commonmeta-ruby 3.0.10 → 3.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: dbd0cff9167f3cf4cbef16d1b2f344dfbaaaa0c5f121f385f8e2703fedd42b0d
-  data.tar.gz: 601f92cc97809057378e7dd89e36d1918a18280201b25a25ad8a13ecd1412a04
+  metadata.gz: 1ff3685620f0d6399524eac22d162f7b32391fa1424783a30e6c2f914d30deea
+  data.tar.gz: bf986a52084af3c28fb163a59022b1ede266b37b77bfd0bf8365c35fd98893b3
 SHA512:
-  metadata.gz: d0e2953f19c0364ad7f774fe38be92bf9df6b975c02568e980ac4cfb7a0fae590aeda39df9d3c80332701db4cc7bfd81648c987b1e96eed6cd1595baf758376d
-  data.tar.gz: 76b133fe3e101ba09c62c362d41035fd323e262575338866bacdbd2e07544b4b1e63583c304c827f9c386c22c7ea45c7f2b0c6eb304cf060b10f8e32e77e3796
+  metadata.gz: 447cc3b60622046224caf62ee2afa70f35f1b47c229c7407f126a3efcc6815cf129386590c6f1114c894111b657326fc35b442427c84907058bd809236a5afff
+  data.tar.gz: 69715e0926e03fc2441b8236a6e6beb0440b69dad8bde707f8d097a3d1922b71b3c80ac4c6286d8fc1fa5d489cc29be02250be6c4a6aadd0747d91bef1251b78

