"use strict";
define([
"jquery",
"underscore",
"backbone",
"rdflib",
"uuid",
"md5",
"collections/SolrResults",
"models/filters/Filter",
"models/DataONEObject",
"models/metadata/ScienceMetadata",
"models/metadata/eml211/EML211",
], function (
$,
_,
Backbone,
rdf,
uuid,
md5,
SolrResults,
Filter,
DataONEObject,
ScienceMetadata,
EML211,
) {
/**
* @class DataPackage
* @classdesc A DataPackage represents a hierarchical collection of
packages, metadata, and data objects, modeling an OAI-ORE RDF graph.
TODO: incorporate Backbone.UniqueModel
* @classcategory Collections
* @name DataPackage
* @extends Backbone.Collection
* @constructor
*/
var DataPackage = Backbone.Collection.extend(
/** @lends DataPackage.prototype */ {
/**
* The name of this type of collection
* @type {string}
*/
type: "DataPackage",
/**
* The package identifier
* @type {string}
*/
id: null,
/**
* The type of the object (DataPackage, Metadata, Data)
* Simple queue to enqueue file transfers. Use push() and shift()
* to add and remove items. If this gets to large/slow, possibly
* switch to http://code.stephenmorley.org/javascript/queues/
* @type {DataPackage|Metadata|Data[]}
*/
transferQueue: [],
/** A flag ued for the package's edit status. Can be
* set to false to 'lock' the package
* @type {boolean}
*/
editable: true,
/**
* The RDF graph representing this data package
* @type {RDFGraph}
*/
dataPackageGraph: null,
/**
* A DataONEObject representing the resource map itself
* @type {DataONEObject}
*/
packageModel: null,
/** The science data identifiers associated with this
* data package (from cito:documents), mapped to the science metadata
* identifier that documents it
* Not to be changed after initial fetch - this is to keep track of the relationships in their original state
* @type {object}
*/
originalIsDocBy: {},
/** An array of ids that are aggregated in the resource map on the server.
* Taken from the original RDF XML that was fetched from the server.
* Used for comparing the original aggregation with the aggregation of this collection.
* @type {string[]}
*/
originalMembers: [],
/**
* Keep the collection sorted by model "sortOrder". The three model types are ordered as:
* Metadata: 1
* Data: 2
* DataPackage: 3
* See getMember(). We do this so that Metadata get rendered first, and Data are
* rendered as DOM siblings of the Metadata rows of the DataPackage table.
* @type {string}
*/
comparator: "sortOrder",
/**
* The nesting level in a data package hierarchy
* @type {number}
*/
nodeLevel: 0,
/**
* The SolrResults collection associated with this DataPackage.
* This can be used to fetch the package from Solr by passing the 'fromIndex' option
* to fetch().
* @type {SolrResults}
*/
solrResults: new SolrResults(),
/**
* A Filter model that should filter the Solr index for only the
* objects aggregated by this package.
* @type {Filter}
*/
filterModel: null,
/** Define the namespaces used in the RDF XML
* @type {object}
*/
namespaces: {
RDF: "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
FOAF: "http://xmlns.com/foaf/0.1/",
OWL: "http://www.w3.org/2002/07/owl#",
DC: "http://purl.org/dc/elements/1.1/",
ORE: "http://www.openarchives.org/ore/terms/",
DCTERMS: "http://purl.org/dc/terms/",
CITO: "http://purl.org/spar/cito/",
XSD: "http://www.w3.org/2001/XMLSchema#",
PROV: "http://www.w3.org/ns/prov#",
PROVONE: "http://purl.dataone.org/provone/2015/01/15/ontology#",
},
sources: [],
derivations: [],
provenanceFlag: null,
sourcePackages: [],
derivationPackages: [],
relatedModels: [],
/**
* Contains provenance relationships added or deleted to this DataONEObject.
* Each entry is [operation ('add' or 'delete'), prov field name, object id], i.e. ['add', 'prov_used', 'urn:uuid:5678']
*/
provEdits: [],
/**
* The number of models that have been updated during the current save().
* This is reset to zero after the current save() is complete.
*/
numSaves: 0,
// Constructor: Initialize a new DataPackage
initialize: function (models, options) {
if (typeof options == "undefined") var options = {};
// Create an rdflib reference
this.rdf = rdf;
// Create an initial RDF graph
this.dataPackageGraph = this.rdf.graph();
//Set the id or create a new one
this.id = options.id || "resource_map_urn:uuid:" + uuid.v4();
let packageModelAttrs = options.packageModelAttrs || {};
if (typeof options.packageModel !== "undefined") {
// use the given package model
this.packageModel = new DataONEObject(options.packageModel);
} else {
// Create a DataONEObject to represent this resource map
this.packageModel = new DataONEObject(
_.extend(packageModelAttrs, {
formatType: "RESOURCE",
type: "DataPackage",
formatId: "http://www.openarchives.org/ore/terms",
childPackages: {},
id: this.id,
latestVersion: this.id,
}),
);
}
this.id = this.packageModel.id;
//Create a Filter for this DataPackage using the id
this.filterModel = new Filter({
fields: ["resourceMap"],
values: [this.id],
matchSubstring: false,
});
//If the id is ever changed, update the id in the Filter
this.listenTo(this.packageModel, "change:id", function () {
this.filterModel.set("values", [this.packageModel.get("id")]);
});
this.on("add", this.handleAdd);
this.on("add", this.triggerComplete);
this.on("successSaving", this.updateRelationships);
return this;
},
// Build the DataPackage URL based on the MetacatUI.appModel.objectServiceUrl
// and id or seriesid
url: function (options) {
if (options && options.update) {
return (
MetacatUI.appModel.get("objectServiceUrl") +
(encodeURIComponent(this.packageModel.get("oldPid")) ||
encodeURIComponent(this.packageModel.get("seriesid")))
);
} else {
//URL encode the id or seriesId
var encodedId =
encodeURIComponent(this.packageModel.get("id")) ||
encodeURIComponent(this.packageModel.get("seriesid"));
//Use the object service URL if it is available (when pointing to a MN)
if (MetacatUI.appModel.get("objectServiceUrl")) {
return MetacatUI.appModel.get("objectServiceUrl") + encodedId;
}
//Otherwise, use the resolve service URL (when pointing to a CN)
else {
return MetacatUI.appModel.get("resolveServiceUrl") + encodedId;
}
}
},
/*
* The DataPackage collection stores DataPackages and
* DataONEObjects, including Metadata and Data objects.
* Return the correct model based on the type
*/
model: function (attrs, options) {
switch (attrs.formatid) {
case "http://www.openarchives.org/ore/terms":
return new DataPackage(null, { packageModel: attrs }); // TODO: is this correct?
case "eml://ecoinformatics.org/eml-2.0.0":
return new EML211(attrs, options);
case "eml://ecoinformatics.org/eml-2.0.1":
return new EML211(attrs, options);
case "eml://ecoinformatics.org/eml-2.1.0":
return new EML211(attrs, options);
case "eml://ecoinformatics.org/eml-2.1.1":
return new EML211(attrs, options);
case "eml://ecoinformatics.org/eml-2.1.1":
return new EML211(attrs, options);
case "-//ecoinformatics.org//eml-access-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-access-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-attribute-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-attribute-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-constraint-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-constraint-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-coverage-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-coverage-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-dataset-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-distribution-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-distribution-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-entity-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-entity-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-literature-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-literature-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-party-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-party-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-physical-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-physical-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-project-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-project-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-protocol-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-protocol-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-resource-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-resource-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-software-2.0.0beta4//EN":
return new ScienceMetadata(attrs, options);
case "-//ecoinformatics.org//eml-software-2.0.0beta6//EN":
return new ScienceMetadata(attrs, options);
case "FGDC-STD-001-1998":
return new ScienceMetadata(attrs, options);
case "FGDC-STD-001.1-1999":
return new ScienceMetadata(attrs, options);
case "FGDC-STD-001.2-1999":
return new ScienceMetadata(attrs, options);
case "INCITS-453-2009":
return new ScienceMetadata(attrs, options);
case "ddi:codebook:2_5":
return new ScienceMetadata(attrs, options);
case "http://datacite.org/schema/kernel-3.0":
return new ScienceMetadata(attrs, options);
case "http://datacite.org/schema/kernel-3.1":
return new ScienceMetadata(attrs, options);
case "http://datadryad.org/profile/v3.1":
return new ScienceMetadata(attrs, options);
case "http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd":
return new ScienceMetadata(attrs, options);
case "http://ns.dataone.org/metadata/schema/onedcx/v1.0":
return new ScienceMetadata(attrs, options);
case "http://purl.org/dryad/terms/":
return new ScienceMetadata(attrs, options);
case "http://purl.org/ornl/schema/mercury/terms/v1.0":
return new ScienceMetadata(attrs, options);
case "http://rs.tdwg.org/dwc/xsd/simpledarwincore/":
return new ScienceMetadata(attrs, options);
case "http://www.cuahsi.org/waterML/1.0/":
return new ScienceMetadata(attrs, options);
case "http://www.cuahsi.org/waterML/1.1/":
return new ScienceMetadata(attrs, options);
case "http://www.esri.com/metadata/esriprof80.dtd":
return new ScienceMetadata(attrs, options);
case "http://www.icpsr.umich.edu/DDI":
return new ScienceMetadata(attrs, options);
case "http://www.isotc211.org/2005/gmd":
return new ScienceMetadata(attrs, options);
case "http://www.isotc211.org/2005/gmd-noaa":
return new ScienceMetadata(attrs, options);
case "http://www.loc.gov/METS/":
return new ScienceMetadata(attrs, options);
case "http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2":
return new ScienceMetadata(attrs, options);
default:
return new DataONEObject(attrs, options);
}
},
/**
* Overload fetch calls for a DataPackage
*
* @param {Object} [options] - Optional options for this fetch that get sent with the XHR request
* @property {boolean} fetchModels - If false, this fetch will not fetch
* each model in the collection. It will only get the resource map object.
* @property {boolean} fromIndex - If true, the collection will be fetched from Solr rather than
* fetching the system metadata of each model. Useful when you only need to retrieve limited information about
* each package member. Set query-specific parameters on the `solrResults` SolrResults set on this collection.
*/
fetch: function (options) {
// Fetch the system metadata for this resource map
this.packageModel.fetch();
if (typeof options == "object") {
// If the fetchModels property is set to false,
if (options.fetchModels === false) {
// Save the property to the Collection itself so it is accessible in other functions
this.fetchModels = false;
// Remove the property from the options Object since we don't want to send it with the XHR
delete options.fetchModels;
this.once("reset", this.triggerComplete);
}
// If the fetchFromIndex property is set to true
else if (options.fromIndex) {
this.fetchFromIndex();
return;
}
}
// Set some custom fetch options
var fetchOptions = _.extend({ dataType: "text" }, options);
var thisPackage = this;
// Function to retry fetching with user login details if the initial fetch fails
var retryFetch = function () {
// Add the authorization options
var authFetchOptions = _.extend(
fetchOptions,
MetacatUI.appUserModel.createAjaxSettings(),
);
// Fetch the resource map RDF XML with user login details
return Backbone.Collection.prototype.fetch
.call(thisPackage, authFetchOptions)
.fail(function () {
// trigger failure()
console.log("Fetch failed");
thisPackage.trigger("fetchFailed", thisPackage);
});
};
// Fetch the resource map RDF XML
return Backbone.Collection.prototype.fetch
.call(this, fetchOptions)
.fail(function () {
// If the initial fetch fails, retry with user login details
return retryFetch();
});
},
/*
* Deserialize a Package from OAI-ORE RDF XML
*/
parse: function (response, options) {
//Save the raw XML in case it needs to be used later
this.objectXML = response;
var RDF = this.rdf.Namespace(this.namespaces.RDF),
FOAF = this.rdf.Namespace(this.namespaces.FOAF),
OWL = this.rdf.Namespace(this.namespaces.OWL),
DC = this.rdf.Namespace(this.namespaces.DC),
ORE = this.rdf.Namespace(this.namespaces.ORE),
DCTERMS = this.rdf.Namespace(this.namespaces.DCTERMS),
CITO = this.rdf.Namespace(this.namespaces.CITO),
PROV = this.rdf.Namespace(this.namespaces.PROV),
XSD = this.rdf.Namespace(this.namespaces.XSD);
var memberStatements = [],
atLocationStatements = [], // array to store atLocation statements
memberURIParts,
memberPIDStr,
memberPID,
memberPIDs = [],
memberModel,
documentsStatements,
objectParts,
objectPIDStr,
objectPID,
objectAtLocationValue,
scimetaID, // documentor
scidataID, // documentee
models = []; // the models returned by parse()
try {
//First, make sure we are only using one CN Base URL in the RDF or the RDF parsing will fail.
