.Catchesbygears
COMPUTE_FISHERIES_INDICATORS_FROM_OWN_FORMATTED_DATASET=org.gcube.dataanalysis.executor.rscripts.Computefisheriesindicatorsfromownformatteddataset
IMPORT_FISHERIES_FORMATTED_DATASET___QUICK_IMPORT=org.gcube.dataanalysis.executor.rscripts.ImportFisheriesFormattedDatasetQuickimport
CATCHES_AGGREGATED_FOLLOWING_A_SELECT_VARIABLE=org.gcube.dataanalysis.executor.rscripts.Catchesaggregatedfollowingaselectvariable
WTG=org.gcube.dataanalysis.executor.rscripts.WTG
FEED_FORWARD_NEURAL_NETWORK_TRAINER=org.gcube.data.analysis.algorithms.neuralnetworks.feedforward.FeedForwardNeuralNetworkTrainer
NCOUTPUTS2CSV_VPA_ICCAT_BFT_E=org.gcube.dataanalysis.executor.rscripts.ncOutputs2csvVPAICCATBFTE
FEED_FORWARD_NEURAL_NETWORK_REGRESSOR=org.gcube.data.analysis.algorithms.neuralnetworks.feedforward.FeedForwardNeuralNetworkRegressor
CMSY_2=org.gcube.dataanalysis.executor.rscripts.CMSY2
CATCHES_INDICATORS_IOTC_REST_SERVICES=org.gcube.dataanalysis.executor.rscripts.catchesindicatorsiotcrestservices
STAT_VAL_UNIPARTITE_NET=org.gcube.dataanalysis.executor.rscripts.STATVALUNIPARTITENET
GEOGRSF_INTERSECTS=org.gcube.dataanalysis.executor.rscripts.GeoGRSFIntersects
TESTING_ALGORITHM=org.gcube.dataanalysis.executor.rscripts.TestingAlgorithm
SPATIAL_DISTRIBUTION_OF_CORRELATION=org.gcube.dataanalysis.executor.rscripts.SPATIALDISTRIBUTIONOFCORRELATION
KAPPA_COEFFICIENT=org.gcube.data.analysis.algorithms.kstatistics.KStatistics
TRANSFORM_IOTC_CATCH_AND_EFFORT_DSD_CECOASTAL_AND_CESURFACE=org.gcube.dataanalysis.executor.rscripts.TransformIOTCCatchandeffortDSDCECoastalandCESurface
LOAD_CATCHES_DATASET_IN_SARDARA=org.gcube.dataanalysis.executor.rscripts.Loadcatchesdatasetinsardara
LOAD_EFFORTS_DATASET_IN_SARDARA=org.gcube.dataanalysis.executor.rscripts.Loadeffortsdatasetinsardara
SCATTERPLOT_DIAGRAM=org.gcube.dataanalysis.executor.rscripts.SCATTERPLOTDIAGRAM
SPATIAL_DENSITY_DISTRIBUTION=org.gcube.dataanalysis.executor.rscripts.SPATIALDENSITYDISTRIBUTION
GEOGRSF_BBOXLIST=org.gcube.dataanalysis.executor.rscripts.GeoGRSFBboxlist
SHAPEFILE_IMPORTER=org.gcube.data.analysis.algorithms.shapefileimporter.ShapefileImporter
MATLAS_OPTICS_CLUSTERING=it.cnr.isti.kdd.matlas.optics.Optics
MATLAS_TRAJECTORY_BUILDER=it.cnr.isti.kdd.matlas.trajectoryBuilder.TrajectoryBuilder
ENGLISH_NAMED_ENTITY_RECOGNIZER=org.gcube.data.analysis.algorithms.samplepipeline.SamplePipeline
TWITTER_MONITOR=it.cnr.iit.wafi.gcube.twmon.sched.TwMonScheduler
ENGLISH_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline01
ENGLISH_NAMED_ENTITY_RECOGNIZER=org.gcube.data.analysis.algorithms.samplepipeline.AbstractPipeline