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    commonmeta-ruby (3.0.10)
+    commonmeta-ruby (3.2.0)
       activesupport (>= 4.2.5, < 8.0)
       addressable (~> 2.8.1, < 2.8.2)
       base32-url (>= 0.5.0, < 1)
@@ -13,7 +13,7 @@ PATH
       gender_detector (~> 2.0)
       http (~> 5.1, >= 5.1.1)
       json-ld-preloaded (~> 3.2, >= 3.2.2)
-      json_schemer (~> 0.2.23)
+      json_schemer (~> 1.0.1)
       jsonlint (~> 0.3.0)
       loofah (~> 2.19)
       namae (~> 1.0)
@@ -25,7 +25,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.4.3)
+    activesupport (7.0.5)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -57,14 +57,12 @@ GEM
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    ebnf (2.3.2)
+    ebnf (2.3.3)
       htmlentities (~> 4.3)
       rdf (~> 3.2)
       scanf (~> 1.0)
       sxp (~> 1.2)
       unicode-types (~> 1.8)
-    ecma-re-validator (0.4.0)
-      regexp_parser (~> 2.2)
     edtf (3.1.1)
       activesupport (>= 3.0, < 8.0)
     ffi (1.15.5)
@@ -86,25 +84,24 @@ GEM
     http-cookie (1.0.5)
       domain_name (~> 0.5)
     http-form_data (2.3.0)
-    i18n (1.12.0)
+    i18n (1.14.0)
       concurrent-ruby (~> 1.0)
     json (2.6.3)
-    json-canonicalization (0.3.1)
-    json-ld (3.2.3)
+    json-canonicalization (0.3.2)
+    json-ld (3.2.5)
       htmlentities (~> 4.3)
-      json-canonicalization (~> 0.3)
+      json-canonicalization (~> 0.3, >= 0.3.2)
       link_header (~> 0.0, >= 0.0.8)
       multi_json (~> 1.15)
-      rack (~> 2.2)
-      rdf (~> 3.2, >= 3.2.9)
+      rack (>= 2.2, < 4)
+      rdf (~> 3.2, >= 3.2.10)
     json-ld-preloaded (3.2.2)
       json-ld (~> 3.2)
       rdf (~> 3.2)
-    json_schemer (0.2.24)
-      ecma-re-validator (~> 0.3)
+    json_schemer (1.0.1)
       hana (~> 1.3)
       regexp_parser (~> 2.0)
-      uri_template (~> 0.7)
+      simpleidn (~> 0.2)
     jsonlint (0.3.0)
       oj (~> 3)
       optimist (~> 3)
@@ -113,19 +110,19 @@ GEM
     llhttp-ffi (0.4.0)
       ffi-compiler (~> 1.0)
       rake (~> 13.0)
-    loofah (2.20.0)
+    loofah (2.21.3)
       crass (~> 1.0.2)
-      nokogiri (>= 1.5.9)
+      nokogiri (>= 1.12.0)
     matrix (0.4.2)
     minitest (5.18.0)
     multi_json (1.15.0)
     namae (1.1.1)
-    nokogiri (1.14.3-arm64-darwin)
+    nokogiri (1.15.2-arm64-darwin)
       racc (~> 1.4)
-    oj (3.14.3)
+    oj (3.15.0)
     optimist (3.0.1)
-    parallel (1.22.1)
-    parser (3.2.2.0)
+    parallel (1.23.0)
+    parser (3.2.2.1)
       ast (~> 2.4.1)
     postrank-uri (1.1)
       addressable (>= 2.4.0)
@@ -133,12 +130,12 @@ GEM
       public_suffix (>= 4.0.0, < 5)
     public_suffix (4.0.7)
     racc (1.6.2)
-    rack (2.2.6.4)
+    rack (3.0.7)
     rack-test (2.1.0)
       rack (>= 1.3)
     rainbow (3.1.1)
     rake (13.0.6)
-    rdf (3.2.9)
+    rdf (3.2.10)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (3.2.1)
       rdf (~> 3.2)
@@ -158,20 +155,20 @@ GEM
     rdf-turtle (3.2.1)
       ebnf (~> 2.3)
       rdf (~> 3.2)
-    rdf-vocab (3.2.5)
+    rdf-vocab (3.2.6)
       rdf (~> 3.2, >= 3.2.4)
     rdf-xsd (3.2.1)
       rdf (~> 3.2)
       rexml (~> 3.2)
-    regexp_parser (2.7.0)
+    regexp_parser (2.8.0)
     rexml (3.2.5)
     rspec (3.12.0)
       rspec-core (~> 3.12.0)
       rspec-expectations (~> 3.12.0)
       rspec-mocks (~> 3.12.0)
-    rspec-core (3.12.1)
+    rspec-core (3.12.2)
       rspec-support (~> 3.12.0)
-    rspec-expectations (3.12.2)
+    rspec-expectations (3.12.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
     rspec-mocks (3.12.5)
@@ -181,7 +178,7 @@ GEM
     rspec-xsd (0.1.0)
       nokogiri (~> 1.6)
       rspec (~> 3)
-    rubocop (1.50.1)
+    rubocop (1.52.0)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.2.0.0)
@@ -191,18 +188,21 @@ GEM
       rubocop-ast (>= 1.28.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.28.0)
+    rubocop-ast (1.29.0)
       parser (>= 3.2.1.0)
-    rubocop-capybara (2.17.1)
+    rubocop-capybara (2.18.0)
       rubocop (~> 1.41)
-    rubocop-performance (1.17.1)
+    rubocop-factory_bot (2.23.1)
+      rubocop (~> 1.33)
+    rubocop-performance (1.18.0)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
     rubocop-rake (0.6.0)
       rubocop (~> 1.0)
-    rubocop-rspec (2.19.0)
+    rubocop-rspec (2.22.0)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
+      rubocop-factory_bot (~> 2.22)
     ruby-progressbar (1.13.0)
     scanf (1.0.0)
     simplecov (0.22.0)
@@ -211,11 +211,13 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
-    sxp (1.2.3)
+    simpleidn (0.2.1)
+      unf (~> 0.1.4)
+    sxp (1.2.4)
       matrix (~> 0.4)
       rdf (~> 3.2)
-    temple (0.10.0)
-    thor (1.2.1)
+    temple (0.10.2)
+    thor (1.2.2)
     tilt (2.1.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
@@ -224,7 +226,6 @@ GEM
     unf_ext (0.0.8.2)
     unicode-display_width (2.4.2)
     unicode-types (1.8.0)
-    uri_template (0.7.0)
     vcr (6.1.0)
     webmock (3.18.1)
       addressable (>= 2.8.0)

data/commonmeta.gemspec

@@ -30,7 +30,7 @@ Gem::Specification.new do |s|
   s.add_dependency 'http', '~> 5.1', '>= 5.1.1'
   s.add_dependency 'json-ld-preloaded', '~> 3.2', '>= 3.2.2'
   s.add_dependency 'jsonlint', '~> 0.3.0'
-  s.add_dependency 'json_schemer', '~> 0.2.23'
+  s.add_dependency 'json_schemer', '~> 1.0.1'
   s.add_dependency 'loofah', '~> 2.19'
   s.add_dependency 'namae', '~> 1.0'
   s.add_dependency 'postrank-uri', '~> 1.1'

