molgenis.properties

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# MOLGENIS configuration file                                 #
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# 1. FILES DESCRIBING YOUR DESIGN USING MOLGENIS XML LANGUAGE 
# can be multiple files ',' separated
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# xml file with data model in terms of 'entity' descriptions
model_database = molgenis_db.xml

# xml file with user screen descriptions in terms of 'form', 'menu',..
model_userinterface = molgenis_ui.xml

example_data_dir = data

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# 2. DATABASE SETTINGS
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#if jpa is used define database properties in META-INF/persistence.xml
#mapper_implementation = jpa

# MySQL:
# jdbc compatible connection parameters to a database (see doc of database supplier)
 db_driver = com.mysql.jdbc.Driver
 db_user = molgenis
 db_password = molgenis
 db_uri= jdbc:mysql://localhost/molgenis?innodb_autoinc_lock_mode=2

# PostgreSQL: experimental!
# jdbc compatible connection parameters to a database (see doc of database supplier)
# db_driver = org.postgresql.Driver
# db_user = molgenis
# db_password = molgenis
# db_uri = jdbc:postgresql://localhost/molgenis
# db_jndiname = jdbc/molgenisdb

# HypersonicSQL: embedded and filebased system, experimental!
# jdbc compatible connection parameters to a database (see doc of database supplier)
# db_driver = org.hsqldb.jdbcDriver
# db_user = sa
# no password needed 
# path needs to be fully qualliefied path
# db_uri = jdbc:hsqldb:file:c:/molgenis/molgenisdb;shutdown=true
 
#absolute path where attached files should be stored (if <field type="file" ...> is used)
db_filepath = attachedfiles

#jndi name, should be unique if you have multiple molgenises
db_jndiname = jdbc/molgenisdb

###############################################################
# 3. EMAIL settings if you want to email from within MOLGENIS plugins
# If you use smpts you may need to certify that you trust the server
# see http://blogs.sun.com/andreas/entry/no_more_unable_to_find
###############################################################

mail_smtp_from = noreply@molgenis.org
mail_smtp_protocol = smtps 
# protocol is either smtp or smtps
mail_smtp_hostname = smtp.gmail.com
mail_smtp_port = 465
mail_smtp_user = molgenis
mail_smtp_password = molgenispass 
 
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# 4. EXPERT OPTIONS (only change when you know what you are doing)
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# select components to be generated
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generate_data = true
generate_gui = true
generate_doc = true
generate_webservices = true 
generate_R = true

# Output options 
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# the directory where the source files are generated into
output_src = generated/java
# the directory where the sql create file are generated into
output_sql = generated/sql
# the directory where the documentation is generated into 
output_doc = WebContent/generated-doc
# the directory where the documentation is generated into 
output_web = WebContent
# the directory where handwritten plugins are stored
output_hand = handwritten/java

# advanced generator options
###############################################################

exclude_system = true

# use mysql optimized statements instead of prepared statements (mysql only)
mysql_multiquery = true

# mapping strategy of inheritance on database tables (subclass_per_tabel, class_per_table, hierarchy_per_table)
mapping_type = subclass_per_table

molgenis_servlet = app.servlet.MolgenisServlet

#auth_loginclass = plugin.login.SimpleLogin
#