stash-merritt 0.0.1

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Files changed (50) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +193 -0
  3. data/.rubocop.yml +32 -0
  4. data/.ruby-version +1 -0
  5. data/.travis.yml +12 -0
  6. data/Gemfile +6 -0
  7. data/Gemfile.lock +326 -0
  8. data/LICENSE.md +22 -0
  9. data/README.md +53 -0
  10. data/Rakefile +49 -0
  11. data/lib/datacite/mapping/datacite_xml_factory.rb +212 -0
  12. data/lib/stash/merritt/ezid_helper.rb +50 -0
  13. data/lib/stash/merritt/module_info.rb +12 -0
  14. data/lib/stash/merritt/repository.rb +17 -0
  15. data/lib/stash/merritt/submission_job.rb +90 -0
  16. data/lib/stash/merritt/submission_package/data_one_manifest_builder.rb +41 -0
  17. data/lib/stash/merritt/submission_package/merritt_datacite_builder.rb +22 -0
  18. data/lib/stash/merritt/submission_package/merritt_delete_builder.rb +25 -0
  19. data/lib/stash/merritt/submission_package/merritt_oaidc_builder.rb +130 -0
  20. data/lib/stash/merritt/submission_package/stash_wrapper_builder.rb +59 -0
  21. data/lib/stash/merritt/submission_package.rb +125 -0
  22. data/lib/stash/merritt/sword_helper.rb +58 -0
  23. data/lib/stash/merritt.rb +5 -0
  24. data/lib/stash.rb +5 -0
  25. data/spec/.rubocop.yml +10 -0
  26. data/spec/config/app_config.yml +3 -0
  27. data/spec/config/database.yml +7 -0
  28. data/spec/config/licenses.yml +18 -0
  29. data/spec/data/archive/mrt-datacite.xml +121 -0
  30. data/spec/data/archive/mrt-dataone-manifest.txt +32 -0
  31. data/spec/data/archive/mrt-oaidc.xml +38 -0
  32. data/spec/data/archive/stash-wrapper.xml +213 -0
  33. data/spec/data/archive.zip +0 -0
  34. data/spec/data/dc4-with-funding-references.xml +123 -0
  35. data/spec/db/datacite/mapping/datacite_xml_factory_spec.rb +56 -0
  36. data/spec/db/stash/merritt/merritt_oaidc_builder_spec.rb +72 -0
  37. data/spec/db/stash/merritt/submission_package_spec.rb +174 -0
  38. data/spec/db/stash/merritt/sword_helper_spec.rb +162 -0
  39. data/spec/db_spec_helper.rb +31 -0
  40. data/spec/rspec_custom_matchers.rb +92 -0
  41. data/spec/spec_helper.rb +86 -0
  42. data/spec/unit/stash/merritt/ezid_helper_spec.rb +88 -0
  43. data/spec/unit/stash/merritt/repository_spec.rb +19 -0
  44. data/spec/unit/stash/merritt/submission_job_spec.rb +127 -0
  45. data/spec/util/resource_builder.rb +333 -0
  46. data/stash-merritt.gemspec +48 -0
  47. data/stash-merritt.iml +147 -0
  48. data/stash-merritt.ipr +127 -0
  49. data/travis-local-deps.sh +43 -0
  50. metadata +337 -0
@@ -0,0 +1,125 @@
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+ require 'fileutils'
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+ require 'tmpdir'
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+ require 'stash_engine'
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+ require 'stash_datacite'
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+ require 'zip'
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+ require 'datacite/mapping/datacite_xml_factory'
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+ require 'stash/merritt/submission_package/data_one_manifest_builder'
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+ require 'stash/merritt/submission_package/merritt_datacite_builder'
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+ require 'stash/merritt/submission_package/merritt_delete_builder'
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+ require 'stash/merritt/submission_package/merritt_oaidc_builder'
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+ require 'stash/merritt/submission_package/stash_wrapper_builder'
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+
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+ module Stash
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+ module Merritt
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+ class SubmissionPackage
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+ attr_reader :resource
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+ attr_reader :zipfile
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+
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+ def initialize(resource:)
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+ raise ArgumentError, "Resource (#{resource.id}) must have an identifier before submission" unless resource.identifier_str
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+ @resource = resource
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+ @zipfile = create_zipfile
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+ end
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+
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+ def resource_id
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+ resource.id
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+ end
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+
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+ def dc3_xml
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+ @dc3_xml ||= datacite_xml_factory.build_datacite_xml(datacite_3: true)
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+ end
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+
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+ def resource_title
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+ primary_title = resource.titles.where(title_type: nil).first
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+ primary_title.title.to_s if primary_title
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+ end
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+
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+ def create_zipfile
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+ StashDatacite::PublicationYear.ensure_pub_year(resource)
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+ zipfile_path = File.join(workdir, "#{resource_id}_archive.zip")
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+ Zip::File.open(zipfile_path, Zip::File::CREATE) do |zipfile|
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+ builders.each { |builder| write_to_zipfile(zipfile, builder) }
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+ uploads.each { |upload| add_to_zipfile(zipfile, upload) }
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+ end
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+ zipfile_path
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+ end
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+
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+ def cleanup!
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+ FileUtils.remove_dir(workdir)
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+ @zipfile = nil
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+ end
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+
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+ def to_s
