@base <http://www.w3.org/2005/04/swls/chemistryCanvas>

@prefix	dc:			<http://purl.org/dc/elements/1.1/>
@prefix	hs:			<http://haystack.lcs.mit.edu/schemata/haystack#>
@prefix	ozone:		<http://haystack.lcs.mit.edu/schemata/ozone#>
@prefix	task:		<http://haystack.lcs.mit.edu/schemata/task#>
@prefix	applet:		<http://haystack.lcs.mit.edu/schemata/ozoneapplet#>
@prefix	slide:		<http://haystack.lcs.mit.edu/schemata/ozoneslide#> 
@prefix	vc:			<http://haystack.lcs.mit.edu/ui/viewContainer#> 
@prefix	layout:		<http://haystack.lcs.mit.edu/schemata/layout#>
@prefix	summary:	<http://haystack.lcs.mit.edu/ui/summaryView#> 
@prefix	data:		<http://haystack.lcs.mit.edu/schemata/dataProvider#>
@prefix op:			<http://haystack.lcs.mit.edu/schemata/operation#>
@prefix	modeless:	<http://haystack.lcs.mit.edu/schemata/ozonemodeless#>
@prefix	create:		<http://haystack.lcs.mit.edu/programs/create#> 
@prefix	marble:		<http://haystack.lcs.mit.edu/ui/marble#>
@prefix	cv:			<http://haystack.lcs.mit.edu/ui/collectionView#> 
@prefix	metadata:	<http://haystack.lcs.mit.edu/ui/metadataEditor#> 
@prefix help:		<http://haystack.lcs.mit.edu/programs/help#>
@prefix	lensui:		<http://haystack.lcs.mit.edu/ui/lens#> 
@prefix graph:		<http://haystack.lcs.mit.edu/programs/graphExplorer#>
@prefix	vowl:		<http://haystack.lcs.mit.edu/schemata/vowl#> 
@prefix biopax:		<http://www.biopax.org/release/biopax-level1.owl#>
@prefix opdata:		<http://haystack.lcs.mit.edu/data/operations#>
@prefix gsk: 		<http://www.w3.org/2005/04/swls/gsk3b/gsk#>
@prefix ls:			<http://www.w3.org/2005/04/swls/ls-ont-1.0#>
@prefix :			<http://www.w3.org/2005/04/swls/chemistryCanvas#>

################################################################################
# Sample data

add { :testCanvas
	rdfs:label			"Example chemistry canvas" ;
	rdf:type			:ChemistryCanvas ;
	:chemicalLibrary	:chemlib1 ;
	:chemicalLibrary	:chemlib2 ;
	:target				<http://www.w3.org/2005/04/swls/gsk3b/gsk#CaseinKinaseI_Tgt> ;
	:target				<http://www.w3.org/2005/04/swls/gsk3b/gsk#GSK3beta_Tgt> ;
	:relationship		:magicallyMutatesInto ;
	:relationship		:smellsLike ;
	:extraChemical		:silver
}

add { :magicallyMutatesInto
	rdfs:label	"Magically mutates into" ;
	rdf:type	rdf:Property
}

add { :smellsLike
	rdfs:label	"Smells like" ;
	rdf:type	rdf:Property
}

add { :chemlib1
	dc:title	"Chemical library alpha" ;
	rdf:type	hs:Collection ;
	hs:member	:diphenylketone
}

add { :chemlib2
	dc:title	"Chemical library beta" ;
	rdf:type	hs:Collection ;
	hs:member	:gold
}

add { :gold rdfs:label "Gold" }
add { :silver rdfs:label "Silver" }
add { :diphenylketone rdfs:label "Diphenylketone" }

add { :diphenylketone :smellsLike <http://www.w3.org/2005/04/swls/gsk3b/gsk#CHIR98014> }
add { <http://www.w3.org/2005/04/swls/gsk3b/gsk#CHIR98014> :magicallyMutatesInto :gold }
add { <http://www.w3.org/2005/04/swls/gsk3b/gsk#CHIR98014> :magicallyMutatesInto :silver }
add { <http://www.w3.org/2005/04/swls/gsk3b/gsk#ARA014418> :magicallyMutatesInto <http://www.w3.org/2005/04/swls/gsk3b/gsk#SB216763> }

add { <http://www.w3.org/2005/04/swls/gsk3b/topicView#demo>
	hs:member	:testCanvas ;
	hs:member	:createBlankCanvas ;
	hs:member	:sampleChemicalRelations
}

add { :sampleChemicalRelations
	rdf:type	hs:Collection ;
	rdfs:label	"Sample chemical relations" ;
	hs:member	ls:coProducedWith ;
	hs:member	ls:conceptFrom ;
	hs:member	ls:derivedFrom ;
	hs:member	ls:metabolizesTo ;
	hs:member	ls:patentCovered ;
	hs:member	ls:synthesizedFrom
}

