wiki:DespoinaLog/2010/04/21

Version 1 (modified by trac, 14 years ago) (diff)

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Installation Notes .

  • Got mysqldump from Mark.
    • * * * $ sudo ./mysqlimport5 -u molgenis -p a.sql > database_test
    • (permission denied!)
  • Fixing error in molgenis new distro (hvp_pilot ) missing molgenis jar files.
  • Just noticed that Molgenis has also common_collections jar file . Maybe conflict with peregrine there .
  • Lucene @ mac :
    • Fix classpath at .profile (Users ~ home directory) :
      • * export CLASSPATH=/Users/despoina/Documents/Lucene/lucene-3.0.1/lucene-core-3.0.1.jar:/Users/despoina/Documents/Lucene/lucene-3.0.1/lucene-demos-3.0.1.jar
    • In order to create an index for a directory ".../path/", run :
      • prompt $ java org.apache.lucene.demo.IndexFiles /...path/
      • Search the created index by :
      • Locate the database files and create an index on them :
        • Successfully build an index in a.sql dump file of Syndrome book data . Unfortunately when searching a term that exists more that once, only one reference is found ! -->
          • * Enter query:
          • acetylgalactosaminyltransferase
          • Searching for: acetylgalactosaminyltransferase
          • 1 total matching documents
          • 1. /Users/despoina/Documents/SyndromeBookDATA/a.sql
        • So maybe if they are on different tables, or on an xml file !
          • TODO : will try that on the tables of hvp_pilot :
            • TODO : fill some data
              • TODO increase gene_description size.
                • * changed * <field name="geneDescription" /> TO <field name="geneDescription" type="text" />
        • TODO : COmmit svn : (problem with javahl --> chflags -R nouchg .)
        • or ....http://kalanir.blogspot.com/2008/06/indexing-database-using-apache-lucene.html
  • MYSQL on mac : bins @ /opt/local/var/macports/software/mysql5/5.1.45_0/opt/local/bin
    • dbs @ /opt/local/var/db/mysql5 * *