GERMAN_NAMED_ENTITY_RECOGNIZER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline02
LANGUAGE_IDENTIFICATION_FOR_TWEETS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline03
ENGLISH_TWEET_TOKENIZER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline04
FRENCH_NAMED_ENTITY_RECOGNIZER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline05
PART_OF_SPEECH_TAGGER_FOR_TWEETS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline06
CYMRIE_WELSH_NAMED_ENTITY_RECOGNIZER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline07
FRENCH_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline08
GERMAN_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline09
ENGLISH_PART_OF_SPEECH_AND_MORPHOLOGY_ANAYLIZER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline10
NOUN_PHRASE_CHUNKER=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline11
MEASUREMENT_EXPRESSION_ANNOTATOR=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline12
ANNIE_PLUS_MEASUREMENTS=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline13
GENERIC_OPINION_MINING_ENGLISH=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline14
DECARBONET_ENVIRONMENTAL_ANNOTATOR=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline15
DECARBONET_GERMAN_ENVIRONMENTAL_ANNOTATOR=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline16
TWITTER_OPINION_MINING_ENGLISH=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline17
THE_BREXIT_ANALYZER_PIPELINE=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline18
SUMMA_TEXT_SUMMARIZATION_EN=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline19
SUMMA_TEXT_SUMMARIZATION_ES=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline20
OPEN_NLP_ENGLISH_PIPELINE=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline21
OPEN_NLP_GERMAN_PIPELINE=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline22
OPEN_NLP_DUTCH_PIPELINE=org.gcube.data.analysis.algorithms.samplepipeline.Pipeline23
SMOOTH_SCATTERPLOT_DIAGRAM=org.gcube.dataanalysis.executor.rscripts.SMOOTHSCATTERPLOTDIAGRAM
ENRICHMENT_FROM_NETCDF=org.gcube.dataanalysis.executor.rscripts.EnrichmentFromNetcdf
CREATE_YOUR_OWN_VERSION_OF_THE_TUNA_ATLAS=org.gcube.dataanalysis.executor.rscripts.CreateyourownversionoftheTunaAtlas
LOAD_A_DATASET_IN_SARDARA_DATABASE=org.gcube.dataanalysis.executor.rscripts.LoadadatasetinSardaraDatabase
SAMPLE_KNIME_WORKFLOW=org.gcube.dataanalysis.executor.rscripts.SampleKnimeWorkflow
KNIME_WORKSPACE_FILE_UPLOADER=org.gcube.dataanalysis.executor.rscripts.KnimeWorkspaceFileUploader
