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authorBryan Newbold <bnewbold@archive.org>2021-05-27 11:57:04 -0700
committerBryan Newbold <bnewbold@archive.org>2021-05-27 11:57:04 -0700
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notes on large-domain ingest tweaks
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+
+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})
+