b1776731-62d7-41a7-882d-6a5b4760db75

Committed 14 May 2024 12:28PM UTC coverage: 79.223% (-16.7%) from 95.9%

Build # b1776731-62d7-41a7-882d-6a5b4760db75

Build Type

push

circleci

Committed by

carolyncole

Commit Message

Adding a submission completion page

fixes #1791

Run Details

9 of 9 new or added lines in 2 files covered. (100.0%)

567 existing lines in 42 files now uncovered.

2692 of 3398 relevant lines covered (79.22%)

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82.76

/app/services/work_preservation_service.rb

# frozen_string_literal: true

# A service to create and store the preservation data for a given work.
# Currently it assumes this data will be stored in an AWS S3 bucket accessible with our AWS credentials.
# This preservation bucket is configured in our s3.yml file and we store it in a different availability region
# to make sure the data is properly distributed.
class WorkPreservationService
  PRESERVATION_DIRECTORY = "princeton_data_commons"

  # @param work_id [Integer] The ID of the work to preserve.
  # @param path [String] The path where the work will be preserved.
  # @param localhost [Bool] Set to true to preserve the files locally, i.e. not in AWS
  def initialize(work_id:, path:, localhost: false)
    @work = Work.find(work_id)
    @path = path
    @localhost = localhost
    @s3_query_service = nil
  end

  # Creates and stores the preservation files for the work.
  # @return [String] The AWS S3 path where the files were stored
  def preserve!
    create_preservation_directory
    preserve_file(io: metadata_io, filename: "metadata.json")
    preserve_file(io: datacite_io, filename: "datacite.xml")
    preserve_file(io: provenance_io, filename: "provenance.json")
    Rails.logger.info "Preservation files for work #{@work.id} saved to #{target_location}"
    target_location
  end

  def preservation_metadata
    # Always use the post-curation file list
    metadata = JSON.parse(@work.to_json(force_post_curation: true))
    # Make sure we don't include the preservation files as part of
    # the work's preservation metadata.
    metadata["files"] = metadata["files"].map do |file|
      if file["filename"].include?("/#{PRESERVATION_DIRECTORY}/")
        nil
      else
        file
      end
    end.compact
    metadata.to_json
  end

  private

    def local?
      @localhost
    end

    def target_location
      if local?
        "file://" + File.join(Dir.pwd, preservation_directory)
      else
        "s3://#{bucket_name}/#{preservation_directory}"
      end
    end

    def metadata_io
      StringIO.new(preservation_metadata)
    end

    def datacite_io
      StringIO.new(@work.to_xml)
    end

    def provenance_io
      StringIO.new(@work.work_activity.to_json)
    end

    def preservation_directory
      Pathname.new(@path).join("#{PRESERVATION_DIRECTORY}/")
    end

    def s3_query_service
      @s3_query_service ||= S3QueryService.new(@work, "preservation")
    end

    def bucket_name
      s3_query_service.bucket_name
    end

    def create_preservation_directory
      if local?
        FileUtils.mkdir_p preservation_directory.to_s
      else
        s3_query_service.client.put_object({ bucket: bucket_name, key: preservation_directory.to_s, content_length: 0 })
      end
    end

    def preserve_file(io:, filename:)
      if local?
        save_local_file(io:, filename:)
      else
        upload_file(io:, filename:)
      end
    end

    def upload_file(io:, filename:)
      md5_digest = @work.s3_query_service.md5(io:)
      key = preservation_directory.join(filename).to_s
      s3_query_service.client.put_object(bucket: bucket_name, key:, body: io, content_md5: md5_digest)
      key
    end

    def save_local_file(io:, filename:)
      full_filename = preservation_directory.join(filename).to_s
      File.open(full_filename, "w") do |file|
        file.puts(io.read)
      end
      full_filename
    end
end