var cnResolveUrl = MetacatUI.appModel.get("resolveServiceUrl");
var cnURLs = _.uniq(
response.match(
/cn\S+\.test\.dataone\.org\/cn\/v\d\/resolve|cn\.dataone\.org\/cn\/v\d\/resolve/g,
),
);
if (cnURLs.length > 1) {
response = response.replace(
/cn\S+\.test\.dataone\.org\/cn\/v\d\/resolve|cn\.dataone\.org\/cn\/v\d\/resolve/g,
cnResolveUrl.substring(cnResolveUrl.indexOf("https://") + 8),
);
}
this.rdf.parse(
response,
this.dataPackageGraph,
this.url(),
"application/rdf+xml",
);
// List the package members
memberStatements = this.dataPackageGraph.statementsMatching(
undefined,
ORE("aggregates"),
undefined,
undefined,
);
// Get system metadata for each member to eval the formatId
_.each(
memberStatements,
function (memberStatement) {
memberURIParts = memberStatement.object.value.split("/");
memberPIDStr = _.last(memberURIParts);
memberPID = decodeURIComponent(memberPIDStr);
if (memberPID) memberPIDs.push(memberPID);
//TODO: Test passing merge:true when adding a model and this if statement may not be necessary
//Create a DataONEObject model to represent this collection member and add to the collection
if (!_.contains(this.pluck("id"), memberPID)) {
memberModel = new DataONEObject({
id: memberPID,
resourceMap: [this.packageModel.get("id")],
collections: [this],
});
models.push(memberModel);
}
//If the model already exists, add this resource map ID to it's list of resource maps
else {
memberModel = this.get(memberPID);
models.push(memberModel);
var rMaps = memberModel.get("resourceMap");
if (
rMaps &&
Array.isArray(rMaps) &&
!_.contains(rMaps, this.packageModel.get("id"))
)
rMaps.push(this.packageModel.get("id"));
else if (rMaps && !Array.isArray(rMaps))
rMaps = [rMaps, this.packageModel.get("id")];
else rMaps = [this.packageModel.get("id")];
}
},
this,
);
//Save the list of original ids
this.originalMembers = memberPIDs;
// Get the isDocumentedBy relationships
documentsStatements = this.dataPackageGraph.statementsMatching(
undefined,
CITO("documents"),
undefined,
undefined,
);
var sciMetaPids = [];
_.each(
documentsStatements,
function (documentsStatement) {
// Extract and URI-decode the metadata pid
scimetaID = decodeURIComponent(
_.last(documentsStatement.subject.value.split("/")),
);
sciMetaPids.push(scimetaID);
// Extract and URI-decode the data pid
scidataID = decodeURIComponent(
_.last(documentsStatement.object.value.split("/")),
);
// Store the isDocumentedBy relationship
if (typeof this.originalIsDocBy[scidataID] == "undefined")
this.originalIsDocBy[scidataID] = [scimetaID];
else if (
Array.isArray(this.originalIsDocBy[scidataID]) &&
!_.contains(this.originalIsDocBy[scidataID], scimetaID)
)
this.originalIsDocBy[scidataID].push(scimetaID);
else
this.originalIsDocBy[scidataID] = _.uniq([
this.originalIsDocBy[scidataID],
scimetaID,
]);
//Find the model in this collection for this data object
//var dataObj = this.get(scidataID);
var dataObj = _.find(models, function (m) {
return m.get("id") == scidataID;
});
if (dataObj) {
//Get the isDocumentedBy field
var isDocBy = dataObj.get("isDocumentedBy");
if (
isDocBy &&
Array.isArray(isDocBy) &&
!_.contains(isDocBy, scimetaID)
)
isDocBy.push(scimetaID);
else if (isDocBy && !Array.isArray(isDocBy))
isDocBy = [isDocBy, scimetaID];
else isDocBy = [scimetaID];
//Set the isDocumentedBy field
dataObj.set("isDocumentedBy", isDocBy);
}
},
this,
);
//Save the list of science metadata pids
this.sciMetaPids = sciMetaPids;
// Parse atLocation
var atLocationObject = {};
atLocationStatements = this.dataPackageGraph.statementsMatching(
undefined,
PROV("atLocation"),
undefined,
undefined,
);
const ref = this;
// Get atLocation information for each statement in the resourceMap
_.each(
atLocationStatements,
function (atLocationStatement) {
objectParts = atLocationStatement.subject.value.split("/");
objectPIDStr = _.last(objectParts);
objectPID = decodeURIComponent(objectPIDStr);
objectAtLocationValue = atLocationStatement.object.value;
atLocationObject[objectPID] = ref.getAbsolutePath(
objectAtLocationValue,
);
},
this,
);
this.atLocationObject = atLocationObject;
//Put the science metadata pids first
memberPIDs = _.difference(memberPIDs, sciMetaPids);
_.each(_.uniq(sciMetaPids), function (id) {
memberPIDs.unshift(id);
});
//Don't fetch each member model if the fetchModels property on this Collection is set to false
if (this.fetchModels !== false) {
//Add the models to the collection now, silently
//this.add(models, {silent: true});
//Retrieve the model for each member
_.each(
models,
function (memberModel) {
var collection = this;
memberModel.fetch();
memberModel.once("sync", function (oldModel) {
//Get the right model type based on the model values
var newModel = collection.getMember(oldModel);
//If the model type has changed, then mark the model as unsynced, since there may be custom fetch() options for the new model
if (oldModel.type != newModel.type) {
// DataPackages shouldn't be fetched until we support nested packages better in the UI
if (newModel.type == "DataPackage") {
//Trigger a replace event so other parts of the app know when a model has been replaced with a different type
oldModel.trigger("replace", newModel);
} else {
newModel.set("synced", false);
newModel.fetch();
newModel.once("sync", function (fetchedModel) {
fetchedModel.set("synced", true);
//Remove the model from the collection and add it back
collection.remove(oldModel);
collection.add(fetchedModel);
//Trigger a replace event so other parts of the app know when a model has been replaced with a different type
oldModel.trigger("replace", newModel);
if (newModel.type == "EML")
collection.trigger("add:EML");
});
}
} else {
newModel.set("synced", true);
collection.add(newModel, {
merge: true,
});
if (newModel.type == "EML") collection.trigger("add:EML");
}
});
},
this,
);
}
} catch (error) {
console.log(error);
}
// trigger complete if fetchModel is false and this is the only object in the package
if (this.fetchModels == false && models.length == 1)
this.triggerComplete();
return models;
},
/* Parse the provenance relationships from the RDF graph, after all DataPackage members
have been fetched, as the prov info will be stored in them.
*/
parseProv: function () {
try {
/* Now run the SPARQL queries for the provenance relationships */
var provQueries = [];
/* result: pidValue, wasDerivedFromValue (prov_wasDerivedFrom) */
provQueries["prov_wasDerivedFrom"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_wasDerivedFrom \n" +
"WHERE { \n" +
"?derived_data prov:wasDerivedFrom ?primary_data . \n" +
"?derived_data dcterms:identifier ?pid . \n" +
"?primary_data dcterms:identifier ?prov_wasDerivedFrom . \n" +
"} \n" +
"]]>";
/* result: pidValue, generatedValue (prov_generated) */
provQueries["prov_generated"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_generated \n" +
"WHERE { \n" +
"?result prov:wasGeneratedBy ?activity . \n" +
"?activity prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?result dcterms:identifier ?prov_generated . \n" +
"?program dcterms:identifier ?pid . \n" +
"} \n" +
"]]>";
/* result: pidValue, wasInformedByValue (prov_wasInformedBy) */
provQueries["prov_wasInformedBy"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_wasInformedBy \n" +
"WHERE { \n" +
"?activity prov:wasInformedBy ?previousActivity . \n" +
"?activity dcterms:identifier ?pid . \n" +
"?previousActivity dcterms:identifier ?prov_wasInformedBy . \n" +
"} \n" +
"]]> \n";
/* result: pidValue, usedValue (prov_used) */
provQueries["prov_used"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_used \n" +
"WHERE { \n" +
"?activity prov:used ?data . \n" +
"?activity prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?program dcterms:identifier ?pid . \n" +
"?data dcterms:identifier ?prov_used . \n" +
"} \n" +
"]]> \n";
/* result: pidValue, programPidValue (prov_generatesByProgram) */
provQueries["prov_generatedByProgram"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_generatedByProgram \n" +
"WHERE { \n" +
"?derived_data prov:wasGeneratedBy ?execution . \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?program dcterms:identifier ?prov_generatedByProgram . \n" +
"?derived_data dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* result: pidValue, executionPidValue */
provQueries["prov_generatedByExecution"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_generatedByExecution \n" +
"WHERE { \n" +
"?derived_data prov:wasGeneratedBy ?execution . \n" +
"?execution dcterms:identifier ?prov_generatedByExecution . \n" +
"?derived_data dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* result: pidValue, pid (prov_generatedByProgram) */
provQueries["prov_generatedByUser"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_generatedByUser \n" +
"WHERE { \n" +
"?derived_data prov:wasGeneratedBy ?execution . \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:agent ?prov_generatedByUser . \n" +
"?derived_data dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, programPidValue (prov_usedByProgram) */
provQueries["prov_usedByProgram"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_usedByProgram \n" +
"WHERE { \n" +
"?execution prov:used ?primary_data . \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?program dcterms:identifier ?prov_usedByProgram . \n" +
"?primary_data dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, executionIdValue (prov_usedByExecution) */
provQueries["prov_usedByExecution"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_usedByExecution \n" +
"WHERE { \n" +
"?execution prov:used ?primary_data . \n" +
"?primary_data dcterms:identifier ?pid . \n" +
"?execution dcterms:identifier ?prov_usedByExecution . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, pid (prov_usedByUser) */
provQueries["prov_usedByUser"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_usedByUser \n" +
"WHERE { \n" +
"?execution prov:used ?primary_data . \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:agent ?prov_usedByUser . \n" +
"?primary_data dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, executionIdValue (prov_wasExecutedByExecution) */
provQueries["prov_wasExecutedByExecution"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_wasExecutedByExecution \n" +
"WHERE { \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?execution dcterms:identifier ?prov_wasExecutedByExecution . \n" +
"?program dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, pid (prov_wasExecutedByUser) */
provQueries["prov_wasExecutedByUser"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_wasExecutedByUser \n" +
"WHERE { \n" +
"?execution prov:qualifiedAssociation ?association . \n" +
"?association prov:hadPlan ?program . \n" +
"?association prov:agent ?prov_wasExecutedByUser . \n" +
"?program dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, derivedDataPidValue (prov_hasDerivations) */
provQueries["prov_hasDerivations"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"PREFIX cito: <http://purl.org/spar/cito/> \n" +
"SELECT ?pid ?prov_hasDerivations \n" +
"WHERE { \n" +
"?derived_data prov:wasDerivedFrom ?source_data . \n" +
"?source_data dcterms:identifier ?pid . \n" +
"?derived_data dcterms:identifier ?prov_hasDerivations . \n" +
"} \n" +
"]]> \n";
/* results: pidValue, pid (prov_instanceOfClass) */
provQueries["prov_instanceOfClass"] =
"<![CDATA[ \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
"PREFIX prov: <http://www.w3.org/ns/prov#> \n" +
"PREFIX provone: <http://purl.dataone.org/provone/2015/01/15/ontology#> \n" +
"PREFIX ore: <http://www.openarchives.org/ore/terms/> \n" +
"PREFIX dcterms: <http://purl.org/dc/terms/> \n" +
"SELECT ?pid ?prov_instanceOfClass \n" +
"WHERE { \n" +
"?subject rdf:type ?prov_instanceOfClass . \n" +
"?subject dcterms:identifier ?pid . \n" +
"} \n" +
"]]> \n";
// These are the provenance fields that are currently searched for in the provenance queries, but
// not all of these fields are displayed by any view.
