Class: DataPackage

DataPackage()

A DataPackage represents a hierarchical collection of packages, metadata, and data objects, modeling an OAI-ORE RDF graph.

Constructor

new DataPackage()

Source:

Extends

  • Backbone.Collection

Members

comparator :string

Used to 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
Source:

dataPackageGraph :RDFGraph

The RDF graph representing this data package
Type:
  • RDFGraph
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derivations :Array.<DataONEObject>

Package members that are derivations in provenance relationships.
Type:
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editable :boolean

A flag used for the package's edit status. Can be set to false to 'lock' the package
Type:
  • boolean
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filterModel :Filter

A Filter model that should filter the Solr index for only the objects aggregated by this package.
Type:
Source:

id :string

The package identifier
Type:
  • string
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namespaces :object

Namespaces used in the RDF XML. The key is the prefix and the value is the namespace URI.
Type:
  • object
Source:

nodeLevel :number

The nesting level in a data package hierarchy
Type:
  • number
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numSaves :number

The number of models that have been updated during the current save(). This is reset to zero after the current save() is complete.
Type:
  • number
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originalIsDocBy :object

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
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originalMembers :Array.<string>

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:
  • Array.<string>
Source:

packageModel :DataONEObject

A DataONEObject representing the resource map itself
Type:
Source:

provEdits :Array.<Array.<string>>

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']
Type:
  • Array.<Array.<string>>
Source:

provenanceFlag :string|null

Set to "complete" to signal that all prov queries have finished
Type:
  • string | null
Source:

solrResults :SolrResults

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:
Source:

sources :Array.<DataONEObject>

Package members that are sources in provenance relationships.
Type:
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transferQueue :DataPackage|Metadata|Array.<Data>

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:
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type :string

The name of this type of collection
Type:
  • string
Source:

Methods

addNewModel(model)

Adds a DataONEObject model to this DataPackage collection
Parameters:
Name Type Description
model DataONEObject The DataONEObject model to add
Source:

addProgramToGraph(programId) → {string}

Add a program identifier to the RDF graph and create an execution node
Parameters:
Name Type Description
programId string The program identifier
Source:
Returns:
The execution identifier
Type
string

addToAggregation(id)

Adds a new object to the resource map RDF graph
Parameters:
Name Type Description
id string The identifier of the object to add
Source:

addToGraph(subject, predicate, object)

Add the specified relationship to the RDF graph only if it has not already been added.
Parameters:
Name Type Description
subject object The subject of the statement to add
predicate object The predicate of the statement to add
object object The object of the statement to add
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broadcastAccessPolicy(accessPolicy)

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.
Parameters:
Name Type Description
accessPolicy AccessPolicy The accessPolicy to broadcast
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cloneNode(nodeToClone) → {Node}

Clone an rdflib.js Node by creaing a new node based on the original node RDF term type and data type.
Parameters:
Name Type Description
nodeToClone Node The node to clone
Source:
Returns:
- The cloned node
Type
Node

fetch(sourceOptionsopt) → {Promise}

Overload fetch calls for a DataPackage This fetch function will fetch the resource map RDF XML for this package + Example 1: `this.fetch();` + Example 2: `this.fetch({fetchModels: false});` + Example 3: `this.fetch({fromIndex: true});` + Example 4: ``` this.fetch() .then(function() { console.log("Fetch complete!"); }) .catch(function() { console.log("Fetch failed!"); }); ```
Parameters:
Name Type Attributes Description
sourceOptions object <optional>
 Optional options for this fetch that get sent with the XHR request
Properties:
Name Type Description
fetchModels boolean If false, this fetch will not fetch each model in the collection. It will only get the resource map object.
fromIndex boolean 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.
Source:
Returns:
A promise that resolves when the fetch is complete
Type
Promise

fetchFromIndex()

Fetches this DataPackage from the Solr index by using a SolrResults collection and merging the models in.
Source:

fetchMemberModels(models, batchSizeopt, timeoutopt, maxRetriesopt) → {Promise}

Fetches member models in batches to avoid fetching all members simultaneously.
Parameters:
Name Type Attributes Description
models Array.<Backbone.Model> The array of member models to fetch.
batchSize number <optional>
 The number of models to fetch in each batch.
timeout number <optional>
 The timeout for each fetch request in milliseconds. If set to anything other than a positive number greater than 0, the fetch will never timeout.
maxRetries number <optional>
 The maximum number of retries for each fetch request.
Since:
  • 2.32.0
Source:
Returns:
A promise that resolves when all models have been fetched.
Type
Promise

fetchPromise(model) → {object}

Fetch a model using Backbone's fetch method but return a promise that resolves when the fetch is complete, along with the XHR object
Parameters:
Name Type Description
model DataONEObject The model to fetch
Since:
  • 2.32.1
Source:
Returns:
An object with a promise and an XHR reference
Type
object

fetchWithRetryAndTimeout(memberModel, maxRetries, timeout, attemptopt) → {DataONEObject}

