diff --git a/lib/summarize/summarizeActivity.js b/lib/summarize/summarizeActivity.js index 20916d41..17125622 100644 --- a/lib/summarize/summarizeActivity.js +++ b/lib/summarize/summarizeActivity.js @@ -10,10 +10,10 @@ var ProvActivity = require('sboljs/lib/ProvActivity') function summarizeActivity (activity, req, sbol, remote, graphUri) { if (activity instanceof URI) { - return uriToMeta(activity) + return uriToMeta(activity, req) } if (!(activity instanceof ProvActivity)) { - return uriToMeta(activity.uri) + return uriToMeta(activity.uri, req) } var summary = { diff --git a/lib/summarize/summarizeAssociation.js b/lib/summarize/summarizeAssociation.js index c87a937b..ea96a85b 100644 --- a/lib/summarize/summarizeAssociation.js +++ b/lib/summarize/summarizeAssociation.js @@ -7,10 +7,10 @@ var ProvAssociation = require('sboljs/lib/ProvAssociation') function summarizeAssociation (association, req, sbol, remote, graphUri) { if (association instanceof URI) { - return uriToMeta(association) + return uriToMeta(association, req) } if (!(association instanceof ProvAssociation)) { - return uriToMeta(association.uri) + return uriToMeta(association.uri, req) } var plan diff --git a/lib/summarize/summarizeAttachment.js b/lib/summarize/summarizeAttachment.js index 855e888e..be0b8aa3 100644 --- a/lib/summarize/summarizeAttachment.js +++ b/lib/summarize/summarizeAttachment.js @@ -7,10 +7,10 @@ var Attachment = require('sboljs/lib/Attachment') function summarizeAttachment (attachment, req, sbol, remote, graphUri) { if (attachment instanceof URI) { - return uriToMeta(attachment) + return uriToMeta(attachment, req) } if (!(attachment instanceof Attachment)) { - return uriToMeta(attachment.uri) + return uriToMeta(attachment.uri, req) } var attachmentType = attachment.format.toString() diff --git a/lib/summarize/summarizeCollection.js b/lib/summarize/summarizeCollection.js index a84d1c95..c4f1d2ea 100644 --- a/lib/summarize/summarizeCollection.js +++ b/lib/summarize/summarizeCollection.js @@ -5,10 +5,10 @@ var Collection = require('sboljs/lib/Collection') function summarizeCollection (collection, req, sbol, remote, graphUri) { if (collection instanceof URI) { - return uriToMeta(collection) + return uriToMeta(collection, req) } if (!(collection instanceof Collection)) { - return uriToMeta(collection.uri) + return uriToMeta(collection.uri, req) } return summarizeTopLevel(collection, req, sbol, remote, graphUri) } diff --git a/lib/summarize/summarizeCombinatorialDerivation.js b/lib/summarize/summarizeCombinatorialDerivation.js index 7a5a8b55..bfd7bc6b 100644 --- a/lib/summarize/summarizeCombinatorialDerivation.js +++ b/lib/summarize/summarizeCombinatorialDerivation.js @@ -7,10 +7,10 @@ var CombinatorialDerivation = require('sboljs/lib/CombinatorialDerivation') function summarizeCombinatorialDerivation (combinatorialDerivation, req, sbol, remote, graphUri) { if (combinatorialDerivation instanceof URI) { - return uriToMeta(combinatorialDerivation) + return uriToMeta(combinatorialDerivation, req) } if (!(combinatorialDerivation instanceof CombinatorialDerivation)) { - return uriToMeta(combinatorialDerivation.uri) + return uriToMeta(combinatorialDerivation.uri, req) } var template = summarizeComponentDefinition(combinatorialDerivation.template, req, sbol, remote, graphUri) diff --git a/lib/summarize/summarizeComponent.js b/lib/summarize/summarizeComponent.js index 408eb8b1..6e221cb8 100644 --- a/lib/summarize/summarizeComponent.js +++ b/lib/summarize/summarizeComponent.js @@ -7,10 +7,10 @@ var Component = require('sboljs/lib/Component') function summarizeComponent (component, req, sbol, remote, graphUri) { if (component instanceof URI) { - return uriToMeta(component) + return uriToMeta(component, req) } if (!