// Note: this list is different than the prov list returned by MetacatUI.appSearchModel.getProvFields()
this.provFields = [
"prov_wasDerivedFrom",
"prov_generated",
"prov_wasInformedBy",
"prov_used",
"prov_generatedByProgram",
"prov_generatedByExecution",
"prov_generatedByUser",
"prov_usedByProgram",
"prov_usedByExecution",
"prov_usedByUser",
"prov_wasExecutedByExecution",
"prov_wasExecutedByUser",
"prov_hasDerivations",
"prov_instanceOfClass",
];
// Process each SPARQL query
var keys = Object.keys(provQueries);
this.queriesToRun = keys.length;
//Bind the onResult and onDone functions to the model so they can be called out of context
this.onResult = _.bind(this.onResult, this);
this.onDone = _.bind(this.onDone, this);
/* Run queries for all provenance fields.
Each query may have multiple solutions and each solution will trigger a callback
to the 'onResult' function. When each query has completed, the 'onDone' function
is called for that query.
*/
for (var iquery = 0; iquery < keys.length; iquery++) {
var eq = rdf.SPARQLToQuery(
provQueries[keys[iquery]],
false,
this.dataPackageGraph,
);
this.dataPackageGraph.query(
eq,
this.onResult,
this.url(),
this.onDone,
);
}
} catch (error) {
console.log(error);
}
},
// The return values have to be extracted from the result.
getValue: function (result, name) {
var res = result[name];
// The result is of type 'NamedNode', just return the string value
if (res) {
return res.value;
} else return " ";
},
/* This callback is called for every query solution of the SPARQL queries. One
query may result in multple queries solutions and calls to this function.
Each query result returns two pids, i.e. pid: 1234 prov_generated: 5678,
which corresponds to the RDF triple '5678 wasGeneratedBy 1234', or the
DataONE solr document for pid '1234', with the field prov_generated: 5678.
The result can look like this:
[?pid: t, ?prov_wasDerivedFrom: t, ?primary_data: t, ?derived_data: t]
?derived_data : t {termType: "NamedNode", value: "https://cn-stage.test.dataone.org/cn/v2/resolve/urn%3Auuid%3Adbbb9a2e-af64-452a-b7b9-122861a5dbb2"}
?pid : t {termType: "Literal", value: "urn:uuid:dbbb9a2e-af64-452a-b7b9-122861a5dbb2", datatype: t}
?primary_data : t {termType: "NamedNode", value: "https://cn-stage.test.dataone.org/cn/v2/resolve/urn%3Auuid%3Aaae9d025-a331-4c3a-b399-a8ca0a2826ef"}
?prov_wasDerivedFrom : t {termType: "Literal", value: "urn:uuid:aae9d025-a331-4c3a-b399-a8ca0a2826ef", datatype: t}]
*/
onResult: function (result) {
var currentPid = this.getValue(result, "?pid");
var resval;
var provFieldResult;
var provFieldValues;
// If there is a solution for this query, assign the value
// to the prov field attribute (e.g. "prov_generated") of the package member (a DataONEObject)
// with id = '?pid'
if (typeof currentPid !== "undefined" && currentPid !== " ") {
var currentMember = null;
var provFieldValues;
var fieldName = null;
var vals = [];
var resultMember = null;
currentMember = this.find(function (model) {
return model.get("id") === currentPid;
});
if (typeof currentMember === "undefined") {
return;
}
// Search for a provenenace field value (i.e. 'prov_wasDerivedFrom') that was
// returned from the query. The current prov queries all return one prov field each
// (see this.provFields).
// Note: dataPackage.provSources and dataPackage.provDerivations are accumulators for
// the entire DataPackage. member.sources and member.derivations are accumulators for
// each package member, and are used by functions such as ProvChartView().
for (var iFld = 0; iFld < this.provFields.length; iFld++) {
fieldName = this.provFields[iFld];
resval = "?" + fieldName;
// The pid corresponding to the object of the RDF triple, with the predicate
// of 'prov_generated', 'prov_used', etc.
// getValue returns a string value.
provFieldResult = this.getValue(result, resval);
if (provFieldResult != " ") {
// Find the Datapacakge member for the result 'pid' and add the result
// prov_* value to it. This is the package member that is the 'subject' of the
// prov relationship.
// The 'resultMember' could be in the current package, or could be in another 'related' package.
resultMember = this.find(function (model) {
return model.get("id") === provFieldResult;
});
if (typeof resultMember !== "undefined") {
// If this prov field is a 'source' field, add it to 'sources'
if (currentMember.isSourceField(fieldName)) {
// Get the package member that the id of the prov field is associated with
if (
_.findWhere(this.sources, {
id: provFieldResult,
}) == null
) {
this.sources.push(resultMember);
}
// Only add the result member if it has not already been added.
if (
_.findWhere(currentMember.get("provSources"), {
id: provFieldResult,
}) == null
) {
vals = currentMember.get("provSources");
vals.push(resultMember);
currentMember.set("provSources", vals);
}
} else if (currentMember.isDerivationField(fieldName)) {
// If this prov field is a 'derivation' field, add it to 'derivations'
if (
_.findWhere(this.derivations, {
id: provFieldResult,
}) == null
) {
this.derivations.push(resultMember);
}
if (
_.findWhere(currentMember.get("provDerivations"), {
id: provFieldResult,
}) == null
) {
vals = currentMember.get("provDerivations");
vals.push(resultMember);
currentMember.set("provDerivations", vals);
}
}
// Get the existing values for this prov field in the package member
vals = currentMember.get(fieldName);
// Push this result onto the prov file list if it is not there, i.e.
if (!_.contains(vals, resultMember)) {
vals.push(resultMember);
currentMember.set(fieldName, vals);
}
//provFieldValues = _.uniq(provFieldValues);
// Add the current prov valid (a pid) to the current value in the member
//currentMember.set(fieldName, provFieldValues);
//this.add(currentMember, { merge: true });
} else {
// The query result field is not the identifier of a packge member, so it may be the identifier
// of another 'related' package, or it may be a string value that is the object of a prov relationship,
// i.e. for 'prov_instanceOfClass' == 'http://purl.dataone.org/provone/2015/01/15/ontology#Data',
// so add the value to the current member.
vals = currentMember.get(fieldName);
if (!_.contains(vals, provFieldResult)) {
vals.push(provFieldResult);
currentMember.set(fieldName, vals);
}
}
}
}
}
},
/* This callback is called when all queries have finished. */
onDone: function () {
if (this.queriesToRun > 1) {
this.queriesToRun--;
} else {
// Signal that all prov queries have finished
this.provenanceFlag = "complete";
this.trigger("queryComplete");
}
},
/*
* Use the DataONEObject parseSysMeta() function
*/
parseSysMeta: function () {
return DataONEObject.parseSysMeta.call(this, arguments[0]);
},
/**
* Overwrite the Backbone.Collection.sync() function to set custom options
* @param {Object} [options] - Options for this DataPackage save
* @param {Boolean} [options.sysMetaOnly] - If true, only the system metadata of this Package will be saved.
* @param {Boolean} [options.resourceMapOnly] - If true, only the Resource Map/Package object will be saved. Metadata and Data objects aggregated by the package will be skipped.
*/
save: function (options) {
if (!options) var options = {};
this.packageModel.set("uploadStatus", "p");
//Get the system metadata first if we haven't retrieved it yet
if (!this.packageModel.get("sysMetaXML")) {
var collection = this;
this.packageModel.fetch({
success: function () {
collection.save(options);
},
});
return;
}
//If we want to update the system metadata only,
// then update via the DataONEObject model and exit
if (options.sysMetaOnly) {
this.packageModel.save(null, options);
return;
}
if (options.resourceMapOnly !== true) {
//Sort the models in the collection so the metadata is saved first
var metadataModels = this.where({ type: "Metadata" });
var dataModels = _.difference(this.models, metadataModels);
var sortedModels = _.union(metadataModels, dataModels);
var modelsInProgress = _.filter(sortedModels, function (m) {
return (
m.get("uploadStatus") == "p" ||
m.get("sysMetaUploadStatus") == "p"
);
});
var modelsToBeSaved = _.filter(sortedModels, function (m) {
//Models should be saved if they are in the save queue, had an error saving earlier,
//or they are Science Metadata model that is NOT already in progress
return (
(m.get("type") == "Metadata" && m.get("uploadStatus") == "q") ||
(m.get("type") == "Data" &&
m.get("hasContentChanges") &&
m.get("uploadStatus") != "p" &&
m.get("uploadStatus") != "c" &&
m.get("uploadStatus") != "e") ||
(m.get("type") == "Metadata" &&
m.get("uploadStatus") != "p" &&
m.get("uploadStatus") != "c" &&
m.get("uploadStatus") != "e" &&
m.get("uploadStatus") !== null)
);
});
//Get an array of data objects whose system metadata should be updated.
var sysMetaToUpdate = _.reject(dataModels, function (m) {
// Find models that don't have any content changes to save,
// and whose system metadata is not already saving
return (
!m.hasUpdates() ||
m.get("hasContentChanges") ||
m.get("sysMetaUploadStatus") == "p" ||
m.get("sysMetaUploadStatus") == "c" ||
m.get("sysMetaUploadStatus") == "e"
);
});
//First quickly validate all the models before attempting to save any
var allValid = _.every(modelsToBeSaved, function (m) {
if (m.isValid()) {
m.trigger("valid");
return true;
} else {
return false;
}
});
// If at least once model to be saved is invalid,
// or the metadata failed to save, cancel the save.
if (
!allValid ||
_.contains(
_.map(metadataModels, function (model) {
return model.get("uploadStatus");
}),
"e",
)
) {
this.packageModel.set("changed", false);
this.packageModel.set("uploadStatus", "q");
this.trigger("cancelSave");
return;
}
//If we are saving at least one model in this package, then serialize the Resource Map RDF XML
if (modelsToBeSaved.length) {
try {
//Set a new id and keep our old id
if (!this.packageModel.isNew()) {
//Update the identifier for this object
this.packageModel.updateID();
}
//Create the resource map XML
var mapXML = this.serialize();
} catch (serializationException) {
//If serialization failed, revert back to our old id
this.packageModel.resetID();
//Cancel the save and show an error message
this.packageModel.set("changed", false);
this.packageModel.set("uploadStatus", "q");
this.trigger(
"errorSaving",
"There was a Javascript error during the serialization process: " +
serializationException,
);
return;
}
}
//First save all the models of the collection, if needed
_.each(
modelsToBeSaved,
function (model) {
//If the model is saved successfully, start this save function again
this.stopListening(model, "successSaving", this.save);
this.listenToOnce(model, "successSaving", this.save);
//If the model fails to save, start this save function
this.stopListening(model, "errorSaving", this.save);
this.listenToOnce(model, "errorSaving", this.save);
//If the model fails to save, start this save function
this.stopListening(model, "cancelSave", this.save);
this.listenToOnce(model, "cancelSave", this.save);
//Save the model and watch for fails
model.save();
//Add it to the list of models in progress
modelsInProgress.push(model);
this.numSaves++;
},
this,
);
//Save the system metadata of all the Data objects
_.each(
sysMetaToUpdate,
function (dataModel) {
//When the sytem metadata has been saved, save this resource map
this.listenTo(dataModel, "change:sysMetaUploadStatus", this.save);
//Update the system metadata
dataModel.updateSysMeta();
//Add it to the list of models in progress
modelsInProgress.push(dataModel);
this.numSaves++;
},
this,
);
//If there are still models in progress of uploading, then exit. (We will return when they are synced to upload the resource map)
if (modelsInProgress.length) return;
}
//If we are saving the resource map object only, and there are changes to save, serialize the RDF XML
else if (this.needsUpdate()) {
try {
//Set a new id and keep our old id
if (!this.packageModel.isNew()) {
//Update the identifier for this object
this.packageModel.updateID();
}
//Create the resource map XML
var mapXML = this.serialize();
} catch (serializationException) {
//If serialization failed, revert back to our old id
this.packageModel.resetID();
//Cancel the save and show an error message
this.packageModel.set("changed", false);
this.packageModel.set("uploadStatus", "q");
this.trigger(
"errorSaving",
"There was a Javascript error during the serialization process: " +
serializationException,
);
return;
}
}
//If we are saving the resource map object only, and there are no changes to save, exit the function
else if (!this.needsUpdate()) {
return;
}
//If no models were saved and this package has no changes, we can exit without saving the resource map
if (this.numSaves < 1 && !this.needsUpdate()) {
this.numSaves = 0;
this.packageModel.set(
"uploadStatus",
this.packageModel.defaults().uploadStatus,
);
this.trigger("successSaving", this);
return;
}
//Reset the number of models saved since they should all be completed by now
this.numSaves = 0;
//Determine the HTTP request type
var requestType;
if (this.packageModel.isNew()) {
requestType = "POST";
} else {
requestType = "PUT";
}
//Create a FormData object to send data with the XHR
var formData = new FormData();
//Add the identifier to the XHR data
if (this.packageModel.isNew()) {
formData.append("pid", this.packageModel.get("id"));
} else {
//Add the ids to the form data
formData.append("newPid", this.packageModel.get("id"));
formData.append("pid", this.packageModel.get("oldPid"));
}
//Do a fresh re-serialization of the RDF XML, in case any pids in the package have changed.