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+ "#{self.class}: submission package for resource #{resource_id} (#{resource_title}"
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+ end
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+
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+ private
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+
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+ def write_to_zipfile(zipfile, builder)
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+ return unless (file = builder.write_file(workdir))
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+ zipfile.add(builder.file_name, file)
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+ end
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+
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+ def add_to_zipfile(zipfile, upload)
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+ path = File.join(resource.upload_dir, upload.upload_file_name)
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+ raise ArgumentError("Upload file '#{upload.upload_file_name}' not found in directory #{resource.upload_dir}") unless File.exist?(path)
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+ zipfile.add(upload.upload_file_name, path)
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+ end
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+
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+ def builders
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+ [stash_wrapper_builder, mrt_datacite_builder, mrt_oaidc_builder, mrt_dataone_manifest_builder, mrt_delete_builder]
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+ end
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+
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+ def stash_wrapper_builder
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+ @stash_wrapper_builder ||= StashWrapperBuilder.new(dcs_resource: dc4_resource, version_number: version_number, uploads: uploads)
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+ end
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+
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+ def mrt_datacite_builder
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+ @mrt_datacite_builder ||= MerrittDataciteBuilder.new(datacite_xml_factory)
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+ end
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+
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+ def mrt_oaidc_builder
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+ @mrt_oaidc_builder ||= MerrittOAIDCBuilder.new(resource_id: resource_id)
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+ end
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+
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+ def mrt_dataone_manifest_builder
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+ @mrt_dataone_manifest_builder ||= DataONEManifestBuilder.new(uploads)
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+ end
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+
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+ def mrt_delete_builder
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+ @mrt_delete_builder ||= MerrittDeleteBuilder.new(resource_id: resource_id)
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+ end
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+
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+ def total_size_bytes
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+ @total_size_bytes ||= uploads.inject(0) { |sum, u| sum + u.upload_file_size }
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+ end
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+
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+ def version_number
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+ @version_number ||= resource.version_number
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+ end
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+
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+ def uploads
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+ resource.current_file_uploads
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+ end
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+
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+ def datacite_xml_factory
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+ @datacite_xml_factory ||= Datacite::Mapping::DataciteXMLFactory.new(doi_value: resource.identifier_value, se_resource_id: resource_id, total_size_bytes: total_size_bytes, version: version_number)
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+ end
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+
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+ def dc4_resource
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+ @dc4_resource ||= datacite_xml_factory.build_resource
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+ end
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+
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+ def workdir
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+ @workdir ||= begin
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+ path = resource.upload_dir
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+ FileUtils.mkdir_p(path)
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+ tmpdir = Dir.mktmpdir('uploads', path)
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+ File.absolute_path(tmpdir)
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+ end
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+ end
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+
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+ end
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+ end
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+ end
@@ -0,0 +1,58 @@
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+ require 'stash/sword'
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+
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+ module Stash
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+ module Merritt
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+ class SwordHelper
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+ attr_reader :logger
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+ attr_reader :package
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+
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+ def initialize(package:, logger: nil)
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+ @logger = logger
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+ @package = package
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+ end
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+
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+ def submit!
