merge develop into vue

proteinevolution · Jan 3, 2019 · 70d51cc · 70d51cc
2 parents f2789d6 + 56aa40f
commit 70d51cc
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Showing 5 changed files with 111 additions and 73 deletions.
diff --git a/conf/application.conf b/conf/application.conf
@@ -14,7 +14,7 @@ akka {
       hostname = localhost        # external (logical) hostname
       port = 1234                 # external (logical) port
 
-      bind-hostname = 172.18.0.2  # internal (bind) hostname
+      bind-hostname = 174.18.0.2  # internal (bind) hostname
       bind-port = 1234            # internal (bind) port
     }
   }
@@ -44,23 +44,27 @@ play.http {
   }
 }
 
+
 # Actors
 play.modules {
   enabled += "modules.ActorModule"
   enabled += "play.modules.reactivemongo.ReactiveMongoModule"
 }
 
+
 # The application languages
 # ~~~~~
 play.i18n.langs = ["en"]
 
+
 # Play Framework cache name definitons
 # ~~~~~
 play.cache {
   createBoundCaches = false
   bindCaches = ["userCache", "wsActorCache", "resultCache"]
 }
 
+
 # Play Framework filters config
 # ~~~~~
 play.filters {
@@ -75,7 +79,6 @@ play.filters {
 
   # CORS Configuration
   cors {
-
     # The path prefixes to filter. TODO just allow "/api" and put all the api functionality behind it
     pathPrefixes = ["/"]
 
@@ -113,13 +116,15 @@ play.filters {
   }
 }
 
+
 # Play Framework assets configuration
 # ~~~~~
 play.assets {
   path = "/public"
   urlPrefix = "/assets"
 }
 
+
 # Mailer
 # ~~~~~
 # This configures the E-Mail server connection
@@ -140,17 +145,15 @@ play.application.loader = ToolkitAppLoader
 
 ####################################################################################
 
-base_path = "/ebio/abt1_share"
-base_path = ${?TK_BASE_PATH}
-
 # geoIP
-maxmind_db = ${base_path}"/toolkit_support1/data/GeoLite2-City.mmdb"
+maxmind_db = "/root/GeoLite2-City.mmdb"
 maxmind_db = ${?MAXMIND_DB}
 
-mongodb.uri = "mongodb://balata.eb.local:27017/tkplay_dev"
+# mongo address with auth for local docker
+mongodb.uri = "mongodb://root:rootPassXX@174.18.0.3:27017/tkplay_dev?authenticationDatabase=admin"
 mongodb.uri = ${?MONGODB_URI}
 
-modeller_key = "unset"
+modeller_key = ""
 modeller_key = ${?MODELLER_KEY}
 
 # scripts
@@ -160,14 +163,12 @@ server_scripts = ${?SCRIPT_URL}
 job_path = "development"
 job_path = ${?JOB_PATH}
 
-#DYNAMIC PROP KEY/VALUE PAIRS
-db_root = ${base_path}"/toolkit_sync/databases"
-standard_db = ${db_root}"/standard"
+db_root = "/root/Toolkit/databases"
 
-bioprogs_root = ${base_path}"/toolkit_support1/code"
+bioprogs_root = "/root/Toolkit/bioprogs"
 
-#Set the full path to this file in application-ext.conf
-#The SGE nodes will need the full path to source this file.
+# Set the full path to this file in application-ext.conf
+# The SGE nodes will need the full path to source this file.
 environment = "tel/env/environment.sh"
 
 helper_scripts = ${bioprogs_root}"/bioprogs/helpers"
@@ -178,9 +179,17 @@ perl_lib = ${bioprogs_root}"/bioprogs/lib"
 # However, qstat-related functions (e.g. cluster load calculation) will not work in this mode.
 submit_mode=sge
 
-#Accessible SGE nodes for execution of jobs
-#e.g. "'node502|node503|node504'"
+# Accessible SGE nodes for execution of jobs
+# e.g. "'node502|node503|node504'"
 sge_nodes = "'*'"
 