(component instanceof Component)) { - return uriToMeta(component.uri) + return uriToMeta(component.uri, req) } var summary = { diff --git a/lib/summarize/summarizeComponentDefinition.js b/lib/summarize/summarizeComponentDefinition.js index 33f7431f..9be4bbdc 100644 --- a/lib/summarize/summarizeComponentDefinition.js +++ b/lib/summarize/summarizeComponentDefinition.js @@ -9,7 +9,6 @@ const summarizeSequenceConstraint = require('./summarizeSequenceConstraint') const summarizeRoles = require('./summarizeRoles') const getDisplayList = require('visbol').getDisplayList const config = require('../config') -const uriToUrl = require('../uriToUrl') const uriToMeta = require('../uriToMeta') const URI = require('sboljs').URI const ComponentDefinition = require('sboljs/lib/ComponentDefinition') @@ -17,10 +16,10 @@ const lookupType = require('../type') function summarizeComponentDefinition (componentDefinition, req, sbol, remote, graphUri) { if (componentDefinition instanceof URI) { - return uriToMeta(componentDefinition) + return uriToMeta(componentDefinition, req) } if (!(componentDefinition instanceof ComponentDefinition)) { - return uriToMeta(componentDefinition.uri) + return uriToMeta(componentDefinition.uri, req) } var components = summarizeComponents(componentDefinition, req, sbol, remote, graphUri) @@ -155,7 +154,6 @@ function summarizeSequences (componentDefinition, req, sbol, remote, graphUri) { return summarizeSequence(sequence, req, sbol, remote, graphUri) }) sequences.forEach((sequence) => { - sequence.url = uriToUrl(sequence) if (req.params.version === 'current') { sequence.url = sequence.url.toString().replace('/' + sequence.version, '/current') sequence.version = 'current' diff --git a/lib/summarize/summarizeComponentInstance.js b/lib/summarize/summarizeComponentInstance.js index 87f87b00..4a0947a0 100644 --- a/lib/summarize/summarizeComponentInstance.js +++ b/lib/summarize/summarizeComponentInstance.js @@ -6,7 +6,7 @@ var URI = require('sboljs').URI function summarizeComponentInstance (componentInstance, req, sbol, remote, graphUri) { if (componentInstance instanceof URI) { - return uriToMeta(componentInstance) + return uriToMeta(componentInstance, req) } var summarizeComponentDefinition = require('./summarizeComponentDefinition') diff --git a/lib/summarize/summarizeExperiment.js b/lib/summarize/summarizeExperiment.js index 9460d247..39b643a2 100644 --- a/lib/summarize/summarizeExperiment.js +++ b/lib/summarize/summarizeExperiment.js @@ -6,10 +6,10 @@ var Experiment = require('sboljs/lib/Experiment') function summarizeExperiment (experiment, req, sbol, remote, graphUri) { if (experiment instanceof URI) { - return uriToMeta(experiment) + return uriToMeta(experiment, req) } if (!(experiment instanceof Experiment)) { - return uriToMeta(experiment.uri) + return uriToMeta(experiment.uri, req) } var summary = { @@ -23,6 +23,7 @@ function summarizeExperimentalData (experiment, req, sbol, remote, graphUri) { experiment.experimentalData.forEach((experimentalDatum) => { experimentalData.push(summarizeGenericTopLevel(experimentalDatum, req, sbol, remote, graphUri)) }) + console.log(JSON.stringify(experimentalData)) return experimentalData } diff --git a/lib/summarize/summarizeFunctionalComponent.js b/lib/summarize/summarizeFunctionalComponent.js index 4632e7ae..90012b26 100644 --- a/lib/summarize/summarizeFunctionalComponent.js +++ b/lib/summarize/summarizeFunctionalComponent.js @@ -5,10 +5,10 @@ var FunctionalComponent = require('sboljs/lib/FunctionalComponent') function summarizeFunctionalComponent (functionalComponent, req, sbol, remote, graphUri) { if (functionalComponent instanceof URI) { - return uriToMeta(functionalComponent) + return uriToMeta(functionalComponent, req) } if (!