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| -rw-r--r-- | commands.md | 23 |
1 files changed, 16 insertions, 7 deletions
diff --git a/commands.md b/commands.md index b4a4e04..7508842 100644 --- a/commands.md +++ b/commands.md @@ -8,22 +8,31 @@ Dependencies: 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 + wget https://archive.org/download/s2-cord19-dataset/cord19.2020-03-27.csv + mv cord19.2020-03-27.csv metadata + ./scripts/parse_cord19_csv.py metadata/cord19.2020-03-27.csv > metadata/cord19.2020-03-27.json + cat metadata/cord19.2020-03-27.json | parallel -j10 --linebuffer --round-robin --pipe ./scripts/cord19_fatcat_enrich.py - | pv -l > metadata/cord19.2020-03-27.enrich.json + cat metadata/cord19.2020-03-27.enrich.json | jq 'select(.release_id == null) | .cord19_paper' -c > metadata/cord19.2020-03-27.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$' | ./fatcat_transform.py elasticsearch-releases - - | pv -l > cord19.2020-03-20.fatcat_es.json + cat /srv/covid19.fatcat.wiki/src/metadata/cord19.2020-03-27.enrich.json | jq .fatcat_release -c | rg -v '^null$' | ./fatcat_transform.py elasticsearch-releases - - | pv -l > cord19.2020-03-27.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 + cat metadata/cord19.2020-03-27.enrich.json | jq .fatcat_release -c | parallel -j20 --linebuffer --round-robin --pipe ./scripts/deliver_file2disk.py --disk-dir fulltext_web - | pv -l > fatcat_web_20200327.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 +## ES Indices + +Create and index existing `fatcat_release` schema: + + http put :9200/covid19_fatcat_release < release_schema.json + + # in fatcat python directory, pipenv shell + export LC_ALL=C.UTF-8 + cat /srv/covid19.fatcat.wiki/src/metadata/cord19.2020-03-27.enrich.json | jq .fatcat_release -c | rg -v '^null$' | pv -l | ./fatcat_transform.py elasticsearch-releases - - | esbulk -verbose -size 1000 -id ident -w 8 -index covid19_fatcat_release -type release |