adiwg-mdtranslator 0.8.0

data/lib/adiwg/mdtranslator/readers/adiwgJson/adiwgJson_validator.rb

@@ -0,0 +1,115 @@
+# Get minor version of ADIwg JSON V1
+
+# History:
+# 	Stan Smith 2014-07-09 original script
+#   Stan Smith 2014-07-21 added json structure validation method
+#   Stan Smith 2014-08-21 parsed json-schema validation message to readable text
+#   Stan Smith 2014-09-26 added processing of minor release numbers
+
+require 'json'
+require 'json-schema'
+require 'adiwg-json_schemas'
+#json-schema patch
+require 'validator.rb'
+
+module AdiwgJsonValidation
+
+	def self.validate(file)
+
+		# set the anticipated format of the input file based on the reader specified
+		$response[:readerFormat] = 'json'
+
+		# validate the input file structure
+		# test for valid json syntax by attempting to parse the file
+		begin
+			hashObj = JSON.parse(file)
+			$response[:readerStructurePass] = true
+		rescue JSON::JSONError => err
+			$response[:readerStructurePass] = false
+			$response[:readerStructureMessages] << err
+			return
+		end
+
+		# find name and version of input json file
+		if hashObj.has_key?('version')
+			hVersion = hashObj['version']
+		else
+			$response[:readerStructurePass] = false
+			$response[:readerStructureMessages] << 'input file is missing the version:{} block'
+			return
+		end
+
+		# get the version name
+		if hVersion.has_key?('name')
+			s = hVersion['name']
+			if !s.nil?
+				$response[:readerNameFound] = s
+				if s != 'adiwgJson'
+					$response[:readerStructurePass] = false
+					$response[:readerStructureMessages] << "input file version name must be 'adiwgJson'"
+					$response[:readerStructureMessages] << "found version name '#{s}'"
+					return
+				end
+			end
+		else
+			$response[:readerStructurePass] = false
+			$response[:readerStructureMessages] << "input file version:{} block is missing the 'name' attribute"
+			return
+		end
+
+		# get version number
+		if hVersion.has_key?('version')
+			requestReaderVersion = hVersion['version']
+			$response[:readerVersionFound] = requestReaderVersion
+			# test if reader version is supported
+			# remove minor release number
+			# ...and look for a module folder name ending with the requested version
+			# ...example: 'modules_1.2.0'
+			if !requestReaderVersion.nil?
+				aVersionParts = requestReaderVersion.split('.')
+				readerVersion = aVersionParts[0] +'.' + aVersionParts[1] + '.0'
+				dir = File.join(File.dirname(__FILE__),'modules_' + readerVersion)
+				if !File.directory?(dir)
+					$response[:readerStructurePass] = false
+					$response[:readerStructureMessages] << 'input file version is not supported'
+					$response[:readerStructureMessages] << "adiwgJson version requested was '#{requestReaderVersion}'"
+					return
+				end
+				$response[:readerVersionUsed] = readerVersion
+			end
+		else
+			$response[:readerStructurePass] = false
+			$response[:readerStructureMessages] << "input file version:{} block is missing the 'version' attribute"
+			return
+		end
+
+		# validate json against the adiwg-json_schemas
+		# only one schema version is supported at this time
+		begin
+
+			schema = ADIWG::JsonSchemas::Utils.schema_path
+			aValErrs = Array.new
+			if $response[:readerValidationLevel] == 'strict'
+				aValErrs = JSON::Validator.fully_validate(schema, file, :strict => true, :errors_as_objects => true)
+			elsif $response[:readerValidationLevel] == 'normal'
+				aValErrs = JSON::Validator.fully_validate(schema, file, :errors_as_objects => true)
+			end
+
+			if aValErrs.length > 0
+				$response[:readerValidationPass] = false
+				$response[:readerValidationMessages] = aValErrs
+				return
+			end
+
+		rescue JSON::Schema::ValidationError
+			$response[:readerValidationPass] = false
+			$response[:readerValidationMessages] << $!.message
+			return
+		end
+
+		$response[:readerValidationPass] = true
+		return
+
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_address.rb