Fetch a model with a timeout and a maximum number of retries. Fetch a model with a timeout, aborting the fetch if it takes too long.
Parameters:
Name Type Attributes Description
memberModel DataONEObject The model to fetch
maxRetries number The maximum number of retries
timeout number The timeout in milliseconds. If set to anything other than a positive number greater than 0, the fetch will not have a timeout (i.e., will wait indefinitely)
attempt number <optional>
 The current attempt number
Since:
  • 2.32.1
Source:
Returns:
The fetched model
Type
DataONEObject

getAbsolutePath(relativePath) → {string}

Get the absolute path from a relative path, handling '~', '..', and '.'.
Parameters:
Name Type Description
relativePath string The relative path to be converted to an absolute path.
Since:
  • 2.28.0
Source:
Returns:
The absolute path after processing '~', '..', and '.'. If the result is empty, returns '/'.
Type
string

getAtLocation() → {object}

Returns atLocation information found in this resourceMap for all the PIDs in this resourceMap
Since:
  • 2.28.0
Source:
Returns:
- object with PIDs as key and atLocation paths as values
Type
object

getCnURI() → {string}

Parses out the CN Resolve URL from the existing statements in the RDF or if not found in the RDF, from the app configuration.
Source:
Returns:
- The CN resolve URL
Type
string

getExecutionId(programId) → {string}

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.
Parameters:
Name Type Description
programId string The program identifier
Source:
Returns:
The execution identifier
Type
string

getExecutionNode(executionId) → {object}

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.
Parameters:
Name Type Description
executionId string The execution identifier
Source:
Returns:
The RDF node for the execution
Type
object

getMember(context) → {Backbone.Model}

When a data package member updates, we evaluate it for its formatid, and update it appropriately if it is not a data object only
Parameters:
Name Type Description
context Backbone.Model The model that was updated
Source:
Returns:
The updated model
Type
Backbone.Model

getQueue() → {Array}

Gets objects not yet uploaded to the DataONE server
Source:
Returns:
An array of models that are in the queue or in progress of uploading
Type
Array

getURIFromRDF(id) → {string}

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.
Parameters:
Name Type Description
id string The identifier to search for
Source:
Returns:
- The full URI for the given id as it exists in the RDF.
Type
string

getValue(result, name) → {string}

The return values have to be extracted from the result.
Parameters:
Name Type Description
result object The result of the SPARQL query
name string The name of the field to extract
Source:
Returns:
- The value of the result
Type
string

handleAdd(dataONEObject)

Actions ot perform when a DataONEObject model is added to this collection
Parameters:
Name Type Description
dataONEObject DataONEObject The DataONEObject model that was added
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handleMemberFetchError(failedModels, errors)

Handle errors that occur when fetching member models
Parameters:
Name Type Description
failedModels Array.<DataONEObject> The models that were being fetched
errors Array.<Error> The errors that occurred
Since:
  • 2.32.1
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initialize()

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mergeModels(otherModels, fieldsToMergeopt)

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.
Parameters:
Name Type Attributes Description
otherModels Array.<Backbone.Model> the other models to merge with the models in this collection
fieldsToMerge Array.<string> <optional>
 If specified, only these fields will be extracted from the otherModels
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model(attrs, options) → {DataONEObject|ScienceMetadata|EML211|DataPackage}

The DataPackage collection stores DataPackages and DataONEObjects, including Metadata and Data objects. Return the correct model based on the type
Parameters:
Name Type Description
attrs object The attributes of the model
options object Options to pass to the instantiated model
Source:
Returns:
The model
Type
DataONEObject | ScienceMetadata | EML211 | DataPackage

needsUpdate() → {boolean}

Checks if this resource map has had any changes that requires an update
Source:
Returns:
- True if the resource map needs to be updated
Type
boolean

onDone()

This callback is called when all queries have finished.
Source:

onResult(result)

