diff options
Diffstat (limited to 'extra/bulk_edits/2022-02-04_deleted_dois.md')
| -rw-r--r-- | extra/bulk_edits/2022-02-04_deleted_dois.md | 154 |
1 files changed, 154 insertions, 0 deletions
diff --git a/extra/bulk_edits/2022-02-04_deleted_dois.md b/extra/bulk_edits/2022-02-04_deleted_dois.md new file mode 100644 index 00000000..83c7d697 --- /dev/null +++ b/extra/bulk_edits/2022-02-04_deleted_dois.md @@ -0,0 +1,154 @@ + +## Wild Volume/Issue Numbers + + fatcat-cli search release --count 'volume:99999 author:xxxxxxxxxx doi:* !release_type:stub' + # 37 + +A number of these have duplicated PMID/PMCID + +Should update with: + + release_type:stub release_stage: pmid: pmcid: wikidata_qid: volume: issue: pages: + + export FATCAT_AUTH_WORKER_CLEANUP=[...] + export FATCAT_API_AUTH_TOKEN=$FATCAT_AUTH_WORKER_CLEANUP + fatcat-cli search releases 'volume:99999 author:xxxxxxxxxx doi:* !release_type:stub' --entity-json --limit 50 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub volume= issue= container_id= pages= pmid= pmcid= wikidata_qid= --description "Cleanup of de-registered/stub Crossref DOIs" + # editgroup_exitdv37d5h5zlhmnc6bkwpz6a + +This small batch seems to just be partial/bad metadata, but real releases: + + fatcat-cli search release --count 'volume:9999 issue:9999 container_id:4ozjmpq3dvd2xjdnavdvvq3bam' + # 7 + + fatcat-cli search releases 'volume:9999 issue:9999 container_id:4ozjmpq3dvd2xjdnavdvvq3bam' --entity-json --limit 50 \ + | jq 'select(.volume == "9999")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub volume= issue= container_id= pages= pmid= pmcid= wikidata_qid= --description "Cleanup of bad volume/issue numbers" + # editgroup_bba357rix5g4znbyyz5pu4tjki + +Oops, that was too agressive, not merging. + + fatcat-cli search releases 'volume:9999 issue:9999 container_id:4ozjmpq3dvd2xjdnavdvvq3bam' --entity-json --limit 50 \ + | jq 'select(.volume == "9999")' -c \ + | pv -l \ + | fatcat-cli batch update release volume= issue= --description "Cleanup of bad volume/issue numbers" + # editgroup_vablvgsdpvexvf55zerugkcm6q + +Did some other manual cleanups. + +These are just bad metadata, not stubs: + + fatcat-cli search release 'volume:999 issue:999' --count + # 456 + + # first limit 50 with no auto-merge, then ran the remainder + fatcat-cli search releases 'volume:999 issue:999' --entity-json --limit 50 \ + | jq 'select(.volume == "999")' -c \ + | pv -l \ + | fatcat-cli batch update release volume= issue= --description "Cleanup of bad volume/issue numbers" + # editgroup_xsmvljqware4reixxw7xhuywqq + + # ok, now auto for the rest + fatcat-cli search releases 'volume:999 issue:999' --entity-json --limit 500 \ + | jq 'select(.volume == "999")' -c \ + | pv -l \ + | fatcat-cli batch update release volume= issue= --description "Cleanup of bad volume/issue numbers" --auto-accept + +## "CrossRef Listing Of Deleted DOIs" + +42 releases have the same container, which was misnamed: `container_5hsepvqrxrakvcg4to77yuhbdi` + +Updated that container manually. + + fatcat-cli search releases 'publisher:"Test accounts" journal:"CrossRef Listing of Deleted DOIs" doi:* !release_type:stub' --count + # 52773 + + # start small + fatcat-cli search releases 'publisher:"Test accounts" journal:"CrossRef Listing of Deleted DOIs" doi:* !release_type:stub' --entity-json --limit 50 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub volume= issue= container_id= pages= pmid= pmcid= wikidata_qid= --description "Cleanup of de-registered/stub Crossref DOIs" + # editgroup_hhdr2ptknjemrjwx7kum6a4c6y + +Looks good, though not really any point in removing volume/issue/pages if we +are removing `container_id`, so I won't remove that. + + fatcat-cli search releases 'publisher:"Test accounts" journal:"CrossRef Listing of Deleted DOIs" doi:* !release_type:stub' --entity-json --limit 53000 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub container_id= pmid= pmcid= wikidata_qid= --description "Cleanup of de-registered/stub Crossref DOIs" --auto-accept + + +## "Test Papers" + + fatcat-cli search releases 'title:"test paper" title:ignore author:Alejandro container_id:tol7woxlqjeg5bmzadeg6qrg3e' --count + # 38 + + fatcat-cli search releases 'title:"test paper" title:ignore author:Alejandro container_id:tol7woxlqjeg5bmzadeg6qrg3e' --entity-json --limit 50 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub --description "Mark 'testing' / 'debug' works as stubs" + # editgroup_ikgq6flyhjds7mxe3pig3pvduu + + fatcat-cli search releases 'title:ABCDEF author:EFGH container_id:"dem5zlrvj5fozg4qkmp46jeb4a" !release_type:stub' --count + 104 + + fatcat-cli search releases 'title:ABCDEF author:EFGH container_id:"dem5zlrvj5fozg4qkmp46jeb4a" !release_type:stub' --entity-json --limit 200 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub --description "Mark 'testing' / 'debug' works as stubs" + # editgroup_x2ki7xw35nablf3trjt43zxhpm + # editgroup_2kinca3wgbgujiu634l6g2bxpq + # editgroup_utkdkgvfcvbu5nr4ebiz35a5m4 + + fatcat-cli search releases 'doi_prefix:10.1254 title:ABCDEF author:EFGH !type:stub' --entity-json --limit 50 \ + | jq 'select(.release_type != "stub")' -c \ + | pv -l \ + | fatcat-cli batch update release release_type=stub volume= release_stage= --description "Mark 'testing' / 'debug' works as stubs" + # editgroup_ge26fv3gqncvde47peu67dwkn4 + + +## Bogus DOIs (10.5555) + + fatcat-cli search releases 'doi_prefix:10.5555 pmcid:* !type:stub' --count + 133 + + fatcat-cli search releases 'doi_prefix:10.5555 pmcid:* !type:stub container_id:w46j4of25bd4bjrfy4botn5ezi' --count + 119 + +These seem to all be bogus, never-registered DOIs. Going to remove them from the release entities. + + fatcat-cli search releases 'doi_prefix:10.5555 pmcid:* !type:stub container_id:w46j4of25bd4bjrfy4botn5ezi' --entity-json --limit 120 \ + | pv -l \ + | fatcat-cli batch update release doi= --description "Remove some non-existant DOIs from PMCID works" + # editgroup_5xzb5d2fh5goremlrrwtlp372i + # editgroup_rkcgwcideza4vguje2vonsyeua + # editgroup_nfh7yg4l75fjdbjsvle2otz4ee + +## PsycEXTRA + + fatcat-cli search releases 'journal:PsycEXTRA publisher:"Test accounts" doi_registrar:crossref !type:stub' --count + 13354 + +Not sure what the deal is. These seem to all have been de-registered? But not +confident enough to run import. We have many of these crawled and archived. + +## null/null DOIs + + fatcat-cli search releases 'title:null author:null !type:stub' --count + 16 + +These are not all necessarily deleted. Went through manually. Many seemed to be withdrawn, not stubs. + +## Known Crossref Test Stuff + +For now, not going to remove or mark these. + +"The Journal Of Test Deposits": https://fatcat.wiki/container/7wqkwve2ezbtfn7gkorcuvjd3m + +"Journal of Psychoceramics": https://fatcat.wiki/container/u6q4326uzjak3jx7qjmj7742ea + +"Annals of Psychoceramics B": https://fatcat.wiki/container/ywwmljqajvam7gzhwpjmvahs5y |