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Observation has no observable errors in ontario models #59

Closed lambdatronic closed 12 years ago

lambdatronic commented 12 years ago

@fvilla @lambdatronic @bvoigt

AFAICT, all my source, sink, use, and routing models in core.models.sediment-ontario and core.models.water-ontario are running correctly at the Thinklab shell. However, when I build an identification observation containing all of them (except the probabilistic-measurement BN "undiscretizers"), I get an error that appears to be popping out of my local PostGIS database.

Here are the two trouble-makers:


> model -d core.models.water-ontario/all-water-data core.contexts.ontario/lakeofthewoods-wgs84
model -d core.models.water-ontario/all-water-data core.contexts.ontario/lakeofthewoods-wgs84
259200 possible observation(s) found
2012-02-24 16:42:30,284 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:snow_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:snow_low
2012-02-24 16:42:30,324 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:snow_low
2012-02-24 16:42:30,582 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:population_density_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:population_density_low
2012-02-24 16:42:30,602 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:population_density_low
2012-02-24 16:42:30,953 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:soil_drainage_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:soil_drainage_low
2012-02-24 16:42:30,980 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:soil_drainage_low
2012-02-24 16:42:31,201 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#global:impervious_global
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=global:impervious_global
2012-02-24 16:42:31,221 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for global:impervious_global
2012-02-24 16:42:31,643 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:slope20m_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:slope20m_low
2012-02-24 16:42:31,662 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:slope20m_low
2012-02-24 16:42:31,925 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:dem20m_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:dem20m_low
2012-02-24 16:42:31,945 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:dem20m_low
org.integratedmodelling.thinklab.exception.ThinklabValidationException: observation urn:uuid:ins:ac518c2a-7f00-4fa1-84ec-9c54d34c0a57 has no observable
    at org.integratedmodelling.corescience.implementations.observations.Observation.initialize(Observation.java:260)
    at org.integratedmodelling.thinklab.owlapi.ThinklabOWLManager.getInstanceImplementation(ThinklabOWLManager.java:353)
    at org.integratedmodelling.thinklab.owlapi.Instance.getImplementation(Instance.java:188)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:260)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:255)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:255)
    at org.integratedmodelling.thinklab.owlapi.Instance.validate(Instance.java:227)
    at org.integratedmodelling.thinklab.owlapi.Session.createObject(Session.java:384)
    at org.integratedmodelling.modelling.model.ModelFactory$ContextualizingModelResult.getResult(ModelFactory.java:272)
    at org.integratedmodelling.modelling.commands.ModelCommand.execute(ModelCommand.java:156)
    at org.integratedmodelling.thinklab.command.CommandManager.submitCommand(CommandManager.java:163)
    at org.integratedmodelling.thinklab.commandline.Shell.startConsole(Shell.java:100)
    at org.integratedmodelling.thinklab.shell.ShellApplication.startApplication(ShellApplication.java:116)
    at org.java.plugin.boot.Boot.boot(Boot.java:346)
    at org.java.plugin.boot.Boot.main(Boot.java:243)
 error: observation urn:uuid:ins:ac518c2a-7f00-4fa1-84ec-9c54d34c0a57 has no observable

> model -d core.models.sediment-ontario/all-sediment-data core.contexts.ontario/lakeofthewoods-wgs84
4320000 possible observation(s) found
2012-02-24 16:41:28,975 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:stream_gradient_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:stream_gradient_low
2012-02-24 16:41:29,000 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:stream_gradient_low
2012-02-24 16:41:29,244 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:canopy_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:canopy_low
2012-02-24 16:41:29,261 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:canopy_low
2012-02-24 16:41:29,504 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:lulc2000_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:lulc2000_low
2012-02-24 16:41:29,524 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:lulc2000_low
2012-02-24 16:41:29,687 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:slope20m_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:slope20m_low
2012-02-24 16:41:29,707 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:slope20m_low
2012-02-24 16:41:29,981 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:soil_drainage_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:soil_drainage_low
2012-02-24 16:41:30,000 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:soil_drainage_low
2012-02-24 16:41:30,204 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:successional_stage_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:successional_stage_low
2012-02-24 16:41:30,224 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:successional_stage_low
2012-02-24 16:41:30,496 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:precipitation_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:precipitation_low
2012-02-24 16:41:30,516 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:precipitation_low
2012-02-24 16:41:30,639 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:evapotranspiration_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:evapotranspiration_low
2012-02-24 16:41:30,667 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:evapotranspiration_low
2012-02-24 16:41:30,889 [main] INFO  org.integratedmodelling.geospace.Geospace reading WCS source http://ecoinformatics.uvm.edu/geoserver/wcs#ontario:snow_low
accessing: http://ecoinformatics.uvm.edu/geoserver/wcs?service=WCS&version=1.0.0&request=DescribeCoverage&coverage=ontario:snow_low
2012-02-24 16:41:30,911 [main] INFO  org.integratedmodelling.geospace.Geospace parsing descriptor for ontario:snow_low
2012-02-24 16:41:31,302 [main] INFO  org.integratedmodelling.thinklab.riskwiz.RiskWizPlugin bayesian engine set to genie
org.integratedmodelling.thinklab.exception.ThinklabValidationException: observation urn:uuid:ins:52fcd5fe-a13a-4edd-8ad5-646dc96c5182 has no observable
    at org.integratedmodelling.corescience.implementations.observations.Observation.initialize(Observation.java:260)
    at org.integratedmodelling.thinklab.owlapi.ThinklabOWLManager.getInstanceImplementation(ThinklabOWLManager.java:353)
    at org.integratedmodelling.thinklab.owlapi.Instance.getImplementation(Instance.java:188)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:260)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:255)
    at org.integratedmodelling.thinklab.owlapi.Instance.validateInternal(Instance.java:255)
    at org.integratedmodelling.thinklab.owlapi.Instance.validate(Instance.java:227)
    at org.integratedmodelling.thinklab.owlapi.Session.createObject(Session.java:384)
    at org.integratedmodelling.modelling.model.ModelFactory$ContextualizingModelResult.getResult(ModelFactory.java:272)
    at org.integratedmodelling.modelling.commands.ModelCommand.execute(ModelCommand.java:156)
    at org.integratedmodelling.thinklab.command.CommandManager.submitCommand(CommandManager.java:163)
    at org.integratedmodelling.thinklab.commandline.Shell.startConsole(Shell.java:100)
    at org.integratedmodelling.thinklab.shell.ShellApplication.startApplication(ShellApplication.java:116)
    at org.java.plugin.boot.Boot.boot(Boot.java:346)
    at org.java.plugin.boot.Boot.main(Boot.java:243)
 error: observation urn:uuid:ins:52fcd5fe-a13a-4edd-8ad5-646dc96c5182 has no observable
fvilla commented 12 years ago

You made ontario:AllWaterData (and others) an observation:Observation - which in thinklab triggers the creation of the Java peer object linked to observation:Observation, which obviously has several semantic constraints including that of having a functional relationship with an observable. Thinklab creates an instance of whatever observable you pass, and what you see is the result of validating that instance.

One of the main tenets of the approach (as you presented in Vienna) is that observations and observables are orthogonal, so you shouldn't make an observable an observation. Just make it whatever you feel like, this is just the concept that identifies a collection of observations so even a owl:Thing will do.