//The hope is that any errors during the serialization process have already been caught during the first serialization above
try {
var mapXML = this.serialize();
} catch (serializationException) {
//Cancel the save and show an error message
this.packageModel.set("changed", false);
this.packageModel.set("uploadStatus", "q");
this.trigger(
"errorSaving",
"There was a Javascript error during the serialization process: " +
serializationException,
);
return;
}
//Make a Blob object from the serialized RDF XML
var mapBlob = new Blob([mapXML], { type: "application/xml" });
//Get the size of the new resource map
this.packageModel.set("size", mapBlob.size);
//Get the new checksum of the resource map
var checksum = md5(mapXML);
this.packageModel.set("checksum", checksum);
this.packageModel.set("checksumAlgorithm", "MD5");
//Set the file name based on the id
this.packageModel.set(
"fileName",
this.packageModel.get("id").replace(/[^a-zA-Z0-9]/g, "_") +
".rdf.xml",
);
//Create the system metadata
var sysMetaXML = this.packageModel.serializeSysMeta();
//Send the system metadata
var xmlBlob = new Blob([sysMetaXML], {
type: "application/xml",
});
//Add the object XML and System Metadata XML to the form data
//Append the system metadata first, so we can take advantage of Metacat's streaming multipart handler
formData.append("sysmeta", xmlBlob, "sysmeta");
formData.append("object", mapBlob);
var collection = this;
var requestSettings = {
url: this.packageModel.isNew()
? this.url()
: this.url({ update: true }),
type: requestType,
cache: false,
contentType: false,
processData: false,
data: formData,
success: function (response) {
//Update the object XML
collection.objectXML = mapXML;
collection.packageModel.set(
"sysMetaXML",
collection.packageModel.serializeSysMeta(),
);
//Reset the upload status for all members
_.each(collection.where({ uploadStatus: "c" }), function (m) {
m.set("uploadStatus", m.defaults().uploadStatus);
});
// Reset oldPid to null so we know we need to update the ID
// in the future
collection.packageModel.set("oldPid", null);
//Reset the upload status for the package
collection.packageModel.set(
"uploadStatus",
collection.packageModel.defaults().uploadStatus,
);
// Reset the content changes status
collection.packageModel.set("hasContentChanges", false);
// This package is no longer new, so mark it as such
collection.packageModel.set("isNew", false);
collection.trigger("successSaving", collection);
collection.packageModel.fetch({ merge: true });
_.each(sysMetaToUpdate, function (dataModel) {
dataModel.set("sysMetaUploadStatus", "c");
});
},
error: function (data) {
//Reset the id back to its original state
collection.packageModel.resetID();
//Reset the upload status for all members
_.each(collection.where({ uploadStatus: "c" }), function (m) {
m.set("uploadStatus", m.defaults().uploadStatus);
});
//When there is no network connection (status == 0), there will be no response text
if (data.status == 408 || data.status == 0) {
var parsedResponse =
"There was a network issue that prevented this file from uploading. " +
"Make sure you are connected to a reliable internet connection.";
} else {
var parsedResponse = $(data.responseText)
.not("style, title")
.text();
}
//Save the error message in the model
collection.packageModel.set("errorMessage", parsedResponse);
//Reset the upload status for the package
collection.packageModel.set("uploadStatus", "e");
collection.trigger("errorSaving", parsedResponse);
// Track this error in our analytics
MetacatUI.analytics?.trackException(
`DataPackage save error: ${parsedResponse}`,
collection.packageModel.get("id"),
true,
);
},
};
$.ajax(
_.extend(
requestSettings,
MetacatUI.appUserModel.createAjaxSettings(),
),
);
},
/*
* When a data package member updates, we evaluate it for its formatid,
* and update it appropriately if it is not a data object only
*/
getMember: function (context, args) {
var memberModel = {};
switch (context.get("formatId")) {
case "http://www.openarchives.org/ore/terms":
context.attributes.id = context.id;
context.attributes.type = "DataPackage";
context.attributes.childPackages = {};
memberModel = new DataPackage(null, {
packageModel: context.attributes,
});
this.packageModel.get("childPackages")[
memberModel.packageModel.id
] = memberModel;
break;
case "eml://ecoinformatics.org/eml-2.0.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new EML211(context.attributes);
break;
case "eml://ecoinformatics.org/eml-2.0.1":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new EML211(context.attributes);
break;
case "eml://ecoinformatics.org/eml-2.1.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new EML211(context.attributes);
break;
case "eml://ecoinformatics.org/eml-2.1.1":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new EML211(context.attributes);
break;
case "https://eml.ecoinformatics.org/eml-2.2.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new EML211(context.attributes);
break;
case "-//ecoinformatics.org//eml-access-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-access-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-attribute-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-attribute-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-constraint-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-constraint-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-coverage-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-coverage-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-dataset-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-distribution-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-distribution-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-entity-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-entity-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-literature-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-literature-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-party-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-party-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-physical-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-physical-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-project-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-project-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-protocol-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-protocol-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-resource-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-resource-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-software-2.0.0beta4//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "-//ecoinformatics.org//eml-software-2.0.0beta6//EN":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "FGDC-STD-001-1998":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "FGDC-STD-001.1-1999":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "FGDC-STD-001.2-1999":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "INCITS-453-2009":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "ddi:codebook:2_5":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://datacite.org/schema/kernel-3.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://datacite.org/schema/kernel-3.1":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://datadryad.org/profile/v3.1":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://ns.dataone.org/metadata/schema/onedcx/v1.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://purl.org/dryad/terms/":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://purl.org/ornl/schema/mercury/terms/v1.0":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://rs.tdwg.org/dwc/xsd/simpledarwincore/":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.cuahsi.org/waterML/1.0/":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.cuahsi.org/waterML/1.1/":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.esri.com/metadata/esriprof80.dtd":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.icpsr.umich.edu/DDI":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.isotc211.org/2005/gmd":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.isotc211.org/2005/gmd-noaa":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.loc.gov/METS/":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
case "http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2":
context.set({ type: "Metadata", sortOrder: 1 });
memberModel = new ScienceMetadata(context.attributes);
break;
default:
// For other data formats, keep just the DataONEObject sysmeta
context.set({ type: "Data", sortOrder: 2 });
memberModel = context;
}
if (memberModel.type == "DataPackage") {
// We have a nested collection
memberModel.packageModel.set(
"nodeLevel",
this.packageModel.get("nodeLevel") + 1,
);
} else {
// We have a model
memberModel.set("nodeLevel", this.packageModel.get("nodeLevel")); // same level for all members
}
return memberModel;
},
triggerComplete: function (model) {
//If the last fetch did not fetch the models of the collection, then mark as complete now.
if (this.fetchModels === false) {
// Delete the fetchModels property since it is set only once per fetch.
delete this.fetchModels;
this.trigger("complete", this);
return;
}
//Check if the collection is done being retrieved
var notSynced = this.reject(function (m) {
return m.get("synced") || m.get("id") == model.get("id");
});
//If there are any models that are not synced yet, the collection is not complete
if (notSynced.length > 0) {
return;
}
//If the number of models in this collection does not equal the number of objects referenced in the RDF XML, the collection is not complete
if (this.originalMembers.length > this.length) return;
this.sort();
this.trigger("complete", this);
},
/* Accumulate edits that are made to the provenance relationships via the ProvChartView. these
edits are accumulated here so that they are available to any package member or view.
*/
recordProvEdit: function (operation, subject, predicate, object) {
if (!this.provEdits.length) {
this.provEdits = [[operation, subject, predicate, object]];
} else {
// First check if the edit already exists in the list. If yes, then
// don't add it again! This could occur if an edit icon was clicked rapidly
// before it is dismissed.
var editFound = _.find(this.provEdits, function (edit) {
return (
edit[0] == operation &&
edit[1] == subject &&
edit[2] == predicate &&
edit[3] == object
);
});
if (typeof editFound != "undefined") {
return;
}
// If this is a delete operation, then check if a matching operation
// is in the edit list (i.e. the user may have changed their mind, and
// they just want to cancel an edit). If yes, then just delete the
// matching add edit request
var editListSize = this.provEdits.length;
var oppositeOp = operation == "delete" ? "add" : "delete";
this.provEdits = _.reject(this.provEdits, function (edit) {
var editOperation = edit[0];
var editSubjectId = edit[1];
var editPredicate = edit[2];
var editObject = edit[3];
if (
editOperation == oppositeOp &&
editSubjectId == subject &&
editPredicate == predicate &&
editObject == object
) {
return true;
}
});
// If we cancelled out edit containing inverse of the current edit
// then the edit list will now be one edit shorter. Test for this
// and only save the current edit if we didn't remove the inverse.
if (editListSize >= this.provEdits.length) {
this.provEdits.push([operation, subject, predicate, object]);
}
}
},
// Return true if the prov edits list is not empty
provEditsPending: function () {
if (this.provEdits.length) return true;
return false;
},
/* If provenance relationships have been modified by the provenance editor (in ProvChartView), then
update the ORE Resource Map and save it to the server.
*/
saveProv: function () {
var rdf = this.rdf;
var graph = this.dataPackageGraph;
var provEdits = this.provEdits;
if (!provEdits.length) {
return;
}
var RDF = rdf.Namespace(this.namespaces.RDF),
PROV = rdf.Namespace(this.namespaces.PROV),
PROVONE = rdf.Namespace(this.namespaces.PROVONE),
DCTERMS = rdf.Namespace(this.namespaces.DCTERMS),
CITO = rdf.Namespace(this.namespaces.CITO),
XSD = rdf.Namespace(this.namespaces.XSD);
var cnResolveUrl = this.getCnURI();
/* Check if this package member had provenance relationships added
or deleted by the provenance editor functionality of the ProvChartView
*/
_.each(
provEdits,
function (edit) {
var operation, subject, predicate, object;
var provStatements;
operation = edit[0];
subject = edit[1];
predicate = edit[2];
object = edit[3];
// The predicates of the provenance edits recorded by the ProvChartView
// indicate which W3C PROV relationship has been recorded.
// First check if this relationship alread exists in the RDF graph.
