Merge pull request #55 from metabolomics-us/QA

FIEHNLAB-1783/Fix Null Pointer
metabolomics-us · May 31, 2022 · 643f923 · 643f923
2 parents f7992f2 + 4d4cc69
commit 643f923
Show file tree

Hide file tree

Showing 6 changed files with 138 additions and 39 deletions.
diff --git a/...omain/src/main/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/msp/MSPWriter.scala b/...omain/src/main/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/msp/MSPWriter.scala
@@ -96,28 +96,6 @@ class MSPWriter extends DomainWriter {
     }
   }
 
-  /**
-   * Writes InChI metadata string if one is present exists
-   *
-   * @param spectrum
-   * @param writer
-   */
-  def buildCompoundInChi(spectrum: Spectrum, writer: PrintWriter): Unit = {
-    val compound: Compound = spectrum.compound.find(_.kind == "biological").getOrElse(spectrum.compound.head)
-
-    if (compound != null) {
-      if(compound.inchi != null && compound.inchi.nonEmpty) {
-        writer.println(s"InChI: ${compound.inchi}")
-      }
-      else {
-        val metaData: Option[MetaData] = compound.metaData.find(_.name == "InChI")
-
-        if (metaData.isDefined) {
-          writer.println(s"InChI: ${metaData.get.value}")
-        }
-      }
-    }
-  }
   /**
     * Writes the comment string containing all available metadata in the format "name=value"
     *
@@ -185,7 +163,6 @@ class MSPWriter extends DomainWriter {
     // MetaData
     p.println(s"DB#: ${spectrum.id}")
     buildCompoundInchiKey(spectrum, p)
-    buildCompoundInChi(spectrum, p)
     buildMetaData(spectrum.metaData, "Precursor_type", "precursor type", p)
     buildMetaData(spectrum.metaData, "Spectrum_type", "ms level", p)
     buildMetaData(spectrum.metaData, "PrecursorMZ", "precursor m/z", p)

diff --git a/...omain/src/main/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/sdf/SDFWriter.scala b/...omain/src/main/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/sdf/SDFWriter.scala
@@ -94,13 +94,6 @@ class SDFWriter extends DomainWriter{
     }
   }
 
-  def buildCompoundInChI(compound: Compound, writer: PrintWriter): Unit = {
-    if (compound.inchi != null && compound.inchiKey.nonEmpty) {
-      printMetaData("INCHI", compound.inchi, writer)
-    } else {
-      buildMetaData(compound.metaData, "InChI", "INCHI", writer)
-    }
-  }
 
   /**
     * Writes the comment string containing all available metadata in the format "name=value"
@@ -165,7 +158,6 @@ class SDFWriter extends DomainWriter{
     buildMetaData(spectrum.metaData, "COLLISION ENERGY", "collision energy", p)
     buildMetaData(spectrum.metaData, "ION MODE", "ionization mode", p, x => x.charAt(0).toUpper.toString)
     buildCompoundInchiKey(compound, p)
-    buildCompoundInChI(compound, p)
     buildMetaData(compound.metaData, "FORMULA", "molecular formula", p)
     buildMetaData(compound.metaData, "EXACT MASS", "total exact mass", p)
     buildMetaData(compound.metaData, "MW", "total exact mass", p, x => (x.toDouble + 0.2).toInt.toString)

diff --git a/...n/src/test/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/sdf/SDFWriterTest.scala b/...n/src/test/scala/edu/ucdavis/fiehnlab/mona/backend/core/domain/io/sdf/SDFWriterTest.scala
@@ -52,10 +52,6 @@ class SDFWriterTest extends AnyWordSpec {
         assert(out.toString.contains(">  <INCHIKEY>\r\nQASFUMOKHFSJGL-LAFRSMQTSA-N"))
       }
 
-      "InChI" in {
-        assert(out.toString.contains(">  <INCHI>\r\nInChI=1S/C27H41NO2/c1-15-11-24-25(28-14-15)17(3)27(30-24)10-8-20-21-6-5-18-12-19(29)7-9-26(18,4)23(21)13-22(20)16(27)2/h5,15,17,19-21,23-25,28-29H,6-14H2,1-4H3/t15-,17+,19-,20-,21-,23-,24+,25-,26-,27-/m0/s1"))
-      }
-
       "molecular weight" in {
         assert(out.toString.contains(">  <MW>\r\n411"))
       }
@@ -124,10 +120,6 @@ class SDFWriterTest extends AnyWordSpec {
         assert(out.toString.contains(">  <INCHIKEY>\r\nQKLPUVXBJHRFQZ-UHFFFAOYSA-N"))
       }
 
-      "InChI" in {
-        assert(out.toString.contains(">  <INCHI>\r\nInChI=1S/C10H9ClN4O2S/c11-9-5-13-6-10(14-9)15-18(16,17)8-3-1-7(12)2-4-8/h1-6H,12H2,(H,14,15)"))
-      }
-
       "molecular formula" in {
         assert(out.toString.contains(">  <FORMULA>\r\nC10H9ClN4O2S"))
       }

diff --git a/backend/docker-compose-dev.yml b/backend/docker-compose-dev.yml
@@ -17,6 +17,9 @@ services:
     volumes:
       - mongo-data:/data/db
     command: --wiredTigerCacheSizeGB 10
+    logging:
+      options:
+        max-size: "100M"
 
   # Elasticsearch master and entrypoint
   elasticsearch_master:
@@ -25,17 +28,26 @@ services:
     ports:
       - "9200:9200"
       - "9300:9300"
+    logging:
+      options:
+        max-size: "100M"
 