data/lib/commonmeta/metadata_utils.rb

@@ -13,6 +13,7 @@ require_relative 'readers/codemeta_reader'
 require_relative 'readers/crossref_reader'
 require_relative 'readers/crossref_xml_reader'
 require_relative 'readers/datacite_reader'
+require_relative 'readers/json_post_reader'
 require_relative 'readers/npm_reader'
 require_relative 'readers/ris_reader'
 require_relative 'readers/schema_org_reader'
@@ -46,6 +47,7 @@ module Commonmeta
     include Commonmeta::Readers::CrossrefXmlReader
     include Commonmeta::Readers::CslReader
     include Commonmeta::Readers::DataciteReader
+    include Commonmeta::Readers::JsonPostReader
     include Commonmeta::Readers::NpmReader
     include Commonmeta::Readers::RisReader
     include Commonmeta::Readers::SchemaOrgReader

data/lib/commonmeta/readers/json_post_reader.rb

@@ -0,0 +1,78 @@
+# frozen_string_literal: true
+
+module Commonmeta
+  module Readers
+    module JsonPostReader
+      def get_json_post(id: nil, **_options)
+        return { "string" => nil, "state" => "not_found" } unless id.present?
+
+        url = normalize_id(id)
+        response = HTTP.get(url)
+        return { "string" => nil, "state" => "not_found" } unless response.status.success?
+  
+        { "string" => response.body.to_s }
+      end
+
+      def read_json_post(string: nil, **options)
+        read_options = ActiveSupport::HashWithIndifferentAccess.new(options.except(:doi, :id, :url,
+                                                                                   :sandbox, :validate, :ra))
+
+        meta = string.present? ? JSON.parse(string) : {}
+
+        id = options[:doi] ? normalize_doi(options[:doi]) : normalize_id(meta.fetch("id", nil))
+        url = normalize_url(meta.fetch("url", nil))
+        type = "Article"
+        creators = if meta.fetch("authors", nil).present?
+            get_authors(from_json_post(Array.wrap(meta.fetch("authors"))))
+          else
+            [{ "type" => "Organization", "name" => ":(unav)" }]
+          end
+        titles = [{ "title" => meta.fetch("title", nil) }]
+        publisher = { "name" => meta.dig("blog", "title") }
+
+        date = {}
+        date["published"] = get_iso8601_date(meta.dig("date_published")) if meta.dig("date_published").present?
+        date["updated"] = get_iso8601_date(meta.dig("date_modified")) if meta.dig("date_modified").present?
+
+        license = if meta.dig("blog", "license").present?
+            hsh_to_spdx("rightsURI" => meta.dig("blog", "license"))
+          end
+        home_page_url = normalize_url(meta.dig("blog", "home_page_url"))
+        container = if meta.dig("blog", "title").present?
+            { "type" => "Periodical",
+              "title" => meta.dig("blog", "title"),
+              "identifier" => home_page_url,
+              "identifierType" => "URL" }
+          end
+
+        descriptions = if meta.fetch("summary", nil).present?
+            [{ "description" => sanitize(meta.fetch("summary", nil)),
+               "descriptionType" => "Abstract" }]
+          else
+            []
+          end
+        language = meta.fetch("language", nil) || meta.fetch("blog", "language", nil)
+        state = id.present? || read_options.present? ? "findable" : "not_found"
+        subjects = Array.wrap(meta.fetch("tags", nil)).reduce([]) do |sum, subject|
+          sum += name_to_fos(subject)
+
+          sum
+        end
+
+        { "id" => id,
+          "type" => type,
+          "url" => url,
+          "titles" => titles,
+          "creators" => creators,
+          "publisher" => publisher,
+          "container" => container,
+          "date" => date,
+          "language" => language,
+          "descriptions" => descriptions,
+          "license" => license,
+          "subjects" => subjects.presence,
+          "state" => state }.compact.merge(read_options)
+      end
+    end
+  end
+end

data/lib/commonmeta/utils.rb

@@ -468,6 +468,8 @@ module Commonmeta
         "cff"
       elsif %r{\A(http|https):/(/)?github\.com/(.+)\z}.match?(id)
         "cff"
+      elsif %r{\A(http|https):/(/)?rogue-scholar\.org/api/posts/(.+)\z}.match?(id)
+        "json_post"
       else
         "schema_org"
       end
@@ -875,6 +877,12 @@ module Commonmeta
       }
     end
 
