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diff --git a/notes/ingest/2021-05_daily_improvements.md b/notes/ingest/2021-05_daily_improvements.md new file mode 100644 index 0000000..e8748fa --- /dev/null +++ b/notes/ingest/2021-05_daily_improvements.md @@ -0,0 +1,480 @@ + +Summary of top large broken domains (2021-04-21 "30 day" snapshot): + +## acervus.unicamp.br + + domain | status | count +---------------------------------------+-------------------------+-------- + acervus.unicamp.br | | 1967 + acervus.unicamp.br | no-pdf-link | 1853 + +select * from ingest_file_result where updated >= '2021-03-01' and terminal_url like '%acervus.unicamp.br%' and status = 'no-pdf-link' limit 5; + +http://acervus.unicamp.br/index.asp?codigo_sophia=963332 + +seems like many of these were captures with a blank page? or a redirect to +the homepage? + +http://web.archive.org/web/20200129110523/http://acervus.unicamp.br/index.html + +messy, going to move on. + + +## apex.ipk-gatersleben.de + +apex.ipk-gatersleben.de | | 1253 +apex.ipk-gatersleben.de | no-pdf-link | 1132 + +select * from ingest_file_result where updated >= '2021-03-01' and terminal_url like '%apex.ipk-gatersleben.de%' and status = 'no-pdf-link' limit 5; + +https://doi.org/10.25642/ipk/rescoll/4886 +https://apex.ipk-gatersleben.de/apex/f?p=PGRDOI:RESOLVE:::NO:RP:DOI:10.25642/IPK/RESCOLL/7331 + +seem to be datasets/species, not articles. + +prefix: 10.25642/ipk + +## crossref.org + + apps.crossref.org | | 4693 + apps.crossref.org | no-pdf-link | 4075 + +https://doi.org/10.1515/9781501747045-013 +https://apps.crossref.org/coaccess/coaccess.html?doi=10.1515%2F9781501747045-013 + +Derp, they are doing a dynamic/AJAX thing, so access links are not in the HTML. + +## openeditiong + + books.openedition.org | | 1784 + books.openedition.org | no-pdf-link | 1466 + +https://doi.org/10.4000/books.pul.34492 +https://books.openedition.org/pul/34492 + +these are not actually OA books (or at least, not all are) + +## chemrxiv.org (figshare) + + chemrxiv.org | | 857 + chemrxiv.org | no-pdf-link | 519 + +https://doi.org/10.26434/chemrxiv.14411081 +https://chemrxiv.org/articles/preprint/Prediction_and_Optimization_of_Ion_Transport_Characteristics_in_Nanoparticle-Based_Electrolytes_Using_Convolutional_Neural_Networks/14411081 + +these all seem to be *multi-file* entities, thus not good for single file ingest pipeline. + +## direct.mit.edu + + direct.mit.edu | | 996 + direct.mit.edu | no-pdf-link | 869 + +https://doi.org/10.7551/mitpress/14056.003.0004 +https://direct.mit.edu/books/monograph/5111/chapter-abstract/3060134/Adding-Technology-to-Contact-Tracing?redirectedFrom=fulltext + +"not available" + +https://doi.org/10.7551/mitpress/12444.003.0004 + +"not available" + + +## dlc.library.columbia.edu + + dlc.library.columbia.edu | | 4225 + dlc.library.columbia.edu | no-pdf-link | 2395 + dlc.library.columbia.edu | spn2-wayback-error | 1568 + +https://doi.org/10.7916/d8-506w-kk49 +https://dlc.library.columbia.edu/durst/cul:18931zcrk9 + +document repository. +this one goes to IA! actually many seem to. +added extractor, should re-ingest with: + + publisher:"Columbia University" doi_prefix:10.7916 !journal:* + +actually, that is like 600k+ results and many are not digitized, so perhaps not. + +## doi.ala.org.au + + doi.ala.org.au | | 2570 + doi.ala.org.au | no-pdf-link | 2153 + +https://doi.org/10.26197/ala.811d55e3-2ff4-4501-b3e7-e19249507052 +https://doi.ala.org.au/doi/811d55e3-2ff4-4501-b3e7-e19249507052 + +this is a data repository, with filesets, not papers. datacite metadata