Changes between Initial Version and Version 1 of MolgenisFromExisting

Timestamp:

2009-08-22T23:25:27+02:00 (15 years ago)

Author:

Morris Swertz

Comment:

--

MolgenisFromExisting

@@ +1 @@
+= Generate a MOLGENIS from existing database =
+
+There is legacy of existing databases, which you may inherit or get your hands on via SQL dumps/TEXT downloads. Below we will first generate a MOLGENIS for an existing database by automatically extracting the MOLGENIS data model from it. Second you will learn how to batch-load existing data sets from delimited text files.
+
+== Generating a MOLGENIS for an existing database ==
+ 1. Edit the database connection settings in the `molgenis.properties` file to refer to an existing database. See !MolgenisPropertiesFile. In this example it is assumed you connect to the Address Book database from the !AddressBookExample. Alternatively you can download a database dump of your choice or connect to a remote database (assuming proper DatabasePermissions).
+ 1. Run !handwritten/java/!MolgenisExtractModel.java. The extraction tool will connect to your selected database and extract a model from its table structure. An example output for the Address Book Application[[BR]][[BR]]todo screenie[[BR]]
+ 1. Copy-paste the parts of XML you want to use in your *_db.xml file. Then add a suitable *_ui.xml. Then adapt the `molgenis.properties` file accordingly and generate,compile,run to view the results (as learned in the previous section).
+
+== Batch loading of data ==
+MOLGENIS also provides methods to quickly load large data sets from comma or tab separated data files, both in the MolgenisUserInterfaceas well as in the MolgenisJavaApi . This works if:
+
+ * The column headers match the entity `field `definitions as defined in !MolgenisDatabaseXml file(order      doesn’t matter)
+ * A special case are !XrefFields that either can use the      xref_field or the xref_label. For example in the case of AddressBookExample ‘contact_id’      and ‘contact_displayname’.
+
+For example: Load data for Contact. Within the MOLGENIS user interface for Contacts choose ‘File’ and then ‘Add in batch’.
+
+In the CSV data dialog paste the following comma seperated values:
+
+{{{
+displayname,lastname,firstname,mid_initials,birthday
+
+Prof.dr. R Bischoff,Bischoff,Rainer,,
+
+Dr. R Breitling,Breitling,Rainer,,
+
+Prof.dr. RC Jansen,Ritsert,Jansen,C,
+}}}
+Load data for Address. In the dialog for Example data for Address again choose ‘File’ and then ‘Add in batch’. Set the ‘address_type’ to ‘work’ as constant for all addresses to be loaded (otherwise you get an error!). Then paste in the CSV data dialog:
+
+{{{
+phone,contact_displayname
+
++31 (0)50 3633338,Prof.dr. R Bischoff
+
++31 (0)50-3638088,Dr. R Breitling
+
++31 (0)50-3638089,Prof.dr. RC Jansen
+}}}
+Notice the cross reference by ‘xref_label’ using ‘contact_displayname’!
+
+----
+[http://gbic.target.rug.nl/#_ftnref1 "[1]"] These example data was copied from http://www.nbic.nl/nbic/network/?city=Groningen