MAXANDSAM_NETWORK_RECONTRUCTION_METHOD=org.gcube.dataanalysis.executor.rscripts.MaxAndSamNetworkRecontructionMethod
DEBTRANK_SYSTEMIC_RISK_ESTIMATION=org.gcube.dataanalysis.executor.rscripts.DebtRankSystemicRiskEstimation
TRANSFORM_CCSBT_TASK2_LONGLINE=org.gcube.dataanalysis.executor.rscripts.TransformCCSBTtask2Longline
PROJECT_SIMULFISHKPIS_DEV=org.gcube.dataanalysis.executor.rscripts.ProjectSimulFishKPIsDEV
AAPS_STAGING_PUBLISHER=org.gcube.dataanalysis.executor.rscripts.AAPSstagingpublisher
STEP_1___VPA_ICCAT_BFT_E_RETROS_ONERUN=org.gcube.dataanalysis.executor.rscripts.STEP1VPAICCATBFTERetrosOneRun
R_SAMPLE=org.gcube.dataanalysis.executor.rscripts.RSAMPLE
STANBOL_WRAPPER=org.gcube.data.analysis.algorithms.stanbolwrapper.StanbolWrapper
AAPS_NASO_PUBLISHER=org.gcube.dataanalysis.executor.rscripts.AAPSnasopublisher
GEOGRAPHIC_PROXIMITY_TOOL=org.gcube.dataanalysis.executor.rscripts.GeographicProximityTool
SCUBE=it.di.unipi.kdd.segregation.scube.SCubeGui
GEOGRSF_INTERSECTS_BATCH=org.gcube.dataanalysis.executor.rscripts.GeoGRSFIntersectsBatch
CSV_TO_NETCDF_CONVERTER_XY=org.gcube.data.analysis.algorithms.csvtonetcdfconverter.CsvToNetcdfConverterWrapperXY
CSV_TO_NETCDF_CONVERTER_XYZ=org.gcube.data.analysis.algorithms.csvtonetcdfconverter.CsvToNetcdfConverterWrapperXYZ
CSV_TO_NETCDF_CONVERTER_XYT=org.gcube.data.analysis.algorithms.csvtonetcdfconverter.CsvToNetcdfConverterWrapperXYT
CSV_TO_NETCDF_CONVERTER_XYZT=org.gcube.data.analysis.algorithms.csvtonetcdfconverter.CsvToNetcdfConverterWrapperXYZT
STEP_1___VPA_ICCAT_BFT_E_RETROS=org.gcube.dataanalysis.executor.rscripts.STEP1VPAICCATBFTERETROS
AAPS_PUBLIC_PUBLISHER=org.gcube.dataanalysis.executor.rscripts.AAPSpublicpublisher
SIMULFISHKPIS_PRE=org.gcube.dataanalysis.executor.rscripts.SIMULFISHKPISPRE
CSV_TO_NETCDF_CONVERTER_DIMCHAR=org.gcube.data.analysis.algorithms.csvtonetcdfconverter.CsvToNetcdfConverterWrapperDimChar
MPASINTERSECTIONANALYSIS=org.gcube.dataanalysis.executor.rscripts.MPAsIntersectionAnalysis
VSURF=org.gcube.dataanalysis.executor.rscripts.VSURF
TRAIN=org.gcube.dataanalysis.executor.rscripts.train
MPA_INTERSECT_V3=org.gcube.dataanalysis.executor.rscripts.MpaIntersectV3
SUPPORT_VECTOR_MACHINE_TRAINER=org.gcube.data.analysis.algorithms.supportvectormachine.SupportVectorMachine
MPA_INTERSECT_V3_2=org.gcube.dataanalysis.executor.rscripts.MpaIntersectV32
SUPPORT_VECTOR_MACHINE_TRAINER=org.gcube.data.analysis.algorithms.supportvectormachine.SupportVectorMachineTrainer
SUPPORT_VECTOR_MACHINE_REGRESSOR=org.gcube.data.analysis.algorithms.supportvectormachine.SupportVectorMachineRegressor
WEBTG_V2=org.gcube.dataanalysis.executor.rscripts.WebTGV2
