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Collectory GBIF DOI citations lookup
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| #!/usr/local/bin/bash | |
| # | |
| # Iterate over list of GBIF DOI keys from data_resource table and get a count of the | |
| # distinct publication citations via GBIF API by storing each citation DOI (ID) in an | |
| # associative array and then reading the length of the this array. | |
| # | |
| # Requires BASH version > 4 and JQ command line tool (https://github.com/stedolan/jq) | |
| # | |
| # SQL: select gbif_registry_key from data_resource where gbif_registry_key <> ''; | |
| # | |
| # run as ./collectory-doi-counts.sh gbif_registry_key_list.txt | |
| # | |
| GBIF_URL_PREFIX="https://www.gbif.org/api/resource/search?limit=999&contentType=literature&gbifDatasetKey=" | |
| if [[ ! -r "$1" ]]; then | |
| echo "unable to read file '$1'" | |
| exit 1 | |
| fi | |
| declare -Ag doiHashMap | |
| count=0 | |
| while read key; do | |
| echo -n "$((count = count + 1)) $key " | |
| citations=$(curl -s "$GBIF_URL_PREFIX$key" | jq -r '.results[].identifiers.doi') | |
| while IFS= read -r doi ; do echo -n "."; key=${doi:-2}; doiHashMap["$key"]=1; done <<< "$citations" | |
| echo "unique DOIs = ${#doiHashMap[@]}" | |
| done < <(cat $1) | |
| echo "Total DOIs = ${#doiHashMap[@]}" | |
| printf "%s\n" "${!doiHashMap[@]}" |
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