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calacademy-research / antcat

World Catalog of Ants
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Script: Re-use/rescue orphaned `ReferenceDocument`s with hardcoded "antcat.org" `url`s pointing to them #1307

Closed jonkerz closed 3 years ago

jonkerz commented 3 years ago

For https://github.com/calacademy-research/antcat-issues/issues/114

Script

```ruby EDIT_SUMMARY = 'Re-use/rescue orphaned `ReferenceDocument`s with hardcoded "antcat.org" `url`s pointing to them, see %github1307' ANTCATBOT = User.find_by!(name: 'AntCatBot') RequestStore.store[:current_request_uuid] = SecureRandom.uuid PaperTrail.request.whodunnit = ANTCATBOT.id class HardcodedUrlCleaner def initialize hardcoded_url_document raise '???' unless hardcoded_url_document.url @hardcoded_url_document = hardcoded_url_document @hardcoded_url = hardcoded_url_document.url end def puts_info puts <<~STR document_id: #{hardcoded_url_document.id} url: #{hardcoded_url} reference_id: #{hardcoded_url_document.reference_id} - #{hardcoded_url_document.reference.type} STR end def all_orphans ReferenceDocument.left_joins(:reference).where(references: { id: nil }) end def same_url_hardcoded_more_than_once? ReferenceDocument.where(url: hardcoded_url_document.url).count > 1 end def hardcoded_usage ReferenceDocument.where("url LIKE ?", "%antcat.org/documents/#{hardcoded_url_document.id}/%") end def hardcoded_usage_info "hardcoded_usage: #{hardcoded_usage.pluck(:id, :url)}" end def doc_id_from_url return @_doc_id_from_url if defined?(@_doc_id_from_url) @_doc_id_from_url = hardcoded_url.scan(/(?:antcat\.org\/documents\/)(\d+)/).flatten.first end def target_orphan return @_target_orphan if defined?(@_target_orphan) @_target_orphan = all_orphans.find_by(id: doc_id_from_url) end def replace_with_target_orphan? target_orphan.file_file_name.present? end def puts_target_orphan_info puts " found orphaned ReferenceDocument: #{target_orphan.id}" if target_orphan.file_file_name.present? puts " and it has file: #{target_orphan.file_file_name}".green else puts " but it has no file".red end end def replace_with_target! raise '???' unless (reference = hardcoded_url_document.reference) puts "Replacing...".green puts " hardcoded_url_document.id: #{hardcoded_url_document.id}" puts " hardcoded_url_document.reference_id: #{reference.id}" puts " hardcoded_url_document.url: #{hardcoded_url_document.url}" puts " target_orphan.id: #{target_orphan.id}" puts " target_orphan.reference_id: #{target_orphan.reference_id}" puts " target_orphan.file_file_name: #{target_orphan.file_file_name}" hardcoded_url_document.transaction do hardcoded_url_document.destroy! target_orphan.update!(reference: reference) end end private attr_reader :hardcoded_url_document, :hardcoded_url end ReferenceDocument.joins(:reference).where("url LIKE ?", "%antcat\.org%").find_each do |doc_w_hardcoded_url| cleaner = HardcodedUrlCleaner.new(doc_w_hardcoded_url) if cleaner.hardcoded_usage.any? puts "Skipping - hard harcoded usage".red puts cleaner.hardcoded_usage_info.yellow cleaner.puts_info puts next end if cleaner.same_url_hardcoded_more_than_once? puts "Skipping - the same url is hardcoded more than once".red cleaner.puts_info puts next end if cleaner.target_orphan if cleaner.replace_with_target_orphan? cleaner.replace_with_target! else puts "Ignoring target orphan without a filename".red cleaner.puts_target_orphan_info end else puts " found nothing".red end puts end; nil Activity.execute_script_activity User.find_by!(name: 'Fredrik Palmkron'), EDIT_SUMMARY ```

Output (first run)

```ruby Replacing... hardcoded_url_document.id: 5816 hardcoded_url_document.reference_id: 142323 hardcoded_url_document.url: http://antcat.org/documents/5815/bharti_-_sharma_2013_j_asia-pac_entomol-new-myrmica-from-india.pdf target_orphan.id: 5815 target_orphan.reference_id: target_orphan.file_file_name: bharti_-_sharma_2013_j_asia-pac_entomol-new-myrmica-from-india.pdf Replacing... hardcoded_url_document.id: 6655 hardcoded_url_document.reference_id: 142917 hardcoded_url_document.url: http://antcat.org/documents/6545/chomicki_et_al_2015_prsb_pseudomyrmex_ants_and_their_antplants_incl_suppl_material.pdf target_orphan.id: 6545 target_orphan.reference_id: target_orphan.file_file_name: chomicki_et_al_2015_prsb_pseudomyrmex_ants_and_their_antplants_incl_suppl_material.pdf Replacing... hardcoded_url_document.id: 6656 hardcoded_url_document.reference_id: 143001 hardcoded_url_document.url: http://antcat.org/documents/6652/trichomyrmex_of_arabia.pdf target_orphan.id: 6652 target_orphan.reference_id: target_orphan.file_file_name: trichomyrmex_of_arabia.pdf Skipping - the same url is hardcoded more than once document_id: 6662 url: http://antcat.org/documents/6660/chen_etal_2016_far_eastern_entomol_cerapachys_bispinatus.pdf reference_id: 143009 - ArticleReference Replacing... hardcoded_url_document.id: 6666 hardcoded_url_document.reference_id: 143010 hardcoded_url_document.url: http://antcat.org/documents/6665/hita_garcia_et_al_2017_taxonomy_of_the_ant_genus_nesomyrmex.pdf target_orphan.id: 6665 target_orphan.reference_id: target_orphan.file_file_name: hita_garcia_et_al_2017_taxonomy_of_the_ant_genus_nesomyrmex.pdf Replacing... hardcoded_url_document.id: 6674 hardcoded_url_document.reference_id: 143013 hardcoded_url_document.url: http://antcat.org/documents/6669/journal-pone-0049485.pdf target_orphan.id: 6669 target_orphan.reference_id: target_orphan.file_file_name: journal-pone-0049485.pdf Replacing... hardcoded_url_document.id: 6693 hardcoded_url_document.reference_id: 142679 hardcoded_url_document.url: http://antcat.org/documents/6314/talavera_et_al_2014_j_biogeo_lasius_balearicus_n-sp.pdf target_orphan.id: 6314 target_orphan.reference_id: target_orphan.file_file_name: talavera_et_al_2014_j_biogeo_lasius_balearicus_n-sp.pdf Replacing... hardcoded_url_document.id: 6698 hardcoded_url_document.reference_id: 143038 hardcoded_url_document.url: http://antcat.org/documents/6697/sosa-calvo_et_al_2017_plos_one_mycetosoritis.pdf target_orphan.id: 6697 target_orphan.reference_id: target_orphan.file_file_name: sosa-calvo_et_al_2017_plos_one_mycetosoritis.pdf Replacing... hardcoded_url_document.id: 6714 hardcoded_url_document.reference_id: 143050 hardcoded_url_document.url: http://antcat.org/documents/6709/vasquez__2011.pdf target_orphan.id: 6709 target_orphan.reference_id: target_orphan.file_file_name: vasquez__2011.pdf Replacing... hardcoded_url_document.id: 6726 hardcoded_url_document.reference_id: 131351 hardcoded_url_document.url: http://antcat.org/documents/3893/14645.pdf target_orphan.id: 3893 target_orphan.reference_id: target_orphan.file_file_name: 14645.pdf Replacing... hardcoded_url_document.id: 6728 hardcoded_url_document.reference_id: 131557 hardcoded_url_document.url: http://antcat.org/documents/4899/Johnson_2000_Seed_harvester_ants.pdf target_orphan.id: 4899 target_orphan.reference_id: target_orphan.file_file_name: Johnson_2000_Seed_harvester_ants.pdf Replacing... hardcoded_url_document.id: 6730 hardcoded_url_document.reference_id: 133069 hardcoded_url_document.url: http://antcat.org/documents/5705/dlussky_2012_paleontol_j-myrmeciinae-fossil-from-germany.pdf target_orphan.id: 5705 target_orphan.reference_id: target_orphan.file_file_name: dlussky_2012_paleontol_j-myrmeciinae-fossil-from-germany.pdf Replacing... hardcoded_url_document.id: 6739 hardcoded_url_document.reference_id: 134418 hardcoded_url_document.url: http://antcat.org/documents/5724/xu_2012_sociobiology-furcotanilla.pdf target_orphan.id: 5724 target_orphan.reference_id: target_orphan.file_file_name: xu_2012_sociobiology-furcotanilla.pdf Replacing... hardcoded_url_document.id: 6743 hardcoded_url_document.reference_id: 143079 hardcoded_url_document.url: http://antcat.org/documents/6742/hita_garcia_et_al_2017_afrotropical_zasphinctus.pdf target_orphan.id: 6742 target_orphan.reference_id: target_orphan.file_file_name: hita_garcia_et_al_2017_afrotropical_zasphinctus.pdf Replacing... hardcoded_url_document.id: 6749 hardcoded_url_document.reference_id: 143083 hardcoded_url_document.url: http://antcat.org/documents/6747/barden_etal_2017_syst_entomol_burmese_amber_haidomyrmecini_linguamyrmex.pdf target_orphan.id: 6747 target_orphan.reference_id: target_orphan.file_file_name: barden_etal_2017_syst_entomol_burmese_amber_haidomyrmecini_linguamyrmex.pdf Skipping - the same url is hardcoded more than once document_id: 6761 url: http://antcat.org/documents/6759/2017-desquivel_et_al-thaumatomyrmex_fraxini.pdf reference_id: 143099 - ArticleReference Replacing... hardcoded_url_document.id: 6784 hardcoded_url_document.reference_id: 130720 hardcoded_url_document.url: http://antcat.org/documents/3795/baroni_urbani__c-__de_andrade__m-l-_2003b-_the_ant_genus_proceratium.pdf target_orphan.id: 3795 target_orphan.reference_id: target_orphan.file_file_name: baroni_urbani__c-__de_andrade__m-l-_2003b-_the_ant_genus_proceratium.pdf Replacing... hardcoded_url_document.id: 6788 hardcoded_url_document.reference_id: 143122 hardcoded_url_document.url: http://antcat.org/documents/6785/mackay__dash_-_2016_-_a_revision_of_the_phalangium_species_complex_of_the_ant_genus_aphaenogaster_-hymenoptera_formicidae_myrmicinae.pdf target_orphan.id: 6785 target_orphan.reference_id: target_orphan.file_file_name: mackay__dash_-_2016_-_a_revision_of_the_phalangium_species_complex_of_the_ant_genus_aphaenogaster_-hymenoptera_formicidae_myrmicinae.pdf Replacing... hardcoded_url_document.id: 6800 hardcoded_url_document.reference_id: 143095 hardcoded_url_document.url: http://antcat.org/documents/6754/agavekar_et_al_2017_taxonomic_overview_of_the_hyperdiverse_ant_genus_tetramorium_in_india.pdf target_orphan.id: 6754 target_orphan.reference_id: target_orphan.file_file_name: agavekar_et_al_2017_taxonomic_overview_of_the_hyperdiverse_ant_genus_tetramorium_in_india.pdf Replacing... hardcoded_url_document.id: 6815 hardcoded_url_document.reference_id: 143129 hardcoded_url_document.url: http://antcat.org/documents/6795/archibald_etal_2018_okanagan_hymenos.pdf target_orphan.id: 6795 target_orphan.reference_id: target_orphan.file_file_name: archibald_etal_2018_okanagan_hymenos.pdf Replacing... hardcoded_url_document.id: 6856 hardcoded_url_document.reference_id: 