+    def from_json_post(element)
+      mapping = { "url" => "id" }
+
+      map_hash_keys(element: element, mapping: mapping)
+    end
+
     def from_csl(element)
       Array.wrap(element).map do |a|
         if a["literal"].present?
@@ -1068,6 +1076,8 @@ module Commonmeta
 
       return iso8601_time.split(".").first + "Z" if iso8601_time.to_s.include? "."
 
+      return iso8601_time.split("+").first + "Z" if iso8601_time.to_s.include? "+"
+
       iso8601_time
     end
 
@@ -1084,6 +1094,15 @@ module Commonmeta
       dd.fetch("date", nil)
     end
 
+    def get_link(links, link_type)
+      ll = Array.wrap(links).find { |d| d["rel"] == link_type } || {}
+      ll.fetch("href", nil)
+    end
+
+    def rogue_scholar_api_url(id, _options = {})
+      "https://rogue-scholar.org/api/posts/#{id}"
+    end
+
     # convert commonmeta dates to DataCite format
     def get_dates_from_date(date)
       return nil if date.nil?

data/lib/commonmeta/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Commonmeta
-  VERSION = '3.0.10'
+  VERSION = '3.2.0'
 end

data/spec/author_utils_spec.rb

@@ -40,6 +40,16 @@ describe Commonmeta::Metadata, vcr: true do
       expect(subject.is_personal_name?(name: author['name'])).to be true
     end
 
+    it 'has unknown given name' do
+      author = { 'name' => 'Rintze Zelle' }
+      expect(subject.is_personal_name?(name: author['name'])).to be false
+    end
+
+    it 'has middle initial' do
+      author = { 'name' => 'Martin H. Fenner' }
+      expect(subject.is_personal_name?(name: author['name'])).to be true
+    end
+
     it 'has no info' do
       author = { 'name' => 'M Fenner' }
       expect(subject.is_personal_name?(name: author['name'])).to be false