// See DataPackage.parseProv for a description of how relationships from an ORE resource map
// are parsed and stored in DataONEObjects. Here we are reversing the process, so may need
// The representation of the PROVONE data model is simplified in the ProvChartView, to aid
// legibility for users not familiar with the details of the PROVONE model. In this simplification,
// a provone:Program has direct inputs and outputs. In the actual model, a prov:Execution has
// inputs and outputs and is connected to a program via a prov:association. We must 'expand' the
// simplified provenance updates recorded by the editor into the fully detailed representation
// of the actual model.
var executionId, executionURI, executionNode;
var programId, programURI, programNode;
var dataId, dataURI, dataNode;
var derivedDataURI, derivedDataNode;
var lastRef = false;
//var graph = this.dataPackageGraph;
//Create a node for the subject and object
var subjectNode = rdf.sym(this.getURIFromRDF(subject)),
objectNode = rdf.sym(this.getURIFromRDF(object));
switch (predicate) {
case "prov_wasDerivedFrom":
derivedDataNode = subjectNode;
dataNode = objectNode;
if (operation == "add") {
this.addToGraph(dataNode, RDF("type"), PROVONE("Data"));
this.addToGraph(
derivedDataNode,
RDF("type"),
PROVONE("Data"),
);
this.addToGraph(
derivedDataNode,
PROV("wasDerivedFrom"),
dataNode,
);
} else {
graph.removeMatches(
derivedDataNode,
PROV("wasDerivedFrom"),
dataNode,
);
this.removeIfLastProvRef(
dataNode,
RDF("type"),
PROVONE("Data"),
);
this.removeIfLastProvRef(
derivedDataNode,
RDF("type"),
PROVONE("Data"),
);
}
break;
case "prov_generatedByProgram":
programId = object;
dataNode = subjectNode;
var removed = false;
if (operation == "add") {
// 'subject' is the program id, which is a simplification of the PROVONE model for display.
// In the PROVONE model, execution 'uses' and input, and is associated with a program.
executionId = this.addProgramToGraph(programId);
//executionNode = rdf.sym(cnResolveUrl + encodeURIComponent(executionId));
executionNode = this.getExecutionNode(executionId);
this.addToGraph(dataNode, RDF("type"), PROVONE("Data"));
this.addToGraph(
dataNode,
PROV("wasGeneratedBy"),
executionNode,
);
} else {
executionId = this.getExecutionId(programId);
executionNode = this.getExecutionNode(executionId);
graph.removeMatches(
dataNode,
PROV("wasGeneratedBy"),
executionNode,
);
removed = this.removeProgramFromGraph(programId);
this.removeIfLastProvRef(
dataNode,
RDF("type"),
PROVONE("Data"),
);
}
break;
case "prov_usedByProgram":
programId = object;
dataNode = subjectNode;
if (operation == "add") {
// 'subject' is the program id, which is a simplification of the PROVONE model for display.
// In the PROVONE model, execution 'uses' and input, and is associated with a program.
executionId = this.addProgramToGraph(programId);
//executionNode = rdf.sym(cnResolveUrl + encodeURIComponent(executionId));
executionNode = this.getExecutionNode(executionId);
this.addToGraph(dataNode, RDF("type"), PROVONE("Data"));
this.addToGraph(executionNode, PROV("used"), dataNode);
} else {
executionId = this.getExecutionId(programId);
executionNode = this.getExecutionNode(executionId);
graph.removeMatches(executionNode, PROV("used"), dataNode);
removed = this.removeProgramFromGraph(programId);
this.removeIfLastProvRef(
dataNode,
RDF("type"),
PROVONE("Data"),
);
}
break;
case "prov_hasDerivations":
dataNode = subjectNode;
derivedDataNode = objectNode;
if (operation == "add") {
this.addToGraph(dataNode, RDF("type"), PROVONE("Data"));
this.addToGraph(
derivedDataNode,
RDF("type"),
PROVONE("Data"),
);
this.addToGraph(
derivedDataNode,
PROV("wasDerivedFrom"),
dataNode,
);
} else {
graph.removeMatches(
derivedDataNode,
PROV("wasDerivedFrom"),
dataNode,
);
this.removeIfLastProvRef(
dataNode,
RDF("type"),
PROVONE("Data"),
);
this.removeIfLastProvRef(
derivedDataNode,
RDF("type"),
PROVONE("Data"),
);
}
break;
case "prov_instanceOfClass":
var entityNode = subjectNode;
var classNode = PROVONE(object);
if (operation == "add") {
this.addToGraph(entityNode, RDF("type"), classNode);
} else {
// Make sure there are no other references to this
this.removeIfLastProvRef(entityNode, RDF("type"), classNode);
}
break;
default:
// Print error if predicate for prov edit not found.
}
},
this,
);
// When saving provenance only, we only have to save the Resource Map/Package object.
// So we will send the resourceMapOnly flag with the save function.
this.save({
resourceMapOnly: true,
});
},
/* Add the specified relationship to the RDF graph only if it
has not already been added. */
addToGraph: function (subject, predicate, object) {
var graph = this.dataPackageGraph;
var statements = graph.statementsMatching(subject, predicate, object);
if (!statements.length) {
graph.add(subject, predicate, object);
}
},
/* Remove the statement fromn the RDF graph only if the subject of this
relationship is not referenced by any other provenance relationship, i.e.
for example, the prov relationship "id rdf:type provone:data" is only
needed if the subject ('id') is referenced in another relationship.
Also don't remove it if the subject is in any other prov statement,
meaning it still references another prov object.
*/
removeIfLastProvRef: function (subjectNode, predicateNode, objectNode) {
var graph = this.dataPackageGraph;
var stillUsed = false;
var PROV = rdf.Namespace(this.namespaces.PROV);
var PROVONE = rdf.Namespace(this.namespaces.PROVONE);
// PROV namespace value, used to identify PROV statements
var provStr = PROV("").value;
// PROVONE namespace value, used to identify PROVONE statements
var provoneStr = PROVONE("").value;
// Get the statements from the RDF graph that reference the subject of the
// statement to remove.
var statements = graph.statementsMatching(
undefined,
undefined,
subjectNode,
);
var found = _.find(
statements,
function (statement) {
if (
statement.subject == subjectNode &&
statement.predicate == predicateNode &&
statement.object == objectNode
)
return false;
var pVal = statement.predicate.value;
// Now check if the subject is referenced in a prov statement
// There is another statement that references the subject of the
// statement to remove, so it is still being used and don't
// remove it.
if (pVal.indexOf(provStr) != -1) return true;
if (pVal.indexOf(provoneStr) != -1) return true;
return false;
},
this,
);
// IF not found in the first test, keep looking.
if (typeof found == "undefined") {
// Get the statements from the RDF where
var statements = graph.statementsMatching(
subjectNode,
undefined,
undefined,
);
found = _.find(
statements,
function (statement) {
if (
statement.subject == subjectNode &&
statement.predicate == predicateNode &&
statement.object == objectNode
)
return false;
var pVal = statement.predicate.value;
// Now check if the subject is referenced in a prov statement
if (pVal.indexOf(provStr) != -1) return true;
if (pVal.indexOf(provoneStr) != -1) return true;
// There is another statement that references the subject of the
// statement to remove, so it is still being used and don't
// remove it.
return false;
},
this,
);
}
// The specified statement term isn't being used for prov, so remove it.
if (typeof found == "undefined") {
graph.removeMatches(
subjectNode,
predicateNode,
objectNode,
undefined,
);
}
},
/**
* Remove orphaned blank nodes from the model's current graph
*
* This was put in to support replacing package members who are
* referenced by provenance statements, specifically members typed as
* Programs. rdflib.js will throw an error when serializing if any
* statements in the graph have objects that are blank nodes when no
* other statements in the graph have subjects for the same blank node.
* i.e., blank nodes references that aren't defined.
*
* Should be called during a call to serialize() and mutates
* this.dataPackageGraph directly as a side-effect.
*/
removeOrphanedBlankNodes: function () {
if (!this.dataPackageGraph || !this.dataPackageGraph.statements) {
return;
}
// Collect an array of statements to be removed
var toRemove = [];
_.each(
this.dataPackageGraph.statements,
function (statement) {
if (statement.object.termType !== "BlankNode") {
return;
}
// For this statement, look for other statments about it
var matches = 0;
_.each(this.dataPackageGraph.statements, function (other) {
if (
other.subject.termType === "BlankNode" &&
other.subject.id === statement.object.id
) {
matches += 1;
}
});
// If none are found, add it to our list
if (matches === 0) {
toRemove.push(statement);
}
},
this,
);
// Remove collected statements
_.each(
toRemove,
function (statement) {
this.dataPackageGraph.removeStatement(statement);
},
this,
);
},
/* Get the execution identifier that is associated with a program id.
This will either be in the 'prov_wasExecutedByExecution' of the package member
for the program script, or available by tracing backward in the RDF graph from
the program node, through the assocation to the related execution.
*/
getExecutionId: function (programId) {
var rdf = this.rdf;
var graph = this.dataPackageGraph;
var stmts = null;
var cnResolveUrl = this.getCnURI();
var RDF = rdf.Namespace(this.namespaces.RDF),
DCTERMS = rdf.Namespace(this.namespaces.DCTERMS),
PROV = rdf.Namespace(this.namespaces.PROV),
PROVONE = rdf.Namespace(this.namespaces.PROVONE);
var member = this.get(programId);
var executionId = member.get("prov_wasExecutedByExecution");
if (executionId.length > 0) {
return executionId[0];
} else {
var programNode = rdf.sym(this.getURIFromRDF(programId));
// Get the executionId from the RDF graph
// There can be only one plan for an association
stmts = graph.statementsMatching(
undefined,
PROV("hadPlan"),
programNode,
);
if (typeof stmts == "undefined") return null;
var associationNode = stmts[0].subject;
// There should be only one execution for this assocation.
stmts = graph.statementsMatching(
undefined,
PROV("qualifiedAssociation"),
associationNode,
);
if (typeof stmts == "undefined") return null;
return stmts[0].subject;
}
},
/* Get the RDF node for an execution that is associated with the execution identifier.
The execution may have been created in the resource map as a 'bare' urn:uuid
(no resolveURI), or as a resolve URL, so check for both until the id is
found.
*/
getExecutionNode: function (executionId) {
var rdf = this.rdf;
var graph = this.dataPackageGraph;
var stmts = null;
var testNode = null;
var cnResolveUrl = this.getCnURI();
// First see if the execution exists in the RDF graph as a 'bare' idenfier, i.e.
// a 'urn:uuid'.
stmts = graph.statementsMatching(
rdf.sym(executionId),
undefined,
undefined,
);
if (typeof stmts == "undefined" || !stmts.length) {
// The execution node as urn was not found, look for fully qualified version.
testNode = rdf.sym(this.getURIFromRDF(executionId));
stmts = graph.statementsMatching(
rdf.sym(executionId),
undefined,
undefined,
);
if (typeof stmts == "undefined") {
// Couldn't find the execution, return the standard RDF node value
executionNode = rdf.sym(this.getURIFromRDF(executionId));
return executionNode;
} else {
return testNode;
}
} else {
// The executionNode was found in the RDF graph as a urn
var executionNode = stmts[0].subject;
return executionNode;
}
},
addProgramToGraph: function (programId) {
var rdf = this.rdf;
var graph = this.dataPackageGraph;
var RDF = rdf.Namespace(this.namespaces.RDF),
DCTERMS = rdf.Namespace(this.namespaces.DCTERMS),
PROV = rdf.Namespace(this.namespaces.PROV),
PROVONE = rdf.Namespace(this.namespaces.PROVONE),
XSD = rdf.Namespace(this.namespaces.XSD);
var member = this.get(programId);
var executionId = member.get("prov_wasExecutedByExecution");
var executionNode = null;
var programNode = null;
var associationId = null;
var associationNode = null;
var cnResolveUrl = this.getCnURI();
if (!executionId.length) {
// This is a new execution, so create new execution and association ids
executionId = "urn:uuid:" + uuid.v4();
member.set("prov_wasExecutedByExecution", [executionId]);
// Blank node id. RDF validator doesn't like ':' so don't use in the id
//executionNode = rdf.sym(cnResolveUrl + encodeURIComponent(executionId));
executionNode = this.getExecutionNode(executionId);
//associationId = "_" + uuid.v4();
associationNode = graph.bnode();
} else {
executionId = executionId[0];
// Check if an association exists in the RDF graph for this execution id
//executionNode = rdf.sym(cnResolveUrl + encodeURIComponent(executionId));
executionNode = this.getExecutionNode(executionId);
// Check if there is an association id for this execution.