CMSY_FOR_DLM_TOOL=org.gcube.dataanalysis.executor.rscripts.CMSYFORDLMTOOL
TEST_SAI_WS_INTERACTION=org.gcube.dataanalysis.executor.rscripts.TESTSAIWSINTERACTION
GEO_INTERPOLATION=org.gcube.dataanalysis.seadatanet.SeaDataNetConnector_AutoCorrelation

46
smartgears/dataminer_app/files/userperspective.properties Normal file
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@ -0,0 +1,46 @@
FILTERING=HCAF_FILTER
OCCURRENCES=OCCURRENCES_SUBTRACTION,OCCURRENCES_MERGER,OCCURRENCES_INTERSECTOR,ABSENCE_CELLS_FROM_AQUAMAPS,OCCURRENCES_DUPLICATES_DELETER,OCCURRENCES_MARINE_TERRESTRIAL,PRESENCE_CELLS_GENERATION,ABSENCE_GENERATION_FROM_OBIS
CLIMATE=BIOCLIMATE_HCAF,BIOCLIMATE_HSPEC,BIOCLIMATE_HSPEN
TAXA=BIONYM_LOCAL,BIONYM,BIONYM_BIODIV
TIME_SERIES=HCAF_INTERPOLATION,TIME_SERIES_ANALYSIS
OBIS_OBSERVATIONS_SPECIES_DATA=MOST_OBSERVED_SPECIES,MOST_OBSERVED_TAXA,SPECIES_OBSERVATIONS_PER_AREA
OBIS_OBSERVATIONS_TRENDS=SPECIES_OBSERVATIONS_TREND_PER_YEAR,SPECIES_OBSERVATION_LME_AREA_PER_YEAR,SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR,TAXONOMY_OBSERVATIONS_TREND_PER_YEAR
DATABASES=GETTABLEDETAILS,LISTDBINFO,LISTDBNAMES,LISTDBSCHEMA,LISTTABLES,RANDOMSAMPLEONTABLE,SAMPLEONTABLE,SMARTSAMPLEONTABLE,SUBMITQUERY
GEO_PROCESSING=XYEXTRACTOR,XYEXTRACTOR_TABLE,ZEXTRACTION,ZEXTRACTION_TABLE,TIMEEXTRACTION,TIMEEXTRACTION_TABLE,SEADATANET_INTERPOLATOR,ESRI_GRID_EXTRACTION,OCCURRENCE_ENRICHMENT,CSQUARES_TO_COORDINATES,CSQUARE_COLUMN_CREATOR,FAO_OCEAN_AREA_COLUMN_CREATOR,FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT,GRID_CWP_TO_COORDINATES,CSV_TO_NETCDF_CONVERTER_XY,CSV_TO_NETCDF_CONVERTER_XYZ,CSV_TO_NETCDF_CONVERTER_XYT,CSV_TO_NETCDF_CONVERTER_XYZT,CSV_TO_NETCDF_CONVERTER_DIMCHAR,GEO_INTERPOLATION
CHARTS=TIME_GEO_CHART,TIME_SERIES_CHARTS,GEO_CHART,GENERIC_CHARTS
STOCK_ASSESSMENT=KNITR_COMPILER,ECOPATH_WITH_ECOSIM,ENSEMBLE_MODEL,CCAMLR_EXPORTER_TOOL,CMSY_2,CMSY_FOR_DLM_TOOL
VESSELS=SGVM_INTERPOLATION,ESTIMATE_FISHING_ACTIVITY,ESTIMATE_MONTHLY_FISHING_EFFORT
BAYESIAN_METHODS=MAX_ENT_NICHE_MODELLING,LWR,CMSY,FAOMSY,FEED_FORWARD_A_N_N_DISTRIBUTION,FEED_FORWARD_NEURAL_NETWORK_TRAINER,FEED_FORWARD_NEURAL_NETWORK_REGRESSOR,FEED_FORWARD_NEURAL_NETWORK_CLOUD_REGRESSOR
PUBLISHING=RASTER_DATA_PUBLISHER,WEB_APP_PUBLISHER,SHAPEFILE_PUBLISHER,SHAPEFILE_IMPORTER
MAPS=POLYGONS_TO_MAP,SPECIES_MAP_FROM_CSQUARES,SPECIES_MAP_FROM_POINTS,POINTS_TO_MAP,MAPS_COMPARISON
EGIP=EGIP_ENERGY_AGGREGATED_DISTRIBUTION,EGIP_ENERGY_COUNTRY_DISTRIBUTION,EGIP_ENERGY_TRENDS,EGIP_ENERGY_YEAR_DISTRIBUTION
CORRELATION_ANALYSIS=HRS,KAPPA_COEFFICIENT