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+ if (update_uri = resource.update_uri)
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+ do_update(update_uri)
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+ else
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+ do_create
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+ end
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+ resource.version_zipfile = zipfile
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+ resource.save!
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+ end
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+
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+ private
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+
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+ def resource
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+ package.resource
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+ end
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+
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+ def tenant
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+ resource.tenant
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+ end
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+
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+ def identifier_str
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+ resource.identifier_str
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+ end
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+
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+ def zipfile
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+ package.zipfile
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+ end
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+
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+ def sword_client
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+ @sword_client ||= Stash::Sword::Client.new(logger: logger, **tenant.sword_params)
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+ end
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+
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+ def do_create
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+ receipt = sword_client.create(doi: identifier_str, zipfile: zipfile)
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+ resource.download_uri = receipt.em_iri
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+ resource.update_uri = receipt.edit_iri
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+ end
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+
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+ def do_update(update_uri)
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+ sword_client.update(edit_iri: update_uri, zipfile: zipfile)
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+ end
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+
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+ end
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+ end
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+ end
@@ -0,0 +1,5 @@
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+ module Stash
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+ module Merritt
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+ Dir.glob(File.expand_path('../merritt/*.rb', __FILE__)).sort.each(&method(:require))
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+ end
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+ end
data/lib/stash.rb ADDED
@@ -0,0 +1,5 @@
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+ require 'logger'
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+
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+ module Stash
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+ Dir.glob(File.expand_path('../stash/*.rb', __FILE__)).sort.each(&method(:require))
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+ end
data/spec/.rubocop.yml ADDED
@@ -0,0 +1,10 @@
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+ inherit_from: ../.rubocop.yml
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+
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+ Metrics/MethodLength:
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+ Enabled: false
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+
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+ Metrics/ModuleLength:
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+ Enabled: false
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+
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+ Metrics/BlockLength:
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+ Enabled: false
@@ -0,0 +1,3 @@
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+ test:
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+ feedback_email_from: stash-noreply@example.edu
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+ feedback_email_to: [stash-dev@example.edu, stash-ops@example.edu]
@@ -0,0 +1,7 @@
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+ # TODO: separate database
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+ test:
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+ host: localhost
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+ adapter: mysql2
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+ database: stash_merritt
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+ username: travis
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+ encoding: utf8mb4
@@ -0,0 +1,18 @@
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+ # this file has license information starting with an identifier for the license
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+ # and then uri and name
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+
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+ cc0:
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+ uri: https://creativecommons.org/publicdomain/zero/1.0/
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+ name: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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+ explanation: >
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+ This releases your work to the public domain for any use.
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+ badge: icon_cc-zero.svg
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+
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+
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+ cc_by:
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+ uri: https://creativecommons.org/licenses/by/4.0/
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+ name: Creative Commons Attribution 4.0 International (CC BY 4.0)
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+ explanation: >
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+ This license lets others distribute, modify, and build upon your work, even commercially, as
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+ long as they credit you for the original creation.
