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java-jsi-clus-fr: update parent Docker image and update tests
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Lines changed: 103 additions & 35 deletions

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‎java-jsi-clus-fr/Dockerfile‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ COPY src/ /project/src
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RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
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&& mvn -Dmaven.test.skip=true package site
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FROM hbpmip/java-jsi-clus:latest
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FROM hbpmip/java-jsi-clus:0.4.5
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MAINTAINER martin.breskvar@ijs.si
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‎java-jsi-clus-fr/tests/docker-compose.yml‎

Lines changed: 83 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ services:
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- db
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woken_db_setup:
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image: "hbpmip/woken-db-setup:latest"
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image: "hbpmip/woken-db-setup:1.2.1"
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container_name: "woken-db-setup"
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restart: "no"
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environment:
@@ -63,46 +63,97 @@ services:
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clus_fr_regression_st:
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image: "hbpmip/java-jsi-clus-fr:latest"
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container_name: "clus-fr-regression-st"
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restart: "no"
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environment:
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NODE: job_test
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JOB_ID: 1
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IN_JDBC_DRIVER: org.postgresql.Driver
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IN_JDBC_URL: jdbc:postgresql://db:5432/features
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IN_JDBC_USER: features
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IN_JDBC_PASSWORD: featurespwd
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OUT_JDBC_DRIVER: org.postgresql.Driver
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IN_DBAPI_DRIVER: postgresql
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IN_USER: features
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IN_PASSWORD: featurespwd
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IN_HOST: db
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IN_PORT: 5432
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IN_DATABASE: features
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OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
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OUT_JDBC_USER: woken
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OUT_JDBC_PASSWORD: wokenpwd
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PARAM_variables: "score_test1"
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PARAM_covariables: "stress_before_test1,iq,cognitive_task2,practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2"
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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"
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FUNCTION: java-jsi-clus-fr
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OUT_DBAPI_DRIVER: postgresql
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OUT_USER: woken
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OUT_PASSWORD: wokenpwd
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OUT_HOST: db
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OUT_PORT: 5432
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OUT_DATABASE: woken
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PARAM_variables: "minimentalstate"
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PARAM_covariables: "subjectageyears,rightsogsuperioroccipitalgyrus"
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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)"
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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\"}}"
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MODEL_PARAM_size: 100
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links:
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- "db:db"
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clus_fr_regression_mt:
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image: "hbpmip/java-jsi-clus-fr:latest"
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container_name: "clus-fr-regression-mt"
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restart: "no"
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pfa_validator_regression_st:
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image: "hbpmip/pfa-validator:0.10.1-2"
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container_name: "pfa-validator"
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environment:
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NODE: job_test
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JOB_ID: 2
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IN_JDBC_DRIVER: org.postgresql.Driver
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IN_JDBC_URL: jdbc:postgresql://db:5432/features
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IN_JDBC_USER: features
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IN_JDBC_PASSWORD: featurespwd
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OUT_JDBC_DRIVER: org.postgresql.Driver
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OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
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OUT_JDBC_USER: woken
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OUT_JDBC_PASSWORD: wokenpwd
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PARAM_variables: "score_test1,stress_before_test1,iq,cognitive_task2"
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PARAM_covariables: "practice_task2,response_time_task2,college_math,score_math_course1,score_math_course2"
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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"
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FUNCTION: java-jsi-clus-fr
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MODEL_PARAM_size: 100
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INPUT_METHOD: POSTGRESQL
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JOB_ID: 1
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DB_HOST: db
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DB_PORT: 5432
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DB_NAME: woken
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DB_USER: woken
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DB_PASSWORD: wokenpwd
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DB_TABLE: job_result
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DB_COLUMN: data
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FEATURES_DB_HOST: db
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FEATURES_DB_PORT: 5432
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FEATURES_DB_NAME: features
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FEATURES_DB_USER: features
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FEATURES_DB_PASSWORD: featurespwd
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FEATURES_DB_TABLE: cde_features_a
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links:
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- "db:db"
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# clus_fr_regression_mt:
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# image: "hbpmip/java-jsi-clus-fr:latest"
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# restart: "no"
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# environment:
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# NODE: job_test
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# JOB_ID: 2
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# IN_JDBC_URL: jdbc:postgresql://db:5432/features
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# IN_DBAPI_DRIVER: postgresql
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# IN_USER: features
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# IN_PASSWORD: featurespwd
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# IN_HOST: db
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# IN_PORT: 5432
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# IN_DATABASE: features
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# OUT_JDBC_URL: jdbc:postgresql://db:5432/woken
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# OUT_DBAPI_DRIVER: postgresql
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# OUT_USER: woken
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# OUT_PASSWORD: wokenpwd
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# OUT_HOST: db
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# OUT_PORT: 5432
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# OUT_DATABASE: woken
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# PARAM_variables: "minimentalstate,subjectageyears"
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# PARAM_covariables: "rightsogsuperioroccipitalgyrus,leftsogsuperioroccipitalgyrus"
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# 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)"
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# 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\"}}"
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# MODEL_PARAM_size: 100
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#
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# pfa_validator_regression_mt:
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# image: "hbpmip/pfa-validator:0.10.1-2"
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# container_name: "pfa-validator"
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# environment:
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# INPUT_METHOD: POSTGRESQL
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# JOB_ID: 2
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# DB_HOST: db
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# DB_PORT: 5432
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# DB_NAME: woken
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# DB_USER: woken
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# DB_PASSWORD: wokenpwd
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# DB_TABLE: job_result
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# DB_COLUMN: data
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# FEATURES_DB_HOST: db
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# FEATURES_DB_PORT: 5432
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# FEATURES_DB_NAME: features
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# FEATURES_DB_USER: features
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# FEATURES_DB_PASSWORD: featurespwd
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# FEATURES_DB_TABLE: cde_features_a
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# links:
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# - "db:db"

‎java-jsi-clus-fr/tests/test.sh‎

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,15 @@ get_script_dir () {
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cd "$(get_script_dir)"
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cleanup=1
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for param in "$@"
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do
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if [ "--no-cleanup" == "$param" ]; then
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cleanup=0
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echo "INFO: --no-cleanup option detected !"
27+
fi
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done
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2130
if [[ $NO_SUDO || -n "$CIRCLECI" ]]; then
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DOCKER_COMPOSE="docker-compose"
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elif groups $USER | grep &>/dev/null '\bdocker\b'; then
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$DOCKER_COMPOSE rm -f > /dev/null 2> /dev/null | true
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exit $error_code
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}
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if [[ "$cleanup" == 1 ]]; then
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trap _cleanup EXIT INT TERM
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fi
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echo "Starting the databases..."
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$DOCKER_COMPOSE up -d --remove-orphans db
@@ -49,8 +61,13 @@ $DOCKER_COMPOSE run woken_db_setup
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echo
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echo "Run the CLUS feature ranking algorithm for single-target regression..."
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$DOCKER_COMPOSE run clus_fr_regression_st compute
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echo "Run the CLUS feature ranking algorithm for multi-target regression..."
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$DOCKER_COMPOSE run clus_fr_regression_mt compute
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# echo "Run the CLUS feature ranking algorithm for multi-target regression..."
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# $DOCKER_COMPOSE run clus_fr_regression_mt compute
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echo
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echo "Run PFA validator..."
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$DOCKER_COMPOSE run pfa_validator_regression_st
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# $DOCKER_COMPOSE run pfa_validator_regression_mt
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echo
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# Cleanup
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_cleanup

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