Test

CitationWrapper

given an empty citation

#constructor

should return a CitationWrapper

#toString

should return undefined

should be settable by changing the title

#constructor

should return a CitationWrapper

#toString

should return the expected string

Test whether conversion of Phyx files to an OWL ontology occurs predictably.

Test all correct example Phyx files

should be loadable

should validate against our JSON schema

should be able to convertible to an OWL Ontology

should generate the same OWL ontology as it generated earlier

should be convertible to n-quads

should generate the same n-quads ontology as it generated earlier

Test incorrect example Phyx files that should fail validation

should not validate against our JSON schema

Test whether the expected JSON-LD files pass testing using JPhyloRef.

download JPhyloRef

has already been downloaded

should be downloadable

test example JSON-LD files using JPhyloRef

TaxonNameWrapper

#getNomenclaturalCodes

should provide a non-empty list with the expected keys

#getNomenCodeDetails

should provide details for some built-in codes

#nomenclaturalCodeDetails

should provide nomenclatural code details for an example taxon name

TaxonConceptWrapper

#nomenCode

should return UNKNOWN_CODE if one is not set

should return the default nomenclatural code if one is provided

PhyxWrapper

should use the defaultNomenclaturalCodeIRI for phylogeny nodes

should use the inferred nomenclatural code for phylogeny nodes

Test whether normalization of phyloreferences and phylogenies work as expected. This test does not cover Phyx normalization.

Test all normalization Phyx files

Test phylogenies

These tests have not yet been implemented since we don't have an urgent need for them.

Test phyloreferences

should have multiple same phyloreferences for testing

should not have any duplicate phylorefs (which would be pointless)

should have pairs of _same phylorefs that are different, but are identical after normalization

should have pairs of _different phylorefs that are different before and after normalization

PhylogenyWrapper

#constructor

when used to wrap an empty object

should return a PhylogenyWrapper object

#getErrorsInNewickString

when given a correct Newick string

should return an empty list of errors

when given an empty Newick string

should return a single "No phylogeny entered" error

when given an unbalanced Newick string

should report how many parentheses are missing

when given an incomplete Newick string

should report an error parsing the phylogeny

#getNodeLabels

For a particular Newick phylogeny

should return a list of all node labels by default

should return a list of internal labels when asked for internal labels

should return a list of terminal labels when asked for terminal labels

given a particular phylogeny with additional node properties

#getNodeLabels

should return the list of node labels from the Newick string

#getTaxonomicUnitsForNodeLabel

should return the list of taxonomic units using information from additional node properties

#getNodeLabelsMatchedBySpecifier

should match a specifier to MVZ225749 based on occurrence ID

should match a specifier to MVZ191016 based on occurrence ID

should match a specifier to node "Rana boylii" based on the parsed scientific name

#asJSONLD

should preserve an existing @id on input phylogenies

should generate a new @id on input phylorefs

should generate the phylogeny in JSON-LD as expected

#getParsedNewickWithIRIs

should be able to parse a provided Newick string as expected

PhylorefWrapper

given an empty phyloreference

#constructor

should return a PhylorefWrapper

#label

should return undefined

should be settable by assigning to .label

#specifiers

should initially return an empty list

should initially return a nomenclatural code of unknown

when a new external specifier is added using .externalSpecifiers

should return a list with the new specifier

should return a nomenclatural code of ICZN

when a new external specifier is added using .externalSpecifiers

should return a list with the new specifier

should return two nomenclatural codes, one for each specifier

should still return a nomenclatural code of ICZN

when a new internal specifier is added using .internalSpecifiers

should return a list with the new specifier

should return three nomenclatural codes, one for each specifier

should change to a default nomenclatural code of owlterms.UNKNOWN_CODE

when specifiers are deleted using .deleteSpecifier

should return the updated list

when a specifier is added using .externalSpecifiers

should return the updated list

when a specifier is changed to an internal specifier using .setSpecifierType

should remain in the list of specifiers

when a specifier is added using .internalSpecifiers

should be included in the list of all specifiers

#getSpecifierType

should return the correct specifier type for each specifier

#getSpecifierLabel as TaxonomicUnitWrapper

should return the correct label for each specifier

given a particular phylogeny

#getExpectedNodeLabels

should be able to determine expected node labels for a phylogeny

given an empty phyloreference

#getCurrentStatus

should return "pso:draft" as the default initial status

#setStatus

should throw an error if given a mistyped status

#getStatusChanges

should return the empty list

when modified by using .setStatus

should return the updated list

#asJSONLD

should preserve an existing @id on input phylorefs

should generate a new @id on input phylorefs

should generate the expected equivClass expression for 1 int, 1 ext phyloref

should generate the expected equivClass expression for 2 int phyloref

should work without any arguments

should support --help

should be able to convert brochu_2003.json

should be able to convert the entire test/examples/correct directory

should give an error if no JSON files could be found

bin/resolve.js

should work without any arguments

should support --help

should provide the expected results on the brochu_2003.json example file

should correctly report errors with certain phyloreferences

SpecimenWrapper

#constructor

should be able to wrap an empty specimen

should be able to wrap a specimen with an empty occurenceID

should be able to extract an occurenceID and catalogNumber from simple specimen IDs

should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination

should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples

should be able to extract the same occurrenceID from different representations

should not attempt to split a URN into occurenceID, institutionCode and catalogNumber

should not attempt to split a URL into occurenceID, institutionCode and catalogNumber

should be able to create a specimen JSON record from an occurrence ID

TaxonNameWrapper

#constructor

should accept empty taxon names without errors

should be able to parse uninomial names as such

should be able to parse binomial names into genus and specific epithet

should be able to parse trinomial names into genus, specific epithet and infraspecific epithet

should ignore authority after a binomial name

should be able to use default nomenclatural codes

TaxonomicUnitWrapper

#constructor given no arguments

should create an empty TaxonomicUnitWrapper without a defined label

#label given a taxonomic unit

should return a wrapped scientific name

should return a wrapped specimen identifier preceded by "Specimen"

should return specimens with an occurrenceID as well as a taxon concept

should ignore occurrence ID if typed as a taxon concept

should return a wrapped external reference by surrounding it with "<>"

should provide both taxon name and occurrence ID in label, but ignore external reference

#fromLabel

should return empty lists when inputs are empty or undefined

when given a scientific name, it should return a list of a single TU wrapping a scientific name

when given a scientific name separated with underscores, it should return a list of a single TU wrapping the scientific name

#asOWLEquivClass

when given a taxon concept, only the complete name should be present in the equivClass

when given a specimen, only the occurrence ID should be present in the equivClass

TaxonomicUnitMatcher

#matchByNameComplete

should be able to match tunit1 and tunit2 by complete name

#matchByExternalReferences

should be able to match tunit3 and tunit4 by external references

#matchByOccurrenceID

should be able to match tunit2 and tunit3 by specimen identifiers

#matched and #matchReason

should match tunit1 and tunit2 on the basis of identical complete names

should match tunit3 and tunit4 by identical external reference

should match tunit2 and tunit3 by identical specimen identifier