is +incorrect. + +## fldeploc.dep.state.fl.us + + fldeploc.dep.state.fl.us | | 774 + fldeploc.dep.state.fl.us | no-pdf-link | 718 + + +https://doi.org/10.35256/ic29 +http://fldeploc.dep.state.fl.us/geodb_query/fgs_doi.asp?searchCode=IC29 + +re-ingest with: + + # only ~800 works + doi_prefix:10.35256 publisher:Florida + +## geoscan.nrcan.gc.ca + + geoscan.nrcan.gc.ca | | 2056 + geoscan.nrcan.gc.ca | no-pdf-link | 2019 + +https://doi.org/10.4095/295366 +https://geoscan.nrcan.gc.ca/starweb/geoscan/servlet.starweb?path=geoscan/fulle.web&search1=R=295366 + +this is a geographic repository, not papers. + +## kiss.kstudy.com + + kiss.kstudy.com | | 747 + kiss.kstudy.com | no-pdf-link | 686 + +https://doi.org/10.22143/hss21.12.1.121 +http://kiss.kstudy.com/thesis/thesis-view.asp?key=3862523 + +Korean. seems to not actually be theses? can't download. + +## linkinghub.elsevier.com + + linkinghub.elsevier.com | | 5079 + linkinghub.elsevier.com | forbidden | 2226 + linkinghub.elsevier.com | spn2-wayback-error | 1625 + linkinghub.elsevier.com | spn2-cdx-lookup-failure | 758 + +skipping for now, looks like mostly 'forbidden'? + +## osf.io + +These are important! + + osf.io | | 3139 + osf.io | not-found | 2288 + osf.io | spn2-wayback-error | 582 + +https://doi.org/10.31219/osf.io/jux3w +https://accounts.osf.io/login?service=https://osf.io/jux3w/download + +many of these are 404s by browser as well. what does that mean? + +## peerj.com + + peerj.com | | 785 + peerj.com | no-pdf-link | 552 + +https://doi.org/10.7287/peerj.11155v0.1/reviews/2 +https://peerj.com/articles/11155/reviews/ + +these are HTML reviews, not papers + +## preprints.jmir.org + + preprints.jmir.org | | 763 + preprints.jmir.org | no-pdf-link | 611 + +https://doi.org/10.2196/preprints.22556 +https://preprints.jmir.org/preprint/22556 + +UGH, looks simple, but javascript. + +could try to re-write URL into S3 format? meh. + +## psyarxiv.com (OSF?) + + psyarxiv.com | | 641 + psyarxiv.com | no-pdf-link | 546 + +https://doi.org/10.31234/osf.io/5jaqg +https://psyarxiv.com/5jaqg/ + +Also infuriatingly Javascript, but can do URL hack. + +Should reingest, and potentially force-recrawl: + + # about 67k + publisher:"Center for Open Science" in_ia:false + +## publons.com + + publons.com | | 6998 + publons.com | no-pdf-link | 6982 + +https://doi.org/10.1002/jmor.21338/v2/review1 +https://publons.com/publon/40260824/ + +These are just HTML reviews, not papers. + +## saemobilus.sae.org + + saemobilus.sae.org | | 795 + saemobilus.sae.org | no-pdf-link | 669 + +https://doi.org/10.4271/as1426c +https://saemobilus.sae.org/content/as1426c + +These seem to be standards, and are not open access (paywall) + +## scholar.dkyobobook.co.kr + + scholar.dkyobobook.co.kr | | 1043 + scholar.dkyobobook.co.kr | no-pdf-link | 915 + +https://doi.org/10.22471/crisis.2021.6.1.18 +http://scholar.dkyobobook.co.kr/searchDetail.laf?barcode=4010028199536 + +Korean. complex javascript, skipping. + +## unreserved.rba.gov.au + + unreserved.rba.gov.au | | 823 + unreserved.rba.gov.au | no-pdf-link | 821 + +https://doi.org/10.47688/rba_archives_2006/04129 +https://unreserved.rba.gov.au/users/login + +Don't need to login when I tried in browser? document repo, not papers. + +## wayf.switch.ch + + wayf.switch.ch | | 1169 + wayf.switch.ch | no-pdf-link | 809 + +https://doi.org/10.24451/arbor.11128 +https://wayf.switch.ch/SWITCHaai/WAYF?entityID=https%3A%2F%2Farbor.bfh.ch%2Fshibboleth&return=https%3A%2F%2Farbor.bfh.ch%2FShibboleth.sso%2FLogin%3FSAMLDS%3D1%26target%3Dss%253Amem%253A5056fc0a97aeab16e5007ca63bede254cb5669d94173064d6c74c62a0f88b022 + +Loginwall + +## + + www.bloomsburycollections.com | | 1745 + www.bloomsburycollections.com | no-pdf-link | 1571 + +https://doi.org/10.5040/9781849664264.0008 +https://www.bloomsburycollections.com/book/the-political-economies-of-media-the-transformation-of-the-global-media-industries/the-political-economies-of-media-and-the-transformation-of-the-global-media-industries + +These are primarily not OA/available. + +## + + www.emc2020.eu | | 791 + www.emc2020.eu | no-pdf-link | 748 + +https://doi.org/10.22443/rms.emc2020.146 +https://www.emc2020.eu/abstract/evaluation-of-different-rectangular-scan-strategies-for-hrstem-imaging.html + +These are just abstracts, not papers. + +## Emerald + + www.emerald.com | | 2420 + www.emerald.com | no-pdf-link | 1986 + +https://doi.org/10.1108/ramj-11-2020-0065 +https://www.emerald.com/insight/content/doi/10.1108/RAMJ-11-2020-0065/full/html + +Note that these URLs are already HTML fulltext. but the PDF is also available and easy. + +re-ingest: + + # only ~3k or so missing + doi_prefix:10.1108 publisher:emerald in_ia:false is_oa:true + +## + + www.humankineticslibrary.com | | 1122 + www.humankineticslibrary.com | no-pdf-link | 985 + +https://doi.org/10.5040/9781718206625.ch-002 +https://www.humankineticslibrary.com/encyclopedia-chapter?docid=b-9781718206625&tocid=b-9781718206625-chapter2 + +paywall + +## + + www.inderscience.com | | 1532 + www.inderscience.com | no-pdf-link | 1217 + +https://doi.org/10.1504/ijdmb.2020.10036342 +https://www.inderscience.com/info/ingeneral/forthcoming.php?jcode=ijdmb + +paywall + +## + + www.ingentaconnect.com | | 885 + www.ingentaconnect.com | no-pdf-link | 783 + +https://doi.org/10.15258/sst.2021.49.1.07 +https://www.ingentaconnect.com/content/ista/sst/pre-prints/content-7_sst.2021.49.1_63-71;jsessionid=1joc5mmi1juht.x-ic-live-02 + +Annoying javascript, but easy to work around. + +re-ingest: + + # only a couple hundred; also re-ingest + doi_prefix:10.15258 in_ia:false year:>2018 + +## + + www.nomos-elibrary.de | | 2235 + www.nomos-elibrary.de | no-pdf-link | 1128 + www.nomos-elibrary.de | spn2-wayback-error | 559 + +https://doi.org/10.5771/9783748907084-439 +https://www.nomos-elibrary.de/10.5771/9783748907084-439/verzeichnis-der-autorinnen-und-autoren + +Javascript obfuscated download button? + +## + + www.oecd-ilibrary.org | | 3046 + www.oecd-ilibrary.org | no-pdf-link | 2869 + +https://doi.org/10.1787/543e84ed-en +https://www.oecd-ilibrary.org/development/applying-evaluation-criteria-thoughtfully_543e84ed-en + +Paywall. + +## + + www.osapublishing.org | | 821 + www.osapublishing.org | no-pdf-link | 615 + +https://doi.org/10.1364/boe.422199 +https://www.osapublishing.org/boe/abstract.cfm?doi=10.1364/BOE.422199 + +Some of these are "pre-registered" DOIs, not published yet. Many of the +remaining are actually HTML articles, and/or have some stuff in the +`citation_pdf_url`. A core problem is captchas. + +Have started adding support to fatcat for HTML crawl type based on container. + +re-ingest: + + container_twtpsm6ytje3nhuqfu3pa7ca7u (optica) + container_cg4vcsfty5dfvgmat5wm62wgie (optics express) + +## + + www.oxfordscholarlyeditions.com | | 759 + www.oxfordscholarlyeditions.com | no-pdf-link | 719 + +https://doi.org/10.1093/oseo/instance.00266789 +https://www.oxfordscholarlyeditions.com/view/10.1093/actrade/9780199593668.book.1/actrade-9780199593668-div1-27 + +loginwall/paywall + +## + + www.schweizerbart.de | | 730 + www.schweizerbart.de | no-pdf-link | 653 + +https://doi.org/10.1127/zfg/40/1996/461 +https://www.schweizerbart.de/papers/zfg/detail/40/97757/Theoretical_model_of_surface_karstic_processes?af=crossref + +paywall + +## + + www.sciencedirect.com | | 14757 + www.sciencedirect.com | no-pdf-link | 12733 + www.sciencedirect.com | spn2-wayback-error | 1503 + +https://doi.org/10.1016/j.landurbplan.2021.104104 +https://www.sciencedirect.com/science/article/pii/S0169204621000670 + +Bunch of crazy new hacks, but seems to be working! + +re-ingest: + + # to start! about 50k + doi_prefix:10.1016 is_oa:true year:2021 + +## + + www.sciendo.com | | 1955 + www.sciendo.com | no-pdf-link | 1176 + +https://doi.org/10.2478/awutm-2019-0012 +https://www.sciendo.com/article/10.2478/awutm-2019-0012 + +uses lots of javascript, hard to scrape. + + +## Others (for reference) + + | | 725990 + | no-pdf-link | 209933 + | success | 206134 + | spn2-wayback-error | 127015 + | spn2-cdx-lookup-failure | 53384 + | blocked-cookie | 35867 + | link-loop | 25834 + | too-many-redirects | 16430 + | redirect-loop | 14648 + | forbidden | 13794 + | terminal-bad-status | 8055 + | not-found | 6399 + | remote-server-error | 2402 + | wrong-mimetype | 2011 + | spn2-error:unauthorized | 912 + | bad-redirect | 555 + | read-timeout | 530 + +## Re-ingests + +All the above combined: + + container_twtpsm6ytje3nhuqfu3pa7ca7u (optica) + container_cg4vcsfty5dfvgmat5wm62wgie (optics express) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html container --container-id twtpsm6ytje3nhuqfu3pa7ca7u + => Counter({'ingest_request': 1142, 'elasticsearch_release': 1142, 'estimate': 1142, 'kafka': 1142}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --ingest-type html container --container-id cg4vcsfty5dfvgmat5wm62wgie + => Counter({'elasticsearch_release': 33482, 'estimate': 33482, 'ingest_request': 32864, 'kafka': 32864}) + + # only ~800 works + doi_prefix:10.35256 publisher:Florida + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query "doi_prefix:10.35256 publisher:Florida" + => Counter({'ingest_request': 843, 'elasticsearch_release': 843, 'estimate': 843, 'kafka': 843}) + + # only ~3k or so missing + doi_prefix:10.1108 publisher:emerald in_ia:false is_oa:true + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1108 publisher:emerald" + => Counter({'ingest_request': 3812, 'elasticsearch_release': 3812, 'estimate': 3812, 'kafka': 3812}) + + + # only a couple hundred; also re-ingest + doi_prefix:10.15258 in_ia:false year:>2018 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa --force-recrawl query "doi_prefix:10.15258 year:>2018" + => Counter({'ingest_request': 140, 'elasticsearch_release': 140, 'estimate': 140, 'kafka': 140}) + + # to start! about 50k + doi_prefix:10.1016 is_oa:true year:2020 + doi_prefix:10.1016 is_oa:true year:2021 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1016 year:2020" + => Counter({'ingest_request': 75936, 'elasticsearch_release': 75936, 'estimate': 75936, 'kafka': 75936}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi_prefix:10.1016 year:2021" + => Counter({'ingest_request': 54824, 'elasticsearch_release': 54824, 'estimate': 54824, 'kafka': 54824}) + + pmcid:* year:2018 + pmcid:* year:2019 + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --force-recrawl query "pmcid:* year:2018" + => Counter({'ingest_request': 25366, 'elasticsearch_release': 25366, 'estimate': 25366, 'kafka': 25366}) + + ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --force-recrawl query "pmcid:* year:2019" + => Counter({'ingest_request': 55658, 'elasticsearch_release': 55658, 'estimate': 55658, 'kafka': 55658}) + |