diff --git a/sdoi.sh b/sdoi.sh index 4fc15ab..37f3b48 100755 --- a/sdoi.sh +++ b/sdoi.sh @@ -26,25 +26,7 @@ doi=$1 fn=$2 set -e #exit if an error - -uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "[0-9]+" | sed -E "s|([0-9]+)|\1|") - -tmpBib=$(mktemp -p --suffix=.bib) - -if [ -z "$uid" ]; then - fetchBib_doiDotOrg -else - fetchBib_pubmed -fi - -if [ -s "$tmpBib" ]; then - import_bib -else - echo "sorry, doi not found.." - clean_up -fi - - +# set -v -x -e #debugging function import_bib { #decide whether to process and move an associated pdf or just exit @@ -111,3 +93,21 @@ function clean_up { exit 1 } + +uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "[0-9]+" | sed -E "s|([0-9]+)|\1|") + +tmpBib=$(mktemp -p ./ --suffix=.bib) + +if [ -z "$uid" ]; then + fetchBib_doiDotOrg +else + fetchBib_pubmed +fi + +if [ -s "$tmpBib" ]; then + import_bib +else + echo "sorry, doi not found.." + clean_up +fi + diff --git a/spubmed.sh b/spubmed.sh index 4d9cd20..2a68313 100755 --- a/spubmed.sh +++ b/spubmed.sh @@ -30,7 +30,8 @@ year=$3 set -e #exit if an error -uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$author[au]+AND+$journal[ta]+AND+$year[dp]&retmode=xml" | grep -E "[0-9]+" | sed -E "s#([0-9]+)#\1#") +#curl's option globoff needed for using brackets in a uri +uid=$(curl -s --globoff "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$author[au]+AND+$journal[ta]+AND+$year[dp]&retmode=xml" | grep -E "[0-9]+" | sed -E "s#([0-9]+)#\1#") if [ -z "$uid" ]; then echo "pubmed id not found"