   # Elasticsearch node, which may be scaled
   elasticsearch_node:
     image: elasticsearch:2.4
     command: [ elasticsearch, -Des.cluster.name=mona-cluster, -Dnetwork.host=0.0.0.0, -Des.index.query.bool.max_clause_count=10240 ]
+    logging:
+      options:
+        max-size: "100M"
 
   rabbitmq:
     image: rabbitmq:3.6-management
     ports:
       - "15672:15672"
       - "5672:5672"
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -56,6 +68,9 @@ services:
       - JAVA_OPTS='-Xmx4g -XX:+UseParallelGC'
       - GIT_USER=${GIT_USER}
       - GIT_PASS=${GIT_PASS}
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -68,6 +83,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx6g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Webhook support to notify external apis
   webhooks:
@@ -77,6 +95,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Scheduler for curation jobs
   curationScheduler:
@@ -86,6 +107,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Serves the content of MoNA as a repository
   repository:
@@ -97,6 +121,9 @@ services:
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
     volumes:
       - repository-data:/data
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -109,11 +136,17 @@ services:
     depends_on:
       - curationScheduler
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx6g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Main authentication service
   auth:
     image: public.ecr.aws/fiehnlab/mona-auth-server:test
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # MoNA similarity service
   similarity:
@@ -123,6 +156,9 @@ services:
     depends_on:
       - curationScheduler
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx8g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -139,6 +175,9 @@ services:
     environment:
       - VIRTUAL_HOST='mona.fiehnlab.ucdavis.edu'
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xss4m -Xmx4g -XX:+UseParallelGC -XX:+UseCompressedOops -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Download service for scheduling and running download jobs
   downloader:
@@ -150,10 +189,16 @@ services:
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx6g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
     volumes:
       - downloader-data:/data
+    logging:
+      options:
+        max-size: "100M"
 
   # Run scheduled curation tasks
   curationRunner:
     image: public.ecr.aws/fiehnlab/mona-curation-runner:test
     depends_on:
       - persistence
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
diff --git a/backend/docker-compose-prod.yml b/backend/docker-compose-prod.yml
@@ -17,6 +17,9 @@ services:
     volumes:
       - mongo-data:/data/db
     command: --wiredTigerCacheSizeGB 48
+    logging:
+      options:
+        max-size: "100M"
 
   # Elasticsearch master and entrypoint
   elasticsearch_master:
@@ -25,17 +28,26 @@ services:
     ports:
       - "9200:9200"
       - "9300:9300"
+    logging:
+      options:
+        max-size: "100M"
 
   # Elasticsearch node, which may be scaled
   elasticsearch_node:
     image: elasticsearch:2.4
     command: [ elasticsearch, -Des.cluster.name=mona-cluster, -Dnetwork.host=0.0.0.0, -Des.index.query.bool.max_clause_count=10240 ]
+    logging:
+      options:
+        max-size: "100M"
 
   rabbitmq:
     image: rabbitmq:3.6-management
     ports:
       - "15672:15672"
       - "5672:5672"
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -54,6 +66,9 @@ services:
       - ./nginx_v2/certs:/etc/letsencrypt
       - ./nginx_v2/config/mona.fiehnlab.ucdavis.edu.conf:/etc/nginx/conf.d/mona.fiehnlab.ucdavis.edu.conf
       - ./nginx_v2/config/massbank.us.conf:/etc/nginx/conf.d/massbank.us.conf
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -74,6 +89,9 @@ services:
       - JAVA_OPTS='-Xmx4g -XX:+UseParallelGC'
       - GIT_USER=${GIT_USER}
       - GIT_PASS=${GIT_PASS}
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -86,6 +104,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx6g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Webhook support to notify external apis
   webhooks:
@@ -95,6 +116,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Scheduler for curation jobs
   curationScheduler:
@@ -104,6 +128,9 @@ services:
     depends_on:
       - discovery
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Serves the content of MoNA as a repository
   repository:
@@ -115,6 +142,9 @@ services:
     entrypoint: bash -c "./wait-for-it.sh discovery:8761 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
     volumes:
       - repository-data:/data
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -127,13 +157,19 @@ services:
     depends_on:
       - curationScheduler
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx6g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Main authentication service
   auth:
     image: public.ecr.aws/fiehnlab/mona-auth-server:prod
     depends_on:
       - curationScheduler
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx4g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # MoNA similarity service
   similarity:
@@ -143,6 +179,9 @@ services:
     depends_on:
       - curationScheduler
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx8g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
 
   #
@@ -159,6 +198,9 @@ services:
     environment:
       - VIRTUAL_HOST='mona.fiehnlab.ucdavis.edu'
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xss4m -Xmx4g -XX:+UseParallelGC -XX:+UseCompressedOops -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"
 
   # Download service for scheduling and running download jobs
   downloader:
@@ -170,10 +212,16 @@ services:
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx8g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
     volumes:
       - downloader-data:/data
+    logging:
+      options:
+        max-size: "100M"
 
   # Run scheduled curation tasks
   curationRunner:
     image: public.ecr.aws/fiehnlab/mona-curation-runner:prod
     depends_on:
       - persistence
     entrypoint: bash -c "./wait-for-it.sh webhooks:4444 -t 3600 --strict -- java -Xmx8g -XX:+UseParallelGC -Dspring.cloud.config.uri=http://discovery:8761/config -Dspring.profiles.active=docker -jar *.jar"
+    logging:
+      options:
+        max-size: "100M"