// If this execution is newly created (via the editor (existing would
// be parsed from the resmap), then create a new association id.
var stmts = graph.statementsMatching(
executionNode,
PROV("qualifiedAssociation"),
undefined,
);
// IF an associati on was found, then use it, else geneate a new one
// (Associations aren't stored in the )
if (stmts.length) {
associationNode = stmts[0].object;
//associationId = stmts[0].object.value;
} else {
//associationId = "_" + uuid.v4();
associationNode = graph.bnode();
}
}
//associationNode = graph.bnode(associationId);
//associationNode = graph.bnode();
programNode = rdf.sym(this.getURIFromRDF(programId));
try {
this.addToGraph(
executionNode,
PROV("qualifiedAssociation"),
associationNode,
);
this.addToGraph(executionNode, RDF("type"), PROVONE("Execution"));
this.addToGraph(
executionNode,
DCTERMS("identifier"),
rdf.literal(executionId, undefined, XSD("string")),
);
this.addToGraph(associationNode, PROV("hadPlan"), programNode);
this.addToGraph(programNode, RDF("type"), PROVONE("Program"));
} catch (error) {
console.log(error);
}
return executionId;
},
// Remove a program identifier from the RDF graph and remove associated
// linkage between the program id and the exection, if the execution is not
// being used by any other statements.
removeProgramFromGraph: function (programId) {
var graph = this.dataPackageGraph;
var rdf = this.rdf;
var stmts = null;
var cnResolveUrl = this.getCnURI();
var RDF = rdf.Namespace(this.namespaces.RDF),
DCTERMS = rdf.Namespace(this.namespaces.DCTERMS),
PROV = rdf.Namespace(this.namespaces.PROV),
PROVONE = rdf.Namespace(this.namespaces.PROVONE),
XSD = rdf.Namespace(this.namespaces.XSD);
var associationNode = null;
var executionId = this.getExecutionId(programId);
if (executionId == null) return false;
//var executionNode = rdf.sym(cnResolveUrl + encodeURIComponent(executionId));
var executionNode = this.getExecutionNode(executionId);
var programNode = rdf.sym(this.getURIFromRDF(programId));
// In order to remove this program from the graph, we have to first determine that
// nothing else is using the execution that is associated with the program (the plan).
// There may be additional 'used', 'geneated', 'qualifiedGeneration', etc. items that
// may be pointing to the execution. If yes, then don't delete the execution or the
// program (the execution's plan).
try {
// Is the program in the graph? If the program is not in the graph, then
// we don't know how to remove the proper execution and assocation.
stmts = graph.statementsMatching(undefined, undefined, programNode);
if (typeof stmts == "undefined" || !stmts.length) return false;
// Is anything else linked to this execution?
stmts = graph.statementsMatching(executionNode, PROV("used"));
if (!typeof stmts == "undefined" || stmts.length) return false;
stmts = graph.statementsMatching(
undefined,
PROV("wasGeneratedBy"),
executionNode,
);
if (!typeof stmts == "undefined" || stmts.length) return false;
stmts = graph.statementsMatching(
executionNode,
PROV("qualifiedGeneration"),
undefined,
);
if (!typeof stmts == "undefined" || stmts.length) return false;
stmts = graph.statementsMatching(
undefined,
PROV("wasInformedBy"),
executionNode,
);
if (!typeof stmts == "undefined" || stmts.length) return false;
stmts = graph.statementsMatching(
undefined,
PROV("wasPartOf"),
executionNode,
);
if (!typeof stmts == "undefined" || stmts.length) return false;
// get association
stmts = graph.statementsMatching(
undefined,
PROV("hadPlan"),
programNode,
);
associationNode = stmts[0].subject;
} catch (error) {
console.log(error);
}
// The execution isn't needed any longer, so remove it and the program.
try {
graph.removeMatches(programNode, RDF("type"), PROVONE("Program"));
graph.removeMatches(associationNode, PROV("hadPlan"), programNode);
graph.removeMatches(
associationNode,
RDF("type"),
PROV("Association"),
);
graph.removeMatches(associationNode, PROV("Agent"), undefined);
graph.removeMatches(executionNode, RDF("type"), PROVONE("Execution"));
graph.removeMatches(
executionNode,
DCTERMS("identifier"),
rdf.literal(executionId, undefined, XSD("string")),
);
graph.removeMatches(
executionNode,
PROV("qualifiedAssociation"),
associationNode,
);
} catch (error) {
console.log(error);
}
return true;
},
/*
* Serialize the DataPackage to OAI-ORE RDF XML
*/
serialize: function () {
//Create an RDF serializer
var serializer = this.rdf.Serializer(),
oldPidVariations,
modifiedDate,
subjectClone,
predicateClone,
objectClone;
serializer.store = this.dataPackageGraph;
//Define the namespaces
var ORE = this.rdf.Namespace(this.namespaces.ORE),
CITO = this.rdf.Namespace(this.namespaces.CITO),
DC = this.rdf.Namespace(this.namespaces.DC),
DCTERMS = this.rdf.Namespace(this.namespaces.DCTERMS),
FOAF = this.rdf.Namespace(this.namespaces.FOAF),
RDF = this.rdf.Namespace(this.namespaces.RDF),
XSD = this.rdf.Namespace(this.namespaces.XSD);
//Get the pid of this package - depends on whether we are updating or creating a resource map
var pid = this.packageModel.get("id"),
oldPid = this.packageModel.get("oldPid"),
cnResolveUrl = this.getCnURI();
//Get a list of the model pids that should be aggregated by this package
var idsFromModel = [];
this.each(function (packageMember) {
//If this object isn't done uploading, don't aggregate it.
//Or if it failed to upload, don't aggregate it.
//But if the system metadata failed to update, it can still be aggregated.
if (
packageMember.get("uploadStatus") !== "p" ||
packageMember.get("uploadStatus") !== "e" ||
packageMember.get("sysMetaUploadStatus") == "e"
) {
idsFromModel.push(packageMember.get("id"));
}
});
this.idsToAggregate = idsFromModel;
//Update the pids in the RDF graph only if we are updating the resource map with a new pid
if (!this.packageModel.isNew()) {
// Remove all describes/isDescribedBy statements (they'll be rebuilt)
this.dataPackageGraph.removeMany(
undefined,
ORE("describes"),
undefined,
undefined,
undefined,
);
this.dataPackageGraph.removeMany(
undefined,
ORE("isDescribedBy"),
undefined,
undefined,
undefined,
);
//Create variations of the resource map ID using the resolve URL so we can always find it in the RDF graph
oldPidVariations = [
oldPid,
encodeURIComponent(oldPid),
cnResolveUrl + oldPid,
cnResolveUrl + encodeURIComponent(oldPid),
this.getURIFromRDF(oldPid),
];
//Using the isAggregatedBy statements, find all the DataONE object ids in the RDF graph
var idsFromXML = [];
var identifierStatements = this.dataPackageGraph.statementsMatching(
undefined,
DCTERMS("identifier"),
undefined,
);
_.each(
identifierStatements,
function (statement) {
idsFromXML.push(
statement.object.value,
encodeURIComponent(statement.object.value),
cnResolveUrl + encodeURIComponent(statement.object.value),
cnResolveUrl + statement.object.value,
);
},
this,
);
//Get all the child package ids
var childPackages = this.packageModel.get("childPackages");
if (typeof childPackages == "object") {
idsFromModel = _.union(idsFromModel, Object.keys(childPackages));
}
//Find the difference between the model IDs and the XML IDs to get a list of added members
var addedIds = _.without(
_.difference(idsFromModel, idsFromXML),
oldPidVariations,
);
//Start an array to track all the member id variations
var allMemberIds = idsFromModel;
//Add the ids with the CN Resolve URLs
_.each(idsFromModel, function (id) {
allMemberIds.push(
cnResolveUrl + encodeURIComponent(id),
cnResolveUrl + id,
encodeURIComponent(id),
);
});
//Find the identifier statement in the resource map
var idNode = this.rdf.lit(oldPid);
var idStatements = this.dataPackageGraph.statementsMatching(
undefined,
undefined,
idNode,
);
//Change all the resource map identifier literal node in the RDF graph
if (idStatements.length) {
var idStatement = idStatements[0];
//Remove the identifier statement
try {
this.dataPackageGraph.remove(idStatement);
} catch (error) {
console.log(error);
}
//Replace the id in the subject URI with the new id
var newRMapURI = "";
if (idStatement.subject.value.indexOf(oldPid) > -1) {
newRMapURI = idStatement.subject.value.replace(oldPid, pid);
} else if (
idStatement.subject.value.indexOf(encodeURIComponent(oldPid)) > -1
) {
newRMapURI = idStatement.subject.value.replace(
encodeURIComponent(oldPid),
encodeURIComponent(pid),
);
}
//Create resource map nodes for the subject and object
var rMapNode = this.rdf.sym(newRMapURI),
rMapIdNode = this.rdf.lit(pid);
//Add the triple for the resource map id
this.dataPackageGraph.add(
rMapNode,
DCTERMS("identifier"),
rMapIdNode,
);
}
//Get all the isAggregatedBy statements
var aggByStatements = $.extend(
true,
[],
this.dataPackageGraph.statementsMatching(
undefined,
ORE("isAggregatedBy"),
),
);
// Remove any other isAggregatedBy statements that are not listed as members of this model
_.each(
aggByStatements,
function (statement) {
if (!_.contains(allMemberIds, statement.subject.value)) {
this.removeFromAggregation(statement.subject.value);
}
},
this,
);
// Change all the statements in the RDF where the aggregation is the subject, to reflect the new resource map ID
var aggregationNode;
_.each(
oldPidVariations,
function (oldPid) {
//Create a node for the old aggregation using this pid variation
aggregationNode = this.rdf.sym(oldPid + "#aggregation");
var aggregationLitNode = this.rdf.lit(
oldPid + "#aggregation",
"",
XSD("anyURI"),
);
//Get all the triples where the old aggregation is the subject
var aggregationSubjStatements = _.union(
this.dataPackageGraph.statementsMatching(aggregationNode),
this.dataPackageGraph.statementsMatching(aggregationLitNode),
);
if (aggregationSubjStatements.length) {
_.each(
aggregationSubjStatements,
function (statement) {
//Clone the subject
subjectClone = this.cloneNode(statement.subject);
//Clone the predicate
predicateClone = this.cloneNode(statement.predicate);
//Clone the object
objectClone = this.cloneNode(statement.object);
//Set the subject value to the new aggregation id
subjectClone.value =
this.getURIFromRDF(pid) + "#aggregation";
//Add a new statement with the new aggregation subject but the same predicate and object
this.dataPackageGraph.add(
subjectClone,
predicateClone,
objectClone,
);
},
this,
);
//Remove the old aggregation statements from the graph
this.dataPackageGraph.removeMany(aggregationNode);
}
// Change all the statements in the RDF where the aggregation is the object, to reflect the new resource map ID
var aggregationObjStatements = _.union(
this.dataPackageGraph.statementsMatching(
undefined,
undefined,
aggregationNode,
),
this.dataPackageGraph.statementsMatching(
undefined,
undefined,
aggregationLitNode,
),
);
if (aggregationObjStatements.length) {
_.each(
aggregationObjStatements,
function (statement) {
//Clone the subject, object, and predicate
subjectClone = this.cloneNode(statement.subject);
predicateClone = this.cloneNode(statement.predicate);
objectClone = this.cloneNode(statement.object);
//Set the object to the new aggregation pid
objectClone.value =
this.getURIFromRDF(pid) + "#aggregation";
//Add the statement with the old subject and predicate but new aggregation object
this.dataPackageGraph.add(
subjectClone,
predicateClone,
objectClone,
);
},
this,
);
//Remove all the old aggregation statements from the graph
this.dataPackageGraph.removeMany(
undefined,
undefined,
aggregationNode,
);
}
// Change all the resource map subject nodes in the RDF graph
var rMapNode = this.rdf.sym(this.getURIFromRDF(oldPid));
var rMapStatements = $.extend(
true,
[],
this.dataPackageGraph.statementsMatching(rMapNode),
);
// then repopulate them with correct values
_.each(
rMapStatements,
function (statement) {
subjectClone = this.cloneNode(statement.subject);
predicateClone = this.cloneNode(statement.predicate);
objectClone = this.cloneNode(statement.object);
// In the case of modified date, reset it to now()
if (predicateClone.value === DC("modified")) {
objectClone.value = new Date().toISOString();
}
//Update the subject to the new pid
subjectClone.value = this.getURIFromRDF(pid);
//Remove the old resource map statement
this.dataPackageGraph.remove(statement);
//Add the statement with the new subject pid, but the same predicate and object
this.dataPackageGraph.add(
subjectClone,
predicateClone,
objectClone,
);
},
this,
);
},
this,
);
// Add the describes/isDescribedBy statements back in
this.dataPackageGraph.add(
this.rdf.sym(this.getURIFromRDF(pid)),
ORE("describes"),
this.rdf.sym(this.getURIFromRDF(pid) + "#aggregation"),
);
this.dataPackageGraph.add(
this.rdf.sym(this.getURIFromRDF(pid) + "#aggregation"),
ORE("isDescribedBy"),
this.rdf.sym(this.getURIFromRDF(pid)),
);
//Add nodes for new package members
_.each(
addedIds,
function (id) {
this.addToAggregation(id);
},
this,
);
} else {
// Create the OAI-ORE graph from scratch
this.dataPackageGraph = this.rdf.graph();
cnResolveUrl = this.getCnURI();
//Create a resource map node
var rMapNode = this.rdf.sym(this.getURIFromRDF(this.packageModel.id));
//Create an aggregation node
var aggregationNode = this.rdf.sym(
this.getURIFromRDF(this.packageModel.id) + "#aggregation",
);
// Describe the resource map with a Creator
var creatorNode = this.rdf.blankNode();
var creatorName = this.rdf.lit(
(MetacatUI.appUserModel.get("firstName") || "") +
" " +
(MetacatUI.appUserModel.get("lastName") || ""),
"",
XSD("string"),
);
this.dataPackageGraph.add(creatorNode, FOAF("name"), creatorName);
this.dataPackageGraph.add(creatorNode, RDF("type"), DCTERMS("Agent"));
this.dataPackageGraph.add(rMapNode, DC("creator"), creatorNode);
// Set the modified date
modifiedDate = this.rdf.lit(
new Date().toISOString(),
"",
XSD("dateTime"),
);
this.dataPackageGraph.add(
rMapNode,
DCTERMS("modified"),
modifiedDate,
);
this.dataPackageGraph.add(rMapNode, RDF("type"), ORE("ResourceMap"));
this.dataPackageGraph.add(
rMapNode,
ORE("describes"),
aggregationNode,
);
var idLiteral = this.rdf.lit(this.packageModel.id, "", XSD("string"));
this.dataPackageGraph.add(rMapNode, DCTERMS("identifier"), idLiteral);
// Describe the aggregation
this.dataPackageGraph.add(
aggregationNode,
ORE("isDescribedBy"),
rMapNode,
);
// Aggregate each package member
_.each(
idsFromModel,
function (id) {
this.addToAggregation(id);
},
this,
);
}
// Remove any references to blank nodes not already cleaned up.