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+ badge: icon_cc-by.svg
@@ -0,0 +1,121 @@
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+ <?xml version='1.0'?>
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+ <resource xsi:schemaLocation='http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns='http://datacite.org/schema/kernel-3'>
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+ <identifier identifierType='DOI'>10.15146/R3RG6G</identifier>
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+ <creators>
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+ <creator>
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+ <creatorName>Chen, Hao</creatorName>
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+ <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>0123-4567-8910-1112</nameIdentifier>
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+ <affiliation>North Carolina Central University</affiliation>
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+ </creator>
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+ </creators>
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+ <titles>
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+ <title>A Zebrafish Model for Studies on Esophageal Epithelial Biology</title>
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+ <title titleType='Subtitle'>
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+ Characterizing a region of stratified squamous epithelium in the zebrafish
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+ upper digestive tract
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+ </title>
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+ </titles>
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+ <publisher>DataONE</publisher>
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+ <publicationYear>2016</publicationYear>
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+ <subjects>
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+ <subject>Zebrafish</subject>
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+ <subject>Epithelium</subject>
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+ <subject>Barrett&apos;s esophagus</subject>
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+ </subjects>
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+ <contributors>
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+ <contributor contributorType='ProjectMember'>
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+ <contributorName>Chen, Xiaoxin</contributorName>
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+ <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>1234-5678-9101-1121</nameIdentifier>
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+ <affiliation>University of North Carolina at Chapel Hill</affiliation>
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+ </contributor>
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+ <contributor contributorType='DataManager'>
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+ <contributorName>Wilson, James</contributorName>
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+ </contributor>
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+ <contributor contributorType="Funder">
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+ <contributorName>U.S. Environmental Protection Agency</contributorName>
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+ </contributor>
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+ <contributor contributorType="Funder">
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+ <contributorName>
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+ CYBER-ShARE Center of Excellence National Science Foundation (NSF) CREST grants
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+ </contributorName>
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+ </contributor>
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+ <contributor contributorType="Funder">
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+ <contributorName>CI-Team Grant</contributorName>
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+ </contributor>
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+ </contributors>
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+ <dates>
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+ <date dateType='Available'>2015-12-02</date>
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+ <date dateType='Collected'>2009/2011</date>
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+ </dates>
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+ <language>en</language>
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+ <resourceType resourceTypeGeneral='Dataset'>application/octet-stream</resourceType>
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+ <alternateIdentifiers>
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+ <alternateIdentifier alternateIdentifierType='URL'>
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+ https://oneshare.cdlib.org/xtf/view?docId=dataone/ark%2B%3Dc5146%3Dr3rg6g/mrt-datacite.xml
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+ </alternateIdentifier>
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+ </alternateIdentifiers>
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+ <relatedIdentifiers>
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+ <relatedIdentifier relationType='IsCitedBy' relatedIdentifierType='DOI'>10.1371/journal.pone.0143878</relatedIdentifier>
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+ <relatedIdentifier relationType='IsDocumentedBy' relatedIdentifierType='URL'>http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143878</relatedIdentifier>
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+ </relatedIdentifiers>
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+ <sizes>
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+ <size>3286679 bytes</size>
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+ </sizes>
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+ <formats>
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+ <format>text/plain</format>
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+ <format>text/application/vnd.openxmlformats-officedocument.wordprocessingml.document</format>
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+ <format>application/xml</format>
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+ <format>application/pdf</format>
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+ </formats>
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+ <version>1</version>
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+ <rightsList>
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+ <rights rightsURI='https://creativecommons.org/publicdomain/zero/1.0/'>CC0 1.0 Universal (CC0 1.0) Public Domain Dedication</rights>
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+ </rightsList>
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+ <descriptions>
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+ <description descriptionType='Abstract'>
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+ Mammalian esophagus exhibits a remarkable change in epithelial structure
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+ during the transition from embryo to adult. However, the molecular
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+ mechanisms of esophageal epithelial development are not well understood.
