java-jsi-clus-fire: update parent Docker image + update tests + show stack trace when entrypoint catches an exception with no error message

Author: mirco-nasuti

java-jsi-clus-fire/Dockerfile

@@ -10,7 +10,7 @@ COPY src/ /project/src
 RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
     && mvn -Dmaven.test.skip=true package site
 
-FROM hbpmip/java-jsi-clus:latest
+FROM hbpmip/java-jsi-clus:0.4.3
 
 MAINTAINER martin.breskvar@ijs.si
 

java-jsi-clus-fire/src/main/java/eu/humanbrainproject/mip/algorithms/jsi/clus/fire/Entrypoint.java

@@ -1,7 +1,5 @@
 package eu.humanbrainproject.mip.algorithms.jsi.clus.fire;
 
-import java.util.logging.Logger;
-
 import eu.humanbrainproject.mip.algorithms.jsi.Main;
 import eu.humanbrainproject.mip.algorithms.jsi.common.ClusMeta;
 import eu.humanbrainproject.mip.algorithms.jsi.common.InputData;
@@ -10,6 +8,8 @@
 import eu.humanbrainproject.mip.algorithms.jsi.serializers.pfa.ClusModelPFASerializer;
 import si.ijs.kt.clus.algo.rules.ClusRuleSet;
 
+import java.util.logging.Logger;
+
 /** @author Martin Breskvar */
 public final class Entrypoint {
   private static final Logger LOGGER = Logger.getLogger(Entrypoint.class.getName());
@@ -30,7 +30,13 @@ public static void main(String[] args) {
       entry.run();
 
     } catch (Exception e) {
-      LOGGER.severe(e.getMessage());
+      String errorMessage = e.getMessage();
+      if(errorMessage != null) {
+        LOGGER.severe(errorMessage);
+      }
+      else {
+        e.printStackTrace();
+      }
       System.exit(1);
     }
   }

java-jsi-clus-fire/tests/docker-compose.yml

@@ -48,7 +48,7 @@ services:
       - db
 
   woken_db_setup:
-    image: "hbpmip/woken-db-setup:latest"
+    image: "hbpmip/woken-db-setup:1.2.1"
     container_name: "woken-db-setup"
     restart: "no"
     environment:
@@ -63,55 +63,32 @@ services:
 
   clus_fire_regression_st:
     image: "hbpmip/java-jsi-clus-fire:latest"
-    container_name: "clus-fire-regression-st"
     restart: "no"
     environment:
       NODE: job_test
       JOB_ID: 1
-      IN_JDBC_DRIVER: org.postgresql.Driver
       IN_JDBC_URL: jdbc:postgresql://db:5432/features
-      IN_JDBC_USER: features
-      IN_JDBC_PASSWORD: featurespwd
-      OUT_JDBC_DRIVER: org.postgresql.Driver
+      IN_DBAPI_DRIVER: postgresql
+      IN_USER: features
+      IN_PASSWORD: featurespwd
+      IN_HOST: db
+      IN_PORT: 5432
+      IN_DATABASE: features
       OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
-      OUT_JDBC_USER: woken
-      OUT_JDBC_PASSWORD: wokenpwd
-      PARAM_variables: "score_test1"
-      PARAM_covariables: "stress_before_test1,iq,cognitive_task2,practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2"
-      PARAM_query: "SELECT stress_before_test1,score_test1,iq,cognitive_task2,practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2 FROM SAMPLE_DATA"
-      FUNCTION: java-jsi-clus-fire
-      MODEL_PARAM_size: 10
-      MODEL_PARAM_rules: 15
-    links:
-      - "db:db"
-
-  clus_fire_regression_mt:
-    image: "hbpmip/java-jsi-clus-fire:latest"
-    container_name: "clus-fire-regression-mt"
-    restart: "no"
-    environment:
-      NODE: job_test
-      JOB_ID: 2
-      IN_JDBC_DRIVER: org.postgresql.Driver
-      IN_JDBC_URL: jdbc:postgresql://db:5432/features
-      IN_JDBC_USER: features
-      IN_JDBC_PASSWORD: featurespwd
-      OUT_JDBC_DRIVER: org.postgresql.Driver
-      OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
-      OUT_JDBC_USER: woken
-      OUT_JDBC_PASSWORD: wokenpwd
-      PARAM_variables: "score_test1,stress_before_test1,iq,cognitive_task2"
-      PARAM_covariables: "practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2"
-      PARAM_query: "SELECT stress_before_test1,score_test1,iq,cognitive_task2,practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2 FROM SAMPLE_DATA"
-      FUNCTION: java-jsi-clus-fire
-      MODEL_PARAM_size: 15
-      MODEL_PARAM_rules: 15
-    links:
-      - "db:db"
+      OUT_DBAPI_DRIVER: postgresql
+      OUT_USER: woken
+      OUT_PASSWORD: wokenpwd
+      OUT_HOST: db
+      OUT_PORT: 5432
+      OUT_DATABASE: woken
+      PARAM_variables: "minimentalstate"
+      PARAM_covariables: "subjectageyears,rightsogsuperioroccipitalgyrus"
+      PARAM_query: "SELECT minimentalstate,subjectageyears,rightsogsuperioroccipitalgyrus FROM cde_features_a WHERE minimentalstate IS NOT NULL AND subjectageyears IS NOT NULL AND rightsogsuperioroccipitalgyrus IS NOT NULL AND dataset IN ('desd-synthdata') EXCEPT ALL (SELECT minimentalstate,subjectageyears,rightsogsuperioroccipitalgyrus FROM cde_features_a WHERE minimentalstate IS NOT NULL AND subjectageyears IS NOT NULL AND rightsogsuperioroccipitalgyrus IS NOT NULL AND dataset IN ('desd-synthdata') OFFSET 349 LIMIT 349)"
+      PARAM_meta: "{\"rightsogsuperioroccipitalgyrus\":{\"description\":\"\",\"methodology\":\"lren-nmm-volumes\",\"label\":\"Right superior occipital gyrus\",\"code\":\"rightsogsuperioroccipitalgyrus\",\"units\":\"cm3\",\"type\":\"real\"},\"subjectageyears\":{\"description\":\"Subject age in years.\",\"methodology\":\"mip-cde\",\"label\":\"Age Years\",\"minValue\":0,\"code\":\"subjectageyears\",\"units\":\"years\",\"length\":3,\"maxValue\":130.0,\"type\":\"integer\"},\"minimentalstate\":{\"description\":\"The Mini–Mental State Examination (MMSE) or Folstein test is a 30-point questionnaire that is used extensively in clinical and research settings to measure cognitive impairment. It is commonly used to screen for dementia.\",\"methodology\":\"mip-cde\",\"label\":\"MMSE - Mini Mental State Examination\",\"minValue\":0,\"code\":\"minimentalstate\",\"maxValue\":30.0,\"type\":\"integer\"}}"
 