+# what to override in application-ext.conf
+# play.http.secret.key = ""
+# play.mailer.host = localhost
+# play.mailer.user = ""
+# play.mailer.password = ""
+# modeller_key = ""
+# mongodb.uri = ""
+
 # include extending file with secrets
-include "application-ext"
+include "application-ext"
diff --git a/conf/ehcache.xml b/conf/ehcache.xml
@@ -1,57 +1,48 @@
 <!--
   ~ Copyright (C) 2009-2017 Lightbend Inc. <https://www.lightbend.com>
   -->
-<ehcache xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ehcache.xsd" updateCheck="false">
-
-<sizeOfPolicy maxDepth="10000000" maxDepthExceededBehavior="abort" />
+<ehcache xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ehcache.xsd"
+         updateCheck="false">
 
+    <sizeOfPolicy maxDepth="10000000" maxDepthExceededBehavior="abort"/>
 
     <cache name="userCache"
-            maxBytesLocalHeap="512M"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            maxElementsOnDisk="10000000"
-            diskPersistent="false"
-            diskExpiryThreadIntervalSeconds="120"
-            memoryStoreEvictionPolicy="LRU"
-    />
+           maxBytesLocalHeap="256M"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
 
     <cache name="wsActorCache"
-            maxElementsInMemory="10000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            maxElementsOnDisk="10000000"
-            diskPersistent="false"
-            diskExpiryThreadIntervalSeconds="120"
-            memoryStoreEvictionPolicy="LRU"
-    />
+           maxElementsInMemory="10000"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
 
     <cache name="resultCache"
-            maxBytesLocalHeap="1g"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            maxElementsOnDisk="10000000"
-            diskPersistent="false"
-            diskExpiryThreadIntervalSeconds="120"
-            memoryStoreEvictionPolicy="LRU"
-    />
+           maxBytesLocalHeap="512M"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
 
     <defaultCache
-            maxBytesLocalHeap="1g"
-            eternal="false"
             timeToIdleSeconds="120"
             timeToLiveSeconds="120"
             overflowToDisk="false"
             maxElementsOnDisk="10000000"
             diskPersistent="false"
             diskExpiryThreadIntervalSeconds="120"
-            memoryStoreEvictionPolicy="LRU"
-    />
+            memoryStoreEvictionPolicy="LRU"/>
 </ehcache>
 
diff --git a/conf/ehcache.xml.template b/conf/ehcache.xml.template
@@ -0,0 +1,48 @@
+<!--
+  ~ Copyright (C) 2009-2017 Lightbend Inc. <https://www.lightbend.com>
+  -->
+<ehcache xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ehcache.xsd"
+         updateCheck="false">
+
+    <sizeOfPolicy maxDepth="10000000" maxDepthExceededBehavior="abort"/>
+
+    <cache name="userCache"
+           maxBytesLocalHeap="256M"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
+
+    <cache name="wsActorCache"
+           maxElementsInMemory="10000"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
+
+    <cache name="resultCache"
+           maxBytesLocalHeap="512M"
+           timeToIdleSeconds="120"
+           timeToLiveSeconds="120"
+           overflowToDisk="false"
+           maxElementsOnDisk="10000000"
+           diskPersistent="false"
+           diskExpiryThreadIntervalSeconds="120"
+           memoryStoreEvictionPolicy="LRU"/>
+
+    <defaultCache
+            timeToIdleSeconds="120"
+            timeToLiveSeconds="120"
+            overflowToDisk="false"
+            maxElementsOnDisk="10000000"
+            diskPersistent="false"
+            diskExpiryThreadIntervalSeconds="120"
+            memoryStoreEvictionPolicy="LRU"/>
+</ehcache>
+
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -28,10 +28,10 @@ services:
     image: mongo:4.0
     container_name: tk-mongodb
     environment:
-      - MONGO_DATA_DIR=/data/db
-      - MONGO_LOG_DIR=/data/log
-      - MONGO_INITDB_ROOT_USERNAME=root
-      - MONGO_INITDB_ROOT_PASSWORD=rootPassXX
+    - MONGO_DATA_DIR=/data/db
+    - MONGO_LOG_DIR=/data/log
+    - MONGO_INITDB_ROOT_USERNAME=root
+    - MONGO_INITDB_ROOT_PASSWORD=rootPassXX
     volumes:
       - mongodb:/data/db
     ports:

diff --git a/tel/env/environment.sh b/tel/env/environment.sh
@@ -1,22 +1,14 @@
 #!/bin/bash
-#Databases
-
-export TK_ROOT="${BIOPROGSROOT}"
-export BIOPROGS="${TK_ROOT}/bioprogs"
-export STANDARD="${DATABASES}/standard"
-
+export BIOPROGS="${BIOPROGSROOT}/bioprogs"
 #HHomp database
 export HHOMPDBPATH="${DATABASES}/hhomp/db"
-
 #JAVA
 ##########################################################
 export JAVA_HOME="${BIOPROGS}/dependencies/jdk1.8.0"
 export JRE_HOME="${BIOPROGS}/dependencies/jdk1.8.0/jre"
-
 #PERL
 ##########################################################
 export PERL5LIB="${BIOPROGS}/lib"
-
 #COILS/PCOILS
 export COILSDIR="${BIOPROGS}/pcoils"
 #ALI2D
@@ -48,7 +40,7 @@ export PIPRED="${BIOPROGS}/tools/pipred"
 #DeepCoil
 export DEEPCOIL="${BIOPROGS}/tools/deepcoil"
 #Setup HHrepid
-export HHREPIDPATH="${BIOPROGS}/tools/hhrepid" 
+export HHREPIDPATH="${BIOPROGS}/tools/hhrepid"
 #Setup HMMER
 export HMMERPATH="${BIOPROGS}/tools/hmmer/bin"
 export HMMERBINARIES="${BIOPROGS}/tools/hmmer/binaries"
@@ -64,7 +56,6 @@ export PYTHONPATH="${BIOPROGS}/tools/modeller/modlib/:${BIOPROGS}/dependencies/p
 export PHYLIPBIN="${BIOPROGS}/tools/phylip/current/bin64"
 #Reformat version with PHYLIP Support (new reformat.pl does not have this support)
 export REFORMAT_PHYLIP="${BIOPROGS}/helpers/reformat_protblast.pl"
-
 #HHLIB
 #Rye and its nodes have slightly different architectures.
 #hh-suite needs to be compiled separately on them
@@ -77,9 +68,8 @@ else
         export PATH="${BIOPROGS}/tools/hh-suite-build/scripts:${PATH}" #HHSCRIPTS
         export PATH="${BIOPROGS}/tools/hh-suite-build/bin:${PATH}" #HHBINS
 fi
-
 #PATH variable
-export PATH="${BIORPOGS}/dependencies/anaconda3/bin:${PATH}"
+export PATH="${BIOPROGS}/dependencies/anaconda3/bin:${PATH}"
 export PATH="${BIOPROGS}/dependencies/Python-3.5.2/bin:${PATH}" #Python binary
 export PATH="${BIOPROGS}/pcoils:${PATH}" #PCOILS
 export PATH="${BIOPROGS}/dependencies/hh-suite_misc_scripts:${PATH}" # helper scripts from the old Toolkit
@@ -104,7 +94,7 @@ export PATH="${BIOPROGS}/tools/aln2plot:${PATH}"
 export PATH="${BIOPROGS}/tools/phylip:${PATH}" #PHYLIP
 export PATH="${BIOPROGS}/tools/marcoil:${PATH}" #MARCOIL
 export PATH="${BIOPROGS}/tools/modeller/bin:${PATH}" #MODELLER
-export PATH="${BIOPROGS}/dependencies/Python-3.5.2/bin:${PATH}" 
+export PATH="${BIOPROGS}/dependencies/Python-3.5.2/bin:${PATH}"
 export PATH="${BIOPROGS}/tools/hmmer/binaries:${PATH}" #HMMER
 export PATH="${BIOPROGS}/tools/retrieveseq:${PATH}" #RetrieveSeq
 export PATH="${BIOPROGS}/tools/seq2id:${PATH}" #Seq2ID
@@ -120,4 +110,4 @@ export PATH="${BIOPROGS}/tools/Phobius/PolyPhobius:${PATH}" #POLYPHOBIUS
 export PATH="${BIOPROGS}/tools/iupred:${PATH}" #IUPRED
 export PATH="${BIOPROGS}/tools/signalp-4.1:${PATH}" #SIGNALP
 export PATH="${BIOPROGS}/tools/blast-2.2.26/bin:${PATH}" #LEGACY BLAST
-export PATH="${BIOPROGS}/tools/DISOPRED:${PATH}" #DISOPRED
+export PATH="${BIOPROGS}/tools/DISOPRED:${PATH}" #DISOPRED