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+ Zebrafish (Danio rerio), a common model organism for vertebrate
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+ development and gene function, has not previously been characterized as a
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+ model system for esophageal epithelial development. In this study, we
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+ characterized a piece of non-keratinized stratified squamous epithelium
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+ similar to human esophageal epithelium in the upper digestive tract of
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+ developing zebrafish. Under the microscope, this piece was detectable at
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+ 5dpf and became stratified at 7dpf. Expression of esophageal epithelial
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+ marker genes (Krt5, P63, Sox2 and Pax9) was detected by
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+ immunohistochemistry and in situ hybridization. Knockdown of P63, a gene
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+ known to be critical for esophageal epithelium, disrupted the development
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+ of this epithelium. With this model system, we found that Pax9 knockdown
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+ resulted in loss or disorganization of the squamous epithelium, as well as
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+ down-regulation of the differentiation markers Krt4 and Krt5. In summary,
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+ we characterized a region of stratified squamous epithelium in the
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+ zebrafish upper digestive tract which can be used for functional studies
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+ of candidate genes involved in esophageal epithelial biology.
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+ </description>
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+ <description descriptionType='Other'>
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+ Data were created with funding from U.S. Environmental Protection Agency
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+ under grant(s) EPA STAR Fellowship 2011.
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+ </description>
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+ <description descriptionType='Other'>
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+ Data were created with funding from CYBER-ShARE Center of Excellence
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+ National Science Foundation (NSF) CREST grants under grant(s) HRD-0734825
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+ and HRD-1242122.
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+ </description>
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+ <description descriptionType='Other'>
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+ Data were created with funding from CI-Team Grant under grant(s)
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+ OCI-1135525.
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+ </description>
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+ </descriptions>
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+ <geoLocations>
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+ <geoLocation>
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+ <geoLocationBox>37.046 -119.211 37.075 -119.182</geoLocationBox>
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+ <geoLocationPlace>Providence Creek (Lower, Upper and P301)</geoLocationPlace>
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+ </geoLocation>
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+ <geoLocation>
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+ <geoLocationPoint>31.233 -67.302</geoLocationPoint>
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+ <geoLocationBox>41.09 -71.032 42.893 -68.211</geoLocationBox>
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+ <geoLocationPlace>Atlantic Ocean</geoLocationPlace>
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+ </geoLocation>
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+ </geoLocations>
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+ </resource>
@@ -0,0 +1,32 @@
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+ #%dataonem_0.1
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+ #%profile | http://uc3.cdlib.org/registry/ingest/manifest/mrt-dataone-manifest
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+ #%prefix | dom: | http://uc3.cdlib.org/ontology/dataonem
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+ #%prefix | mrt: | http://uc3.cdlib.org/ontology/mom
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+ #%fields | dom:scienceMetadataFile | dom:scienceMetadataFormat | dom:scienceDataFile | mrt:mimeType
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | Laney_300394_Exempt_Determination_Letter.pdf | application/pdf
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | Laney_300394_Exempt_Determination_Letter.pdf | application/pdf
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | Laney_IRBProposal.docx | application/vnd.openxmlformats-officedocument.wordprocessingml.document
9
+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | Laney_IRBProposal.docx | application/vnd.openxmlformats-officedocument.wordprocessingml.document
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | SensorSurvey_Printout.pdf | application/pdf
11
+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | SensorSurvey_Printout.pdf | application/pdf
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | clean_survey_data_no_ids.csv | text/csv
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | clean_survey_data_no_ids.csv | text/csv
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | research_coords.csv | text/csv
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | research_coords.csv | text/csv
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q10/research_sites.R | text/plain
17
+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q10/research_sites.R | text/plain
18
+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q11-23/sensors_platforms.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q11-23/sensors_platforms.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q24/limitsToExpansion.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q24/limitsToExpansion.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q25-32/data_metadata_management.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q25-32/data_metadata_management.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q3-9/respondent_info.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q3-9/respondent_info.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q33-37/networking.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q33-37/networking.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q38-42/publications.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q38-42/publications.R | text/plain
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+ mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey_data_prep.R | text/plain
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+ mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey_data_prep.R | text/plain
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+ #%eof
@@ -0,0 +1,38 @@
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+ <qualifieddc xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xsi:noNamespaceSchemaLocation="http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd">
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+ <dc:creator>Chen, Hao</dc:creator>
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+ <dc:contributor>Chen, Xiaoxin</dc:contributor>
4
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