// rdflib.js will fail to serialize an IndexedFormula (graph) with
// statements whose object is a blank node when the blank node
// is not the subject of any other statements.
this.removeOrphanedBlankNodes();
var xmlString = serializer.statementsToXML(
this.dataPackageGraph.statements,
);
return xmlString;
},
// Clone an rdflib.js Node by creaing a new node based on the
// original node RDF term type and data type.
cloneNode: function (nodeToClone) {
switch (nodeToClone.termType) {
case "NamedNode":
return this.rdf.sym(nodeToClone.value);
break;
case "Literal":
// Check for the datatype for this literal value, e.g. http://www.w3.org/2001/XMLSchema#string"
if (typeof nodeToClone.datatype !== "undefined") {
return this.rdf.literal(
nodeToClone.value,
undefined,
nodeToClone.datatype,
);
} else {
return this.rdf.literal(nodeToClone.value);
}
break;
case "BlankNode":
//Blank nodes don't need to be cloned
return nodeToClone; //(this.rdf.blankNode(nodeToClone.value));
break;
case "Collection":
// TODO: construct a list of nodes for this term type.
return this.rdf.list(nodeToClone.value);
break;
default:
console.log(
"ERROR: unknown node type to clone: " + nodeToClone.termType,
);
}
},
// Adds a new object to the resource map RDF graph
addToAggregation: function (id) {
// Initialize the namespaces
var ORE = this.rdf.Namespace(this.namespaces.ORE),
DCTERMS = this.rdf.Namespace(this.namespaces.DCTERMS),
XSD = this.rdf.Namespace(this.namespaces.XSD),
CITO = this.rdf.Namespace(this.namespaces.CITO);
// Create a node for this object, the identifier, the resource map, and the aggregation
var objectNode = this.rdf.sym(this.getURIFromRDF(id)),
rMapURI = this.getURIFromRDF(this.packageModel.get("id")),
mapNode = this.rdf.sym(rMapURI),
aggNode = this.rdf.sym(rMapURI + "#aggregation"),
idNode = this.rdf.literal(id, undefined, XSD("string")),
idStatements = [],
aggStatements = [],
aggByStatements = [],
documentsStatements = [],
isDocumentedByStatements = [];
// Add the statement: this object isAggregatedBy the resource map aggregation
aggByStatements = this.dataPackageGraph.statementsMatching(
objectNode,
ORE("isAggregatedBy"),
aggNode,
);
if (aggByStatements.length < 1) {
this.dataPackageGraph.add(objectNode, ORE("isAggregatedBy"), aggNode);
}
// Add the statement: The resource map aggregation aggregates this object
aggStatements = this.dataPackageGraph.statementsMatching(
aggNode,
ORE("aggregates"),
objectNode,
);
if (aggStatements.length < 1) {
this.dataPackageGraph.add(aggNode, ORE("aggregates"), objectNode);
}
// Add the statement: This object has the identifier {id} if it isn't present
idStatements = this.dataPackageGraph.statementsMatching(
objectNode,
DCTERMS("identifier"),
idNode,
);
if (idStatements.length < 1) {
this.dataPackageGraph.add(objectNode, DCTERMS("identifier"), idNode);
}
// Find the metadata doc that describes this object
var model = this.findWhere({ id: id }),
isDocBy = model.get("isDocumentedBy"),
documents = model.get("documents");
// Deal with Solr indexing bug where metadata-only packages must "document" themselves
if (isDocBy.length === 0 && documents.length === 0) {
documents.push(model.get("id"));
}
// If this object is documented by any metadata...
if (isDocBy && isDocBy.length) {
// Get the ids of all the metadata objects in this package
var metadataInPackage = _.compact(
_.map(this.models, function (m) {
if (m.get("formatType") == "METADATA") return m;
}),
),
metadataInPackageIDs = _.each(metadataInPackage, function (m) {
return m.get("id");
});
// Find the metadata IDs that are in this package that also documents this data object
var metadataIds = Array.isArray(isDocBy)
? _.intersection(metadataInPackageIDs, isDocBy)
: _.intersection(metadataInPackageIDs, [isDocBy]);
// If this data object is not documented by one of these metadata docs,
// then we should check if it's documented by an obsoleted pid. If so,
// we'll want to change that so it's documented by a current metadata.
if (metadataIds.length == 0) {
for (var i = 0; i < metadataInPackage.length; i++) {
//If the previous version of this metadata documents this data,
if (_.contains(isDocBy, metadataInPackage[i].get("obsoletes"))) {
//Save the metadata id for serialization
metadataIds = [metadataInPackage[i].get("id")];
//Exit the for loop
break;
}
}
}
// For each metadata that documents this object, add a CITO:isDocumentedBy and CITO:documents statement
_.each(
metadataIds,
function (metaId) {
//Create the named nodes and statements
var dataNode = this.rdf.sym(this.getURIFromRDF(id)),
metadataNode = this.rdf.sym(this.getURIFromRDF(metaId)),
isDocByStatement = this.rdf.st(
dataNode,
CITO("isDocumentedBy"),
metadataNode,
),
documentsStatement = this.rdf.st(
metadataNode,
CITO("documents"),
dataNode,
);
// Add the statements
documentsStatements = this.dataPackageGraph.statementsMatching(
metadataNode,
CITO("documents"),
dataNode,
);
if (documentsStatements.length < 1) {
this.dataPackageGraph.add(documentsStatement);
}
isDocumentedByStatements =
this.dataPackageGraph.statementsMatching(
dataNode,
CITO("isDocumentedBy"),
metadataNode,
);
if (isDocumentedByStatements.length < 1) {
this.dataPackageGraph.add(isDocByStatement);
}
},
this,
);
}
// If this object documents a data object
if (documents && documents.length) {
// Create a literal node for it
var metadataNode = this.rdf.sym(this.getURIFromRDF(id));
_.each(
documents,
function (dataID) {
//Make sure the id is one that will be aggregated
if (_.contains(this.idsToAggregate, dataID)) {
//Find the identifier statement for this data object
var dataURI = this.getURIFromRDF(dataID);
//Create a data node using the exact way the identifier URI is written
var dataNode = this.rdf.sym(dataURI);
//Get the statements for data isDocumentedBy metadata
isDocumentedByStatements =
this.dataPackageGraph.statementsMatching(
dataNode,
CITO("isDocumentedBy"),
metadataNode,
);
//If that statement is not in the RDF already...
if (isDocumentedByStatements.length < 1) {
// Create a statement: This data is documented by this metadata
var isDocByStatement = this.rdf.st(
dataNode,
CITO("isDocumentedBy"),
metadataNode,
);
//Add the "isDocumentedBy" statement
this.dataPackageGraph.add(isDocByStatement);
}
//Get the statements for metadata documents data
documentsStatements = this.dataPackageGraph.statementsMatching(
metadataNode,
CITO("documents"),
dataNode,
);
//If that statement is not in the RDF already...
if (documentsStatements.length < 1) {
// Create a statement: This metadata documents data
var documentsStatement = this.rdf.st(
metadataNode,
CITO("documents"),
dataNode,
);
//Add the "isDocumentedBy" statement
this.dataPackageGraph.add(documentsStatement);
}
}
},
this,
);
}
},
/*
* Removes an object from the aggregation in the RDF graph
*/
removeFromAggregation: function (id) {
if (id.indexOf(this.dataPackageGraph.cnResolveUrl) == -1) {
id = this.getURIFromRDF(id);
}
// Create a literal node for the removed object
var removedObjNode = this.rdf.sym(id),
// Get the statements from the RDF where the removed object is the subject or object
statements = $.extend(
true,
[],
_.union(
this.dataPackageGraph.statementsMatching(
undefined,
undefined,
removedObjNode,
),
this.dataPackageGraph.statementsMatching(removedObjNode),
),
);
// Remove all the statements mentioning this object
try {
this.dataPackageGraph.remove(statements);
} catch (error) {
console.log(error);
}
},
/**
* Finds the given identifier in the RDF graph and returns the subject
* URI of that statement. This is useful when adding additional statements
* to the RDF graph for an object that already exists in that graph.
*
* @param {string} id - The identifier to search for
* @return {string} - The full URI for the given id as it exists in the RDF.
*/
getURIFromRDF: function (id) {
//Exit if no id was given
if (!id) return "";
//Create a literal node with the identifier as the value
var XSD = this.rdf.Namespace(this.namespaces.XSD),
DCTERMS = this.rdf.Namespace(this.namespaces.DCTERMS),
idNode = this.rdf.literal(id, undefined, XSD("string")),
//Find the identifier statements for the given id
idStatements = this.dataPackageGraph.statementsMatching(
undefined,
DCTERMS("identifier"),
idNode,
);
//If this object has an identifier statement,
if (idStatements.length > 0) {
//Return the subject of the statement
return idStatements[0].subject.value;
} else {
return this.getCnURI() + encodeURIComponent(id);
}
},
/**
* Parses out the CN Resolve URL from the existing statements in the RDF
* or if not found in the RDF, from the app configuration.
