commonmeta-ruby 3.2.3 → 3.2.4

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Files changed (35) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +1 -1
  3. data/lib/commonmeta/author_utils.rb +11 -0
  4. data/lib/commonmeta/cli.rb +5 -1
  5. data/lib/commonmeta/readers/json_feed_reader.rb +9 -5
  6. data/lib/commonmeta/utils.rb +4 -2
  7. data/lib/commonmeta/version.rb +1 -1
  8. data/spec/author_utils_spec.rb +9 -8
  9. data/spec/cli_spec.rb +1 -1
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post.yml +14 -14
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/all_posts.yml +2625 -0
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/behind_the_science.yml +1176 -0
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +7 -7
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +7 -7
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +196 -0
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +7 -7
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +7 -7
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_feed_url/all_posts.yml +221 -0
  19. data/spec/readers/json_feed_reader_spec.rb +35 -10
  20. data/spec/utils_spec.rb +5 -0
  21. data/spec/writers/citation_writer_spec.rb +1 -1
  22. metadata +6 -15
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/blogger_post.yml +0 -141
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/ghost_post_with_doi.yml +0 -164
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/jekyll_post.yml +0 -134
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/wordpress_post.yml +0 -210
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/blogger_post.yml +0 -94
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/ghost_post.yml +0 -117
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/ghost_post_with_doi.yml +0 -117
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/jekyll_post.yml +0 -170
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/wordpress_post.yml +0 -163
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/blogger_post.yml +0 -141
  33. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/ghost_post_with_doi.yml +0 -164
  34. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/jekyll_post.yml +0 -134
  35. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/wordpress_post.yml +0 -210
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- years and a million links","summary":"As trailed on a Twitter thread last
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- week I’ve been working on a manuscript describing the efforts to map taxonomic
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- names to their original descriptions in the taxonomic literature. Putting
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- week I’ve been working on a manuscript describing the efforts to map taxonomic
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- names to their original descriptions in the taxonomic literature.</p>\n<blockquote
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- class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Putting together a manuscript
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- on linking taxonomic names to the primary literature, basically “um, what,
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- exactly, have you been doing all these years?”. TL;DR Across fungi, plants,
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- and animals approx 1.3 million names have been linked to a persistent identifier
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- for a publication.</p>— Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
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- 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
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- major gap in the biodiversity knowledge graph is a connection between taxonomic
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- names and the taxonomic literature. While both names and publications often
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- have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
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- or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
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- DOIs for publications. This article describes efforts to make those connections
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- across three large taxonomic databases: Index Fungorum, International Plant
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- Names Index (IPNI), and the Index of Organism Names (ION). Over a million
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- names have been matched to DOIs or other persistent identifiers for taxonomic
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- publications. This represents approximately 36% of names for which publication
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- data is available. The mappings between LSIDs and publication PIDs are made
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- available through ChecklistBank. Applications of this mapping are discussed,
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- including a web app to locate the citation of a taxonomic name, and a knowledge
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- graph that uses data on researcher’s ORCID ids to connect taxonomic names
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- and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
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- the work has been linking taxa to names, which still has huge gaps. There
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- are also interesting differences in coverage between plants, animals, and
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- fungi (see preprint for details).</p>\n\n<div class=\"separator\" style=\"clear:
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- both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"
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- class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"
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- border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
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- src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s320/plants-coverage.png\"/></a></div>\n\n\nThere
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- 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
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- 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
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- it compose?","summary":"One question I have increasingly asked myself in the
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- <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
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- question I have increasingly asked myself in the past few years. Meaning </p><blockquote>Can
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- I run this open source software  using Docker containers and a Docker Compose
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- file?</blockquote><p>As the Docker project <a href=\"https://snyk.io/blog/the-docker-project-turns-10/\">turned
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- ten this spring</a>, it has become standard practice to distribute open source
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- software via Docker images and to provide a <a href=\"https://docs.docker.com/compose/\">Docker
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- Compose</a> file to run the software together with other dependencies. The
