diff options
| -rw-r--r-- | commands.md | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/commands.md b/commands.md index 4ef7231..a749ad4 100644 --- a/commands.md +++ b/commands.md @@ -10,8 +10,8 @@ Fetch and transform metadata: mkdir -p metadata fulltext_web 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 + ./bin/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 ./bin/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: @@ -21,7 +21,7 @@ Existing fatcat ES transform: Download fulltext from wayback: - 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 + cat metadata/cord19.2020-03-27.enrich.json | jq .fatcat_release -c | parallel -j20 --linebuffer --round-robin --pipe ./bin/deliver_file2disk.py --disk-dir fulltext_web - | pv -l > fatcat_web_20200327.log Extract text from PDFs: @@ -42,28 +42,28 @@ Convert GROBID XML to JSON: Create large derivatives file (including extracted fulltext): - ./cord19_fatcat_derivatives.py metadata/cord19.2020-03-27.enrich.json --base-dir fulltext_web/ | pv -l > fulltext.json + ./cord19_fatcat_derivatives.py metadata/cord19.2020-03-27.enrich.json --base-dir fulltext_web/ | pv -l > metadata/cord19.2020-03-27.fulltext.json - cat fulltext.json | jq .fulltext_status -r | sort | uniq -c | sort -nr + cat metadata/cord19.2020-03-27.fulltext.json | jq .fulltext_status -r | sort | uniq -c | sort -nr ## ES Indices +Create fulltext index, transform to ES schema and index: + + # if existing, first: http delete :9200/covid19_fatcat_fulltext + http put :9200/covid19_fatcat_fulltext < schema/fulltext_schema.v00.json + + # in fatcat_covid19, pipenv shell + ./elastic_transform.py metadata/cord19.2020-03-27.fulltext.json | pv -l | esbulk -verbose -size 1000 -id fatcat_ident -w 8 -index covid19_fatcat_fulltext -type release + Create and index existing `fatcat_release` schema: http put :9200/covid19_fatcat_release < schema/release_schema_v03b.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$' | pv -l | ./fatcat_transform.py elasticsearch-releases - - | esbulk -verbose -size 1000 -id ident -w 8 -index covid19_fatcat_release -type release - -Create fulltext index: - - http put :9200/covid19_fatcat_fulltext < schema/fulltext_schema_v00.json - -Transform to ES schema and index: - - ./elastic_transform.py cord19.2020-03-27.fulltext.json | pv -l | esbulk -verbose -size 1000 -id fatcat_ident -w 8 -index covid19_fatcat_fulltext -type release + cat /srv/fatcat_covid19/src/metadata/cord19.2020-03-27.enrich.json | jq .fatcat_release -c | rg -v '^null$' | pv -l | ./fatcat_transform.py elasticsearch-releases - - | esbulk -verbose -size 1000 -id ident -w 8 -index covid19_fatcat_release -type release ## GROBID Processing |