@@ -0,0 +1,71 @@
+# unpack address
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-10-21 original script
+
+module Adiwg_Address
+
+	def self.unpack(hConAddress)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intAdd = nil
+
+		unless hConAddress.empty?
+			intAdd = intMetadataClass.newAddress
+
+			# address - delivery point
+			if hConAddress.has_key?('deliveryPoint')
+				dPoint = hConAddress['deliveryPoint']
+				dPoint.each do |addLine|
+					intAdd[:deliveryPoints] << addLine
+				end
+			end
+
+			# address - city
+			if hConAddress.has_key?('city')
+				s = hConAddress['city']
+				if s != ''
+					intAdd[:city] = s
+				end
+			end
+
+			# address - admin area
+			if hConAddress.has_key?('administrativeArea')
+				s = hConAddress['administrativeArea']
+				if s != ''
+					intAdd[:adminArea] = s
+				end
+			end
+
+			# address - postal code
+			if hConAddress.has_key?('postalCode')
+				s = hConAddress['postalCode']
+				if s != ''
+					intAdd[:postalCode] = s
+				end
+			end
+
+			# address - country
+			if hConAddress.has_key?('country')
+				s = hConAddress['country']
+				if s != ''
+					intAdd[:country] = s
+				end
+			end
+
+			# address - email
+			if hConAddress.has_key?('electronicMailAddress')
+				eMailList = hConAddress['electronicMailAddress']
+				eMailList.each do |email|
+					intAdd[:eMailList] << email
+				end
+			end
+
+		end
+
+		return intAdd
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_associatedResource.rb

@@ -0,0 +1,57 @@
+# unpack associated resource
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2014-05-02 original script
+# 	Stan Smith 2014-05-28 added resource identifier section
+# 	Stan Smith 2014-06-02 added resource metadata citation section
+#   Stan Smith 2014-07-08 resolve require statements using Mdtranslator.reader_module
+#   Stan Smith 2014-08-18 moved resourceIdentifier to citation module schema 0.6.0
+
+require ADIWG::Mdtranslator.reader_module('module_citation', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_resourceIdentifier', $response[:readerVersionUsed])
+
+module Adiwg_AssociatedResource
+
+	def self.unpack(hAssocRes)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intAssocRes = intMetadataClass.newAssociatedResource
+
+		# associated resource - resource type - initiativeTypeCode
+		if hAssocRes.has_key?('associationType')
+			s = hAssocRes['associationType']
+			if s != ''
+				intAssocRes[:associationType] = s
+			end
+		end
+
+		# associated resource - association type - associationTypeCode
+		if hAssocRes.has_key?('resourceType')
+			s = hAssocRes['resourceType']
+			if s != ''
+				intAssocRes[:resourceType] = s
+			end
+		end
+
+		# associated resource - resource citation
+		if hAssocRes.has_key?('resourceCitation')
+			hCitation = hAssocRes['resourceCitation']
+			unless hCitation.empty?
+				intAssocRes[:resourceCitation] = Adiwg_Citation.unpack(hCitation)
+			end
+		end
+
+		# associated resource - metadata citation
+		if hAssocRes.has_key?('metadataCitation')
+			hCitation = hAssocRes['metadataCitation']
+			unless hCitation.empty?
+				intAssocRes[:metadataCitation] = Adiwg_Citation.unpack(hCitation)
+			end
+		end
+
+		return intAssocRes
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_boundingBox.rb

