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| -rw-r--r-- | commands.md | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/commands.md b/commands.md new file mode 100644 index 0000000..b4a4e04 --- /dev/null +++ b/commands.md @@ -0,0 +1,29 @@ + +Dependencies: + + sudo apt install poppler-utils + pipenv shell + pip install requests python-magic + +Fetch and transform metadata: + + mkdir -p metadata fulltext_web + wget https://archive.org/download/s2-cord19-dataset/cord19.2020-03-20.csv + mv cord19.2020-03-20.csv metadata + ./scripts/parse_cord19_csv.py metadata/cord19.2020-03-20.csv > metadata/cord19.2020-03-20.json + cat metadata/cord19.2020-03-20.json | parallel -j10 --linebuffer --round-robin --pipe ./scripts/cord19_fatcat_enrich.py - | pv -l > metadata/cord19.2020-03-20.enrich.json + cat metadata/cord19.2020-03-20.enrich.json | jq 'select(.release_id == null) | .cord19_paper' -c > metadata/cord19.2020-03-20.missing.json + +Existing fatcat ES transform: + + cat /srv/covid19.fatcat.wiki/src/metadata/cord19.2020-03-20.enrich.json | jq .fatcat_release -c | rg -v '^null$' | ./fatcat_transform.py elasticsearch-releases - - | pv -l > cord19.2020-03-20.fatcat_es.json + +Download fulltext from wayback: + + cat metadata/cord19.2020-03-20.enrich.json | jq .fatcat_release -c | parallel -j20 --linebuffer --round-robin --pipe ./scripts/deliver_file2disk.py --disk-dir fulltext_web - | pv -l > fatcat_web_20200320.log + +Extract text from PDFs: + + ls fulltext_web/pdf/ | parallel mkdir -p fulltext_web/pdftotext/{} + fd .pdf fulltext_web/pdf/ | cut -c18-60 | parallel -j10 pdftotext fulltext_web/pdf/{}.pdf fulltext_web/pdftotext/{}.txt + |