stash-merritt 0.0.1

data/spec/util/resource_builder.rb

@@ -0,0 +1,333 @@
+require 'datacite/mapping'
+require 'stash/wrapper'
+require 'time'
+
+# TODO: Get rid of this and use FactoryGirl or something
+module StashDatacite
+  class ResourceBuilder # rubocop:disable Metrics/ClassLength
+    DESCRIPTION_TYPE = Datacite::Mapping::DescriptionType
+
+    attr_reader :user_id
+    attr_reader :dcs_resource
+    attr_reader :stash_files
+    attr_reader :upload_time
+
+    def initialize(user_id:, dcs_resource:, stash_files:, upload_date:)
+      @user_id = user_id
+      @dcs_resource = ResourceBuilder.dcs_resource(dcs_resource)
+      @stash_files = ResourceBuilder.stash_files(stash_files)
+      @upload_time = upload_date.to_time
+    end
+
+    def self.dcs_resource(dcs_resource)
+      return dcs_resource if dcs_resource.is_a?(Datacite::Mapping::Resource)
+      return dcs_resource if dcs_resource.to_s =~ /InstanceDouble\(Datacite::Mapping::Resource\)/ # For RSpec tests
+      raise ArgumentError, "dcs_resource does not appear to be a Datacite::Mapping::Resource: #{dcs_resource || 'nil'}"
+    end
+
+    def self.stash_files(stash_files)
+      return stash_files if stash_files.all? do |file|
+        file.is_a?(Stash::Wrapper::StashFile) ||
+        file.to_s =~ /InstanceDouble\(Stash::Wrapper::StashFile\)/ # For RSpec tests
+      end
+      raise ArgumentError, "stash_files does not appear to be an array of Stash::Wrapper::StashFile objects: #{stash_files || 'nil'}"
+    end
+
+    def build
+      populate_se_resource!
+    end
+
+    private
+
+    def se_resource
+      @se_resource ||= StashEngine::Resource.create(user_id: user_id)
+    end
+
+    def se_resource_id
+      se_resource.id
+    end
+
+    def populate_se_resource! # rubocop:disable Metrics/AbcSize
+      set_sd_identifier(dcs_resource.identifier)
+      stash_files.each { |stash_file| add_stash_file(stash_file) }
+      dcs_resource.creators.each { |dcs_creator| add_sd_creator(dcs_creator) }
+      dcs_resource.titles.each { |dcs_title| add_sd_title(dcs_title) }
+      set_sd_publisher(dcs_resource.publisher)
+      set_sd_pubyear(dcs_resource.publication_year)
+      dcs_resource.subjects.each { |dcs_subject| add_sd_subject(dcs_subject) }
+      dcs_resource.contributors.each { |dcs_contributor| add_sd_contributor(dcs_contributor) }
+      dcs_resource.dates.each { |dcs_date| add_sd_date(dcs_date) }
+      set_sd_language(dcs_resource.language)
+      set_sd_resource_type(dcs_resource.resource_type)
+      dcs_resource.alternate_identifiers.each { |dcs_alternate_ident| add_sd_alternate_ident(dcs_alternate_ident) }
+      dcs_resource.related_identifiers.each { |dcs_related_ident| add_sd_related_ident(dcs_related_ident) }
+      dcs_resource.sizes.each { |dcs_size| add_sd_size(dcs_size) }
+      dcs_resource.formats.each { |dcs_format| add_sd_format(dcs_format) }
+      set_sd_version(dcs_resource.version)
+      dcs_resource.rights_list.each { |dcs_rights| add_sd_rights(dcs_rights) }
+      dcs_resource.descriptions.each { |dcs_description| add_sd_description(dcs_description) }
+      dcs_resource.geo_locations.each { |dcs_geo_location| add_sd_geo_location(dcs_geo_location) }
+      dcs_resource.funding_references.each { |dcs_funding_reference| add_funding(dcs_funding_reference) }
+      se_resource.save!
