missing: patching metadata for missing fatcat records

1 files changed, 23 insertions, 0 deletions

diff --git a/notes/missing_2020-03-20.md b/notes/missing_2020-03-20.md
index fa2705b..2576a8e 100644
--- a/notes/missing_2020-03-20.md
+++ b/notes/missing_2020-03-20.md
@@ -280,3 +280,26 @@ Interesting sites to crawl or translate:
         => commerical/national holder of 40+ million papers
         => indexed by EBSCO
 
+## Fetching Metata
+
+    cat metadata/cord19.2020-03-27.missing.json | jq 'select(.doi != "") | .doi' -r | sort -u > missing_doi.tsv
+    cat metadata/cord19.2020-03-27.missing.json | jq 'select(.pubmed_id != "") | .pubmed_id' -r | sort -u > missing_pmid.tsv
+    cat metadata/cord19.2020-03-27.missing.json | jq 'select(.pmcid != "") | .pmcid' -r | sort -u > missing_pmcid.tsv
+
+    cat missing_doi.tsv | parallel -j4 'http --headers head "https://doi.org/{}" | head -n1 | awk "{print \"{}\t\" \$2}"' > missing_doi_status.tsv
+
+    cat missing_doi_status.tsv | rg '404$' | cut -f1 > unregistered_doi.tsv
+
+    cat missing_doi_status.tsv | rg '302$' | cut -f1 | parallel http --json get "https://api.crossref.org/v1/works/http://dx.doi.org/{}" | jq .message -c | pv -l > missing_doi_crossref.json
+
+    mkdir -p pubmed
+    cat missing_pmcid.tsv | parallel -j1 'http get "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=pubmed" > pubmed/{}.xml'
+    cat missing_pmid.tsv | parallel -j1 'http get "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=pubmed" > pubmed/{}.xml'
+
+    cat pubmed/*.xml | rg -v '^<\?xml version' | rg -v '^<!DOCTYPE' | rg -v '^<PubmedArticleSet>' | rg -v '^</PubmedArticleSet>' > pubmed_combined.xml
+
+    # Edit file manually to add `<PubmedArticleSet>` and `</PubmedArticleSet>` wrapper.
+
+    # in prod:
+    ./fatcat_import.py pubmed --do-updates /tmp/pubmed_combined.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt
+