Changeset 351

Timestamp:

05/15/10 20:07:46 (21 months ago)

Author:

AlexanderPico

Message:

updated bacteria script and substituted use of tmp dir

Location:

trunk/dbbuilder/src/org/bridgedb/download

Files:

• bacteria_download.sh (modified) (5 diffs)
• ensembl_download.sh (modified) (1 diff)

trunk/dbbuilder/src/org/bridgedb/download/bacteria_download.sh

@@ +1 @@
+# Update "release-#" below
+
 ftp_site=ftp.ensemblgenomes.org
 species_list=${1?"Usage: $0 species_list"}
 
-mysql=mysql
-mysqlimport=mysqlimport
+mysql='mysql --host=mysql-dev.cgl.ucsf.edu --port=13308'
+mysqlimport='mysqlimport  --host=mysql-dev.cgl.ucsf.edu --port=13308'
 
 cat $species_list | while read species_name
@@ -15 +17 @@
  fi
 
-  export species_name="$species_name"; var=`echo "ls -l /pub/bacteria/release-1/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
+  export species_name="$species_name"; var=`echo "ls -l /pub/bacteria/release-4/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_core"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_db_name=$1
 
   # check variable before proceeding
@@ -29 +31 @@
 
   # get raw tables from ftp site
-  ncftpget ${ftp_site} ./${mysql_db_name} /pub/bacteria/release-1/mysql/${mysql_db_name}/*.txt.table.gz
-  for q in ./${mysql_db_name}/*.txt.table.gz
+  ncftpget ${ftp_site} ./${mysql_db_name} /pub/bacteria/release-4/mysql/${mysql_db_name}/*.txt.gz
+  for q in ./${mysql_db_name}/*.txt.gz
   do
     gunzip $q
   done
 
-  ncftpget ${ftp_site} ./ /pub/bacteria/release-1/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
+  ncftpget ${ftp_site} ./ /pub/bacteria/release-4/mysql/${mysql_db_name}/${mysql_db_name}.sql.gz
   gunzip ./${mysql_db_name}.sql.gz
 
@@ -42 +44 @@
 
   #create local mysql db
-  echo "create database if not exists ${mysql_db_name_local}" | ${mysql} -u genmapp -pfun4genmapp
+  echo "create database if not exists genmapp_${mysql_db_name_local}" | ${mysql} -u genmapp -pfun4genmapp
   #create schema
-  ${mysql} -u genmapp -pfun4genmapp ${mysql_db_name_local} < ./${mysql_db_name}.sql
+  ${mysql} -u genmapp -pfun4genmapp genmapp_${mysql_db_name_local} < ./${mysql_db_name}.sql
    # place in own scope, due to "cd" command
   (
-    cd ./${mysql_db_name}; for table_name in *.txt.table
+    cd ./${mysql_db_name}; for table_name in *.txt
     do
-      #import data
-      cp $table_name /tmp/
-
-      ${mysqlimport} -u genmapp -pfun4genmapp ${mysql_db_name_local} /tmp/${table_name}
-
-      rm /tmp/${table_name}
+      ${mysqlimport} -u genmapp -pfun4genmapp genmapp_${mysql_db_name_local} `pwd`/${table_name}
     done
   )
@@ -60 +57 @@
   # zip, archive and clean up
   gzip ./${mysql_db_name}.sql
-  tar cvzf ./${mysql_db_name}.txt.table.tgz ./${mysql_db_name}/*
+  tar cvzf ./${mysql_db_name}.txt.tgz ./${mysql_db_name}/*
   rm -R ./${mysql_db_name}/
 

trunk/dbbuilder/src/org/bridgedb/download/ensembl_download.sh

@@ -44 +44 @@
    cd ./${mysql_go_name}; for table_name in *.txt
    do
-    #import data
-    cp $table_name /tmp/
-    
-    ${mysqlimport} -u genmapp -pfun4genmapp genmapp_${mysql_go_name} /tmp/${table_name}
-    
-    rm /tmp/${table_name}
+    ${mysqlimport} -u genmapp -pfun4genmapp genmapp_${mysql_go_name} `pwd`/${table_name}
   done
  )