Changes between Version 6 and Version 7 of MolgenisFromExisting


Ignore:
Timestamp:
2009-08-23T19:10:08+02:00 (15 years ago)
Author:
Morris Swertz
Comment:

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  • MolgenisFromExisting

    v6 v7  
    11Back to MolgenisGuide
    22
    3 = Generate a MOLGENIS from existing database =
     3= Extract MOLGENIS model from existing database =
    44There 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.
    55
    … …  
    1212 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).
    1313
    14 == Batch loading of data ==
    15 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:
    16 
    17  * The column headers match the entity `field `definitions as defined in !MolgenisDatabaseXml file(order      doesn’t matter)
    18  * 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’.
    19 
    20 For example: Load data for Contact. Within the MOLGENIS user interface for Contacts choose ‘File’ and then ‘Add in batch’.
    21 
    22 In the CSV data dialog paste the following comma seperated values:
    23 
    24 {{{
    25 displayname,lastname,firstname,mid_initials,birthday
    26 
    27 Prof.dr. R Bischoff,Bischoff,Rainer,,
    28 
    29 Dr. R Breitling,Breitling,Rainer,,
    30 
    31 Prof.dr. RC Jansen,Ritsert,Jansen,C,
    32 }}}
    33 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:
    34 
    35 {{{
    36 phone,contact_displayname
    37 
    38 +31 (0)50 3633338,Prof.dr. R Bischoff
    39 
    40 +31 (0)50-3638088,Dr. R Breitling
    41 
    42 +31 (0)50-3638089,Prof.dr. RC Jansen
    43 }}}
    44 Notice the cross reference by ‘xref_label’ using ‘contact_displayname’!
    45 
    46 ----
    47 [http://gbic.target.rug.nl/#_ftnref1 "[1]"] These example data was copied from http://www.nbic.nl/nbic/network/?city=Groningen