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    Trouble installing OS 2.2 Fresh install

    Technical Questions
    #1

    I am trying to install OpenSpecimen 2.2 on a brand new computer for testing purposes.

    1. I have installed Java JDK 1.8.51 and set the JAVA_HOME = C:\program files (x86)\Java\jdk1.8.0.51.
    2. I installed mySQL 5.6.26.0 and added C:\program files (x86)\mysql\mysql server 5.6\bin to the PATH variable.
    3. I also installed mySQL workbench 6.3.4.
    4. I created a database called catissueplus40 and granted the root user all rights to all database schemas.
    5. I downloaded OpenSpecimen-2.2.RC2-MySQL-Fresh.zip and unzipped it to the PC
    6. I created a folder called c:/OS_data for the adatadir parameter in the install.bat command
    7. I ran the install.bat command
      install.bat -dhost localhost -dport 3306 -dname catissueplus40 -duser root -dpass password -ahome “C:/OpenSpecimen” -ahost localhost -aport 8080 -adatadir “C:/os_data” 2>&1
    8. Then I ran the catalina.bat start command
    9. I then try to access the site from http://localhost:8080/openspecimen and I get an error: HTTP Status 404 The requested resource is not available.

    Any thoughts on what the issue might be. I have attached all the log files that had any content in them.

    localhost_access_log.2015-09-29.txt (87 Bytes)
    localhost.2015-09-29.log (6.7 KB)
    catalina.2015-09-29.log (7.4 KB)

    #2

    I’m getting the attached error when starting catalina. Could this be the issue?

    Error.JPG1172×579 249 KB

    #3

    You may want to grep your catalina log for something like the statement below. It might predate your error, especially if you haven’t dropped your db on a reinstall for testing. This applies to mysql installs only.

    SEVERE : liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/permissible-values.xml::Creating function for getting next PV Id::nmarwaha: Change Set db/2.0/permissible-values.xml::Creating function for getting next PV Id::nmarwaha failed.  Error: java.sql.SQLException: This function has none of DETERMINISTIC, NO SQL, or READS SQL DATA in its declaration and binary logging is enabled (you *might* want to use the less safe log_bin_trust_function_creators variable)
liquibase.exception.DatabaseException: java.sql.SQLException: This function has none of DETERMINISTIC, NO SQL, or READS SQL DATA in its declaration and binary logging is enabled (you *might* want to use the less safe log_bin_trust_function_creators variable)

    The error you posted looks like the db is truncated and it isn’t picking up data from the permissible values table from a statement in the permissible-values.xml. I ran in to this as well from a fresh install of OS 2.2. The bulk of the permissible-values statements that use functions will fail if you have binary logging turned on with mysql. (Which most do from default.) There are a few ways to fix this to get it to load and run the functions in the liquibase files.

    1. Not ideal: turn off bin logging.

    2. Not ideal: Set log_bin_trust_function_creators = 1 in the mysql.ini. (not ideal)

    3. More ideal: Modify the liquibase xml that loads the mysql functions for the permissible values to include:

      “READS SQL DATA
      NOT DETERMINISTIC”

    For testing if you allow/trust function creators it should reload your db correctly with mysql. I’m testing that now.

    Openspecimen team: the mysql functions at lines 22 and 65 of permissible-values.xml need to be modified to allow for mysql master/slave installs where bin logging is required and bin log trust settings need to be set to 0.

    https://github.com/krishagni/openspecimen/blob/OS_v20/WEB-INF/resources/db/2.0/permissible-values.xml#L22

    https://github.com/krishagni/openspecimen/blob/OS_v20/WEB-INF/resources/db/2.0/permissible-values.xml#L65

    See: http://stackoverflow.com/questions/26015160/deterministic-no-sql-or-reads-sql-data-in-its-declaration-and-binary-logging-i

    -Randy

    #4

    Hi @bmumph,

    We have updated the build under releases folder http://demo.openspecimen.org/releases/. Download latest OS-v2.2.RC2 build. You should not face this issue with the new build.

    ~Nitesh

    #5

    The new build fixed the issue.

    Thanks,

    #6

    Can someone point me to the complete OS 2.2 installation documentation? All I have seen is this:

    https://openspecimen.atlassian.net/wiki/display/CAT/Deployment+steps

    Thank you.

    #7

    That is the one. If you find something is missing or should change, feel free to let us know so that we can make it complete.

    ~Sri