adiwg-mdtranslator 1.4.0 → 2.0.0rc2

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_lineage.rb

@@ -1,67 +0,0 @@
-# unpack lineage
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2013-11-26 original script
-#   Stan Smith 2014-07-03 resolve require statements using Mdtranslator.reader_module
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_processStep')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_source')
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module Lineage
-
-                    def self.unpack(hLineage, responseObj)
-
-                        # return nil object if input is empty
-                        intDataLine = nil
-                        return if hLineage.empty?
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intDataLine = intMetadataClass.newLineage
-
-                        # lineage - statement
-                        if hLineage.has_key?('statement')
-                            s = hLineage['statement']
-                            if s != ''
-                                intDataLine[:statement] = s
-                            end
-                        end
-
-                        # lineage - process steps
-                        if hLineage.has_key?('processStep')
-                            aProcSteps = hLineage['processStep']
-                            unless aProcSteps.empty?
-                                aProcSteps.each do |hProcStep|
-                                    intDataLine[:processSteps] << ProcessStep.unpack(hProcStep, responseObj)
-                                end
-                            end
-                        end
-
-                        # lineage - data sources
-                        if hLineage.has_key?('source')
-                            aSources = hLineage['source']
-                            unless aSources.empty?
-                                aSources.each do |hSource|
-                                    intDataLine[:dataSources] << Source.unpack(hSource, responseObj)
-                                end
-                            end
-                        end
-
-                        return intDataLine
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_locale.rb

@@ -1,57 +0,0 @@
-# unpack locale
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2015-07-28 original script
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module Locale
-
-                    def self.unpack(hLocale, responseObj)
-
-                        # return nil object if input is empty
-                        intLocale = nil
-                        return if hLocale.empty?
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intLocale = intMetadataClass.newLocale
-
-                        # locale - language
-                        if hLocale.has_key?('language')
-                            s = hLocale['language']
-                            if s != ''
-                                intLocale[:languageCode] = s
-                            end
-                        end
-
-                        # locale - country
-                        if hLocale.has_key?('country')
-                            s = hLocale['country']
-                            if s != ''
-                                intLocale[:countryCode] = s
-                            end
-                        end
-
-                        # locale - character set
-                        if hLocale.has_key?('characterSet')
-                            s = hLocale['characterSet']
-                            if s != ''
-                                intLocale[:characterEncoding] = s
-                            end
-                        end
-
-                        return intLocale
-
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_mdJson.rb

@@ -1,68 +0,0 @@
-# unpack address
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2014-12-12 original script
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-02-17 added support for multiple data dictionaries
-#   Stan Smith 2015-06-12 moved instantiation of intObj up to module mdJson_reader.rb
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_contacts')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_metadata')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_dataDictionary')
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                def self.unpack(intObj, hMdJson, responseObj)
-
-                    # get json schema name and version
-                    hVersion = hMdJson['version']
-                    intObj[:schema][:name] = hVersion['name']
-                    intObj[:schema][:version] = hVersion['version']
-
-                    # contact array
-                    # load the array of contacts from the json input
-                    if hMdJson.has_key?('contact')
-                    	aContacts = hMdJson['contact']
-                    	aContacts.each do |hContact|
-                    		unless hContact.empty?
-                    			intObj[:contacts] << Contact.unpack(hContact, responseObj)
-                    		end
-                    	end
-                    end
-
-                    # add default contacts
-                    intObj[:contacts].concat(Contact.setDefaultContacts)
-
-                    # metadata section
-                    # load metadata from the hash object
-                    if hMdJson.has_key?('metadata')
-                    	hMetadata = hMdJson['metadata']
-                    	intObj[:metadata] = Metadata.unpack(hMetadata, responseObj)
-                    end
-
-                    # data dictionary section
-                    if hMdJson.has_key?('dataDictionary')
-                        aDictionary = hMdJson['dataDictionary']
-                        aDictionary.each do |hDictionary|
-                            unless hDictionary.empty?
-                                intObj[:dataDictionary] << DataDictionary.unpack(hDictionary, responseObj)
-                            end
-                        end
-                    end
-
-                    # return ADIwg internal container
-                    return intObj
-
-                end
-
-            end
-        end
-    end
-end
-