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.
Parameters:
Name Type Description
result object The result of the SPARQL query
Source:
Example
// 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}]

parse(response, _options) → {Array.<DataPackage>}

Deserialize a Package from OAI-ORE RDF XML
Parameters:
Name Type Description
response string The RDF/XML string to parse
_options object Options for parsing the RDF/XML
Source:
Returns:
- An array of models that were parsed from the RDF/XML
Type
Array.<DataPackage>

parseProv()

Parse the provenance relationships from the RDF graph, after all DataPackage members have been fetched, as the prov info will be stored in them.
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parseSysMeta(sysMeta) → {object}

Use the DataONEObject parseSysMeta() function
Parameters:
Name Type Description
sysMeta object The system metadata object to parse
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Returns:
The parsed system metadata object
Type
object

provEditsPending() → {boolean}

Check if there are any provenance edits pending
Source:
Returns:
Returns true if the prov edits list is not empty, otherwise false.
Type
boolean

recordProvEdit(operation, subject, predicate, object)

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.
Parameters:
Name Type Description
operation string The operation performed on the relationship (add or delete)
subject string The subject of the relationship
predicate string The predicate of the relationship
object string The object of the relationship
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removeFromAggregation(id)

Removes an object from the aggregation in the RDF graph
Parameters:
Name Type Description
id string The identifier of the object to remove
Source:

removeIfLastProvRef(subjectNode, predicateNode, objectNode)

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.
Parameters:
Name Type Description
subjectNode object The subject of the statement to remove
predicateNode object The predicate of the statement to remove
objectNode object The object of the statement to remove
Source:

removeOrphanedBlankNodes()

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.
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removeProgramFromGraph(programId) → {boolean}

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.
Parameters:
Name Type Description
programId string The program identifier
Source:
Returns:
Returns true if the program was removed, otherwise false.
Type
boolean

save(optionsopt)

Overwrite the Backbone.Collection.sync() function to set custom options
Parameters:
Name Type Attributes Description
options object <optional>
 Options for this DataPackage save
Properties
Name Type Attributes Description
sysMetaOnly boolean <optional>
 If true, only the system metadata of this Package will be saved.
resourceMapOnly boolean <optional>
 If true, only the Resource Map/Package object will be saved. Metadata and Data objects aggregated by the package will be skipped.
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saveProv()

If provenance relationships have been modified by the provenance editor (in ProvChartView), then update the ORE Resource Map and save it to the server.
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saveReference(model)

Save a reference to this collection in the model
Parameters:
Name Type Description
model DataONEObject The model to save a reference to
Source:

serialize() → {string}

Serialize the DataPackage to OAI-ORE RDF XML
Source:
Returns:
The serialized RDF/XML
Type
string

setLoadingFiles(dataONEObjectopt)

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.
Parameters:
Name Type Attributes Description
dataONEObject DataONEObject <optional>
 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
Source:

triggerComplete(model)

Trigger the complete event if all models have been fetched
Parameters:
Name Type Description
model Backbone.Model The model that was fetched
Source:

updateLoadingCount(num)

Sets the numLoadingFileMetadata attribute on the package model
Parameters:
Name Type Description
num number The number of models that are currently being fetched
Since:
  • 2.32.1
Source:

updateMemberModelType(memberModel, maxRetries, timeout) → {DataONEObject}

After a member model is fetched, determine whether it needs to: 1) be merged into the collection (the type did NOT change) 2) replace the old model (the type changed to DataPackage) 3) be fetched again, waited for, and then replaced in the collection (the type from the server is different from the type in the collection) Then resolve the promise when the model is fully handled.
Parameters:
Name Type Description
memberModel DataONEObject The model to potentially replace
maxRetries number The maximum number of retries for each fetch request
timeout number The timeout for each fetch request in milliseconds. If set to anything other than a positive number greater than 0, the fetch will never timeout
Since:
  • 2.32.1
Source:
Returns:
The updated model
Type
DataONEObject

updateRelationships()

Update the relationships in this resource map when its been udpated
Source:

url(optionsopt) → {string}

Build the DataPackage URL based on the MetacatUI.appModel.objectServiceUrl and id or seriesid
Parameters:
Name Type Attributes Description
options object <optional>
 Optional options for this URL
Properties
Name Type Attributes Description
update boolean <optional>
 If true, this URL will be for updating the package
Source:
Returns:
The URL for this DataPackage
Type
string