Merge pull request #91 from galaxy-genome-annotation/gnb_sleep

genenotebook: give a few more seconds to startup

tools/genenotebook/launch_gnb.sh

@@ -2,17 +2,26 @@
 
 set -e
 
-mongod --dbpath ./mongo_db/ --unixSocketPrefix `pwd` --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid &
+echo "Running mongod: "
+mongod --dbpath ./mongo_db/ --unixSocketPrefix "$(pwd)" --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid &
 
-sleep 8
+echo "Waiting while mongod starts up"
+
+tries=0
 
 # "Listening on" is for mongodb 5x
-if ! grep -q "Listening on" ./mongod.log; then
-  echo "Failed to launch MongoDB:" 1>&2;
-  cat ./mongod.log 1>&2;
-  kill $GNB_PID;
-  exit 1;
-fi;
+while ! grep -q "Listening on" ./mongod.log; do
+
+  tries=$((tries + 1))
+
+  if [ "$tries" -ge 30 ]; then
+    echo "Failed to launch MongoDB:" 1>&2;
+    cat ./mongod.log 1>&2;
+    exit 1;
+  fi
+
+  sleep 3
+done;
 
 TMP_STORAGE=$(pwd)/tmp_storage
 mkdir "$TMP_STORAGE"
@@ -23,11 +32,18 @@ genoboo run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb
 
 export GNB_PID=$!
 
-sleep 15
+tries_gnb=0
+
+while ! grep -q "GeneNoteBook server started, serving" ./gnb.log; do
+
+  tries_gnb=$((tries_gnb + 1))
+
+  if [ "$tries_gnb" -ge 30 ]; then
+    echo "Failed to launch GeneNoteBook:" 1>&2;
+    cat ./gnb.log 1>&2;
+    kill $GNB_PID $(<"./mongo.pid");
+    exit 1;
+  fi
 
-if ! grep -q "GeneNoteBook server started, serving" ./gnb.log; then
-  echo "Failed to launch GeneNoteBook:" 1>&2;
-  cat ./gnb.log 1>&2;
-  kill $GNB_PID $(<"./mongo.pid");
-  exit 1;
-fi;
+  sleep 3
+done;

tools/genenotebook/macros.xml

@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@TOOL_VERSION@">0.4.9</token>
+    <token name="@TOOL_VERSION@">0.4.12</token>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
 
     <xml name="citation">