stash-merritt 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +193 -0
- data/.rubocop.yml +32 -0
- data/.ruby-version +1 -0
- data/.travis.yml +12 -0
- data/Gemfile +6 -0
- data/Gemfile.lock +326 -0
- data/LICENSE.md +22 -0
- data/README.md +53 -0
- data/Rakefile +49 -0
- data/lib/datacite/mapping/datacite_xml_factory.rb +212 -0
- data/lib/stash/merritt/ezid_helper.rb +50 -0
- data/lib/stash/merritt/module_info.rb +12 -0
- data/lib/stash/merritt/repository.rb +17 -0
- data/lib/stash/merritt/submission_job.rb +90 -0
- data/lib/stash/merritt/submission_package/data_one_manifest_builder.rb +41 -0
- data/lib/stash/merritt/submission_package/merritt_datacite_builder.rb +22 -0
- data/lib/stash/merritt/submission_package/merritt_delete_builder.rb +25 -0
- data/lib/stash/merritt/submission_package/merritt_oaidc_builder.rb +130 -0
- data/lib/stash/merritt/submission_package/stash_wrapper_builder.rb +59 -0
- data/lib/stash/merritt/submission_package.rb +125 -0
- data/lib/stash/merritt/sword_helper.rb +58 -0
- data/lib/stash/merritt.rb +5 -0
- data/lib/stash.rb +5 -0
- data/spec/.rubocop.yml +10 -0
- data/spec/config/app_config.yml +3 -0
- data/spec/config/database.yml +7 -0
- data/spec/config/licenses.yml +18 -0
- data/spec/data/archive/mrt-datacite.xml +121 -0
- data/spec/data/archive/mrt-dataone-manifest.txt +32 -0
- data/spec/data/archive/mrt-oaidc.xml +38 -0
- data/spec/data/archive/stash-wrapper.xml +213 -0
- data/spec/data/archive.zip +0 -0
- data/spec/data/dc4-with-funding-references.xml +123 -0
- data/spec/db/datacite/mapping/datacite_xml_factory_spec.rb +56 -0
- data/spec/db/stash/merritt/merritt_oaidc_builder_spec.rb +72 -0
- data/spec/db/stash/merritt/submission_package_spec.rb +174 -0
- data/spec/db/stash/merritt/sword_helper_spec.rb +162 -0
- data/spec/db_spec_helper.rb +31 -0
- data/spec/rspec_custom_matchers.rb +92 -0
- data/spec/spec_helper.rb +86 -0
- data/spec/unit/stash/merritt/ezid_helper_spec.rb +88 -0
- data/spec/unit/stash/merritt/repository_spec.rb +19 -0
- data/spec/unit/stash/merritt/submission_job_spec.rb +127 -0
- data/spec/util/resource_builder.rb +333 -0
- data/stash-merritt.gemspec +48 -0
- data/stash-merritt.iml +147 -0
- data/stash-merritt.ipr +127 -0
- data/travis-local-deps.sh +43 -0
- metadata +337 -0
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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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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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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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def resource_id
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resource.id
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end
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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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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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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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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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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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private
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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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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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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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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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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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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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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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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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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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def version_number
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@version_number ||= resource.version_number
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end
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def uploads
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resource.current_file_uploads
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end
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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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def dc4_resource
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@dc4_resource ||= datacite_xml_factory.build_resource
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end
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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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end
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end
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end
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require 'stash/sword'
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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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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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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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private
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def resource
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package.resource
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end
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def tenant
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resource.tenant
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end
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def identifier_str
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resource.identifier_str
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end
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def zipfile
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package.zipfile
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end
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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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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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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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end
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end
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end
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data/lib/stash.rb
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data/spec/.rubocop.yml
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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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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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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
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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'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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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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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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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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resulted in loss or disorganization of the squamous epithelium, as well as
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of candidate genes involved in esophageal epithelial biology.</dc:description>
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Pax9) was detected by immunohistochemistry and in situ hybridization.
|
177
|
+
Knockdown of P63, a gene known to be critical for esophageal
|
178
|
+
epithelium, disrupted the development of this epithelium. With this
|
179
|
+
model system, we found that Pax9 knockdown resulted in loss or
|
180
|
+
disorganization of the squamous epithelium, as well as down-regulation
|
181
|
+
of the differentiation markers Krt4 and Krt5. In summary, we
|
182
|
+
characterized a region of stratified squamous epithelium in the
|
183
|
+
zebrafish upper digestive tract which can be used for functional
|
184
|
+
studies of candidate genes involved in esophageal epithelial biology.
|
185
|
+
</description>
|
186
|
+
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|
187
|
+
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188
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189
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190
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|
191
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|
192
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|
193
|
+
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|
194
|
+
</geoLocationBox>
|
195
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<geoLocationPlace>Providence Creek (Lower, Upper and P301)</geoLocationPlace>
|
196
|
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|
197
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|
198
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|
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|
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|
206
|
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|
207
|
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</geoLocationBox>
|
208
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<geoLocationPlace>Atlantic Ocean</geoLocationPlace>
|
209
|
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|
210
|
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|
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</st:stash_descriptive>
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213
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</st:stash_wrapper>
|
Binary file
|