142626 hardcoded_url_document.url: http://antcat.org/documents/6240/boudinot_2014_tricytarus_new_generic_synonym_of_meranoplus.pdf target_orphan.id: 6240 target_orphan.reference_id: target_orphan.file_file_name: boudinot_2014_tricytarus_new_generic_synonym_of_meranoplus.pdf Replacing... hardcoded_url_document.id: 6857 hardcoded_url_document.reference_id: 142603 hardcoded_url_document.url: http://antcat.org/documents/6218/macgown_et_al_2014_zootaxa_nearctic_odontomachus.pdf target_orphan.id: 6218 target_orphan.reference_id: target_orphan.file_file_name: macgown_et_al_2014_zootaxa_nearctic_odontomachus.pdf Replacing... hardcoded_url_document.id: 6859 hardcoded_url_document.reference_id: 143170 hardcoded_url_document.url: http://antcat.org/documents/6858/Ajerrar_et_al_Temnothorax_tamriensis.pdf target_orphan.id: 6858 target_orphan.reference_id: target_orphan.file_file_name: Ajerrar_et_al_Temnothorax_tamriensis.pdf Replacing... hardcoded_url_document.id: 6862 hardcoded_url_document.reference_id: 143172 hardcoded_url_document.url: http://antcat.org/documents/6861/Jaitrong___Yamane_2018_Nat-Hist-Bull-Siam-Soc_Calyptomyrmex_new_species_from_Laos.pdf target_orphan.id: 6861 target_orphan.reference_id: target_orphan.file_file_name: Jaitrong___Yamane_2018_Nat-Hist-Bull-Siam-Soc_Calyptomyrmex_new_species_from_Laos.pdf Replacing... hardcoded_url_document.id: 6864 hardcoded_url_document.reference_id: 143173 hardcoded_url_document.url: http://antcat.org/documents/6863/RAKOTONIRINA__FISHER_-_2018_-_Zootaxa.pdf target_orphan.id: 6863 target_orphan.reference_id: target_orphan.file_file_name: RAKOTONIRINA__FISHER_-_2018_-_Zootaxa.pdf Replacing... hardcoded_url_document.id: 6913 hardcoded_url_document.reference_id: 143180 hardcoded_url_document.url: http://antcat.org/documents/6906/ZK_article_24908.pdf target_orphan.id: 6906 target_orphan.reference_id: target_orphan.file_file_name: ZK_article_24908.pdf Replacing... hardcoded_url_document.id: 6915 hardcoded_url_document.reference_id: 143185 hardcoded_url_document.url: http://antcat.org/documents/6914/Schär_et_al._-_2018_-_Journal_of_Biogeography.pdf target_orphan.id: 6914 target_orphan.reference_id: target_orphan.file_file_name: Schär_et_al._-_2018_-_Journal_of_Biogeography.pdf Skipping - the same url is hardcoded more than once document_id: 6926 url: http://antcat.org/documents/5844/boudinot___fisher_2013_zootaxa_meranoplus_of_madagascar.pdf reference_id: 142345 - ArticleReference Skipping - the same url is hardcoded more than once document_id: 6927 url: http://antcat.org/documents/6774/barden_etal_2017_leptomyrmex-phylogeny.pdf reference_id: 143112 - ArticleReference Replacing... hardcoded_url_document.id: 6928 hardcoded_url_document.reference_id: 130629 hardcoded_url_document.url: http://antcat.org/documents/5750/abouheif_-_wray_2002_sci-evol-wing-poliphenism-ants.pdf target_orphan.id: 5750 target_orphan.reference_id: target_orphan.file_file_name: abouheif_-_wray_2002_sci-evol-wing-poliphenism-ants.pdf Replacing... hardcoded_url_document.id: 6929 hardcoded_url_document.reference_id: 131007 hardcoded_url_document.url: http://antcat.org/documents/4308/Davidson_et_al_2003_Science.pdf target_orphan.id: 4308 target_orphan.reference_id: target_orphan.file_file_name: Davidson_et_al_2003_Science.pdf Skipping - the same url is hardcoded more than once document_id: 6932 url: http://antcat.org/documents/4487/Krieger&Ross_2002_Science.pdf reference_id: 131645 - ArticleReference Replacing... hardcoded_url_document.id: 6943 hardcoded_url_document.reference_id: 122980 hardcoded_url_document.url: http://antcat.org/documents/331/6524.pdf target_orphan.id: 331 target_orphan.reference_id: target_orphan.file_file_name: 6524.pdf Skipping - the same url is hardcoded more than once document_id: 6948 url: http://antcat.org/documents/1454/4031.pdf reference_id: 125216 - ArticleReference Replacing... hardcoded_url_document.id: 6957 hardcoded_url_document.reference_id: 143195 hardcoded_url_document.url: http://antcat.org/documents/6951/Steiner_et_al._-_2018_-_Molecular_Phylogenetics_and_Evolution.pdf target_orphan.id: 6951 target_orphan.reference_id: target_orphan.file_file_name: Steiner_et_al._-_2018_-_Molecular_Phylogenetics_and_Evolution.pdf Skipping - the same url is hardcoded more than once document_id: 6965 url: http://antcat.org/documents/6962/585-2799-1-SM.pdf reference_id: 143203 - ArticleReference Skipping - the same url is hardcoded more than once document_id: 6971 url: http://antcat.org/documents/6968/Da_Silva_Neves_et_al._-_2018_-_Sociobiology.pdf reference_id: 143207 - ArticleReference Replacing... hardcoded_url_document.id: 6974 hardcoded_url_document.reference_id: 123079 hardcoded_url_document.url: http://antcat.org/documents/368/2360.pdf target_orphan.id: 368 target_orphan.reference_id: target_orphan.file_file_name: 2360.pdf Skipping - the same url is hardcoded more than once document_id: 6986 url: http://antcat.org/documents/838/7602.pdf reference_id: 124002 - BookReference Replacing... hardcoded_url_document.id: 7005 hardcoded_url_document.reference_id: 143233 hardcoded_url_document.url: http://antcat.org/documents/7004/Guerrero_2018_Zootaxa_Tapinoma_melanocephalum.pdf target_orphan.id: 7004 target_orphan.reference_id: target_orphan.file_file_name: Guerrero_2018_Zootaxa_Tapinoma_melanocephalum.pdf Replacing... hardcoded_url_document.id: 7009 hardcoded_url_document.reference_id: 143234 hardcoded_url_document.url: http://antcat.org/documents/7008/mn28_25-33_printable.pdf target_orphan.id: 7008 target_orphan.reference_id: target_orphan.file_file_name: mn28_25-33_printable.pdf Replacing... hardcoded_url_document.id: 7016 hardcoded_url_document.reference_id: 143237 hardcoded_url_document.url: http://antcat.org/documents/7015/Odontomachus_ferminae_upload.pdf target_orphan.id: 7015 target_orphan.reference_id: target_orphan.file_file_name: Odontomachus_ferminae_upload.pdf Skipping - the same url is hardcoded more than once document_id: 7019 url: http://antcat.org/documents/7017/Blaimer_et_al_2018_Insect_Syst___Diversity_Crematogastrini_phylogeny.pdf reference_id: 143238 - ArticleReference Replacing... hardcoded_url_document.id: 7021 hardcoded_url_document.reference_id: 143070 hardcoded_url_document.url: http://antcat.org/documents/6735/seifert__b-__d-eustacchio__d-_et_al-_2017-_four_species_within_the_supercolonial_ants_of_the_tapinoma_nigerrimum_complex_revealed_by_integrative_taxonomy.pdf target_orphan.id: 6735 target_orphan.reference_id: target_orphan.file_file_name: seifert__b-__d-eustacchio__d-_et_al-_2017-_four_species_within_the_supercolonial_ants_of_the_tapinoma_nigerrimum_complex_revealed_by_integrative_taxonomy.pdf Skipping - the same url is hardcoded more than once document_id: 7024 url: http://antcat.org/documents/6809/salata-and-borowiec-2018-am010002.pdf reference_id: 143140 - ArticleReference Replacing... hardcoded_url_document.id: 7025 hardcoded_url_document.reference_id: 143240 hardcoded_url_document.url: http://antcat.org/documents/7023/ZK_article_27022.pdf target_orphan.id: 7023 target_orphan.reference_id: target_orphan.file_file_name: ZK_article_27022.pdf Skipping - the same url is hardcoded more than once document_id: 7034 url: http://antcat.org/documents/6997/Wagner_et_al-2018-Scientific_Reports_(1).pdf reference_id: 143231 - ArticleReference Replacing... hardcoded_url_document.id: 7036 hardcoded_url_document.reference_id: 142676 hardcoded_url_document.url: http://antcat.org/documents/6311/sharaf_et_al_2014_plos_one_meranoplus_pulcher_new_species_from_saudi_arabia.pdf target_orphan.id: 6311 target_orphan.reference_id: target_orphan.file_file_name: sharaf_et_al_2014_plos_one_meranoplus_pulcher_new_species_from_saudi_arabia.pdf Replacing... hardcoded_url_document.id: 7038 hardcoded_url_document.reference_id: 123938 hardcoded_url_document.url: http://antcat.org/documents/825/5258.pdf target_orphan.id: 825 target_orphan.reference_id: target_orphan.file_file_name: 5258.pdf Skipping - the same url is hardcoded more than once document_id: 7052 url: http://antcat.org/documents/7050/Yamada__A.__Luong__P.T.H._et_al._2018._Description_of_a_new_species_of_the_ant_genus_Ooceraea.pdf reference_id: 143254 - ArticleReference Replacing... hardcoded_url_document.id: 7057 hardcoded_url_document.reference_id: 143258 hardcoded_url_document.url: http://antcat.org/documents/7056/Reyes-Lopez__J.L.__Carpintero-Ortega__S._2013._Descripcion_de_Temnothorax_bejaraniensis_nov._sp.pdf target_orphan.id: 7056 target_orphan.reference_id: target_orphan.file_file_name: Reyes-Lopez__J.L.__Carpintero-Ortega__S._2013._Descripcion_de_Temnothorax_bejaraniensis_nov._sp.pdf Replacing... hardcoded_url_document.id: 7076 hardcoded_url_document.reference_id: 143269 hardcoded_url_document.url: http://antcat.org/documents/7075/Hosoishi__S.__Ogata__K._2017._Phylogenetic_analysis_and_systematic_position_of_two_new_species_of_the_ant_genus_Crematogaster.pdf target_orphan.id: 7075 target_orphan.reference_id: target_orphan.file_file_name: Hosoishi__S.__Ogata__K._2017._Phylogenetic_analysis_and_systematic_position_of_two_new_species_of_the_ant_genus_Crematogaster.pdf Replacing... hardcoded_url_document.id: 7082 hardcoded_url_document.reference_id: 143273 hardcoded_url_document.url: http://antcat.org/documents/7080/04_Salata_68-4_769-808_(1).pdf target_orphan.id: 7080 target_orphan.reference_id: target_orphan.file_file_name: 04_Salata_68-4_769-808_(1).pdf Replacing... hardcoded_url_document.id: 7083 hardcoded_url_document.reference_id: 143274 hardcoded_url_document.url: http://antcat.org/documents/7081/05_Radchenko_68-4_809-824.pdf target_orphan.id: 7081 target_orphan.reference_id: target_orphan.file_file_name: 05_Radchenko_68-4_809-824.pdf Skipping - 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hardcoded_url_document.id: 7645 hardcoded_url_document.reference_id: 143403 hardcoded_url_document.url: http://antcat.org/documents/7638/lebas___galkowski_2019_notes_sur_le_genre_proformica_ruzsky.pdf target_orphan.id: 7638 target_orphan.reference_id: target_orphan.file_file_name: lebas___galkowski_2019_notes_sur_le_genre_proformica_ruzsky.pdf Skipping - the same url is hardcoded more than once document_id: 7650 url: http://antcat.org/documents/7568/ortiz-sepulveda2019.pdf