inc/request_closest_sql

phylogeny/distTree_inc_init.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 THIS=`dirname $0`
 source $THIS/../bash_common.sh
-if [ $# -ne 12 ]; then
+if [ $# -ne 13 ]; then
   echo "Initialize an incremental distance tree directory"
   echo "#1: output directory"
   echo "#2: grid_min (> 0): min. number of dissimilarity requests to use GRID"
@@ -10,11 +10,12 @@ if [ $# -ne 12 ]; then
   echo "#5: dissim_boundary (> 0 or NAN)"
   echo "#6: genogroup_barrier (> 0 or NAN)"
   echo "#7: complete path to a 'phenotype' directory or ''"
-  echo "#8: large directories (0/1): 1 - files in #1/new/ and #7/ are grouped into subdirectories named file2hash(<file name>)"
-  echo "#9: SQL server name or ''"
-  echo "#10: database name on the SQL server or ''"
-  echo "#11: complete path to a directory for bulk insert into the database or ''"
-  echo "#12: path in Universal Naming Convention to the bulk directory #11 or ''"
+  echo "#8: large (0/1): 1 - files in #1/new/ and #7/ are grouped into subdirectories named file2hash(<file name>)"
+  echo "#9: request_closest_sql (0/1): 1 - request_closest.sh queries an SQL database and the number of concurrent connections is restricted to 30"
+  echo "#10: SQL server name or ''"
+  echo "#11: database name on the SQL server or ''"
+  echo "#12: complete path to a directory for bulk insert into the database or ''"
+  echo "#13: path in Universal Naming Convention to the bulk directory #11 or ''"
   exit 1
 fi
 INC=$1
@@ -23,12 +24,13 @@ VARIANCE="$3"
 HYBRIDNESS_MIN=$4
 DISSIM_BOUNDARY=$5
 GENOGROUP_BARRIER=$6
-PHEN=$7
+PHEN="$7"
 LARGE=$8
-SERVER=$9
-DATABASE=${10}
-BULK_LOCAL=${11}
-BULK_REMOTE=${12}
+REQUEST_CLOSEST_SQL=$9
+SERVER=${10}
+DATABASE=${11}
+BULK_LOCAL=${12}
+BULK_REMOTE=${13}
 
 
 if [ $GRID_MIN -le 0 ]; then
@@ -72,12 +74,14 @@ mkdir $INC/hist
 echo $GRID_MIN > $INC/grid_min
 touch $INC/runlog
 
-echo "$VARIANCE"        > $INC/variance
-echo $DISSIM_BOUNDARY   > $INC/dissim_boundary
-echo $GENOGROUP_BARRIER > $INC/genogroup_barrier
-echo $HYBRIDNESS_MIN    > $INC/hybridness_min
-echo $SERVER            > $INC/server
-echo $DATABASE          > $INC/database
+echo "$VARIANCE"          > $INC/variance
+echo $DISSIM_BOUNDARY     > $INC/dissim_boundary
+echo $GENOGROUP_BARRIER   > $INC/genogroup_barrier
+echo $HYBRIDNESS_MIN      > $INC/hybridness_min
+echo $LARGE               > $INC/large
+echo $REQUEST_CLOSEST_SQL > $INC/request_closest_sql
+echo $SERVER              > $INC/server
+echo $DATABASE            > $INC/database
 
 
 function create_script
@@ -114,7 +118,6 @@ if [ "$PHEN" ]; then
   ln -s $PHEN $INC/phen
 fi
 
-echo $LARGE > $INC/large
 if [ $LARGE == 1 ]; then
   $THIS/../trav 1000 -zero -start 0 "mkdir $INC/new/%n"
 fi

phylogeny/distTree_inc_init_stnd.sh

@@ -26,7 +26,8 @@ fi
 ( sqsh-ms  -S $SERVER  -D $DATABASE  -m bcp  -C "select @@version" > /dev/null ) || error "Database is not available"
 
 
-$THIS/distTree_inc_init.sh $INC 1 "" 0 NAN NAN "" 0 $SERVER $DATABASE $BULK_LOCAL $BULK_REMOTE
+$THIS/distTree_inc_init.sh $INC 1 "" 0 NAN NAN "" 0 0 $SERVER $DATABASE $BULK_LOCAL $BULK_REMOTE
+#                          1    2 3  4 5   6   7  8 9 10       11        12          13
 cp $FROM/* $INC/
 
 

phylogeny/distTree_inc_new.sh

@@ -18,6 +18,7 @@ GRID_MIN=`cat $INC/grid_min`
 QC=""  # -qc  
 RATE=0.015   # PAR
 VARIANCE=`cat $INC/variance`
+REQUEST_CLOSEST_SQL=`cat $INC/request_closest_sql`
 OBJS=`$THIS/tree2obj.sh $INC/tree | wc -l`
 ADD=`echo "$OBJS * $RATE" | bc -l | sed 's/\..*$//1'`  # PAR
 if [ $ADD == 0 ]; then
@@ -88,7 +89,11 @@ if [ $N -gt 0 ]; then
     $THIS/../trav  -step 1  $INC/search "$THIS/distTree_inc_search_init.sh $INC %f" 
   else
     $THIS/../grid_wait.sh 1
-    $THIS/../trav  -step 1  $INC/search "$QSUB_5,ul1=30  -N j%n  %Q$THIS/distTree_inc_search_init.sh $INC %f%Q > /dev/null" 
+    UL1=""
+    if [ $REQUEST_CLOSEST_SQL == 1 ]; then
+      UL1=",ul1=30"
+    fi
+    $THIS/../trav  -step 1  $INC/search "$QSUB_5$UL1  -N j%n  %Q$THIS/distTree_inc_search_init.sh $INC %f%Q > /dev/null" 
     $THIS/../qstat_wait.sh 2000 1
     ls $INC/search/*/request | cut -f 3 -d '/' > $INC/sought.list
       # Will break if "No such file or directory"

version.inc

@@ -1,6 +1,7 @@
 #define VERSION "1.2.3"
 
 
+// 1.3.1  12/18/2020  inc/phen_large --> inc/large; inc/request_closest_sql
 // 1.2.3  10/03/2020  makeDistTree does not stop on criterion increase of dissimilarity types > 1
 // 1.2.2  08/28/2020  distTree_new.cpp accepts a tree file as input
 // 1.2.1  08/20/2020  request2dissim.sh: 4 parameters