From 7f91b5f36a0a73fa3361d984f53ce186d8e6976f Mon Sep 17 00:00:00 2001 From: Andrea Dell'Amico Date: Tue, 19 Sep 2017 14:44:35 +0200 Subject: [PATCH 1/4] dataminer: New workarounds to fix some broken behaviour. --- smartgears/dataminer_app/defaults/main.yml | 12 ++ .../dataminer_app/files/algorithms.properties | 17 ++ .../dataminer_app/files/clusterers.properties | 4 + .../files/dynamictransducerers.properties | 1 + .../dataminer_app/files/evaluators.properties | 4 + .../dataminer_app/files/generators.properties | 3 + .../dataminer_app/files/modelers.properties | 1 + .../dataminer_app/files/models.properties | 3 + .../files/nodealgorithms.properties | 16 ++ .../files/transducerers.properties | 185 ++++++++++++++++++ .../files/userperspective.properties | 46 +++++ .../dataminer_app/tasks/dataminer-app.yml | 18 +- 12 files changed, 309 insertions(+), 1 deletion(-) create mode 100644 smartgears/dataminer_app/files/algorithms.properties create mode 100644 smartgears/dataminer_app/files/clusterers.properties create mode 100644 smartgears/dataminer_app/files/dynamictransducerers.properties create mode 100644 smartgears/dataminer_app/files/evaluators.properties create mode 100644 smartgears/dataminer_app/files/generators.properties create mode 100644 smartgears/dataminer_app/files/modelers.properties create mode 100644 smartgears/dataminer_app/files/models.properties create mode 100644 smartgears/dataminer_app/files/nodealgorithms.properties create mode 100644 smartgears/dataminer_app/files/transducerers.properties create mode 100644 smartgears/dataminer_app/files/userperspective.properties diff --git a/smartgears/dataminer_app/defaults/main.yml b/smartgears/dataminer_app/defaults/main.yml index c62fe605..404354a3 100644 --- a/smartgears/dataminer_app/defaults/main.yml +++ b/smartgears/dataminer_app/defaults/main.yml @@ -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 diff --git a/smartgears/dataminer_app/files/algorithms.properties b/smartgears/dataminer_app/files/algorithms.properties new file mode 100644 index 00000000..48263ebc --- /dev/null +++ b/smartgears/dataminer_app/files/algorithms.properties @@ -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 \ No newline at end of file diff --git a/smartgears/dataminer_app/files/clusterers.properties b/smartgears/dataminer_app/files/clusterers.properties new file mode 100644 index 00000000..f9321de4 --- /dev/null +++ b/smartgears/dataminer_app/files/clusterers.properties @@ -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 \ No newline at end of file diff --git a/smartgears/dataminer_app/files/dynamictransducerers.properties b/smartgears/dataminer_app/files/dynamictransducerers.properties new file mode 100644 index 00000000..aec7a718 --- /dev/null +++ b/smartgears/dataminer_app/files/dynamictransducerers.properties @@ -0,0 +1 @@ +#org.gcube.dataanalysis.geo.wps.factory.DynamicWPSTransducerer \ No newline at end of file diff --git a/smartgears/dataminer_app/files/evaluators.properties b/smartgears/dataminer_app/files/evaluators.properties new file mode 100644 index 00000000..3f438a8a --- /dev/null +++ b/smartgears/dataminer_app/files/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/smartgears/dataminer_app/files/generators.properties b/smartgears/dataminer_app/files/generators.properties new file mode 100644 index 00000000..29071626 --- /dev/null +++ b/smartgears/dataminer_app/files/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 \ No newline at end of file diff --git a/smartgears/dataminer_app/files/modelers.properties b/smartgears/dataminer_app/files/modelers.properties new file mode 100644 index 00000000..d5c652e1 --- /dev/null +++ b/smartgears/dataminer_app/files/modelers.properties @@ -0,0 +1 @@ +HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler \ No newline at end of file diff --git a/smartgears/dataminer_app/files/models.properties b/smartgears/dataminer_app/files/models.properties new file mode 100644 index 00000000..b19d44c7 --- /dev/null +++ b/smartgears/dataminer_app/files/models.properties @@ -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 \ No newline at end of file diff --git