reference_id: 143355 - ArticleReference Replacing... hardcoded_url_document.id: 7654 hardcoded_url_document.reference_id: 143067 hardcoded_url_document.url: http://antcat.org/documents/6731/2017-cardiocondyla_nuda_group.pdf target_orphan.id: 6731 target_orphan.reference_id: target_orphan.file_file_name: 2017-cardiocondyla_nuda_group.pdf Replacing... hardcoded_url_document.id: 7655 hardcoded_url_document.reference_id: 143373 hardcoded_url_document.url: http://antcat.org/documents/7590/09_mostafa_az_69-3_603-608.pdf 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rasnitsyn_1969_hymenoptera_symphyta_origin_evol.pdf Skipping - the same url is hardcoded more than once document_id: 7665 url: http://antcat.org/documents/3996/23195.pdf reference_id: 132090 - ArticleReference Replacing... hardcoded_url_document.id: 7666 hardcoded_url_document.reference_id: 133007 hardcoded_url_document.url: http://antcat.org/documents/6294/Forel_1899i_Formicidae_concl.pdf target_orphan.id: 6294 target_orphan.reference_id: target_orphan.file_file_name: Forel_1899i_Formicidae_concl.pdf Replacing... hardcoded_url_document.id: 7675 hardcoded_url_document.reference_id: 128176 hardcoded_url_document.url: http://antcat.org/documents/6389/ruzsky_m_1902e.pdf target_orphan.id: 6389 target_orphan.reference_id: target_orphan.file_file_name: ruzsky_m_1902e.pdf Replacing... hardcoded_url_document.id: 7678 hardcoded_url_document.reference_id: 143020 hardcoded_url_document.url: http://antcat.org/documents/6675/taylor_etal_2016_ants_mali.pdf target_orphan.id: 6675 target_orphan.reference_id: target_orphan.file_file_name: taylor_etal_2016_ants_mali.pdf Replacing... hardcoded_url_document.id: 7679 hardcoded_url_document.reference_id: 142991 hardcoded_url_document.url: http://antcat.org/documents/6639/polyrhachis_euthiacaena.pdf target_orphan.id: 6639 target_orphan.reference_id: target_orphan.file_file_name: polyrhachis_euthiacaena.pdf Skipping - the same url is hardcoded more than once document_id: 7715 url: http://antcat.org/documents/7713/gathalkar___barsagade_2018_japplbiolbiotech_myrmicinae_myrmicaria_brunnea_cephalic_microstructure.pdf reference_id: 143469 - ArticleReference Replacing... hardcoded_url_document.id: 7769 hardcoded_url_document.reference_id: 130753 hardcoded_url_document.url: http://antcat.org/documents/5821/billen_2009_arthropod_struct_devel_exocrine_glands_in_ant_legs.pdf target_orphan.id: 5821 target_orphan.reference_id: target_orphan.file_file_name: billen_2009_arthropod_struct_devel_exocrine_glands_in_ant_legs.pdf Skipping - the same url is hardcoded more than once document_id: 7774 url: http://antcat.org/documents/7763/schoeters___billen_1999_actcollinsectsoc_neurohemal_organs.pdf reference_id: 143512 - ArticleReference Replacing... hardcoded_url_document.id: 7777 hardcoded_url_document.reference_id: 130769 hardcoded_url_document.url: http://antcat.org/documents/4251/Billen&Wilson_2008_Arthropod_Struct_Devel.pdf target_orphan.id: 4251 target_orphan.reference_id: target_orphan.file_file_name: Billen&Wilson_2008_Arthropod_Struct_Devel.pdf Replacing... hardcoded_url_document.id: 7781 hardcoded_url_document.reference_id: 130756 hardcoded_url_document.url: http://antcat.org/documents/3802/14624.pdf target_orphan.id: 3802 target_orphan.reference_id: target_orphan.file_file_name: 14624.pdf Replacing... hardcoded_url_document.id: 7783 hardcoded_url_document.reference_id: 132450 hardcoded_url_document.url: http://antcat.org/documents/4211/Tijskens_et_al_2002_Neth_J_Zool.pdf target_orphan.id: 4211 target_orphan.reference_id: target_orphan.file_file_name: Tijskens_et_al_2002_Neth_J_Zool.pdf Replacing... hardcoded_url_document.id: 7784 hardcoded_url_document.reference_id: 131372 hardcoded_url_document.url: http://antcat.org/documents/4396/Gobin_et_al_2003_Acta_Zool.pdf target_orphan.id: 4396 target_orphan.reference_id: target_orphan.file_file_name: Gobin_et_al_2003_Acta_Zool.pdf Replacing... hardcoded_url_document.id: 7790 hardcoded_url_document.reference_id: 132811 hardcoded_url_document.url: http://antcat.org/documents/4828/Gobin_et_al_2006_Cell_Tissue_Res Queen-worker spermatheca differences.pdf target_orphan.id: 4828 target_orphan.reference_id: target_orphan.file_file_name: Gobin_et_al_2006_Cell_Tissue_Res Queen-worker spermatheca differences.pdf Replacing... hardcoded_url_document.id: 7791 hardcoded_url_document.reference_id: 131395 hardcoded_url_document.url: http://antcat.org/documents/4411/Grasso_et_al_2005_Zoomorphology.pdf target_orphan.id: 4411 target_orphan.reference_id: target_orphan.file_file_name: Grasso_et_al_2005_Zoomorphology.pdf Replacing... hardcoded_url_document.id: 7792 hardcoded_url_document.reference_id: 132812 hardcoded_url_document.url: http://antcat.org/documents/4829/Gobin_et_al_2008_Naturwissenschaften Degeneration of spermatheca in worker ants.pdf target_orphan.id: 4829 target_orphan.reference_id: target_orphan.file_file_name: Gobin_et_al_2008_Naturwissenschaften Degeneration of spermatheca in worker ants.pdf Skipping - the same url is hardcoded more than once document_id: 7794 url: http://antcat.org/documents/4252/Billen_et_al_2005_Arthropod_Struct_Devel.pdf reference_id: 130768 - ArticleReference Skipping - the same url is hardcoded more than once document_id: 7796 url: http://antcat.org/documents/6044/billen_et_al_2013_arthropod_struct_devel_abdominal_gland_diversity_in_myopias.pdf reference_id: 142489 - ArticleReference Skipping - the same url is hardcoded more than once document_id: 7814 url: http://antcat.org/documents/5878/billen_et_al_2013_arthropod_struct_devel_exocrine_system_of_protanilla.pdf reference_id: 142370 - ArticleReference ```