(functionalComponent instanceof FunctionalComponent)) { - return uriToMeta(functionalComponent.uri) + return uriToMeta(functionalComponent.uri, req) } var summary = { diff --git a/lib/summarize/summarizeGenericTopLevel.js b/lib/summarize/summarizeGenericTopLevel.js index d22f0c87..c8a80cb5 100644 --- a/lib/summarize/summarizeGenericTopLevel.js +++ b/lib/summarize/summarizeGenericTopLevel.js @@ -5,10 +5,10 @@ var GenericTopLevel = require('sboljs/lib/GenericTopLevel') function summarizeGenericTopLevel (genericTopLevel, req, sbol, remote, graphUri) { if (genericTopLevel instanceof URI) { - return uriToMeta(genericTopLevel) + return uriToMeta(genericTopLevel, req) } if (!(genericTopLevel instanceof GenericTopLevel)) { - return uriToMeta(genericTopLevel.uri) + return uriToMeta(genericTopLevel.uri, req) } return summarizeTopLevel(genericTopLevel, req, sbol, remote, graphUri) diff --git a/lib/summarize/summarizeIdentified.js b/lib/summarize/summarizeIdentified.js index 7882fc99..837dfce1 100644 --- a/lib/summarize/summarizeIdentified.js +++ b/lib/summarize/summarizeIdentified.js @@ -16,10 +16,10 @@ var Identified = require('sboljs/lib/Identified') function summarizeIdentified (identified, req, sbol, remote, graphUri) { if (identified instanceof URI) { - return uriToMeta(identified) + return uriToMeta(identified, req) } if (!(identified instanceof Identified)) { - return uriToMeta(identified.uri) + return uriToMeta(identified.uri, req) } var mutableDescriptionSource = identified.getAnnotations(namespace.synbiohub + 'mutableDescription').toString() || '' diff --git a/lib/summarize/summarizeImplementation.js b/lib/summarize/summarizeImplementation.js index 27c161c2..f87abaa2 100644 --- a/lib/summarize/summarizeImplementation.js +++ b/lib/summarize/summarizeImplementation.js @@ -6,10 +6,10 @@ var Implementation = require('sboljs/lib/Implementation') function summarizeImplementation (implementation, req, sbol, remote, graphUri) { if (implementation instanceof URI) { - return uriToMeta(implementation) + return uriToMeta(implementation, req) } if (!(implementation instanceof Implementation)) { - return uriToMeta(implementation.uri) + return uriToMeta(implementation.uri, req) } var built diff --git a/lib/summarize/summarizeInteraction.js b/lib/summarize/summarizeInteraction.js index 023aef2b..cbcbe998 100644 --- a/lib/summarize/summarizeInteraction.js +++ b/lib/summarize/summarizeInteraction.js @@ -9,10 +9,10 @@ var Interaction = require('sboljs/lib/Interaction') function summarizeInteraction (interaction, req, sbol, remote, graphUri) { if (interaction instanceof URI) { - return uriToMeta(interaction) + return uriToMeta(interaction, req) } if (!(interaction instanceof Interaction)) { - return uriToMeta(interaction.uri) + return uriToMeta(interaction.uri, req) } var summary = { diff --git a/lib/summarize/summarizeLocation.js b/lib/summarize/summarizeLocation.js index 3f9d886c..057ed283 100644 --- a/lib/summarize/summarizeLocation.js +++ b/lib/summarize/summarizeLocation.js @@ -8,12 +8,12 @@ var GenericLocation = require('sboljs/lib/GenericLocation') function summarizeLocation (location, req, sbol, remote, graphUri) { if (location instanceof URI) { - return uriToMeta(location) + return uriToMeta(location, req) } if (!(location instanceof Range) && !(location instanceof Cut) && !(location instanceof GenericLocation)) { - return uriToMeta(location.uri) + return uriToMeta(location.uri, req) } var locationStr = '' diff --git a/lib/summarize/summarizeMapsTo.js b/lib/summarize/summarizeMapsTo.js index 34ee989b..393c1672 100644 --- a/lib/summarize/summarizeMapsTo.js +++ b/lib/summarize/summarizeMapsTo.js @@ -5,10 +5,10 @@ var MapsTo = require('sboljs/lib/MapsTo') function summarizeMapsTo (mapsTo, req, sbol, remote, graphUri) { if (mapsTo instanceof URI) { - return uriToMeta(mapsTo) + return uriToMeta(mapsTo, req) } if (!