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_medium.rb

@@ -1,73 +0,0 @@
-# unpack transfer medium
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2015-08-24 original script
-#   Stan Smith 2015-09-18 added capacity and capacity units
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module Medium
-
-                    def self.unpack(hMedium, responseObj)
-
-                        # return nil object if input is empty
-                        intMedium = nil
-                        return if hMedium.empty?
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intMedium = intMetadataClass.newMedium
-
-                        # medium - type
-                        if hMedium.has_key?('name')
-                            s = hMedium['name']
-                            if s != ''
-                                intMedium[:mediumType] = s
-                            end
-                        end
-
-                        # medium - capacity
-                        if hMedium.has_key?('mediumCapacity')
-                            s = hMedium['mediumCapacity']
-                            if s != ''
-                                intMedium[:mediumCapacity] = s
-                            end
-                        end
-
-                        # medium - capacity units
-                        if hMedium.has_key?('mediumCapacityUnits')
-                            s = hMedium['mediumCapacityUnits']
-                            if s != ''
-                                intMedium[:mediumCapacityUnits] = s
-                            end
-                        end
-
-                        # medium - format
-                        if hMedium.has_key?('mediumFormat')
-                            s = hMedium['mediumFormat']
-                            if s != ''
-                                intMedium[:mediumFormat] = s
-                            end
-                        end
-
-                        # medium - note
-                        if hMedium.has_key?('mediumNote')
-                            s = hMedium['mediumNote']
-                            if s != ''
-                                intMedium[:mediumNote] = s
-                            end
-                        end
-
-                        return intMedium
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_metadata.rb

@@ -1,90 +0,0 @@
-# unpack metadata
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2013-08-22 original script
-#   Stan Smith 2013-09-23 added distributor info section
-#   Stan Smith 2013-11-26 added metadata maintenance section
-#   Stan Smith 2013-11-26 added hierarchy section
-#   Stan Smith 2013-11-26 added data quality section
-#   Stan Smith 2013-12-27 added parent identifier
-#   Stan Smith 2014-04-24 reorganized for json schema 0.3.0
-#   Stan Smith 2014-05-02 added associated resources
-#   Stan Smith 2014-05-02 added additional documentation
-#   Stan Smith 2014-07-03 resolve require statements using Mdtranslator.reader_module
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_metadataInfo')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_resourceInfo')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_distributionInfo')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_associatedResource')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_additionalDocumentation')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_citation')
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module Metadata
-
-                    def self.unpack(hMetadata, responseObj)
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intMetadata = intMetadataClass.newMetadata
-
-                        # metadata - metadataInfo
-                        # metadataInfo needs access to resourceInfo to check taxonomy
-                        if hMetadata.has_key?('metadataInfo')
-                            intMetadata[:metadataInfo] = MetadataInfo.unpack(hMetadata,responseObj)
-                        end
-
-                        # metadata - resource identification info
-                        if hMetadata.has_key?('resourceInfo')
-                            hResourceInfo = hMetadata['resourceInfo']
-                            intMetadata[:resourceInfo] = ResourceInfo.unpack(hResourceInfo, responseObj)
-                        end
-
-                        # metadata - distribution info
-                        if hMetadata.has_key?('distributionInfo')
-                            aDistributors = hMetadata['distributionInfo']
-                            unless aDistributors.empty?
-                                aDistributors.each do |hDistributor|
-                                    intMetadata[:distributorInfo] << DistributionInfo.unpack(hDistributor, responseObj)
-                                end
-                            end
-                        end
-
-                        # metadata - associated resources
-                        if hMetadata.has_key?('associatedResource')
-                            aAssocRes = hMetadata['associatedResource']
-                            unless aAssocRes.empty?
-                                aAssocRes.each do |hAssocRes|
-                                    intMetadata[:associatedResources] << AssociatedResource.unpack(hAssocRes, responseObj)
-                                end
-                            end
-                        end
-
-                        # metadata - additional documents
-                        if hMetadata.has_key?('additionalDocumentation')
-                            aAddDocs = hMetadata['additionalDocumentation']
-                            unless aAddDocs.empty?
-                                aAddDocs.each do |hAddDoc|
-                                    intMetadata[:additionalDocuments] << AdditionalDocumentation.unpack(hAddDoc, responseObj)
-                                end
-                            end
-                        end
-
-                        return intMetadata
-
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_metadataExtension.rb

