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    Unable to access OpenSpecimen (First contact, Fresh Install, Tomcat issue)

    Technical Questions
    #1

    Hi everyone. I am new in this community. making my first experience with OpenSpecimen.

    I have build and deployed the current OpenSpecimen version from source according to the instructions on https://openspecimen.atlassian.net/wiki/pages/viewpage.action?pageId=1115955 (the compilation and deployment of the openspecimen was successfull)

    The ploblems appear when I restart de apache tomcat.

    1. The error messages:

    1.1) Oracle Driver:

    English translation:

    05-Jul-2017 11: 23: 35.120 GRAVE [main] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to class listener instance [org.springframework.web.context.ContextLoaderListener]
    Org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘de-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; Nested exception is liquibase.exception.DatabaseException: java.sql.SQLException: Can not load JDBC driver class ‘oracle.jdbc.Driver.OracleDriver’

    Original message:
    05-Jul-2017 11:23:35.120 GRAVE [main] org.apache.catalina.core.StandardContext.listenerStart Excepción enviando evento inicializado de contexto a instancia de escuchador de clase [org.springframework.web.context.ContextLoaderListener]
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘de-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.DatabaseException: java.sql.SQLException: Cannot load JDBC driver class ‘oracle.jdbc.Driver.OracleDriver’

    1.2) English translation:
    At least one JAR, which has been scanned for TLDs, did not yet contain TLDs. Enable debugging history for this historian for a complete list of JARs that were scanned and found to be TLDs.

    Original message:
    05-Jul-2017 11:23:32.839 INFORMACIÓN [main] org.apache.jasper.servlet.TldScanner.scanJars Al menos un JAR, que se ha explorado buscando TLDs, aún no contenía TLDs. Activar historial de depuración para este historiador para una completa lista de los JARs que fueron explorados y de los que nos se halló TLDs. Saltarse JARs no necesarios durante la exploración puede dar lugar a una mejora de tiempo significativa en el arranque y compilación de JSP .
    05-Jul-2017 11:23:35.120 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
    05-Jul-2017 11:23:35.120 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal Falló en arranque del Contexto [/openspecimen] debido a errores previos
    05-Jul-2017 11:23:35.136 ADVERTENCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [openspecimen] appears to have started a thread named [FileWatchdog] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
    java.lang.Thread.sleep(Native Method)
    org.apache.log4j.helpers.FileWatchdog.run(FileWatchdog.java:104)

    Full detail in files:

    catalina.log catalina.2017-07-05.log (35.8 KB)

    localhost.log localhost.2017-07-05.log (15.2 KB)

    1. The emvironment (basics):
      O.S: Microsoft Windows 10 Pro
      O. S: Version: 10.0.10586 N/D Compilation 10586
      O.S. type compilation: Multiprocessor Free
      Hardware RAM) 8.103 MB

    environment datailed: log.ambiente.txt (4.9 KB)
    3) openspecimen configuration:

    context.xml context.xml (1.7 KB)

    Notes:

    1. my user and my_password have the correct values!! I changed it to upload the file
    2. I try whith “oracle.jdbc.Driver.OracleDriver” and “oracle.jdbc.OracleDriver”
    1. my doubts

    4.1) I do not find where I should include in tomcat 9 the equivalent of the file module.xml that the jboss administrator of my company had to define when I installed the jar in the jboss 7.
    Here is he module:

    I think the problem is that I did not establish the relationship between the logical definition of the driver and the ojdbc6.jar file I want to use

    I believe I need to declare that relationship… I am totally wrong?

    4.2) Looking for the error messages in google found answers that indicated to define in the web.xml file the following:

    Oracle Datasource example jdbc / javausecasedb javax.sql.DataSource Container

    I didn’t fount the equivalent of this step in the instructions I followed of: “How to build from source code”

    This was acchieved in other place?

    Thank’s a lot and sorry by my questions.

    Really…many thanks for any help !!

    Gustavo de la Fuente
    Hospital Garrahan
    Buenos Aires - Argentina

    #2

    I apologize for the inconvenience my post may have had.

    I was able to solve the problems (I had several)

    1. the ojdbc6.jar was corrupt, after several attempts, download a new copy from Oracle and it was solved.

    2. Add the dependency and repository of jersey version 1 to the build.gradle file.

    3. run the gradle eclipse command in the directory where the zip was uncompressed instead of doing it in the eclipse worspace directory

    Thanks to all who read my post, and I leave the soculion written in case someone happens to something similar.