@@ -0,0 +1,51 @@
+# unpack bounding box
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-11-07 original script
+#   Stan Smith 2014-04-28 reorganized for json schema 0.3.0
+
+module Adiwg_BoundingBox
+
+	def self.unpack(aBBox)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intGeometry = intMetadataClass.newGeometry
+		intGeometry[:geoType] = 'BoundingBox'
+
+		# unpack GeoJSON bounding box elements
+		intBBox = intMetadataClass.newBoundingBox
+		west = aBBox[0]
+		south = aBBox[1]
+		east = aBBox[2]
+		north = aBBox[3]
+
+		# validate coordinates if easting +/-180 and northing +/-90
+		valid = false
+		if (180 >= west) && (west >= -180)
+			if (90 >= south) && (south >= -90)
+				if (180 >= east) && (east >= -180)
+					if (90 >= north) &&(north >= -90)
+						valid = true
+					end
+				end
+			end
+		end
+
+		# build internal geo element if valid
+		if valid
+			intBBox[:westLong] = west
+			intBBox[:eastLong] = east
+			intBBox[:southLat] = south
+			intBBox[:northLat] = north
+			intGeometry[:geometry] = intBBox
+
+			return intGeometry
+		else
+			return nil
+		end
+
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_browseGraphic.rb

@@ -0,0 +1,52 @@
+# unpack browse graphic
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-10-17 original script
+# 	Stan Smith 2013-11-27 modified to process single browse graphic rather than array
+#   Stan Smith 2014-04-28 modified attribute names to match json schema 0.3.0
+
+module Adiwg_BrowseGraphic
+
+	def self.unpack(hBgraphic)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intBGraphic = intMetadataClass.newBrowseGraphic
+
+		# graphic - file name
+		if hBgraphic.has_key?('fileName')
+			s = hBgraphic['fileName']
+			if s != ''
+				intBGraphic[:bGName] = s
+			end
+		end
+
+		# graphic - file description
+		if hBgraphic.has_key?('fileDescription')
+			s = hBgraphic['fileDescription']
+			if s != ''
+				intBGraphic[:bGDescription] = s
+			end
+		end
+
+		# graphic - file  type
+		if hBgraphic.has_key?('fileType')
+			s = hBgraphic['fileType']
+			if s != ''
+				intBGraphic[:bGType] = s
+			end
+		end
+
+		# graphic - web link
+		if hBgraphic.has_key?('fileUri')
+			s = hBgraphic['fileUri']
+			if s != ''
+				intBGraphic[:bGURI] = s
+			end
+		end
+
+		return intBGraphic
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_citation.rb

@@ -0,0 +1,104 @@
+# unpack citation
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-08-26 original script
+#   Stan Smith 2014-04-25 modified to support json schema 0.3.0
+#   Stan Smith 2014-07-03 resolve require statements using Mdtranslator.reader_module
+#   Stan Smith 2014-08-18 changed additionalIdentifier section to identifier schema 0.6.0
+
+require ADIWG::Mdtranslator.reader_module('module_dateTime', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_responsibleParty', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_onlineResource', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_resourceIdentifier', $response[:readerVersionUsed])
+
+module Adiwg_Citation
+
+	def self.unpack(hCitation)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intCitation = intMetadataClass.newCitation
+
+		# citation - title
+		if hCitation.has_key?('title')
+			s = hCitation['title']
+			if s != ''
+				intCitation[:citTitle] = s
+			end
+		end
+
+		# citation - date
+		if hCitation.has_key?('date')
+			aCitDates = hCitation['date']
+			unless aCitDates.empty?
+				aCitDates.each do |hCitDate|
+					if hCitDate.has_key?('date')
+						s = hCitDate['date']
+						if s != ''
+							intDateTime = Adiwg_DateTime.unpack(s)
+							if hCitDate.has_key?('dateType')
+								s = hCitDate['dateType']
+								if s != ''
+									intDateTime[:dateType] = s
+								end
+							end
+							intCitation[:citDate] << intDateTime
+						end
+					end
+				end
+			end
+		end
+
+		# citation - edition
+		if hCitation.has_key?('edition')
+			s = hCitation['edition']
+			if s != ''
+				intCitation[:citEdition]  = s
+			end
+		end
+
+		# citation - responsible party
+		if hCitation.has_key?('responsibleParty')
+			aRParty = hCitation['responsibleParty']
+			unless aRParty.empty?
+				aRParty.each do |hRParty|
+					intCitation[:citResponsibleParty] << Adiwg_ResponsibleParty.unpack(hRParty)
+				end
+			end
+		end
+
+		# citation - presentation form
+		if hCitation.has_key?('presentationForm')
+			aPForms = hCitation['presentationForm']
+			unless aPForms.empty?
+				aPForms.each do |pForm|
+					intCitation[:citResourceForms] << pForm
+				end
+			end
+		end
+
+		# citation - resource identifiers
+		if hCitation.has_key?('identifier')
+			aResIds = hCitation['identifier']
+			aResIds.each do |hIdentifier|
+				unless hIdentifier.empty?
+					intCitation[:citResourceIDs] << Adiwg_ResourceIdentifier.unpack(hIdentifier)
+				end
+			end
+		end
+
+		# citation - online resources
+		if hCitation.has_key?('onlineResource')
+			aOlRes = hCitation['onlineResource']
+			aOlRes.each do |hOlRes|
+				unless hOlRes.empty?
+					intCitation[:citOlResources] << Adiwg_OnlineResource.unpack(hOlRes)
+				end
+			end
+		end
+
+		return intCitation
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_contacts.rb

