e0eafd3f09d381d9f2ccd04beada00f54c44b115
max
  Thu Jun 20 04:18:03 2024 -0700
make otto job quiet, no redmine

diff --git src/hg/utils/otto/malacards/update.sh src/hg/utils/otto/malacards/update.sh
index d48617e..8abcada 100755
--- src/hg/utils/otto/malacards/update.sh
+++ src/hg/utils/otto/malacards/update.sh
@@ -1,20 +1,20 @@
 #!/bin/bash
 # redmine 14417
 set -e -o pipefail
 now=`date -I`
 cd /hive/data/outside/otto/malacards
-wget https://genecardscustomers.blob.core.windows.net/ucsc/UCSC_DiseaseCentric_dump_MC_current.csv -O oldVersions/$now.csv
+wget -q https://genecardscustomers.blob.core.windows.net/ucsc/UCSC_DiseaseCentric_dump_MC_current.csv -O oldVersions/$now.csv
 # copied from ~/kent/src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh  
 # load malacards table
 hgsql hg38 -e 'drop table malacards; create table malacards (geneSymbol varchar(255), maladySymbol varchar(255), urlSuffix varchar(255), mainName varchar(255), geneScore float, diseaseScore float, isElite bool)'
 hgsql hg38 -e 'create index malacardsGeneIdx on malacards(geneSymbol);'
 s='"'; hgsql hg38  -e "delete from malacards; load data local infile ${s}oldVersions/$now.csv${s} into table malacards columns terminated by ',' enclosed by '$s' escaped by '' ignore 1 lines"
 # load knownToMalacards tables
 kent=~/kent
 for db in hg38 hg19; do 
         hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $db | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt
         hgsql -e "select geneSymbol from malacards" --skip-column-names $db | sort > malacardExists.txt
         join malacardExists.txt  geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2, $1}' > knownToMalacard.txt
         hgLoadSqlTab -notOnServer $db  knownToMalacards $kent/src/hg/lib/knownTo.sql  knownToMalacard.txt
 done
 echo Malacards update OK