a/smartgears/dataminer_app/files/nodealgorithms.properties b/smartgears/dataminer_app/files/nodealgorithms.properties new file mode 100644 index 00000000..2e83be13 --- /dev/null +++ b/smartgears/dataminer_app/files/nodealgorithms.properties @@ -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 diff --git a/smartgears/dataminer_app/files/transducerers.properties b/smartgears/dataminer_app/files/transducerers.properties new file mode 100644 index 00000000..b18cae39 --- /dev/null +++ b/smartgears/dataminer_app/files/transducerers.properties @@ -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 diff --git a/smartgears/dataminer_app/files/userperspective.properties b/smartgears/dataminer_app/files/userperspective.properties new file mode 100644 index 00000000..91c68de6 --- /dev/null +++ b/smartgears/dataminer_app/files/userperspective.properties @@ -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 diff --git a/smartgears/dataminer_app/tasks/dataminer-app.yml b/smartgears/dataminer_app/tasks/dataminer-app.yml index 66eb7e06..92936466 100644 --- a/smartgears/dataminer_app/tasks/dataminer-app.yml +++ b/smartgears/dataminer_app/tasks/dataminer-app.yml @@ -86,7 +86,23 @@ - name: Create a symlink to the gebco_08.nc file 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 From d7a12eb37527ca057b5907f95577228dd77b489b Mon Sep 17 00:00:00 2001 From: Andrea Dell'Amico Date: Tue, 19 Sep 2017 15:13:57 +0200 Subject: [PATCH 2/4] Change the nginx smartgears template to add opencpu as a special case. --- .../generic-smartgears-virtualhost.j2 | 21 ++++++++++++++++--- smartgears/smartgears/defaults/main.yml | 5 ++++- .../smartgears/tasks/smartgears-app.yml | 1 + 3 files changed, 23 insertions(+), 4 deletions(-) diff --git a/smartgears/smartgears-nginx-frontend/templates/generic-smartgears-virtualhost.j2 b/smartgears/smartgears-nginx-frontend/templates/generic-smartgears-virtualhost.j2 index 785fea0c..1510e73d 100644 --- a/smartgears/smartgears-nginx-frontend/templates/generic-smartgears-virtualhost.j2 +++ b/smartgears/smartgears-nginx-frontend/templates/generic-smartgears-virtualhost.j2 @@ -13,7 +13,7 @@ server { {% endif %} access_log /var/log/nginx/{{ item.servername }}_access.log; error_log /var/log/nginx/{{ item.servername }}_error.log; - root /usr/share/nginx/html/; + root {{ item.web_document_root | default('/usr/share/nginx/html/') }}; {% if haproxy_ips is defined %} # We are behind haproxy @@ -90,6 +90,14 @@ server { proxy_pass http://127.0.0.1:{{ smartgears_http_port }}/data-transfer-service; } {% endif %} + {% if remote_opencpu_server is defined and remote_opencpu_server %} + location {{ opencpu_context | default('/ocpu') }} { + {% if smartgears_nginx_cors_enabled %} + include /etc/nginx/snippets/nginx-cors.conf; + {% endif %} + proxy_pass http://{{ remote_opencpu_host }}:{{ opencpu_proxy_port | default('8004') }}{{ opencpu_context | default('/ocpu') }}; + } + {% endif %} {% if rstudio_install_server is defined and rstudio_install_server %} location / { {% if smartgears_nginx_cors_enabled %} @@ -128,8 +136,7 @@ server { access_log /var/log/nginx/{{ item.servername }}_access_ssl.log; error_log /var/log/nginx/{{ item.servername }}_error_ssl.log; - # This is the default for nginx on Ubuntu 14.04 - root /usr/share/nginx/html/; + root {{ item.web_document_root | default('/usr/share/nginx/html/') }}; {% if haproxy_ips is defined %} # We are behind haproxy @@ -206,6 +213,14 @@ server { proxy_pass http://127.0.0.1:{{ smartgears_http_port }}/data-transfer-service; } {% endif %} + {% if remote_opencpu_server is defined and remote_opencpu_server %} + location {{ opencpu_context | default('/ocpu') }} { + {% if smartgears_nginx_cors_enabled %} + include /etc/nginx/snippets/nginx-cors.conf; + {% endif %} + proxy_pass http://{{ remote_opencpu_host }}:{{ opencpu_proxy_port | default('8004') }}{{ opencpu_context | default('/ocpu') }}; + } + {% endif %} {% if rstudio_install_server is defined and rstudio_install_server %} location / { {% if smartgears_nginx_cors_enabled %} diff --git a/smartgears/smartgears/defaults/main.yml b/smartgears/smartgears/defaults/main.yml index 27822ec0..ecf68242 