adiwg-mdtranslator 0.10.2 → 0.12.0

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_legalConstraint.rb

@@ -0,0 +1,56 @@
+# unpack legal constraint
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-11-14 original script
+# 	Stan Smith 2013-11-27 modified to process a single legal constraint
+#   Stan Smith 2014-04-28 modified attribute names to match json schema 0.3.0
+#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module LegalConstraints
+
+                    def self.unpack(hLegalCon)
+
+                        # instance classes needed in script
+                        intMetadataClass = InternalMetadata.new
+                        hIntCon = intMetadataClass.newLegalConstraint
+
+                        # legal constraint - access code
+                        if hLegalCon.has_key?('accessConstraint')
+                            aAccCodes = hLegalCon['accessConstraint']
+                            unless aAccCodes.empty?
+                                hIntCon[:accessCodes] = aAccCodes
+                            end
+                        end
+
+                        # legal constraint - use code
+                        if hLegalCon.has_key?('useConstraint')
+                            aUseCodes = hLegalCon['useConstraint']
+                            unless aUseCodes.empty?
+                                hIntCon[:useCodes] = aUseCodes
+                            end
+                        end
+
+                        # legal constraint - other constraints
+                        if hLegalCon.has_key?('otherConstraint')
+                            aOtherCons = hLegalCon['otherConstraint']
+                            unless aOtherCons.empty?
+                                hIntCon[:otherCons] = aOtherCons
+                            end
+                        end
+
+                        return hIntCon
+
+                    end
+
+                end
+
+            end
+        end
+    end
+end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_lineString.rb

@@ -0,0 +1,36 @@
+# unpack line string
+# line string is coded in GeoJSON
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-11-13 original script
+#   Stan Smith 2014-04-30 reorganized for json schema 0.3.0
+#   Stan Smith 2014-07-07 resolve require statements using Mdtranslator.reader_module
+#   Stan Smith 2014-12-15 refactored to handle namespacing readers and writers
+
+require $ReaderNS.readerModule('module_coordinates')
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module LineString
+
+                    def self.unpack(aCoords, geoType)
+                        intMetadataClass = InternalMetadata.new
+                        intLine = intMetadataClass.newGeometry
+
+                        intLine[:geoType] = geoType
+                        intLine[:geometry] = aCoords
+                        intLine[:dimension] = $ReaderNS::Coordinates.getDimension(aCoords)
+
+                        return intLine
+                    end
+
+                end
+
+            end
+        end
+    end
+end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_lineage.rb

@@ -0,0 +1,61 @@
+# 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
+
+require $ReaderNS.readerModule('module_processStep')
+require $ReaderNS.readerModule('module_source')
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module Lineage
+
+                    def self.unpack(hLineage)
+
+                        # 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] << $ReaderNS::ProcessStep.unpack(hProcStep)
+                                end
+                            end
+                        end
+
+                        # lineage - data sources
+                        if hLineage.has_key?('source')
+                            aSources = hLineage['source']
+                            unless aSources.empty?
+                                aSources.each do |hSource|
+                                    intDataLine[:dataSources] << $ReaderNS::Source.unpack(hSource)
+                                end
+                            end
+                        end
+
+                        return intDataLine
+                    end
+
+                end
+
+            end
+        end
+    end
+end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_mdJson.rb

@@ -0,0 +1,69 @@
+# 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
+
+require $ReaderNS.readerModule('module_contacts')
+require $ReaderNS.readerModule('module_metadata')
+require $ReaderNS.readerModule('module_dataDictionary')
+require 'adiwg/mdtranslator/internal/internal_metadata_obj'
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                def self.unpack(hMdJson)
+
+                    # instance classes needed in script
+                    intMetadataClass = InternalMetadata.new
+
+                    # create new internal metadata container for the reader
+                    intObj = intMetadataClass.newBase
+
+                    # 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
+                    # ... the program uses the 'contactId' provided by the user
+                    # ... to reference a contact
+                    if hMdJson.has_key?('contact')
+                    	aContacts = hMdJson['contact']
+                    	aContacts.each do |hContact|
+                    		unless hContact.empty?
+                    			intObj[:contacts] << $ReaderNS::Contact.unpack(hContact)
+                    		end
+                    	end
+                    end
+
+                    # add default contacts
+                    intObj[:contacts].concat($ReaderNS::Contact.setDefaultContacts)
+
+                    # metadata
+                    # load metadata from the hash object
+                    if hMdJson.has_key?('metadata')
+                    	hMetadata = hMdJson['metadata']
+                    	intObj[:metadata] = $ReaderNS::Metadata.unpack(hMetadata)
+                    end
+
+                    # data dictionary
+                    if hMdJson.has_key?('dataDictionary')
+                    	hDictionary = hMdJson['dataDictionary']
+                    	intObj[:dataDictionary] = $ReaderNS::DataDictionary.unpack(hDictionary)
+                    end
+
+                    # return ADIwg internal container
+                    return intObj
+
+                end
+
+            end
+        end
+    end
+end
+

