OHDSI Home | Forums | Wiki | Github

Error in installing WebAPI


(Lake Park Xpa) #1

Hi i’m trying to install WebAPI and ATLAS for the first time.
When installing some error appeared when i execute
mvn clean package -s WebAPIConfig/settings.xml -P webapi-mssql
the following error occurs

2019-06-19 09:13:28.465 ERROR main org.ohdsi.webapi.db.migartion.V2_7_2_20190515164044__hideSensitiveInfo - - Error migrating file content
java.lang.RuntimeException: Resource not found: /db/migration/java/V2_7_2_20190515164044__hideSensitiveInfo/getSourceData.sql

Jun 19, 2019 9:14:58 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:14:58 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

2019-06-19 09:17:33.074 ERROR http-nio-auto-1-exec-5 org.ohdsi.webapi.estimation.EstimationController - - Failed to import Estimation, empty or not valid source JSON
Jun 19, 2019 9:17:40 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:17:40 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

Jun 19, 2019 9:19:16 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:19:16 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

Jun 19, 2019 9:20:15 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:20:15 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

2019-06-19 09:24:48.759 ERROR http-nio-auto-1-exec-2 org.ohdsi.webapi.prediction.PredictionController - - Failed to import Prediction, empty or not valid source JSON
Jun 19, 2019 9:25:10 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:25:10 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

2019-06-19 09:25:30.460 ERROR http-nio-auto-1-exec-4 org.ohdsi.webapi.service.CohortAnalysisService - - unable to get cohort summary
javax.ws.rs.NotFoundException: There is no cohort definition with id = 0.

2019-06-19 09:25:53.349 ERROR http-nio-auto-1-exec-10 org.ohdsi.webapi.service.SparqlService - - IO exception
2019-06-19 09:27:01.633 WARN http-nio-auto-1-exec-5 org.ohdsi.webapi.service.ConceptSetService - - Failed to delete ConceptSet with ID = 0, {}
org.springframework.dao.EmptyResultDataAccessException: No class org.ohdsi.webapi.conceptset.ConceptSet entity with id 0 exists!

Jun 19, 2019 9:27:02 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:27:02 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.transaction.UnexpectedRollbackException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.transaction.UnexpectedRollbackException[“mostSpecificCause”])

Jun 19, 2019 9:28:25 AM org.glassfish.jersey.server.ServerRuntime$Responder process
SEVERE: Error occurred when processing a response created from an already mapped exception.
Jun 19, 2019 9:28:25 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.ohdsi.webapi.JerseyConfig] in context with path [/WebAPI] threw exception [org.glassfish.jersey.server.internal.process.MappableException: com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])] with root cause
com.fasterxml.jackson.databind.JsonMappingException: Direct self-reference leading to cycle (through reference chain: org.springframework.messaging.support.ErrorMessage[“payload”]->org.springframework.dao.EmptyResultDataAccessException[“mostSpecificCause”])

some error looks repeating

Results :
Tests in error:
org.ohdsi.webapi.test.SecurityIT.testServiceSecurity(org.ohdsi.webapi.test.SecurityIT)

as the result at the bottom is the upper result

currently I’m using
ubuntu 18.04.02 lts
openjdk 1.8.0_212
apache maven : 3.6.0
apache tomcat : 9.0.21

would much appreciate your help!


(Alex Cumarav) #2

Is per error message you see failed test output

Results : Tests in error: org.ohdsi.webapi.test.SecurityIT.testServiceSecurity(org.ohdsi.webapi.test.SecurityIT)

So I suggest to build it skipping the tests, you can achieve that adding -DskipTests to your command line
e.g.:
mvn clean package -s WebAPIConfig/settings.xml -P webapi-mssql -DskipTests

Hope it can help


t