@@ -0,0 +1,121 @@
+# unpack contacts
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-08-20 original script
+# 	Stan Smith 2013-09-25 moved onlineResource to new module
+# 	Stan Smith 2013-10-21 moved address to new module
+#	Stan Smith 2014-04-23 modify for json schema version 0.3.0
+#   Stan Smith 2014-04-24 split default contacts to a separate method
+#   Stan Smith 2014-05-14 combine phone service types
+#   Stan Smith 2014-07-03 added module_path method to support versioning
+
+require ADIWG::Mdtranslator.reader_module('module_address', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_onlineResource', $response[:readerVersionUsed])
+require ADIWG::Mdtranslator.reader_module('module_phone', $response[:readerVersionUsed])
+
+module Adiwg_Contact
+
+	def self.unpack(hContact)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intCont = intMetadataClass.newContact
+
+		# contact ID
+		if hContact.has_key?('contactId')
+			s = hContact['contactId']
+			if s != ''
+				intCont[:contactID] = s
+			end
+		end
+
+		# individual name
+		if hContact.has_key?('individualName')
+			s = hContact['individualName']
+			if s != ''
+				intCont[:indName] = s
+			end
+		end
+
+		# organization name
+		if hContact.has_key?('organizationName')
+			s = hContact['organizationName']
+			if s != ''
+				intCont[:orgName] = s
+			end
+		end
+
+		# position name
+		if hContact.has_key?('positionName')
+			s = hContact['positionName']
+			if s != ''
+				intCont[:position] = s
+			end
+		end
+
+		# online resources
+		if hContact.has_key?('onlineResource')
+			aOlRes = hContact['onlineResource']
+			aOlRes.each do |hOlRes|
+				unless hOlRes.empty?
+					intCont[:onlineRes] << Adiwg_OnlineResource.unpack(hOlRes)
+				end
+			end
+		end
+
+		# contact instructions
+		if hContact.has_key?('contactInstructions')
+			s = hContact['contactInstructions']
+			if s != ''
+				intCont[:contactInstructions] = s
+			end
+		end
+
+		# phones - all service types
+		if hContact.has_key?('phoneBook')
+			aPhones = hContact['phoneBook']
+			aPhones.each do |hPhone|
+				intCont[:phones].concat(Adiwg_Phone.unpack(hPhone))
+			end
+		end
+
+		# address
+		if hContact.has_key?('address')
+			conAddress = hContact['address']
+			intCont[:address] = Adiwg_Address.unpack(conAddress)
+		end
+
+		return intCont
+
+	end
+
+	def self.setDefaultContacts()
+
+		# add default contacts
+		intMetadataClass = InternalMetadata.new
+		aDefContacts = Array.new
+
+		# contact to support biological extensions
+		intCont = intMetadataClass.newContact
+		intCont[:contactID] = 'ADIwgBio'
+		intCont[:orgName] = 'National Biological Information Infrastructure (NBII)'
+		aDefContacts << intCont
+
+		# contact to support doi (digital object identifier)
+		intCont = intMetadataClass.newContact
+		intCont[:contactID] = 'ADIwgDOI'
+		intCont[:orgName] = 'International DOI Foundation (IDF)'
+
+		intOlRes = intMetadataClass.newOnlineResource
+		intOlRes[:olResURI] = 'http://www.doi.org'
+		intCont[:onlineRes] << intOlRes
+
+		aDefContacts << intCont
+
+		return aDefContacts
+
+	end
+
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_coordinates.rb