@@ -1,53 +0,0 @@
-# unpack metadata extension information
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2013-11-22 original script
-#   Stan Smith 2014-05-15 modified for JSON schema 0.4.0
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module MetadataExtension
-
-                    def self.addExtensionISObio(responseObj)
-
-                        intMetadataClass = InternalMetadata.new
-                        intMetaExt = intMetadataClass.newMetadataExtension
-                        intContactRole = intMetadataClass.newRespParty
-
-                        # extension online information
-                        intMetaExt[:onLineResource] = {}
-
-                        # extension entity information
-                        intMetaExt[:extName] = 'Taxonomy System'
-                        intMetaExt[:extShortName] = 'TaxonSys'
-                        intMetaExt[:extDefinition] = 'Documentation of taxonomic sources, procedures, and treatments'
-                        intMetaExt[:obligation] = 'optional'
-                        intMetaExt[:dataType] = 'class'
-                        intMetaExt[:maxOccurrence] = '1'
-                        intMetaExt[:parentEntities] << 'MD_Identification'
-                        intMetaExt[:rule] = 'New Metadata section as a class to MD_Identification'
-                        intMetaExt[:rationales] << 'The set of data elements contained within this class element ' +
-                            'represents an attempt to provide better documentation of ' +
-                            'taxonomic sources, procedures, and treatments.'
-
-                        # source information
-                        intContactRole[:contactId] = 'ADIwgBio'
-                        intContactRole[:roleName] = 'resourceProvider'
-                        intMetaExt[:extSources] << intContactRole
-
-                        return intMetaExt
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_metadataInfo.rb

@@ -1,152 +0,0 @@
-# unpack metadata information block
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2014-04-24 original script - moved from module_metadata
-#   Stan Smith 2014-07-03 resolve require statements using Mdtranslator.reader_module
-#   Stan Smith 2014-09-19 changed metadata identifier type resource identifier json 0.8.0
-#   Stan Smith 2014-09-19 changed parent metadata identifier type citation json 0.8.0
-#   Stan Smith 2014-11-06 removed metadataScope, moved to resourceType under resourceInfo json 0.9.0
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-06-12 added support for metadataCharacterSet
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-#   Stan Smith 2015-07-28 added support for locale
-
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_responsibleParty')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_dateTime')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_resourceMaintenance')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_metadataExtension')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_resourceIdentifier')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_citation')
-require ADIWG::Mdtranslator::Readers::MdJson.readerModule('module_locale')
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module MetadataInfo
-
-                    def self.unpack(hMetadata, responseObj)
-
-                        # return nil object if input is empty
-                        intMetadataInfo = nil
-                        return if hMetadata.empty?
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intMetadataInfo = intMetadataClass.newMetadataInfo
-                        hMetadataInfo = hMetadata['metadataInfo']
-
-                        # metadata - metadata identifier
-                        if hMetadataInfo.has_key?('metadataIdentifier')
-                            hMetadataId = hMetadataInfo['metadataIdentifier']
-                            unless hMetadataId.empty?
-                                intMetadataInfo[:metadataId] = ResourceIdentifier.unpack(hMetadataId, responseObj)
-                            end
-                        end
-
-                        # metadata - parent metadata identifier
-                        if hMetadataInfo.has_key?('parentMetadata')
-                            hParent = hMetadataInfo['parentMetadata']
-                            unless hParent.empty?
-                                intMetadataInfo[:parentMetadata] = Citation.unpack(hParent, responseObj)
-                            end
-                        end
-
-                        # metadata - metadata contacts, custodians
-                        if hMetadataInfo.has_key?('metadataContact')
-                            aCust = hMetadataInfo['metadataContact']
-                            unless aCust.empty?
-                                aCust.each do |rParty|
-                                    intMetadataInfo[:metadataCustodians] << ResponsibleParty.unpack(rParty, responseObj)
-                                end
-                            end
-                        end
-
-                        # metadata - creation date
-                        if hMetadataInfo.has_key?('metadataCreationDate')
-                            s = hMetadataInfo['metadataCreationDate']
-                            if s != ''
-                                hDateTime = DateTime.unpack(s, responseObj)
-                                hDateTime[:dateType] = 'publication'
-                                intMetadataInfo[:metadataCreateDate] = hDateTime
-                            end
-                        end
-
-                        # metadata - date of last metadata update
-                        if hMetadataInfo.has_key?('metadataLastUpdate')
-                            s = hMetadataInfo['metadataLastUpdate']
-                            if s != ''
-                                hDateTime = DateTime.unpack(s, responseObj)
-                                hDateTime[:dateType] = 'revision'
-                                intMetadataInfo[:metadataUpdateDate] = hDateTime
-                            end
-                        end
-
-                        # metadata - characterSet - default 'utf8'
-                        if hMetadataInfo.has_key?('metadataCharacterSet')
-                            s = hMetadataInfo['metadataCharacterSet']
-                            if s != ''
-                                intMetadataInfo[:metadataCharacterSet] = s
-                            else
-                                intMetadataInfo[:metadataCharacterSet] = 'utf8'
-                            end
-                        end
-
-                        # metadata - locale
-                        if hMetadataInfo.has_key?('metadataLocale')
-                            aLocale = hMetadataInfo['metadataLocale']
-                            unless aLocale.empty?
-                                aLocale.each do |hLocale|
-                                    intMetadataInfo[:metadataLocales] << Locale.unpack(hLocale, responseObj)
-                                end
-                            end
-                        end
-
-                        # metadata - metadata URI
-                        if hMetadataInfo.has_key?('metadataUri')
-                            s = hMetadataInfo['metadataUri']
-                            if s != ''
-                                intMetadataInfo[:metadataURI] = s
-                            end
-                        end
-
-                        # metadata - status
-                        if hMetadataInfo.has_key?('metadataStatus')
-                            s = hMetadataInfo['metadataStatus']
-                            if s != ''
-                                intMetadataInfo[:metadataStatus] = s
-                            end
-                        end
-
-                        # metadata - metadata maintenance info
-                        if hMetadataInfo.has_key?('metadataMaintenance')
-                            hMetaMaint = hMetadataInfo['metadataMaintenance']
-                            unless hMetaMaint.empty?
-                                intMetadataInfo[:maintInfo] = ResourceMaintenance.unpack(hMetaMaint, responseObj)
-                            end
-                        end
-
-                        # metadata - extension info - if biological extension
-                        if hMetadata.has_key?('resourceInfo')
-                            resourceInfo = hMetadata['resourceInfo']
-                            if resourceInfo.has_key?('taxonomy')
-                                hTaxonomy = resourceInfo['taxonomy']
-                                unless hTaxonomy.empty?
-                                    intMetadataInfo[:extensions] << MetadataExtension.addExtensionISObio(responseObj)
-                                end
-                            end
-                        end
-
-                        return intMetadataInfo
-
-                    end
-
-                end
-
-            end
-        end
-    end
-end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_v1/module_onlineResource.rb