jonkerz commented 3 years ago
Output (re-run)

```ruby Replacing... hardcoded_url_document.id: 6662 hardcoded_url_document.reference_id: 143009 hardcoded_url_document.url: http://antcat.org/documents/6660/chen_etal_2016_far_eastern_entomol_cerapachys_bispinatus.pdf target_orphan.id: 6660 target_orphan.reference_id: target_orphan.file_file_name: chen_etal_2016_far_eastern_entomol_cerapachys_bispinatus.pdf Replacing... hardcoded_url_document.id: 6761 hardcoded_url_document.reference_id: 143099 hardcoded_url_document.url: http://antcat.org/documents/6759/2017-desquivel_et_al-thaumatomyrmex_fraxini.pdf target_orphan.id: 6759 target_orphan.reference_id: target_orphan.file_file_name: 2017-desquivel_et_al-thaumatomyrmex_fraxini.pdf Replacing... hardcoded_url_document.id: 6926 hardcoded_url_document.reference_id: 142345 hardcoded_url_document.url: http://antcat.org/documents/5844/boudinot___fisher_2013_zootaxa_meranoplus_of_madagascar.pdf target_orphan.id: 5844 target_orphan.reference_id: target_orphan.file_file_name: boudinot___fisher_2013_zootaxa_meranoplus_of_madagascar.pdf Replacing... hardcoded_url_document.id: 6927 hardcoded_url_document.reference_id: 143112 hardcoded_url_document.url: http://antcat.org/documents/6774/barden_etal_2017_leptomyrmex-phylogeny.pdf target_orphan.id: 6774 target_orphan.reference_id: target_orphan.file_file_name: barden_etal_2017_leptomyrmex-phylogeny.pdf Replacing... hardcoded_url_document.id: 6932 hardcoded_url_document.reference_id: 131645 hardcoded_url_document.url: http://antcat.org/documents/4487/Krieger&Ross_2002_Science.pdf target_orphan.id: 4487 target_orphan.reference_id: target_orphan.file_file_name: Krieger&Ross_2002_Science.pdf Replacing... hardcoded_url_document.id: 6948 hardcoded_url_document.reference_id: 125216 hardcoded_url_document.url: http://antcat.org/documents/1454/4031.pdf target_orphan.id: 1454 target_orphan.reference_id: target_orphan.file_file_name: 4031.pdf Replacing... hardcoded_url_document.id: 6965 hardcoded_url_document.reference_id: 143203 hardcoded_url_document.url: http://antcat.org/documents/6962/585-2799-1-SM.pdf target_orphan.id: 6962 target_orphan.reference_id: target_orphan.file_file_name: 585-2799-1-SM.pdf Replacing... hardcoded_url_document.id: 6971 hardcoded_url_document.reference_id: 143207 hardcoded_url_document.url: http://antcat.org/documents/6968/Da_Silva_Neves_et_al._-_2018_-_Sociobiology.pdf target_orphan.id: 6968 target_orphan.reference_id: target_orphan.file_file_name: Da_Silva_Neves_et_al._-_2018_-_Sociobiology.pdf Replacing... hardcoded_url_document.id: 6986 hardcoded_url_document.reference_id: 124002 hardcoded_url_document.url: http://antcat.org/documents/838/7602.pdf target_orphan.id: 838 target_orphan.reference_id: target_orphan.file_file_name: 7602.pdf Replacing... hardcoded_url_document.id: 7019 hardcoded_url_document.reference_id: 143238 hardcoded_url_document.url: http://antcat.org/documents/7017/Blaimer_et_al_2018_Insect_Syst___Diversity_Crematogastrini_phylogeny.pdf target_orphan.id: 7017 target_orphan.reference_id: target_orphan.file_file_name: Blaimer_et_al_2018_Insect_Syst___Diversity_Crematogastrini_phylogeny.pdf Replacing... hardcoded_url_document.id: 7024 hardcoded_url_document.reference_id: 143140 hardcoded_url_document.url: http://antcat.org/documents/6809/salata-and-borowiec-2018-am010002.pdf target_orphan.id: 6809 target_orphan.reference_id: target_orphan.file_file_name: salata-and-borowiec-2018-am010002.pdf Replacing... hardcoded_url_document.id: 7034 hardcoded_url_document.reference_id: 143231 hardcoded_url_document.url: http://antcat.org/documents/6997/Wagner_et_al-2018-Scientific_Reports_(1).pdf target_orphan.id: 6997 target_orphan.reference_id: target_orphan.file_file_name: Wagner_et_al-2018-Scientific_Reports_(1).pdf Replacing... hardcoded_url_document.id: 7052 hardcoded_url_document.reference_id: 143254 hardcoded_url_document.url: http://antcat.org/documents/7050/Yamada__A.__Luong__P.T.H._et_al._2018._Description_of_a_new_species_of_the_ant_genus_Ooceraea.pdf target_orphan.id: 7050 target_orphan.reference_id: target_orphan.file_file_name: Yamada__A.