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/blogger_post.yml

@@ -0,0 +1,94 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://rogue-scholar.org/api/posts/1jgo59el
+    body:
+      encoding: UTF-8
+      string: ''
+    headers:
+      Connection:
+      - close
+      Host:
+      - rogue-scholar.org
+      User-Agent:
+      - http.rb/5.1.1
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Age:
+      - '0'
+      Cache-Control:
+      - public, max-age=0, must-revalidate
+      Content-Length:
+      - '5576'
+      Content-Type:
+      - application/json; charset=utf-8
+      Date:
+      - Sat, 03 Jun 2023 20:04:27 GMT
+      Etag:
+      - '"r6tc4lxjtm4ak"'
+      Server:
+      - Vercel
+      Strict-Transport-Security:
+      - max-age=63072000
+      X-Matched-Path:
+      - "/api/posts/[slug]"
+      X-Vercel-Cache:
+      - MISS
+      X-Vercel-Id:
+      - fra1::iad1::z7sjr-1685822666479-acd9f9ad8646
+      Connection:
+      - close
+    body:
+      encoding: UTF-8
+      string: '{"id":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","short_id":"1jgo59el","url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","title":"Ten
+        years and a million links","summary":"As trailed on a Twitter thread last
+        week I’ve been working on a manuscript describing the efforts to map taxonomic
+        names to their original descriptions in the taxonomic literature. Putting
+        together a...","date_published":"2023-05-31T17:26:00Z","date_modified":null,"authors":[{"url":null,"name":"Roderic
+        Page"}],"image":null,"content_html":"<p>As trailed on a Twitter thread last
+        week I’ve been working on a manuscript describing the efforts to map taxonomic
+        names to their original descriptions in the taxonomic literature.</p>\n<blockquote
+        class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Putting together a manuscript
+        on linking taxonomic names to the primary literature, basically “um, what,
+        exactly, have you been doing all these years?”. TL;DR Across fungi, plants,
+        and animals approx 1.3 million names have been linked to a persistent identifier
+        for a publication.</p>— Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
+        25, 2023</a></blockquote> \n<p>The preprint is on bioRxiv <a href=\"https://doi.org/10.1101/2023.05.29.542697\">doi:10.1101/2023.05.29.542697</a></p>\n<blockquote>\n<p>A
+        major gap in the biodiversity knowledge graph is a connection between taxonomic
+        names and the taxonomic literature. While both names and publications often
+        have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
+        or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
+        DOIs for publications. This article describes efforts to make those connections
+        across three large taxonomic databases: Index Fungorum, International Plant
+        Names Index (IPNI), and the Index of Organism Names (ION). Over a million
+        names have been matched to DOIs or other persistent identifiers for taxonomic
+        publications. This represents approximately 36% of names for which publication
+        data is available. The mappings between LSIDs and publication PIDs are made
+        available through ChecklistBank. Applications of this mapping are discussed,
+        including a web app to locate the citation of a taxonomic name, and a knowledge
+        graph that uses data on researcher’s ORCID ids to connect taxonomic names
+        and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
+        the work has been linking taxa to names, which still has huge gaps. There
+        are also interesting differences in coverage between plants, animals, and
+        fungi (see preprint for details).</p>\n\n<div class=\"separator\" style=\"clear:
+        both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"
+        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
+        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
+        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png\"/></a></div><div
+        class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"
+        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
+        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
+        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s320/fungi-coverage.png\"/></a></div><div
+        class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"
+        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
+        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
+        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s320/plants-coverage.png\"/></a></div>\n\n\nThere
+        is also a simple app to demonstrate these links, see <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
+        with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","blog_id":"tyfqw20","blog":{"id":"tyfqw20","title":"iPhylo","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default?alt=rss","home_page_url":"https://iphylo.blogspot.com/","license":"https://creativecommons.org/licenses/by/4.0/legalcode","category":"Natural
+        Sciences"}}'
+  recorded_at: Sat, 03 Jun 2023 20:04:27 GMT
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+      string: '{"id":"https://doi.org/10.53731/4nwxn-frt36","short_id":"1jgo8yel","url":"https://blog.front-matter.io/posts/does-it-compose/","title":"Does
+        it compose?","summary":"One question I have increasingly asked myself in the
+        past few years. Meaning Can I run this open source software using Docker containers
+        and a Docker Compose file?As the Docker project turned ten this...","date_published":"2023-05-16T11:36:56Z","date_modified":"2023-05-16T11:36:56Z","authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
+        Fenner"}],"image":"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib=rb-4.0.3&q=80&w=2000","content_html":"
+        <p><img src=\"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop&#x3D;entropy&cs&#x3D;tinysrgb&fit&#x3D;max&fm&#x3D;jpg&ixid&#x3D;M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib&#x3D;rb-4.0.3&q&#x3D;80&w&#x3D;2000\"></p><p>One
+        question I have increasingly asked myself in the past few years. Meaning </p><blockquote>Can