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- <a href=\"https://github.com/docker/awesome-compose\">Awesome Compose</a>
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- project has collected many examples, and all you need is a <code>docker-compose.yml</code>file
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- and a recent installation of Docker, e.g. <a href=\"https://www.docker.com/products/docker-desktop/\">Docker
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- Desktop</a>. Be aware that Docker Compose has evolved over the years. It started
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- out as a dedicated Python application but was later integrated into the Docker
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- application (written in Go) as Compose V2.</p><p>Docker and Docker Compose
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- allow you to run pretty complex applications without first addressing a long
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- list of requirements (which might conflict with other software you have installed),
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- or needing a long and complex build step where many things can go wrong. For
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- example a self-hosted instance of Supabase (a hosted Postgres database with
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- additional features) that I installed last week following <a href=\"https://supabase.com/docs/guides/self-hosting/docker\">these
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- instructions</a>.</p><p>An important open source project that I am involved
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- in is <a href=\"https://inveniordm.docs.cern.ch/\">InvenioRDM</a>, the turn-key
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- research data management repository. InvenioRDM started in 2019, with a first
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- production-suitable version in August 2021, and the <a href=\"https://inveniosoftware.org/products/rdm/#status\">next
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- major goal </a>is to have the large and popular <a href=\"https://zenodo.org/\">Zenodo</a>
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- repository running on top of InvenioRDM. Zenodo <a href=\"https://blog.zenodo.org/2023/05/08/2023-05-08-10years/\">turned
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- ten last week</a>, a few weeks after Docker. Interestingly, my personal tenth
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- anniversary was last year in May as I became a full-time software developer
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- and left academic medicine as a medical doctor treating cancer patients in
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- <a href=\"https://doi.org/10.53731/r294649-6f79289-8cw2j\">May 2012</a>.</p><p>Unfortunately,
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- InvenioRDM \"doesn''t compose\" yet. It is very close, but there are no ready-made
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- Docker images to download, and the <a href=\"https://inveniordm.docs.cern.ch/install/\">installation
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- instructions</a> start with installing a Python command-line tool (invenio-cli).
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- So if you have 1-2 hours to play with InvenioRDM and get a first impression,
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- there is no official solution from the InvenioRDM project yet. For this reason,
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- I started the <a href=\"https://github.com/front-matter/docker-invenio-rdm\">docker-invenio-rdm</a>
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- repository on Github. It contains a Docker Compose file that uses pre-built
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- Docker images, and using that file with a <code>docker compose up</code>command
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- on your local computer should give you a running InvenioRDM within 15 minutes:</p><figure
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- 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\"
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- 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
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- 600w, https://blog.front-matter.io/content/images/size/w1000/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
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- 1000w, https://blog.front-matter.io/content/images/size/w1600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
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- 2193w\" sizes=\"(min-width: 720px) 720px\"></figure><p>I started this recently
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- and obviously want to move forward in two directions:</p><ul><li>fine-tune
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- the initial configuration to provide a great initial experience with InvenioRDM,
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- e.g. making it easy to <a href=\"https://inveniordm.docs.cern.ch/develop/topics/theming/\">theme</a>
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- the InvenioRDM instance</li><li>make this an official part of the InvenioRDM
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- project, extending the <a href=\"https://github.com/inveniosoftware/docker-invenio\">docker-invenio</a>
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- GitHub repository that provides Docker base images for InvenioRDM and other
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- projects using the Invenio software.</li></ul><p>But of course, Docker Compose
102
- is not the answer to all questions regarding running Docker-based infrastructure.
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- For production environments, most people shy away from using Docker Compose.
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- The reasons for that and the alternatives will be the topic of a future blog
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- post (spoiler: there is exciting news).</p><p>Docker Compose also needs more
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- work to be set up correctly for development environments. It is a common practice
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- and a workflow I used while working at DataCite (where we launched Docker-based
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- infrastructure in 2016), but for now, the easiest way to set up InvenioRDM
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- development environments is using the <a href=\"https://inveniordm.docs.cern.ch/install/\">invenio-cli
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- tool with a local development environment</a>.</p><p>Please reach out to me
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- with feedback on running Docker Compose for InvenioRDM (use the <a href=\"https://github.com/front-matter/docker-invenio-rdm/discussions\">discussions</a>
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- feature in the GitHub repo), or if you have questions about running InvenioRDM
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- in production.</p> ","tags":["News"],"language":"en","blog_id":"f0m0e38","blog":{"id":"f0m0e38","title":"Front
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