100644 --- a/smartgears/smartgears/defaults/main.yml +++ b/smartgears/smartgears/defaults/main.yml @@ -64,9 +64,12 @@ smartgears_tomcat_listen_address: '127.0.0.1' # The iptables rules use this http_port: '{{ smartgears_http_port }}' +# Used by nginx +smartgears_web_document_root: '/usr/share/nginx/html/' + tomcat_m_webapps_unpack: True tomcat_m_instances: - - { http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', catalina_tmp_directory: '{{ smartgears_tomcat_tmp_dir }}', remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}', access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', skip_smartgears: False,smartgears_id: 1, servername: '{{ ansible_fqdn }}' } + - { http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', catalina_tmp_directory: '{{ smartgears_tomcat_tmp_dir }}', remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}', access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', web_document_root: '{{ smartgears_web_document_root }}' , skip_smartgears: False, smartgears_id: 1, servername: '{{ ansible_fqdn }}' } # To enable debugging: # - Set diff --git a/smartgears/smartgears/tasks/smartgears-app.yml b/smartgears/smartgears/tasks/smartgears-app.yml index b3d6c6fd..6e3ab121 100644 --- a/smartgears/smartgears/tasks/smartgears-app.yml +++ b/smartgears/smartgears/tasks/smartgears-app.yml @@ -119,6 +119,7 @@ become_user: '{{ smartgears_user }}' shell: /usr/local/bin/get-scopes {{ gcube_admin_token | default('') }} when: gcube_admin_token is defined or smartgears_upgrade + ignore_errors: True notify: Restart smartgears tags: [ 'smartgears', 'smartgears_conf', 'tomcat' ] From 02bcd00968636a374655072b228192f13704bbd3 Mon Sep 17 00:00:00 2001 From: Andrea Dell'Amico Date: Tue, 19 Sep 2017 15:37:14 +0200 Subject: [PATCH 3/4] dataminer: Install the war archive by default. --- smartgears/dataminer_app/defaults/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/smartgears/dataminer_app/defaults/main.yml b/smartgears/dataminer_app/defaults/main.yml index 404354a3..cf69727a 100644 --- a/smartgears/dataminer_app/defaults/main.yml +++ b/smartgears/dataminer_app/defaults/main.yml @@ -7,7 +7,7 @@ dataminer_product: prod dataminer_zip_url: 'http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataMinerConfiguration/webapp/{{ dataminer_product }}/wps.zip' # Install from WAR -dataminer_war_install: False +dataminer_war_install: True dataminer_wps_version: latest dataminer_wps_name: wps dataminer_wps_group_id: org.gcube.data-analysis From fc6688b26dcd1d9dc83df6e5199a8d93ec33b3e7 Mon Sep 17 00:00:00 2001 From: Andrea Dell'Amico Date: Tue, 19 Sep 2017 17:11:59 +0200 Subject: [PATCH 4/4] smartgears data-transfer: expand the war file, because we need to put stuff inside. --- smartgears/smartgears/tasks/smartgears-app.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/smartgears/smartgears/tasks/smartgears-app.yml b/smartgears/smartgears/tasks/smartgears-app.yml index 6e3ab121..21bbd96b 100644 --- a/smartgears/smartgears/tasks/smartgears-app.yml +++ b/smartgears/smartgears/tasks/smartgears-app.yml @@ -131,6 +131,20 @@ notify: Restart smartgears tags: [ 'smartgears', 'smartgears_conf', 'tomcat' ] +- name: Create the data transfer webapp directory + become: True + become_user: '{{ smartgears_user }}' + file: path={{ smartgears_instance_path }}/webapps/{{ data_trasfer_service_name }} state=directory + when: data_transfer_service_install + tags: [ 'smartgears', 'smartgears_data_trasfer', 'tomcat' ] + +- name: Unarchive the data transfer webapp directory + become: True + become_user: '{{ smartgears_user }}' + unarchive: src={{ smartgears_instance_path }}/webapps/{{ data_trasfer_service_name }}.war dest={{ smartgears_instance_path }}/webapps/{{ data_trasfer_service_name }} creates={{ smartgears_instance_path }}/webapps/{{ data_trasfer_service_name }}/WEB-INF/gcube-app.xml remote_src=yes + when: data_transfer_service_install + tags: [ 'smartgears', 'smartgears_data_trasfer', 'tomcat' ] + - name: Force a smartgears restart service: name='tomcat-instance-{{ smartgears_http_port }}' state=restarted when: smartgears_force_restart is defined and smartgears_force_restart