@@ -0,0 +1,52 @@
+# repack coordinates
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-11-07 original script
+# 	Stan Smith 2013-11-13 added getDimension
+#   Stan Smith 2014-05-23 added getLevels
+
+module Adiwg_Coordinates
+
+	# repack coordinate array into single string for ISO
+	def self.unpack(aCoords)
+		s = ''
+		i = 0
+		coordCount = aCoords.length
+		aCoords.each do |coord|
+			if coord.kind_of?(Array)
+				s = s + unpack(coord)
+			else
+				i += 1
+				s = s + coord.to_s
+				if i < coordCount
+					s = s + ','
+				end
+				s = s + ' '
+			end
+		end
+
+		return s
+	end
+
+	# get the number of dimensions in a coordinate array
+	def self.getDimension(aCoords)
+		if aCoords[0].kind_of?(Array)
+			coordDim = getDimension(aCoords[0])
+		else
+			coordDim = aCoords.length
+		end
+
+		return coordDim
+	end
+
+	# get the number of levels in the coordinate array
+	def self.getLevels(aCoords)
+		i = 1
+		if aCoords[0].kind_of?(Array)
+			i = i + getLevels(aCoords[0])
+		end
+		return i
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_dataQuality.rb

@@ -0,0 +1,40 @@
+# unpack data quality
+# 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
+
+require ADIWG::Mdtranslator.reader_module('module_lineage', $response[:readerVersionUsed])
+
+module Adiwg_DataQuality
+
+	def self.unpack(hDataQual)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+		intDataQual = intMetadataClass.newDataQuality
+
+		# data quality - scope
+		if hDataQual.has_key?('scope')
+			s = hDataQual['scope']
+			if s != ''
+				intDataQual[:dataScope] = s
+			end
+		end
+
+		# data quality - report
+		# on hold
+
+		# data quality - lineage
+		if hDataQual.has_key?('lineage')
+			hLineage = hDataQual['lineage']
+			unless hLineage.empty?
+				intDataQual[:dataLineage] = Adiwg_Lineage.unpack(hLineage)
+			end
+		end
+
+		return intDataQual
+	end
+
+end

data/lib/adiwg/mdtranslator/readers/adiwgJson/modules_0.8.0/module_dateTime.rb

@@ -0,0 +1,27 @@
+# unpack dateTime
+# Reader - ADIwg JSON V1 to internal data structure
+
+# History:
+# 	Stan Smith 2013-12-11 original script
+
+require 'module_dateTimeFun'
+
+module Adiwg_DateTime
+
+	def self.unpack(sDateTime)
+
+		# instance classes needed in script
+		intMetadataClass = InternalMetadata.new
+
+		# dateTime
+		intDateTime = intMetadataClass.newDateTime
+
+		aDateTimeReturn = AdiwgDateTimeFun.dateTimeFromString(sDateTime)
+		intDateTime[:dateTime] = aDateTimeReturn[0]
+		intDateTime[:dateResolution] = aDateTimeReturn[1]
+
+		return intDateTime
+
+	end
+
+end