1	# frozen_string_literal: true
2
3	# A service to create and store the preservation data for a given work.
4	# Currently it assumes this data will be stored in an AWS S3 bucket accessible with our AWS credentials.
5	# This preservation bucket is configured in our s3.yml file and we store it in a different availability region
6	# to make sure the data is properly distributed.
7	class WorkPreservationService	1✔
8	PRESERVATION_DIRECTORY = "princeton_data_commons"	1✔
9
10	# @param work_id [Integer] The ID of the work to preserve.
11	# @param path [String] The path where the work will be preserved.
12	# @param localhost [Bool] Set to true to preserve the files locally, i.e. not in AWS
13	def initialize(work_id:, path:, localhost: false)	1✔
14	@work = Work.find(work_id)	2✔
15	@path = path	2✔
16	@localhost = localhost	2✔
17	@s3_query_service = nil	2✔
18	end
19
20	# Creates and stores the preservation files for the work.
21	# @return [String] The AWS S3 path where the files were stored
22	def preserve!	1✔
23	create_preservation_directory	2✔
24	preserve_file(io: metadata_io, filename: "metadata.json")	2✔
25	preserve_file(io: datacite_io, filename: "datacite.xml")	2✔
26	preserve_file(io: provenance_io, filename: "provenance.json")	2✔
27	Rails.logger.info "Preservation files for work #{@work.id} saved to #{target_location}"	2✔
28	target_location	2✔
29	end
30
31	def preservation_metadata	1✔
32	# Always use the post-curation file list
33	metadata = JSON.parse(@work.to_json(force_post_curation: true))	2✔
34	# Make sure we don't include the preservation files as part of
35	# the work's preservation metadata.
36	metadata["files"] = metadata["files"].map do \|file\|	2✔
UNCOV 37	if file["filename"].include?("/#{PRESERVATION_DIRECTORY}/")	×
UNCOV 38	nil	×
39	else
UNCOV 40	file	×
41	end
42	end.compact
43	metadata.to_json	2✔
44	end
45
46	private	1✔
47
48	def local?	1✔
49	@localhost	12✔
50	end
51
52	def target_location	1✔
53	if local?	4✔
UNCOV 54	"file://" + File.join(Dir.pwd, preservation_directory)	×
55	else
56	"s3://#{bucket_name}/#{preservation_directory}"	4✔
57	end
58	end
59
60	def metadata_io	1✔
61	StringIO.new(preservation_metadata)	2✔
62	end
63
64	def datacite_io	1✔
65	StringIO.new(@work.to_xml)	2✔
66	end
67
68	def provenance_io	1✔
69	StringIO.new(@work.work_activity.to_json)	2✔
70	end
71
72	def preservation_directory	1✔
73	Pathname.new(@path).join("#{PRESERVATION_DIRECTORY}/")	12✔
74	end
75
76	def s3_query_service	1✔
77	@s3_query_service \|\|= S3QueryService.new(@work, "preservation")	20✔
78	end
79
80	def bucket_name	1✔
81	s3_query_service.bucket_name	12✔
82	end
83
84	def create_preservation_directory	1✔
85	if local?	2✔
UNCOV 86	FileUtils.mkdir_p preservation_directory.to_s	×
87	else
88	s3_query_service.client.put_object({ bucket: bucket_name, key: preservation_directory.to_s, content_length: 0 })	2✔
89	end
90	end
91
92	def preserve_file(io:, filename:)	1✔
93	if local?	6✔
UNCOV 94	save_local_file(io:, filename:)	×
95	else
96	upload_file(io:, filename:)	6✔
97	end
98	end
99
100	def upload_file(io:, filename:)	1✔
101	md5_digest = @work.s3_query_service.md5(io:)	6✔
102	key = preservation_directory.join(filename).to_s	6✔
103	s3_query_service.client.put_object(bucket: bucket_name, key:, body: io, content_md5: md5_digest)	6✔
104	key	6✔
105	end
106
107	def save_local_file(io:, filename:)	1✔
UNCOV 108	full_filename = preservation_directory.join(filename).to_s	×
UNCOV 109	File.open(full_filename, "w") do \|file\|	×
UNCOV 110	file.puts(io.read)	×
111	end
UNCOV 112	full_filename	×
113	end
114	end

pulibrary / pdc_describe / b1776731-62d7-41a7-882d-6a5b4760db75

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