Fix issue with nesting of share links

Author: cjmyers

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 = {

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

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()

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)
 }

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)

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 = {

lib/summarize/summarizeComponentDefinition.js

@@ -17,10 +17,10 @@ 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)

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')

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
 }
 

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 = {

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)

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() || ''

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

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 = {

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 = ''

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')

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)
   }
 

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

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')

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 = {

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 = {

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') {

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 + ''

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

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 = {

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 = {

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 = {

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 = {

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)
   }
 }