+      se_resource
+    end
+
+    def set_sd_identifier(dcs_identifier)
+      return unless dcs_identifier
+      se_resource.identifier_id = StashEngine::Identifier.create(
+        identifier: dcs_identifier.value && dcs_identifier.value.strip,
+        identifier_type: dcs_identifier.identifier_type
+      ).id
+    end
+
+    def add_stash_file(stash_file)
+      StashEngine::FileUpload.create(
+        resource_id: se_resource_id,
+        upload_file_name: stash_file.pathname,
+        upload_content_type: stash_file.mime_type.to_s,
+        upload_file_size: stash_file.size_bytes,
+        upload_updated_at: upload_time,
+        file_state: 'created'
+      )
+    end
+
+    def add_sd_creator(dcs_creator)
+      last_name, first_name = extract_last_first(dcs_creator.name)
+      sd_creator = Creator.create(
+        creator_first_name: first_name,
+        creator_last_name: last_name,
+        name_identifier_id: sd_name_identifier_id_for(dcs_creator.identifier),
+        resource_id: se_resource_id
+      )
+      sd_creator.affiliation_ids = dcs_creator.affiliations.map { |affiliation_str| sd_affiliation_id_for(affiliation_str) }
+      sd_creator
+    end
+
+    def add_sd_title(dcs_title)
+      title_type = dcs_title.type
+      Title.create(
+        title: dcs_title.value && dcs_title.value.strip,
+        title_type_friendly: (title_type.value if title_type),
+        resource_id: se_resource_id
+      )
+    end
+
+    def set_sd_publisher(dcs_publisher)
+      Publisher.create(publisher: dcs_publisher, resource_id: se_resource_id) unless dcs_publisher.blank?
+    end
+
+    def set_sd_pubyear(dcs_publication_year)
+      return if dcs_publication_year.blank?
+      PublicationYear.create(publication_year: dcs_publication_year, resource_id: se_resource_id)
+    end
+
+    def add_sd_subject(dcs_subject)
+      sd_subject_id = sd_subject_id_for(dcs_subject)
+      ResourcesSubjects.create(resource_id: se_resource_id, subject_id: sd_subject_id)
+    end
+
+    def add_sd_contributor(dcs_contributor)
+      contributor_type = dcs_contributor.type
+      sd_contributor = Contributor.create(
+        contributor_name: dcs_contributor.name,
+        contributor_type_friendly: (contributor_type.value if contributor_type),
+        name_identifier_id: sd_name_identifier_id_for(dcs_contributor.identifier),
+        resource_id: se_resource_id
+      )
+      sd_contributor.affiliation_ids = dcs_contributor.affiliations.map { |affiliation_str| sd_affiliation_id_for(affiliation_str) }
+      sd_contributor
+    end
+
+    def add_sd_date(dcs_date)
+      date_type = dcs_date.type
+      DataciteDate.create(
+        date: dcs_date.value && dcs_date.value.strip,
+        date_type_friendly: (date_type.value if date_type),
+        resource_id: se_resource_id
+      )
+    end
+
+    def set_sd_language(dcs_language)
+      return nil if dcs_language.blank?
+      Language.create(language: dcs_language, resource_id: se_resource_id)
+    end
+
+    def set_sd_resource_type(dcs_resource_type)
+      return nil unless dcs_resource_type
+      dcs_resource_type_general = dcs_resource_type.resource_type_general
+      dcs_resource_type_value = dcs_resource_type.value
+      se_resource_type = dcs_resource_type_general.value.downcase
+      resource_type_friendly = (ResourceType::ResourceTypesGeneralLimited.values.include?(se_resource_type) ? se_resource_type : 'other')
+
+      ResourceType.create(
+        resource_id: se_resource_id,
+        resource_type_general: resource_type_friendly,
+        resource_type: dcs_resource_type_value
+      )
+
+      # resource_type_friendly = (ResourceType::ResourceTypesGeneralLimited.values.include?(se_resource_type) ? se_resource_type : 'other')
+      # ResourceType.create(
+      #   resource_id: se_resource_id,
+      #   resource_type_friendly: resource_type_friendly
+      # )
+    end
+
+    def add_sd_alternate_ident(dcs_alternate_ident)
+      AlternateIdentifier.create(
+        alternate_identifier: dcs_alternate_ident.value && dcs_alternate_ident.value.strip,
+        alternate_identifier_type: dcs_alternate_ident.type, # a string, not an enum
+        resource_id: se_resource_id
+      )
+    end
+
+    def add_sd_related_ident(dcs_related_ident)
+      ident_type = dcs_related_ident.identifier_type
+      rel_type = dcs_related_ident.relation_type
+      scheme_uri = dcs_related_ident.scheme_uri
+      RelatedIdentifier.create(
+        related_identifier: dcs_related_ident.value && dcs_related_ident.value.strip,
+        related_identifier_type_friendly: (ident_type.value if ident_type),
+        relation_type_friendly: (rel_type.value if rel_type),
+        related_metadata_scheme: dcs_related_ident.related_metadata_scheme,
+        scheme_URI: (scheme_uri.to_s if scheme_uri),
+        scheme_type: dcs_related_ident.scheme_type,
+        resource_id: se_resource_id
+      )
+    end
+
+    def add_sd_size(dcs_size)
+      return if dcs_size.blank?
+      Size.create(size: dcs_size, resource_id: se_resource_id)
+    end
+
+    def add_sd_format(dcs_format)
+      return if dcs_format.blank?