################################################################################
# Operations

add { :topic
	rdf:type			op:Parameter ;
	rdf:type			daml:ObjectProperty ;
	dc:title			"Topic" ;
	op:required			"true" ;
	rdfs:range			ls:TheraTopic
}

method :createCanvasFromTopic :topic = topic ; 
rdf:type			op:Operation ;
op:primaryParameter	:topic ;
dc:title			"Create chemical canvas from topic" ;
adenine:preload 	"true"
	= x ${
		rdf:type	:ChemistryCanvas ;
		dc:title	"Chemistry canvas"
	}
	
	for y in (query { topic[0] ls:targetGene ?x })
		add { x :target y[0] }
		
	return x

method :createBlankCanvas ; 
rdf:type			op:Operation ;
dc:title			"Create new chemistry canvas" ;
adenine:preload 	"true"
	= x ${
		rdf:type	:ChemistryCanvas ;
		dc:title	"Chemistry canvas"
	}
		
	return x

################################################################################
# Chemistry canvas definition

add { :ChemistryCanvas
	rdf:type		rdfs:Class ;
	rdfs:label		"Chemistry canvas" ;
	hs:classView	:ChemistryCanvasView
}

add { :relationship
	rdfs:label	"Relationships" ;
	rdfs:domain	:ChemistryCanvas
}

add { :chemicalLibrary
	rdfs:label	"Chemical libraries" ;
	rdfs:domain	:ChemistryCanvas
}

add { :extraChemical
	rdfs:label	"Additional chemicals to show" ;
	rdfs:domain	:ChemistryCanvas
}

add { :target
	rdfs:label	"Targets" ;
	rdfs:domain	:ChemistryCanvas
}

################################################################################
# Chemistry canvas view

add { :chemistryCanvasViewPart
	rdf:type						ozone:SWTPart ;
	rdf:type						ozone:Part ;
	rdf:type						ozone:InteractiveViewPart ;
	rdf:type						ozone:ViewPart ;

	###########################################
	# Name of the view class (from above)
	###########################################
	ozone:viewDomain				:ChemistryCanvasView ;

	###########################################
	# View name to show in the left hand side
	###########################################
	vc:toolbarCaption				"Chemistry canvas view" ;

	ozone:cacheStyle				ozone:cacheDisabled ;
	hs:javaImplementation			${ rdf:type hs:JavaClass ; hs:className	"edu.mit.lcs.haystack.ozone.standard.widgets.parts.TemplatePartContainerPart" } ;
	ozone:template ${
		rdf:type			graph:GraphExplorerContainerPart ;
		marble:graphExplorerDataSource ${
			rdf:type				graph:CollectionGraphExplorerSource ;
			marble:extraDataSource ${
				rdf:type		data:MergeSetSource ;
				ozone:dataSource ${
					rdf:type				data:RDFQuerySetSource ;
					data:existentials		@( ?x ?y ) ;
					data:targetExistential	?x ;
					data:statement ${
						data:subjectDataSource	data:underlyingSource ;
						data:predicate			:chemicalLibrary ;
						data:object				?y
					} ;
					data:statement ${
						data:subject	?y ;
						data:predicate	hs:member ;
						data:object		?x
					}
				} ;
				ozone:dataSource ${
					rdf:type				data:RDFQuerySetSource ;
					data:existentials		@( ?x ?y ) ;
					data:targetExistential	?x ;
					data:statement ${
						data:subjectDataSource	data:underlyingSource ;
						data:predicate			:target ;
						data:object				?y
					} ;
					data:statement ${
						data:subject	?y ;
						data:predicate	ls:for ;
						data:object		?x
					}
				} ;
				ozone:dataSource ${
					rdf:type			data:PredicateSetSource ;
					ozone:dataSource	data:underlyingSource ;
					data:predicate		:extraChemical
				}
			} ;
			marble:relationships ${
				rdf:type			data:PredicateSetSource ;
				ozone:dataSource	data:underlyingSource ;
				data:predicate		:relationship
			}
		} ;
		slide:child ${
			rdf:type			layout:Layout ;
			ozone:dataSource ${
				rdf:type		data:DAMLListSource ;
				data:damlList	@( :topPane :bottomPane )
			} ;
			layout:layoutConstraint ${
				rdf:type			layout:RowSplitterConstraint ;
				layout:pack			"last" ;
				layout:constraint	${ layout:element :bottomPane ; layout:dimension "20%" }
			}
		}
	}
}

add { :topPane
	rdf:type	marble:Diagram ;
	ozone:dataSource ${
		rdf:type		marble:ContextHostedSetSource ;
		data:property	marble:graphExplorerDataProvider
	} ;
	marble:arcDataSource ${
		rdf:type	graph:GraphExplorerArcSetSource
	} ;
	layout:focus ${
		rdf:type		data:ContextHostedResourceSource ;
		data:property	layout:focus
	}
}

add { :bottomPane
	rdf:type				slide:Block ;
	slide:cropChildWidth	"true" ;
	slide:child ${
		rdf:type					ozone:DataProviderHost ;
		ozone:hostedDataProvider	data:underlyingSource ;
		ozone:propertyName			lensui:underlyingSource ;
		slide:child ${
			rdf:type				layout:Layout ;
			ozone:dataSource ${
				rdf:type	data:DAMLListSource ;
				data:damlList @(
					:target
					:chemicalLibrary
					:extraChemical
					:relationship
				)
			} ;
			layout:layoutConstraint ${
				rdf:type				layout:VerticalFlowConstraint ;
				layout:minColumnWidth	"350" ;
				ozone:viewPartClass		lensui:IndividualAspectViewPart ;
				layout:spansAllColumnsDataSource ${
					rdf:type		data:StatementExistenceSource ;
					data:predicate	lensui:spansAllColumns ;
					data:object		"true"
				}
			}
		}
	}
}