   pfa_validator_regression_st:
-    image: "hbpmip/pfa-validator:latest"
-    container_name: "pfa-validator-regression-st"
+    image: "hbpmip/pfa-validator:0.10.1-2"
+    container_name: "pfa-validator"
     environment:
       INPUT_METHOD: POSTGRESQL
       JOB_ID: 1
@@ -127,28 +104,53 @@ services:
       FEATURES_DB_NAME: features
       FEATURES_DB_USER: features
       FEATURES_DB_PASSWORD: featurespwd
-      FEATURES_DB_TABLE: sample_data
+      FEATURES_DB_TABLE: cde_features_a
     links:
       - "db:db"
 
-  pfa_validator_regression_mt:
-    image: "hbpmip/pfa-validator:latest"
-    container_name: "pfa-validator-regression-mt"
-    environment:
-      INPUT_METHOD: POSTGRESQL
-      JOB_ID: 2
-      DB_HOST: db
-      DB_PORT: 5432
-      DB_NAME: woken
-      DB_USER: woken
-      DB_PASSWORD: wokenpwd
-      DB_TABLE: job_result
-      DB_COLUMN: data
-      FEATURES_DB_HOST: db
-      FEATURES_DB_PORT: 5432
-      FEATURES_DB_NAME: features
-      FEATURES_DB_USER: features
-      FEATURES_DB_PASSWORD: featurespwd
-      FEATURES_DB_TABLE: sample_data
-    links:
-      - "db:db"
+#   clus_fire_regression_mt:
+#     image: "hbpmip/java-jsi-clus-fire:latest"
+#     restart: "no"
+#     environment:
+#       NODE: job_test
+#       JOB_ID: 2
+#       IN_JDBC_URL: jdbc:postgresql://db:5432/features
+#       IN_DBAPI_DRIVER: postgresql
+#       IN_USER: features
+#       IN_PASSWORD: featurespwd
+#       IN_HOST: db
+#       IN_PORT: 5432
+#       IN_DATABASE: features
+#       OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
+#       OUT_DBAPI_DRIVER: postgresql
+#       OUT_USER: woken
+#       OUT_PASSWORD: wokenpwd
+#       OUT_HOST: db
+#       OUT_PORT: 5432
+#       OUT_DATABASE: woken
+#       PARAM_variables: "minimentalstate,subjectageyears"
+#       PARAM_covariables: "rightsogsuperioroccipitalgyrus,leftsogsuperioroccipitalgyrus"
+#       PARAM_query: "SELECT minimentalstate,subjectageyears,rightsogsuperioroccipitalgyrus,leftsogsuperioroccipitalgyrus FROM cde_features_a WHERE minimentalstate IS NOT NULL AND subjectageyears IS NOT NULL AND rightsogsuperioroccipitalgyrus IS NOT NULL AND leftsogsuperioroccipitalgyrus IS NOT NULL AND dataset IN ('desd-synthdata') EXCEPT ALL (SELECT minimentalstate,subjectageyears,rightsogsuperioroccipitalgyrus,leftsogsuperioroccipitalgyrus FROM cde_features_a WHERE minimentalstate IS NOT NULL AND subjectageyears IS NOT NULL AND rightsogsuperioroccipitalgyrus IS NOT NULL AND rightsogsuperioroccipitalgyrus IS NOT NULL AND dataset IN ('desd-synthdata') OFFSET 349 LIMIT 349)"