+      Format.create(format: dcs_format, resource_id: se_resource_id)
+    end
+
+    def set_sd_version(dcs_version)
+      return if dcs_version.blank?
+      Version.create(version: dcs_version, resource_id: se_resource_id)
+    end
+
+    def add_sd_rights(dcs_rights)
+      rights_uri = dcs_rights.uri
+      Right.create(
+        rights: dcs_rights.value && dcs_rights.value.strip,
+        rights_uri: (rights_uri.to_s if rights_uri),
+        resource_id: se_resource_id
+      )
+    end
+
+    def add_sd_description(dcs_description)
+      desc_type = dcs_description.type
+      if desc_type == DESCRIPTION_TYPE::OTHER && dcs_description.value.start_with?('Data were created with funding')
+        add_sd_award_number(dcs_description.value)
+      else
+        Description.create(
+          description: dcs_description.value && dcs_description.value.strip,
+          description_type_friendly: (desc_type.value if desc_type),
+          resource_id: se_resource_id
+        )
+      end
+    end
+
+    def add_sd_award_number(funding_desc_value)
+      pat = /Data were created with funding from(.*)under grant\(?s?\)?(.*)\.?/m
+      return unless (md = pat.match(funding_desc_value)) && md.size == 3
+
+      contrib_name = md[1].gsub(/\s+/m, ' ').strip
+      award_num = md[2].gsub(/\s+/m, ' ').sub(/.$/, '').strip
+
+      matching_contrib = find_sd_funder(contrib_name)
+      return unless matching_contrib
+
+      matching_contrib.award_number = award_num
+      matching_contrib.save!
+    end
+
+    def find_sd_funder(contrib_name)
+      se_resource.contributors.where(
+        "contributor_name LIKE ? and contributor_type='funder'",
+        "%#{contrib_name.sub(/^[Tt]he ?/, '')}%"
+      ).take
+    end
+
+    def add_sd_geo_location(dcs_geo_location)
+      return unless dcs_geo_location.location?
+      loc = Geolocation.create(resource_id: se_resource_id)
+      add_sd_geo_location_place(loc, dcs_geo_location.place)
+      add_sd_geo_location_point(loc, dcs_geo_location.point)
+      add_sd_geo_location_box(loc, dcs_geo_location.box)
+      loc.save
+    end
+
+    def add_sd_geo_location_place(se_geo_location, dcs_geo_location_place)
+      return if dcs_geo_location_place.blank?
+      se_place = GeolocationPlace.create(geo_location_place: dcs_geo_location_place)
+      se_geo_location.place_id = se_place.id
+    end
+
+    def add_sd_geo_location_point(se_geo_location, dcs_geo_location_point)
+      return unless dcs_geo_location_point
+      se_point = GeolocationPoint.create(
+        latitude: dcs_geo_location_point.latitude,
+        longitude: dcs_geo_location_point.longitude
+      )
+      se_geo_location.point_id = se_point.id
+    end
+
+    def add_sd_geo_location_box(se_geo_location, dcs_geo_location_box)
+      return unless dcs_geo_location_box
+      se_box = GeolocationBox.create(
+        sw_latitude: dcs_geo_location_box.south_latitude,
+        sw_longitude: dcs_geo_location_box.west_longitude,
+        ne_latitude: dcs_geo_location_box.north_latitude,
+        ne_longitude: dcs_geo_location_box.east_longitude
+      )
+      se_geo_location.box_id = se_box.id
+    end
+
+    def add_funding(dcs_funding_reference)
+      award_number = dcs_funding_reference.award_number
+      Contributor.create(
+        contributor_name: dcs_funding_reference.name,
+        contributor_type: Datacite::Mapping::ContributorType::FUNDER.value.downcase,
+        award_number: (award_number.value if award_number),
+        resource_id: se_resource_id
+      )
+    end
+
+    def extract_last_first(name_w_comma)
+      name_w_comma.split(',', 2).map(&:strip)
+    end
+
+    def sd_affiliation_id_for(affiliation_str)
+      sd_affiliations = StashDatacite::Affiliation.where('short_name = ? or long_name = ?', affiliation_str, affiliation_str)
+      return sd_affiliations.first.id unless sd_affiliations.empty?
+      StashDatacite::Affiliation.create(long_name: affiliation_str).id unless affiliation_str.blank?