@@ -1,84 +0,0 @@
-# unpack online resources
-# Reader - ADIwg JSON V1 to internal data structure
-
-# History:
-# 	Stan Smith 2013-09-25 original script
-#   Stan Smith 2014-04-23 modified for json 0.3.0
-#   Stan Smith 2014-08-18 removed doi section for json 0.6.0
-#   Stan Smith 2014-08-21 changed url to uri for json 0.6.0
-#   Stan Smith 2014-12-10 changed to return nil intOlRes if input empty
-#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
-#   Stan Smith 2015-06-22 replace global ($response) with passed in object (responseObj)
-#   Stan Smith 2015-07-14 refactored to remove global namespace constants
-
-module ADIWG
-    module Mdtranslator
-        module Readers
-            module MdJson
-
-                module OnlineResource
-
-                    def self.unpack(hOlResource, responseObj)
-
-                        # return nil object if input is empty
-                        intOLRes = nil
-                        return if hOlResource.empty?
-
-                        # instance classes needed in script
-                        intMetadataClass = InternalMetadata.new
-                        intOLRes = intMetadataClass.newOnlineResource
-
-                        # unpack the online resource
-                        # resource - web link
-                        if hOlResource.has_key?('uri')
-                            s = hOlResource['uri']
-                            if s != ''
-                                intOLRes[:olResURI] = s
-                            else
-                                responseObj[:readerExecutionMessages] << 'Online Resource URI is missing'
-                                responseObj[:readerExecutionPass] = false
-                                return nil
-                            end
-                        end
-
-                        # resource - web link protocol
-                        if hOlResource.has_key?('protocol')
-                            s = hOlResource['protocol']
-                            if s != ''
-                                intOLRes[:olResProtocol] = s
-                            end
-                        end
-
-                        # resource - web link name
-                        if hOlResource.has_key?('name')
-                            s = hOlResource['name']
-                            if s != ''
-                                intOLRes[:olResName] = s
-                            end
-                        end
-
-                        # resource - web link description
-                        if hOlResource.has_key?('description')
-                            s = hOlResource['description']
-                            if s != ''
-                                intOLRes[:olResDesc] = s
-                            end
-                        end
-
-                        # resource - web link function
-                        if hOlResource.has_key?('function')
-                            s = hOlResource['function']
-                            if s != ''
-                                intOLRes[:olResFunction] = s
-                            end
-                        end
-
-                        return intOLRes
-                    end
-
-                end
-
-            end
-        end
-    end
-end