PERFORMANCES_EVALUATION=QUALITY_ANALYSIS,DISCREPANCY_ANALYSIS
DATA_CLUSTERING=DBSCAN,LOF,KMEANS,XMEANS
TRAINING=AQUAMAPSNN,HSPEN,FEED_FORWARD_ANN
SPECIES_SIMULATION=AQUAMAPS_NATIVE,AQUAMAPS_NATIVE_2050,AQUAMAPS_SUITABLE,AQUAMAPS_SUITABLE_2050,AQUAMAPS_NATIVE_NEURALNETWORK,AQUAMAPS_SUITABLE_NEURALNETWORK
SYSTEM=GENERIC_WORKER
ICHTHYOP_MODEL=ICHTHYOP_MODEL_ONE_BY_ONE,ICHTHYOP_MODEL_MULTIPLE_RUNS,MAKE_ICHTHYOP_NETCDF_CF_COMPLIANT,ICHTHYOP_NETCDF_OUTPUT_TO_SHAPEFILE,SPATIAL_DISTRIBUTION_OF_CORRELATION,SCATTERPLOT_DIAGRAM,SPATIAL_DENSITY_DISTRIBUTION,SMOOTH_SCATTERPLOT_DIAGRAM,ENRICHMENT_FROM_NETCDF
ICCAT_EASTERN_BFT_STOCK_ASSESSMENT=STEP_3___VPA_ICCAT_BFT_E_PROJECTION,STEP_2__VPA_ICCAT_BFT_E_VISUALISATION,PARALLELIZED_STEP1_VPA_ICCAT_BFT_E_RETROS,STEP_4_VPA_ICCAT_BFT_E_REPORT,PROJECTIONS_REPORT_VPA_ICCAT_BFT_E,WHOLE_STEPS_VPA_ICCAT_BFT_E,NCOUTPUTS2CSV_VPA_ICCAT_BFT_E,STEP_1___VPA_ICCAT_BFT_E_RETROS_ONERUN,STEP_1___VPA_ICCAT_BFT_E_RETROS
ACCESS_TUNA_ATLAS_DATA=TUNA_ATLAS_DATA_ACCESS,CATCHES_BY_SPECIES,CATCHES_BY_FLAGS,GLOBAL_CATCHES,CATCHES_BY_TYPE_OF_SCHOOL,CATCHES_BY_GEAR_SIMPLIFIED_VERSION,CATCHES_BY_FLAGS_SIMPLIFIED_VERSION,CATCHES_BY_SPECIES_SIMPLIFIED_VERSION,CATCHES_BY_GEARS,COMPUTE_FISHERIES_INDICATORS_FROM_OWN_FORMATTED_DATASET,CATCHES_AGGREGATED_FOLLOWING_A_SELECT_VARIABLE,CATCHES_INDICATORS_IOTC_REST_SERVICES,TRANSFORM_IOTC_CATCH_AND_EFFORT_DSD_CECOASTAL_AND_CESURFACE,LOAD_CATCHES_DATASET_IN_SARDARA,LOAD_EFFORTS_DATASET_IN_SARDARA
FIGIS_SPREAD=FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED,FIGIS_SPATIAL_REALLOCATION_GENERIC,FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED_TABLE
FIGIS_STATS=FIGIS_SDMX_DATA_CONVERTER
SAI_IMPORTED=GENETICALGORITHM,MPA_INTERSECT_V2,QUICK_RANK_TRAIN,QUICK_RANK_TRAIN_NO_VALIDATION,QUICK_RANK_TEST,STAT_VAL,TUNA_ATLAS_INDICATOR_1__SPECIES_BY_OCEAN_,SIMULFISHKPIS,READWFS,STAT_VAL_UNIPARTITE_NET,TESTING_ALGORITHM,MATLAS_OPTICS_CLUSTERING,MATLAS_TRAJECTORY_BUILDER,TWITTER_MONITOR,SCUBE
TRANSFORM_AND_LOAD_TUNA_ATLAS_DATA=IMPORT_FISHERIES_FORMATTED_DATASET___QUICK_IMPORT,LOAD_A_DATASET_IN_SARDARA_DATABASE,TRANSFORM_CCSBT_TASK2_LONGLINE
ENVRI=WTG,WEBTG_V2
GATE_CLOUD=ENGLISH_NAMED_ENTITY_RECOGNIZER,ENGLISH_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS,GERMAN_NAMED_ENTITY_RECOGNIZER,LANGUAGE_IDENTIFICATION_FOR_TWEETS,ENGLISH_TWEET_TOKENIZER,FRENCH_NAMED_ENTITY_RECOGNIZER,PART_OF_SPEECH_TAGGER_FOR_TWEETS,CYMRIE_WELSH_NAMED_ENTITY_RECOGNIZER,FRENCH_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS,GERMAN_NAMED_ENTITY_RECOGNIZER_FOR_TWEETS,ENGLISH_PART_OF_SPEECH_AND_MORPHOLOGY_ANAYLIZER,NOUN_PHRASE_CHUNKER,MEASUREMENT_EXPRESSION_ANNOTATOR,ANNIE_PLUS_MEASUREMENTS,GENERIC_OPINION_MINING_ENGLISH,DECARBONET_ENVIRONMENTAL_ANNOTATOR,DECARBONET_GERMAN_ENVIRONMENTAL_ANNOTATOR,TWITTER_OPINION_MINING_ENGLISH,THE_BREXIT_ANALYZER_PIPELINE,SUMMA_TEXT_SUMMARIZATION_EN,SUMMA_TEXT_SUMMARIZATION_ES,OPEN_NLP_ENGLISH_PIPELINE,OPEN_NLP_GERMAN_PIPELINE,OPEN_NLP_DUTCH_PIPELINE