+    end
+
+    def sd_name_identifier_id_for(dcs_name_identifier)
+      return nil unless dcs_name_identifier
+      scheme_uri = dcs_name_identifier.scheme_uri
+      value = dcs_name_identifier.value
+      sd_name_ident = StashDatacite::NameIdentifier.find_or_create_by(
+        name_identifier: value.to_s.strip,
+        name_identifier_scheme: dcs_name_identifier.scheme,
+        scheme_URI: (scheme_uri if scheme_uri)
+      )
+      sd_name_ident.id
+    end
+
+    def sd_subject_id_for(dcs_subject)
+      return nil unless dcs_subject
+      scheme_uri = dcs_subject.scheme_uri
+      StashDatacite::Subject.find_or_create_by(
+        subject: dcs_subject.value && dcs_subject.value.strip,
+        subject_scheme: dcs_subject.scheme,
+        scheme_URI: (scheme_uri if scheme_uri)
+      ).id
+    end
+  end
+end

data/stash-merritt.gemspec

@@ -0,0 +1,48 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+require 'stash/merritt/module_info'
+require 'uri'
+
+Gem::Specification.new do |spec| # rubocop:disable Metrics/BlockLength
+  spec.name          = Stash::Merritt::NAME
+  spec.version       = Stash::Merritt::VERSION
+  spec.authors       = ['David Moles']
+  spec.email         = ['david.moles@ucop.edu']
+  spec.summary       = 'Merritt integration for Stash'
+  spec.description   = 'Packaging and SWORD deposit module for submitting Stash datasets to Merritt'
+  spec.license       = 'MIT'
+
+  origin = `git config --get remote.origin.url`.chomp
+  origin_uri = origin.start_with?('http') ? URI(origin) : URI(origin.gsub(%r{git@([^:]+)(.com|.org)[^\/]+}, 'http://\1\2'))
+  spec.homepage = URI::HTTP.build(host: origin_uri.host, path: origin_uri.path.chomp('.git')).to_s
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_dependency 'rubyzip', '~> 1.1'
+
+  spec.add_dependency 'stash_ezid_datacite', '~> 0.1' # TODO: fold this in
+
+  spec.add_dependency 'stash_datacite'
+  spec.add_dependency 'stash_engine' # TODO: should stash_datacite export this?
+
+  spec.add_development_dependency 'bundler', '~> 1.7'
+  spec.add_development_dependency 'rake', '~> 10.4'
+  spec.add_development_dependency 'rspec', '~> 3.2'
+  spec.add_development_dependency 'simplecov', '~> 0.9.2'
+  spec.add_development_dependency 'simplecov-console', '~> 0.2.0'
+  spec.add_development_dependency 'rubocop', '~> 0.47'
+  spec.add_development_dependency 'yard', '~> 0.8'
+
+  spec.add_development_dependency 'database_cleaner', '~> 1.5'
+  spec.add_development_dependency 'diffy', '~> 3.1'
+  spec.add_development_dependency 'equivalent-xml', '~> 0.6.0'
+  spec.add_development_dependency 'mysql2', '~> 0.3'
+  spec.add_development_dependency 'webmock', '~> 1.24'
+
+end

data/stash-merritt.iml

@@ -0,0 +1,147 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="RUBY_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$" />
+    <content url="file://$MODULE_DIR$/../stash_engines/stash_engine" />
+    <orderEntry type="jdk" jdkName="ruby-2.2.5-p319" jdkType="RUBY_SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module-library">
+      <library name="stash_datacite (v0.0.5) [path][gem]">
+        <CLASSES>
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/db" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/app" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/bin" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/lib" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/tmp" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/config" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/coverage" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES>
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/db" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/app" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/bin" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/lib" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/tmp" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/config" />
+          <root url="file://$MODULE_DIR$/../stash_engines/stash_datacite/coverage" />
+        </SOURCES>
+      </library>
+    </orderEntry>
+    <orderEntry type="library" scope="PROVIDED" name="actionmailer (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="actionpack (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="actionview (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="activejob (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="activemodel (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="activerecord (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="activesupport (v4.2.7.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="addressable (v2.5.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="amoeba (v3.0.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="arel (v6.0.4, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ast (v2.3.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="builder (v3.2.3, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="carrierwave (v0.10.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="colorize (v0.8.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="concurrent-ruby (v1.0.4, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="crack (v0.4.3, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="database_cleaner (v1.5.3, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="datacite-mapping (v0.2.5, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="diff-lcs (v1.3, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="diffy (v3.1.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="docile (v1.1.5, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="domain_name (v0.5.20161129, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="equivalent-xml (v0.6.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="erubis (v2.7.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ezid-client (v1.5.0, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="faraday (v0.10.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="filesize (v0.1.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="font-awesome-rails (v4.7.0.1, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="globalid (v0.3.7, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="hashdiff (v0.3.2, ruby-2.2.5-p319) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="hashie (v3.5.1, ruby-2.2.5-p319) [gem]" level="application" />
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