+        I run this open source software  using Docker containers and a Docker Compose
+        file?</blockquote><p>As the Docker project <a href=\"https://snyk.io/blog/the-docker-project-turns-10/\">turned
+        ten this spring</a>, it has become standard practice to distribute open source
+        software via Docker images and to provide a <a href=\"https://docs.docker.com/compose/\">Docker
+        Compose</a> file to run the software together with other dependencies. The
+        <a href=\"https://github.com/docker/awesome-compose\">Awesome Compose</a>
+        project has collected many examples, and all you need is a <code>docker-compose.yml</code>file
+        and a recent installation of Docker, e.g. <a href=\"https://www.docker.com/products/docker-desktop/\">Docker
+        Desktop</a>. Be aware that Docker Compose has evolved over the years. It started
+        out as a dedicated Python application but was later integrated into the Docker
+        application (written in Go) as Compose V2.</p><p>Docker and Docker Compose
+        allow you to run pretty complex applications without first addressing a long
+        list of requirements (which might conflict with other software you have installed),
+        or needing a long and complex build step where many things can go wrong. For
+        example a self-hosted instance of Supabase (a hosted Postgres database with
+        additional features) that I installed last week following <a href=\"https://supabase.com/docs/guides/self-hosting/docker\">these
+        instructions</a>.</p><p>An important open source project that I am involved
+        in is <a href=\"https://inveniordm.docs.cern.ch/\">InvenioRDM</a>, the turn-key
+        research data management repository. InvenioRDM started in 2019, with a first
+        production-suitable version in August 2021, and the <a href=\"https://inveniosoftware.org/products/rdm/#status\">next
+        major goal </a>is to have the large and popular <a href=\"https://zenodo.org/\">Zenodo</a>
+        repository running on top of InvenioRDM. Zenodo <a href=\"https://blog.zenodo.org/2023/05/08/2023-05-08-10years/\">turned
+        ten last week</a>, a few weeks after Docker. Interestingly, my personal tenth
+        anniversary was last year in May as I became a full-time software developer
+        and left academic medicine as a medical doctor treating cancer patients in
+        <a href=\"https://doi.org/10.53731/r294649-6f79289-8cw2j\">May 2012</a>.</p><p>Unfortunately,
+        InvenioRDM \"doesn''t compose\" yet. It is very close, but there are no ready-made
+        Docker images to download, and the <a href=\"https://inveniordm.docs.cern.ch/install/\">installation
+        instructions</a> start with installing a Python command-line tool (invenio-cli).
+        So if you have 1-2 hours to play with InvenioRDM and get a first impression,
+        there is no official solution from the InvenioRDM project yet. For this reason,
+        I started the <a href=\"https://github.com/front-matter/docker-invenio-rdm\">docker-invenio-rdm</a>
+        repository on Github. It contains a Docker Compose file that uses pre-built
+        Docker images, and using that file with a <code>docker compose up</code>command
+        on your local computer should give you a running InvenioRDM within 15 minutes:</p><figure
+        class=\"kg-card kg-image-card\"><img src=\"https://blog.front-matter.io/content/images/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png\"
+        class=\"kg-image\" alt loading=\"lazy\" width=\"2000\" height=\"1210\" srcset=\"https://blog.front-matter.io/content/images/size/w600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        600w, https://blog.front-matter.io/content/images/size/w1000/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        1000w, https://blog.front-matter.io/content/images/size/w1600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        1600w, https://blog.front-matter.io/content/images/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
+        2193w\" sizes=\"(min-width: 720px) 720px\"></figure><p>I started this recently
+        and obviously want to move forward in two directions:</p><ul><li>fine-tune
+        the initial configuration to provide a great initial experience with InvenioRDM,
+        e.g. making it easy to <a href=\"https://inveniordm.docs.cern.ch/develop/topics/theming/\">theme</a>
+        the InvenioRDM instance</li><li>make this an official part of the InvenioRDM
+        project, extending the <a href=\"https://github.com/inveniosoftware/docker-invenio\">docker-invenio</a>
+        GitHub repository that provides Docker base images for InvenioRDM and other
+        projects using the Invenio software.</li></ul><p>But of course, Docker Compose
+        is not the answer to all questions regarding running Docker-based infrastructure.
+        For production environments, most people shy away from using Docker Compose.
+        The reasons for that and the alternatives will be the topic of a future blog
+        post (spoiler: there is exciting news).</p><p>Docker Compose also needs more
+        work to be set up correctly for development environments. It is a common practice
+        and a workflow I used while working at DataCite (where we launched Docker-based
+        infrastructure in 2016), but for now, the easiest way to set up InvenioRDM
+        development environments is using the <a href=\"https://inveniordm.docs.cern.ch/install/\">invenio-cli
+        tool with a local development environment</a>.</p><p>Please reach out to me
+        with feedback on running Docker Compose for InvenioRDM (use the <a href=\"https://github.com/front-matter/docker-invenio-rdm/discussions\">discussions</a>
+        feature in the GitHub repo), or if you have questions about running InvenioRDM
+        in production.</p> ","tags":["News"],"language":"en","blog_id":"f0m0e38","blog":{"id":"f0m0e38","title":"Front
+        Matter","language":"en","favicon":"https://blog.front-matter.io/favicon.png","feed_url":"https://blog.front-matter.io/atom/","home_page_url":"https://blog.front-matter.io/","license":"https://creativecommons.org/licenses/by/4.0/legalcode","category":"Engineering
+        and Technology"}}'
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