+#       PARAM_meta: "{\"leftsogsuperioroccipitalgyrus\":{\"description\":\"\",\"methodology\":\"lren-nmm-volumes\",\"label\":\"Left superior occipital gyrus\",\"code\":\"leftsogsuperioroccipitalgyrus\",\"units\":\"cm3\",\"type\":\"real\"},\"rightsogsuperioroccipitalgyrus\":{\"description\":\"\",\"methodology\":\"lren-nmm-volumes\",\"label\":\"Right superior occipital gyrus\",\"code\":\"rightsogsuperioroccipitalgyrus\",\"units\":\"cm3\",\"type\":\"real\"},\"subjectageyears\":{\"description\":\"Subject age in years.\",\"methodology\":\"mip-cde\",\"label\":\"Age Years\",\"minValue\":0,\"code\":\"subjectageyears\",\"units\":\"years\",\"length\":3,\"maxValue\":130.0,\"type\":\"integer\"},\"minimentalstate\":{\"description\":\"The Mini–Mental State Examination (MMSE) or Folstein test is a 30-point questionnaire that is used extensively in clinical and research settings to measure cognitive impairment. It is commonly used to screen for dementia.\",\"methodology\":\"mip-cde\",\"label\":\"MMSE - Mini Mental State Examination\",\"minValue\":0,\"code\":\"minimentalstate\",\"maxValue\":30.0,\"type\":\"integer\"}}"
+#
+#   pfa_validator_regression_mt:
+#     image: "hbpmip/pfa-validator:0.10.1-2"
+#     container_name: "pfa-validator"
+#     environment:
+#       INPUT_METHOD: POSTGRESQL
+#       JOB_ID: 2
+#       DB_HOST: db
+#       DB_PORT: 5432
+#       DB_NAME: woken
+#       DB_USER: woken
+#       DB_PASSWORD: wokenpwd
+#       DB_TABLE: job_result
+#       DB_COLUMN: data
+#       FEATURES_DB_HOST: db
+#       FEATURES_DB_PORT: 5432
+#       FEATURES_DB_NAME: features
+#       FEATURES_DB_USER: features
+#       FEATURES_DB_PASSWORD: featurespwd
+#       FEATURES_DB_TABLE: cde_features_a
+#     links:
+#       - "db:db"

java-jsi-clus-fire/tests/test.sh

@@ -18,6 +18,15 @@ get_script_dir () {
 
 cd "$(get_script_dir)"
 
+cleanup=1
+for param in "$@"
+do
+  if [ "--no-cleanup" == "$param" ]; then
+    cleanup=0
+    echo "INFO: --no-cleanup option detected !"
+  fi
+done
+
 if [[ $NO_SUDO || -n "$CIRCLECI" ]]; then
   DOCKER_COMPOSE="docker-compose"
 elif groups $USER | grep &>/dev/null '\bdocker\b'; then
@@ -34,7 +43,10 @@ function _cleanup() {
   $DOCKER_COMPOSE rm -f > /dev/null 2> /dev/null | true
   exit $error_code
 }
+
+if [[ "$cleanup" == 1 ]]; then
 trap _cleanup EXIT INT TERM
+fi
 
 echo "Starting the databases..."
 $DOCKER_COMPOSE up -d --remove-orphans db
@@ -49,13 +61,15 @@ $DOCKER_COMPOSE run woken_db_setup
 echo
 echo "Run the CLUS FIRE algorithm for single-target regression..."
 $DOCKER_COMPOSE run clus_fire_regression_st compute
-echo "Run the CLUS FIRE algorithm for multi-target regression..."
-$DOCKER_COMPOSE run clus_fire_regression_mt compute
+# echo "Run the CLUS FIRE algorithm for multi-target regression..."
+# $DOCKER_COMPOSE run clus_fire_regression_mt compute
 
 echo
 echo "Run PFA validator..."
 $DOCKER_COMPOSE run pfa_validator_regression_st
-$DOCKER_COMPOSE run pfa_validator_regression_mt
+# $DOCKER_COMPOSE run pfa_validator_regression_mt
 echo
 # Cleanup
+if [[ "$cleanup" == 1 ]]; then
 _cleanup
+fi