CREATE_OWN_TUNA_ATLAS=CREATE_YOUR_OWN_VERSION_OF_THE_TUNA_ATLAS
WORKFLOWS=SAMPLE_KNIME_WORKFLOW,KNIME_WORKSPACE_FILE_UPLOADER
NETWORK_RECONSTRUCTION=MAXANDSAM_NETWORK_RECONTRUCTION_METHOD
SYSTEMIC_RISK_ESTIMATION=DEBTRANK_SYSTEMIC_RISK_ESTIMATION
DEVELOPMENT=PROJECT_SIMULFISHKPIS_DEV
BLACK_BOX=R_SAMPLE
NERLIX_ALGORITHMS=STANBOL_WRAPPER
GEOSPATIAL=GEOGRAPHIC_PROXIMITY_TOOL
GRSF=GEOGRSF_INTERSECTS_BATCH,GEOGRSF_INTERSECTS,GEOGRSF_BBOXLIST
PREPRODUCTION=SIMULFISHKPIS_PRE
BLUEBRIDGE_PROJECT_VRE=MPASINTERSECTIONANALYSIS,MPA_INTERSECT_V3,MPA_INTERSECT_V3_2
STATISTICAL_ALGORITHMS=VSURF,TRAIN
DATA_PUBLISHERS=AAPS_STAGING_PUBLISHER,AAPS_PUBLIC_PUBLISHER,AAPS_NASO_PUBLISHER
MACHINE_LEARNING_METHODS=SUPPORT_VECTOR_MACHINE_TRAINER,SUPPORT_VECTOR_MACHINE_REGRESSOR
TESTS=TEST_SAI_WS_INTERACTION

16
smartgears/dataminer_app/tasks/dataminer-app.yml
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@ -87,6 +87,22 @@
file: src={{ smartgears_user_home }}/data/gebco_08.nc dest={{ smartgears_instance_path }}/webapps/{{ dataminer_wps_name }}/ecocfg/gebco_08.nc state=link
notify: Restart smartgears
- name: Install a couple of jar files under ecocfg
get_url: url=http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/wps/src/main/webapp/ecocfg/{{ item }} dest={{ smartgears_instance_path }}/webapps/{{ dataminer_wps_name }}/ecocfg/{{ item }}
with_items:
- 'YASMEEN-matcher-1.2.0.1.jar'
- 'YASMEEN-parser-1.2.0.jar'
- name: Install a couple of jar files under ecocfg/PARALLEL_PROCESSING
get_url: url=http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/wps/src/main/webapp/ecocfg/{{ item }} dest={{ smartgears_instance_path }}/webapps/{{ dataminer_wps_name }}/ecocfg/PARALLEL_PROCESSING/{{ item }}
with_items:
- 'YASMEEN-matcher-1.2.0.1.jar'
- 'YASMEEN-parser-1.2.0.jar'
- name: Install the old properties files
copy: src={{ item }} dest={{ smartgears_instance_path }}/webapps/{{ dataminer_wps_name }}/ecocfg/{{ item }} force=yes
with_items: '{{ dataminer_properties_files }}'
- name: Install the script that fixes the WPS configuration
become_user: "{{ d4science_ansible_become_user | default('root') }}"
template: src=wps-config-fixer.j2 dest=/usr/local/bin/wps-config-fixer owner=root group=root mode=0555