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_metadata.rb

@@ -0,0 +1,88 @@
+# 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
+
+require $ReaderNS.readerModule('module_metadataInfo')
+require $ReaderNS.readerModule('module_resourceInfo')
+require $ReaderNS.readerModule('module_distributionInfo')
+require $ReaderNS.readerModule('module_associatedResource')
+require $ReaderNS.readerModule('module_additionalDocumentation')
+require $ReaderNS.readerModule('module_citation')
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module Metadata
+
+                    def self.unpack(hMetadata)
+
+                        # 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] = $ReaderNS::MetadataInfo.unpack(hMetadata)
+                        end
+
+                        # metadata - resource identification info
+                        if hMetadata.has_key?('resourceInfo')
+                            hResourceInfo = hMetadata['resourceInfo']
+                            intMetadata[:resourceInfo] = $ReaderNS::ResourceInfo.unpack(hResourceInfo)
+                        end
+
+                        # metadata - distribution info
+                        if hMetadata.has_key?('distributionInfo')
+                            aDistributors = hMetadata['distributionInfo']
+                            unless aDistributors.empty?
+                                aDistributors.each do |hDistributor|
+                                    intMetadata[:distributorInfo] << $ReaderNS::DistributionInfo.unpack(hDistributor)
+                                end
+                            end
+                        end
+
+                        # metadata - associated resources
+                        if hMetadata.has_key?('associatedResource')
+                            aAssocRes = hMetadata['associatedResource']
+                            unless aAssocRes.empty?
+                                aAssocRes.each do |hAssocRes|
+                                    intMetadata[:associatedResources] << $ReaderNS::AssociatedResource.unpack(hAssocRes)
+                                end
+                            end
+                        end
+
+                        # metadata - additional documents
+                        if hMetadata.has_key?('additionalDocumentation')
+                            aAddDocs = hMetadata['additionalDocumentation']
+                            unless aAddDocs.empty?
+                                aAddDocs.each do |hAddDoc|
+                                    intMetadata[:additionalDocuments] << $ReaderNS::AdditionalDocumentation.unpack(hAddDoc)
+                                end
+                            end
+                        end
+
+                        return intMetadata
+
+                    end
+
+                end
+
+            end
+        end
+    end
+end

data/lib/adiwg/mdtranslator/readers/mdJson/modules_0.9/module_metadataExtension.rb

@@ -0,0 +1,51 @@
+# 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
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module MetadataExtension
+
+                    def self.addExtensionISObio()
+
+                        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_0.9/module_metadataInfo.rb

@@ -0,0 +1,123 @@
+# 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
+
+require $ReaderNS.readerModule('module_responsibleParty')
+require $ReaderNS.readerModule('module_dateTime')
+require $ReaderNS.readerModule('module_resourceMaintenance')
+require $ReaderNS.readerModule('module_metadataExtension')
+require $ReaderNS.readerModule('module_resourceIdentifier')
+require $ReaderNS.readerModule('module_citation')
+
+module ADIWG
+    module Mdtranslator
+        module Readers
+            module MdJson
+
+                module MetadataInfo
+
+                    def self.unpack(hMetadata)
+
+                        # 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] = $ReaderNS::ResourceIdentifier.unpack(hMetadataId)
+                            end
+                        end
+
+                        # metadata - parent metadata identifier
+                        if hMetadataInfo.has_key?('parentMetadata')
+                            hParent = hMetadataInfo['parentMetadata']
+                            unless hParent.empty?
+                                intMetadataInfo[:parentMetadata] = $ReaderNS::Citation.unpack(hParent)
+                            end
+                        end
+
+                        # metadata - metadata contacts, custodians
+                        if hMetadataInfo.has_key?('metadataContact')
+                            aCust = hMetadataInfo['metadataContact']
+                            unless aCust.empty?
+                                aCust.each do |rParty|
+                                    intMetadataInfo[:metadataCustodians] << $ReaderNS::ResponsibleParty.unpack(rParty)
+                                end
+                            end
+                        end
+
+                        # metadata - creation date
+                        if hMetadataInfo.has_key?('metadataCreationDate')
+                            s = hMetadataInfo['metadataCreationDate']
+                            if s != ''
+                                hDateTime = $ReaderNS::DateTime.unpack(s)
+                                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 = $ReaderNS::DateTime.unpack(s)
+                                hDateTime[:dateType] = 'revision'
+                                intMetadataInfo[:metadataUpdateDate] = hDateTime
+                            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] = $ReaderNS::ResourceMaintenance.unpack(hMetaMaint)
+                            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] << $ReaderNS::MetadataExtension.addExtensionISObio
+                                end
+                            end
+                        end
+
+                        return intMetadataInfo
+
+                    end
+
+                end
+
+            end
+        end
+    end
+end