(mapsTo instanceof MapsTo)) { - return uriToMeta(mapsTo.uri) + return uriToMeta(mapsTo.uri, req) } var summarizeComponentInstance = require('./summarizeComponentInstance') diff --git a/lib/summarize/summarizeMeasure.js b/lib/summarize/summarizeMeasure.js index 0e3ef119..523f84d4 100644 --- a/lib/summarize/summarizeMeasure.js +++ b/lib/summarize/summarizeMeasure.js @@ -6,15 +6,15 @@ var Measure = require('sboljs/lib/Measure') function summarizeMeasure (measure, req, sbol, remote, graphUri) { if (measure instanceof URI) { - return uriToMeta(measure) + return uriToMeta(measure, req) } if (!(measure instanceof Measure)) { - return uriToMeta(measure.uri) + return uriToMeta(measure.uri, req) } var summary = { value: measure.value, - unit: uriToMeta(measure.unit), + unit: uriToMeta(measure.unit, req), types: summarizeTypes(measure) } diff --git a/lib/summarize/summarizeModel.js b/lib/summarize/summarizeModel.js index d063b585..e9f6e717 100644 --- a/lib/summarize/summarizeModel.js +++ b/lib/summarize/summarizeModel.js @@ -7,10 +7,10 @@ var config = require('../config') function summarizeModel (model, req, sbol, remote, graphUri) { if (model instanceof URI) { - return uriToMeta(model) + return uriToMeta(model, req) } if (!(model instanceof Model)) { - return uriToMeta(model.uri) + return uriToMeta(model.uri, req) } var modelSourceName = model.source.toString().startsWith(config.get('databasePrefix')) ? 'Attachment' : model.source diff --git a/lib/summarize/summarizeModule.js b/lib/summarize/summarizeModule.js index 6298b86c..51152db6 100644 --- a/lib/summarize/summarizeModule.js +++ b/lib/summarize/summarizeModule.js @@ -7,10 +7,10 @@ var Module = require('sboljs/lib/Module') function summarizeModule (module, req, sbol, remote, graphUri) { if (module instanceof URI) { - return uriToMeta(module) + return uriToMeta(module, req) } if (!(module instanceof Module)) { - return uriToMeta(module.uri) + return uriToMeta(module.uri, req) } var summarizeModuleDefinition = require('./summarizeModuleDefinition') diff --git a/lib/summarize/summarizeModuleDefinition.js b/lib/summarize/summarizeModuleDefinition.js index 7a8844f7..8f4358d8 100644 --- a/lib/summarize/summarizeModuleDefinition.js +++ b/lib/summarize/summarizeModuleDefinition.js @@ -19,10 +19,10 @@ var ModuleDefinition = require('sboljs/lib/ModuleDefinition') function summarizeModuleDefinition (moduleDefinition, req, sbol, remote, graphUri) { if (moduleDefinition instanceof URI) { - return uriToMeta(moduleDefinition) + return uriToMeta(moduleDefinition, req) } if (!(moduleDefinition instanceof ModuleDefinition)) { - return uriToMeta(moduleDefinition.uri) + return uriToMeta(moduleDefinition.uri, req) } var summary = { diff --git a/lib/summarize/summarizeParticipation.js b/lib/summarize/summarizeParticipation.js index 779c7cf3..f06c845e 100644 --- a/lib/summarize/summarizeParticipation.js +++ b/lib/summarize/summarizeParticipation.js @@ -10,10 +10,10 @@ var Participation = require('sboljs/lib/Participation') function summarizeParticipation (participation, req, sbol, remote, graphUri) { if (participation instanceof URI) { - return uriToMeta(participation) + return uriToMeta(participation, req) } if (!(participation instanceof Participation)) { - return uriToMeta(participation.uri) + return uriToMeta(participation.uri, req) } var summary = { diff --git a/lib/summarize/summarizeSBOL.js b/lib/summarize/summarizeSBOL.js index a3bfa06d..e76dce14 100644 --- a/lib/summarize/summarizeSBOL.js +++ b/lib/summarize/summarizeSBOL.js @@ -29,7 +29,7 @@ var URI = require('sboljs').URI function summarizeSBOL (typeShortName, topLevel, req, sbol, remote, graphUri) { if (topLevel instanceof URI) { - return uriToMeta(topLevel) + return uriToMeta(topLevel, req) } var meta if (typeShortName === 'Activity') { diff --git a/lib/summarize/summarizeSequence.js b/lib/summarize/summarizeSequence.js index ce564dd0..ad0e3416 100644 --- a/lib/summarize/summarizeSequence.js +++ b/lib/summarize/summarizeSequence.js @@ -8,10 +8,10 @@ var Sequence = require('sboljs/lib/Sequence') function summarizeSequence (sequence, req, sbol, remote, graphUri) { if (sequence instanceof URI) { - return uriToMeta(sequence) + return uriToMeta(sequence, req) } if (!