__Luong__P.T.H._et_al._2018._Description_of_a_new_species_of_the_ant_genus_Ooceraea.pdf Replacing... hardcoded_url_document.id: 7093 hardcoded_url_document.reference_id: 143278 hardcoded_url_document.url: http://antcat.org/documents/7088/Zettel_et_al_2018_ZArbOstEnt_Camponotus_Myrmamblys_from_Southeast_Asia.pdf target_orphan.id: 7088 target_orphan.reference_id: target_orphan.file_file_name: Zettel_et_al_2018_ZArbOstEnt_Camponotus_Myrmamblys_from_Southeast_Asia.pdf Replacing... hardcoded_url_document.id: 7162 hardcoded_url_document.reference_id: 124103 hardcoded_url_document.url: http://antcat.org/documents/862/5664.pdf target_orphan.id: 862 target_orphan.reference_id: target_orphan.file_file_name: 5664.pdf Replacing... hardcoded_url_document.id: 7173 hardcoded_url_document.reference_id: 143016 hardcoded_url_document.url: http://antcat.org/documents/6678/ant_fauna_hymenoptera_formicidae_of_the_socotra_archipelago_yemen_zoogeography_distribution_and_description_of_a_new_species.pdf target_orphan.id: 6678 target_orphan.reference_id: target_orphan.file_file_name: ant_fauna_hymenoptera_formicidae_of_the_socotra_archipelago_yemen_zoogeography_distribution_and_description_of_a_new_species.pdf Replacing... hardcoded_url_document.id: 7175 hardcoded_url_document.reference_id: 143138 hardcoded_url_document.url: http://antcat.org/documents/6807/Sharaf_et_al._-_2018_-_Additions_to_the_ant_fauna_(_Hymenoptera_Formicidae_)_of_Oman_an_updated_list___new_records_and_a_description_o.pdf target_orphan.id: 6807 target_orphan.reference_id: target_orphan.file_file_name: Sharaf_et_al._-_2018_-_Additions_to_the_ant_fauna_(_Hymenoptera_Formicidae_)_of_Oman_an_updated_list___new_records_and_a_description_o.pdf Replacing... hardcoded_url_document.id: 7177 hardcoded_url_document.reference_id: 142632 hardcoded_url_document.url: http://antcat.org/documents/6250/borowiec_2014_catalogue_of_ants_of_europe_low.pdf target_orphan.id: 6250 target_orphan.reference_id: target_orphan.file_file_name: borowiec_2014_catalogue_of_ants_of_europe_low.pdf Replacing... hardcoded_url_document.id: 7188 hardcoded_url_document.reference_id: 130282 hardcoded_url_document.url: http://antcat.org/documents/3650/3462.pdf target_orphan.id: 3650 target_orphan.reference_id: target_orphan.file_file_name: 3462.pdf Replacing... hardcoded_url_document.id: 7190 hardcoded_url_document.reference_id: 130031 hardcoded_url_document.url: http://antcat.org/documents/3438/3276.pdf target_orphan.id: 3438 target_orphan.reference_id: target_orphan.file_file_name: 3276.pdf Replacing... hardcoded_url_document.id: 7214 hardcoded_url_document.reference_id: 130187 hardcoded_url_document.url: http://antcat.org/documents/3570/3386.pdf target_orphan.id: 3570 target_orphan.reference_id: target_orphan.file_file_name: 3386.pdf Replacing... hardcoded_url_document.id: 7250 hardcoded_url_document.reference_id: 130116 hardcoded_url_document.url: http://antcat.org/documents/3511/3336.pdf target_orphan.id: 3511 target_orphan.reference_id: target_orphan.file_file_name: 3336.pdf Replacing... hardcoded_url_document.id: 7259 hardcoded_url_document.reference_id: 123672 hardcoded_url_document.url: http://antcat.org/documents/662/6127.pdf target_orphan.id: 662 target_orphan.reference_id: target_orphan.file_file_name: 6127.pdf Replacing... hardcoded_url_document.id: 7275 hardcoded_url_document.reference_id: 123261 hardcoded_url_document.url: http://antcat.org/documents/497/6779.pdf target_orphan.id: 497 target_orphan.reference_id: target_orphan.file_file_name: 6779.pdf Replacing... hardcoded_url_document.id: 7280 hardcoded_url_document.reference_id: 124151 hardcoded_url_document.url: http://antcat.org/documents/885/8314.pdf target_orphan.id: 885 target_orphan.reference_id: target_orphan.file_file_name: 8314.pdf Replacing... hardcoded_url_document.id: 7296 hardcoded_url_document.reference_id: 142622 hardcoded_url_document.url: http://antcat.org/documents/6315/dlussky_perfilieva_2014_isle_of_wight_eocene_ants.pdf target_orphan.id: 6315 target_orphan.reference_id: target_orphan.file_file_name: dlussky_perfilieva_2014_isle_of_wight_eocene_ants.pdf Replacing... hardcoded_url_document.id: 7302 hardcoded_url_document.reference_id: 142630 hardcoded_url_document.url: http://antcat.org/documents/6341/ward_et_al_2015_syst_entomol_myrmicine_phylogeny_incl_supp_info.pdf target_orphan.id: 6341 target_orphan.reference_id: target_orphan.file_file_name: ward_et_al_2015_syst_entomol_myrmicine_phylogeny_incl_supp_info.pdf Replacing... hardcoded_url_document.id: 7316 hardcoded_url_document.reference_id: 130019 hardcoded_url_document.url: http://antcat.org/documents/3426/10540.pdf target_orphan.id: 3426 target_orphan.reference_id: target_orphan.file_file_name: 10540.pdf Replacing... hardcoded_url_document.id: 7317 hardcoded_url_document.reference_id: 130055 hardcoded_url_document.url: http://antcat.org/documents/3458/3292.pdf target_orphan.id: 3458 target_orphan.reference_id: target_orphan.file_file_name: 3292.pdf Replacing... hardcoded_url_document.id: 7324 hardcoded_url_document.reference_id: 130198 hardcoded_url_document.url: http://antcat.org/documents/3581/3400.pdf target_orphan.id: 3581 target_orphan.reference_id: target_orphan.file_file_name: 3400.pdf Replacing... hardcoded_url_document.id: 7327 hardcoded_url_document.reference_id: 128906 hardcoded_url_document.url: http://antcat.org/documents/5151/2734.pdf target_orphan.id: 5151 target_orphan.reference_id: target_orphan.file_file_name: 2734.pdf Replacing... hardcoded_url_document.id: 7362 hardcoded_url_document.reference_id: 132768 hardcoded_url_document.url: http://antcat.org/documents/4795/Lapeva-Gjonova_et_al_2010_ZooKeys_Catalogue of the ants of Bulgaria.pdf target_orphan.id: 4795 target_orphan.reference_id: target_orphan.file_file_name: Lapeva-Gjonova_et_al_2010_ZooKeys_Catalogue of the ants of Bulgaria.pdf Replacing... hardcoded_url_document.id: 7369 hardcoded_url_document.reference_id: 122149 hardcoded_url_document.url: http://antcat.org/documents/22/6857.pdf target_orphan.id: 22 target_orphan.reference_id: target_orphan.file_file_name: 6857.pdf Replacing... hardcoded_url_document.id: 7370 hardcoded_url_document.reference_id: 131396 hardcoded_url_document.url: http://antcat.org/documents/3894/23047.pdf target_orphan.id: 3894 target_orphan.reference_id: target_orphan.file_file_name: 23047.pdf Replacing... hardcoded_url_document.id: 7416 hardcoded_url_document.reference_id: 133061 hardcoded_url_document.url: http://antcat.org/documents/5676/blaimer_2012_zookeys-crematogaster-orthocrema-of-madagascar.pdf target_orphan.id: 5676 target_orphan.reference_id: target_orphan.file_file_name: blaimer_2012_zookeys-crematogaster-orthocrema-of-madagascar.pdf Replacing... hardcoded_url_document.id: 7417 hardcoded_url_document.reference_id: 142232 hardcoded_url_document.url: http://antcat.org/documents/5746/blaimer_2012_zootaxa-subgeneric-revision-of-crematogaster.pdf target_orphan.id: 5746 target_orphan.reference_id: target_orphan.file_file_name: blaimer_2012_zootaxa-subgeneric-revision-of-crematogaster.pdf Replacing... hardcoded_url_document.id: 7418 hardcoded_url_document.reference_id: 142233 hardcoded_url_document.url: http://antcat.org/documents/5747/blaimer_2012_mol_phylogenet_evol-acrobat-ants-go-global-incl-suppl-data.pdf target_orphan.id: 5747 target_orphan.reference_id: target_orphan.file_file_name: blaimer_2012_mol_phylogenet_evol-acrobat-ants-go-global-incl-suppl-data.pdf Replacing... hardcoded_url_document.id: 7421 hardcoded_url_document.reference_id: 142420 hardcoded_url_document.url: http://antcat.org/documents/5961/blaimer___fisher_2013_eur_j_taxon.pdf target_orphan.id: 5961 target_orphan.reference_id: target_orphan.file_file_name: blaimer___fisher_2013_eur_j_taxon.pdf Replacing... hardcoded_url_document.id: 7465 hardcoded_url_document.reference_id: 133042 hardcoded_url_document.url: http://antcat.org/documents/5654/lacau_et_al_2012_psyche-tatuidris-kapasi-sp-nov.pdf target_orphan.id: 5654 target_orphan.reference_id: target_orphan.file_file_name: lacau_et_al_2012_psyche-tatuidris-kapasi-sp-nov.pdf Replacing... hardcoded_url_document.id: 7466 hardcoded_url_document.reference_id: 132961 hardcoded_url_document.url: http://antcat.org/documents/5399/mariano_et_al_2011_psyche-pachycondyla.pdf target_orphan.id: 5399 target_orphan.reference_id: target_orphan.file_file_name: mariano_et_al_2011_psyche-pachycondyla.pdf Replacing... hardcoded_url_document.id: 7467 hardcoded_url_document.reference_id: 142407 hardcoded_url_document.url: http://antcat.org/documents/5946/joma___mackay_2013_psyche_bothroponera_umgodikulula.pdf target_orphan.id: 5946 target_orphan.reference_id: target_orphan.file_file_name: joma___mackay_2013_psyche_bothroponera_umgodikulula.pdf Replacing... hardcoded_url_document.id: 7468 hardcoded_url_document.reference_id: 132596 hardcoded_url_document.url: http://antcat.org/documents/4760/wernegreen_et_al_2009_bmc_evol_biol.pdf target_orphan.id: 4760 target_orphan.reference_id: target_orphan.file_file_name: wernegreen_et_al_2009_bmc_evol_biol.pdf Replacing... hardcoded_url_document.id: 7469 hardcoded_url_document.reference_id: 132546 hardcoded_url_document.url: http://antcat.org/documents/4745/Wang_et_al_2007_Genome_Biol.pdf target_orphan.id: 4745 target_orphan.reference_id: target_orphan.file_file_name: Wang_et_al_2007_Genome_Biol.pdf Replacing... hardcoded_url_document.id: 7475 hardcoded_url_document.reference_id: 132918 hardcoded_url_document.url: http://antcat.org/documents/5294/peters_et_al_2011_bmc_biol-hymenoptera-phylogeny.pdf target_orphan.id: 5294 target_orphan.reference_id: target_orphan.file_file_name: peters_et_al_2011_bmc_biol-hymenoptera-phylogeny.pdf Replacing... hardcoded_url_document.id: 7476 hardcoded_url_document.reference_id: 131832 hardcoded_url_document.url: http://antcat.org/documents/4545/Maruyama_et_al_2008_BMC_Evol_Biol.pdf target_orphan.id: 4545 target_orphan.reference_id: target_orphan.file_file_name: Maruyama_et_al_2008_BMC_Evol_Biol.pdf Replacing... hardcoded_url_document.id: 7478 hardcoded_url_document.reference_id: 132907 hardcoded_url_document.url: http://antcat.org/documents/5278/kronauer_et_al_2011_frontiers_zool-dorylus-hybridization.pdf target_orphan.id: 5278 target_orphan.reference_id: target_orphan.file_file_name: kronauer_et_al_2011_frontiers_zool-dorylus-hybridization.pdf Replacing... hardcoded_url_document.id: 7479 hardcoded_url_document.reference_id: 131391 hardcoded_url_document.url: http://antcat.org/documents/4175/Gotzek_2010_BMC Evolutionary Biology mt genome evolution in fire ants.pdf target_orphan.id: 4175 target_orphan.reference_id: target_orphan.file_file_name: Gotzek_2010_BMC Evolutionary 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