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 :
      • * prompt: java org.apache.lucene.demo.SearchFiles?
    • 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 .)
        • This problem & solution : ​http://stackoverflow.com/questions/1765232/subclipse-cant-rename-file-os-x
        • Database changed .
        • Text input inserted .
        • Gene description field from table Gene transformed to Text . (in order to increase size).
      • 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 * *