*
* @return {string} - The CN resolve URL
*/
getCnURI: function () {
//If the CN resolve URL was already found, return it
if (this.dataPackageGraph.cnResolveUrl) {
return this.dataPackageGraph.cnResolveUrl;
} else if (this.packageModel.get("oldPid")) {
//Find the identifier statement for the resource map in the RDF graph
var idNode = this.rdf.lit(this.packageModel.get("oldPid")),
idStatements = this.dataPackageGraph.statementsMatching(
undefined,
undefined,
idNode,
),
idStatement = idStatements.length ? idStatements[0] : null;
if (idStatement) {
//Parse the CN resolve URL from the statement subject URI
this.dataPackageGraph.cnResolveUrl =
idStatement.subject.value.substring(
0,
idStatement.subject.value.indexOf(
this.packageModel.get("oldPid"),
),
) ||
idStatement.subject.value.substring(
0,
idStatement.subject.value.indexOf(
encodeURIComponent(this.packageModel.get("oldPid")),
),
);
} else {
this.dataPackageGraph.cnResolveUrl =
MetacatUI.appModel.get("resolveServiceUrl");
}
} else {
this.dataPackageGraph.cnResolveUrl =
MetacatUI.appModel.get("resolveServiceUrl");
}
//Return the CN resolve URL
return this.dataPackageGraph.cnResolveUrl;
},
/**
* Checks if this resource map has had any changes that requires an update
*/
needsUpdate: function () {
//Check for changes to the list of aggregated members
var ids = this.pluck("id");
if (
this.originalMembers.length != ids.length ||
_.intersection(this.originalMembers, ids).length != ids.length
)
return true;
// If the provenance relationships have been updated, then the resource map
// needs to be updated.
if (this.provEdits.length) return true;
//Check for changes to the isDocumentedBy relationships
var isDifferent = false,
i = 0;
//Keep going until we find a difference
while (!isDifferent && i < this.length) {
//Get the original isDocBy relationships from the resource map, and the new isDocBy relationships from the models
var isDocBy = this.models[i].get("isDocumentedBy"),
id = this.models[i].get("id"),
origIsDocBy = this.originalIsDocBy[id];
//Make sure they are both formatted as arrays for these checks
isDocBy = _.uniq(
_.flatten(_.compact(Array.isArray(isDocBy) ? isDocBy : [isDocBy])),
);
origIsDocBy = _.uniq(
_.flatten(
_.compact(
Array.isArray(origIsDocBy) ? origIsDocBy : [origIsDocBy],
),
),
);
//Remove the id of this object so metadata can not be "isDocumentedBy" itself
isDocBy = _.without(isDocBy, id);
origIsDocBy = _.without(origIsDocBy, id);
//Simply check if they are the same
if (origIsDocBy === isDocBy) {
i++;
continue;
}
//Are the number of relationships different?
else if (isDocBy.length != origIsDocBy.length) isDifferent = true;
//Are the arrays the same?
else if (
_.intersection(isDocBy, origIsDocBy).length != origIsDocBy.length
)
isDifferent = true;
i++;
}
return isDifferent;
},
/*
* Returns an array of the models that are in the queue or in progress of uploading
*/
getQueue: function () {
return this.filter(function (m) {
return m.get("uploadStatus") == "q" || m.get("uploadStatus") == "p";
});
},
/*
* Adds a DataONEObject model to this DataPackage collection
*/
addNewModel: function (model) {
//Check that this collection doesn't already contain this model
if (!this.contains(model)) {
this.add(model);
//Mark this data package as changed
this.packageModel.set("changed", true);
this.packageModel.trigger("change:changed");
}
},
handleAdd: function (dataONEObject) {
var metadataModel = this.find(function (m) {
return m.get("type") == "Metadata";
});
// Append to or create a new documents list
if (metadataModel) {
if (!Array.isArray(metadataModel.get("documents"))) {
metadataModel.set("documents", [dataONEObject.id]);
} else {
if (!_.contains(metadataModel.get("documents"), dataONEObject.id))
metadataModel.get("documents").push(dataONEObject.id);
}
// Create an EML Entity for this DataONE Object if there isn't one already
if (
metadataModel.type == "EML" &&
!dataONEObject.get("metadataEntity") &&
dataONEObject.type != "EML"
) {
metadataModel.createEntity(dataONEObject);
metadataModel.set("uploadStatus", "q");
}
}
this.saveReference(dataONEObject);
this.setLoadingFiles(dataONEObject);
//Save a reference to this DataPackage
// If the collections attribute is an array
/* if( Array.isArray(dataONEObject.get("collections")) ){
//Add this DataPackage to the collections list if it's not already in the array
if( !_.contains(dataONEObject.get("collections"), this) ){
dataONEObject.get("collections").push(this);
}
}
//If the collections attribute is not an array but there is a value,
else if(dataONEObject.get("collections")){
//And if the value is not this DataPackage or it's pid, then set it on the model
if( dataONEObject.get("collections") != this && dataONEObject.get("collections") != this.get("id") ){
dataONEObject.set("collections", [dataONEObject.get("collections"), this] );
}
//Otherwise, set the collections attribute to this DataPackage in an array
else {
dataONEObject.set("collections", [this]);
}
}
// If there is no value set on the collections attribute, then set it to
// this DataPackage in an array
else{
dataONEObject.set("collections", [this]);
}
*/
},
/**
* Fetches this DataPackage from the Solr index by using a SolrResults collection
* and merging the models in.
*/
fetchFromIndex: function () {
if (typeof this.solrResults == "undefined" || !this.solrResults) {
this.solrResults = new SolrResults();
}
//If no query is set yet, use the FilterModel associated with this DataPackage
if (!this.solrResults.currentquery.length) {
this.solrResults.currentquery = this.filterModel.getQuery();
}
this.listenToOnce(this.solrResults, "reset", function (solrResults) {
//Merge the SolrResults into this collection
this.mergeModels(solrResults.models);
//Trigger the fetch as complete
this.trigger("complete");
});
//Query the index for this data package
this.solrResults.query();
},
/**
* Merge the attributes of other models into the corresponding models in this collection.
* This should be used when merging models of other types (e.g. SolrResult) that represent the same
* object that the DataONEObject models in the collection represent.
*
* @param {Backbone.Model[]} otherModels - the other models to merge with the models in this collection
* @param {string[]} [fieldsToMerge] - If specified, only these fields will be extracted from the otherModels
*/
mergeModels: function (otherModels, fieldsToMerge) {
//If no otherModels are given, exit the function since there is nothing to merge
if (
typeof otherModels == "undefined" ||
!otherModels ||
!otherModels.length
) {
return false;
}
_.each(
otherModels,
function (otherModel) {
//Get the model from this collection that matches ids with the other model
var modelInDataPackage = this.findWhere({
id: otherModel.get("id"),
});
//If a match is found,
if (modelInDataPackage) {
var valuesFromOtherModel;
//If specific fields to merge are given, get the values for those from the other model
if (fieldsToMerge && fieldsToMerge.length) {
valuesFromOtherModel = _.pick(
otherModel.toJSON(),
fieldsToMerge,
);
}
//If no specific fields are given, merge (almost) all others
else {
//Get the default values for this model type
var otherModelDefaults = otherModel.defaults,
//Get a JSON object of all the attributes on this model
otherModelAttr = otherModel.toJSON(),
//Start an array of attributes to omit during the merge
omitKeys = [];
_.each(otherModelAttr, function (val, key) {
//If this model's attribute is the default, don't set it on our DataONEObject model
// because whatever value is in the DataONEObject model is better information than the default
// value of the other model.
if (otherModelDefaults[key] === val) omitKeys.push(key);
});
//Remove the properties that are still the default value
valuesFromOtherModel = _.omit(otherModelAttr, omitKeys);
}
//Set the values from the other model on the model in this collection
modelInDataPackage.set(valuesFromOtherModel);
}
},
this,
);
},
/**
* Update the relationships in this resource map when its been udpated
*/
updateRelationships: function () {
//Get the old id
var oldId = this.packageModel.get("oldPid");
if (!oldId) return;
//Update the resource map list
this.each(function (m) {
var updateRMaps = _.without(m.get("resourceMap"), oldId);
updateRMaps.push(this.packageModel.get("id"));
m.set("resourceMap", updateRMaps);
}, this);
},
saveReference: function (model) {
//Save a reference to this collection in the model
var currentCollections = model.get("collections");
if (currentCollections.length > 0) {
currentCollections.push(this);
model.set("collections", _.uniq(currentCollections));
} else model.set("collections", [this]);
},
/**
* Broadcast an accessPolicy across members of this package
*
* Note: Currently just sets the incoming accessPolicy on this
* object and doesn't broadcast to other members (such as data).
* How this works is likely to change in the future.
*
* Closely tied to the AccessPolicyView.broadcast property.
*
* @param {AccessPolicy} accessPolicy - The accessPolicy to
* broadcast
*/
broadcastAccessPolicy: function (accessPolicy) {
if (!accessPolicy) {
return;
}
var policy = _.clone(accessPolicy);
this.packageModel.set("accessPolicy", policy);
// Stop now if the package is new because we don't want force
// a save just yet
if (this.packageModel.isNew()) {
return;
}
this.packageModel.on("sysMetaUpdateError", function (e) {
// Show a generic error. Any errors at this point are things the
// user can't really recover from. i.e., we've already checked
// that the user has changePermission perms and we've already
// re-tried the request a few times
var message =
"There was an error sharing your dataset. Not all of your changes were applied.";
// TODO: Is this really the right way to hook into the editor's
// error notification mechanism?
MetacatUI.appView.eml211EditorView.saveError(message);
});
this.packageModel.updateSysMeta();
},
/**
* Tracks the upload status of DataONEObject models in this collection. If they are
* `loading` into the DOM or `in progress` of an upload to the server, they will be considered as "loading" files.
* @param {DataONEObject} [dataONEObject] - A model to begin tracking. Optional. If no DataONEObject is given, then only
* the number of loading files will be calcualted and set on the packageModel.
* @since 2.17.1
*/
setLoadingFiles: function (dataONEObject) {
//Set the number of loading files and the isLoadingFiles flag
let numLoadingFiles =
this.where({ uploadStatus: "l" }).length +
this.where({ uploadStatus: "p" }).length;
this.packageModel.set({
isLoadingFiles: numLoadingFiles > 0,
numLoadingFiles: numLoadingFiles,
});
if (dataONEObject) {
//Listen to the upload status to update the flag
this.listenTo(dataONEObject, "change:uploadStatus", function () {
//If the object is done being successfully saved
if (dataONEObject.get("uploadStatus") == "c") {
let numLoadingFiles =
this.where({ uploadStatus: "l" }).length +
this.where({ uploadStatus: "p" }).length;
//If all models in this DataPackage have finished loading, then mark the loading as complete
if (!numLoadingFiles) {
this.packageModel.set({
isLoadingFiles: false,
numLoadingFiles: numLoadingFiles,
});
} else {
this.packageModel.set("numLoadingFiles", numLoadingFiles);
}
}
});
}
},
/**
* Returns atLocation information found in this resourceMap
* for all the PIDs in this resourceMap
* @returns object with PIDs as key and atLocation paths as values
* @since 2.28.0
*/
getAtLocation: function () {
return this.atLocationObject;
},
/**
* Get the absolute path from a relative path, handling '~', '..', and '.'.
*
* @param {string} relativePath - The relative path to be converted to an absolute path.
* @returns {string} - The absolute path after processing '~', '..', and '.'.
* If the result is empty, returns '/'.
* @since 2.28.0
*/
getAbsolutePath(relativePath) {
// Replace ~ with an empty space
const fullPath = relativePath.replace(/^~(?=$|\/|\\)/, "");
// Process '..' and '.'
const components = fullPath.split("/");
const resolvedPath = components.reduce((accumulator, component) => {
if (component === "..") {
accumulator.pop();
} else if (component !== "." && component !== "") {
accumulator.push(component);
}
return accumulator;
}, []);
// Join the resolved path components with '/'
const result = resolvedPath.join("/");
return result || "/";
},
},
);
return DataPackage;
});