(sequence instanceof Sequence)) { - return uriToMeta(sequence.uri) + return uriToMeta(sequence.uri, req) } var encodingUri = sequence.encoding + '' diff --git a/lib/summarize/summarizeSequenceAnnotation.js b/lib/summarize/summarizeSequenceAnnotation.js index 86b5213e..35709853 100644 --- a/lib/summarize/summarizeSequenceAnnotation.js +++ b/lib/summarize/summarizeSequenceAnnotation.js @@ -8,10 +8,10 @@ var SequenceAnnotation = require('sboljs/lib/SequenceAnnotation') function summarizeSequenceAnnotation (sequenceAnnotation, req, sbol, remote, graphUri) { if (sequenceAnnotation instanceof URI) { - return uriToMeta(sequenceAnnotation) + return uriToMeta(sequenceAnnotation, req) } if (!(sequenceAnnotation instanceof SequenceAnnotation)) { - return uriToMeta(sequenceAnnotation.uri) + return uriToMeta(sequenceAnnotation.uri, req) } var definition diff --git a/lib/summarize/summarizeSequenceConstraint.js b/lib/summarize/summarizeSequenceConstraint.js index 6bea068f..3cd9e4c5 100644 --- a/lib/summarize/summarizeSequenceConstraint.js +++ b/lib/summarize/summarizeSequenceConstraint.js @@ -6,10 +6,10 @@ var SequenceConstraint = require('sboljs/lib/SequenceConstraint') function summarizeSequenceConstraint (sequenceConstraint, req, sbol, remote, graphUri) { if (sequenceConstraint instanceof URI) { - return uriToMeta(sequenceConstraint) + return uriToMeta(sequenceConstraint, req) } if (!(sequenceConstraint instanceof SequenceConstraint)) { - return uriToMeta(sequenceConstraint.uri) + return uriToMeta(sequenceConstraint.uri, req) } var summary = { diff --git a/lib/summarize/summarizeTopLevel.js b/lib/summarize/summarizeTopLevel.js index 8092f9f3..8c047185 100644 --- a/lib/summarize/summarizeTopLevel.js +++ b/lib/summarize/summarizeTopLevel.js @@ -6,7 +6,7 @@ var URI = require('sboljs').URI function summarizeTopLevel (topLevel, req, sbol, remote, graphUri) { if (topLevel instanceof URI) { - return uriToMeta(topLevel) + return uriToMeta(topLevel, req) } var summary = { diff --git a/lib/summarize/summarizeUsage.js b/lib/summarize/summarizeUsage.js index 42b63ffb..3c403b06 100644 --- a/lib/summarize/summarizeUsage.js +++ b/lib/summarize/summarizeUsage.js @@ -7,10 +7,10 @@ var ProvUsage = require('sboljs/lib/ProvUsage') function summarizeUsage (usage, req, sbol, remote, graphUri) { if (usage instanceof URI) { - return uriToMeta(usage) + return uriToMeta(usage, req) } if (!(usage instanceof ProvUsage)) { - return uriToMeta(usage.uri) + return uriToMeta(usage.uri, req) } var summary = { diff --git a/lib/summarize/summarizeVariableComponent.js b/lib/summarize/summarizeVariableComponent.js index 59191bf1..7a5a84d1 100644 --- a/lib/summarize/summarizeVariableComponent.js +++ b/lib/summarize/summarizeVariableComponent.js @@ -6,10 +6,10 @@ var VariableComponent = require('sboljs/lib/VariableComponent') function summarizeVariableComponent (variableComponent, req, sbol, remote, graphUri) { if (variableComponent instanceof URI) { - return uriToMeta(variableComponent) + return uriToMeta(variableComponent, req) } if (!(variableComponent instanceof VariableComponent)) { - return uriToMeta(variableComponent.uri) + return uriToMeta(variableComponent.uri, req) } var summary = { diff --git a/lib/uriToMeta.js b/lib/uriToMeta.js index cbbf1bc2..5d8d6cde 100644 --- a/lib/uriToMeta.js +++ b/lib/uriToMeta.js @@ -1,8 +1,9 @@ var uriToUrl = require('./uriToUrl') -function uriToMeta (uri) { +function uriToMeta (uri, req) { var persId var version + var id if (uri.toString().lastIndexOf('/')) { version = uri.toString().slice(uri.toString().lastIndexOf('/') + 1) if (version.match(/^\d/)) { @@ -19,7 +20,7 @@ function uriToMeta (uri) { id: id, version: version, name: id, - url: uriToUrl(uri) + url: uriToUrl(uri, req) } }