Changes between Version 9 and Version 10 of i2b2 Mapped Importer


Ignore:
Timestamp:
10/03/13 16:41:41 (11 years ago)
Author:
Richard Bramley
Comment:

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  • i2b2 Mapped Importer

    v9 v10  
    9999* JSON
    100100
    101 == Mapping
     101== Entity Mapping
    102102
    103103Mappings are used to specify which field from the source gets used for which field in the output.  These are specified in a YAML file.  By default this file is called mapping.yaml in the application root directory, but the mapping file path can be defined using the {{{-m=xxx}}} or {{{--mappingFilePath=xxx}}} command line arguments.
    104104
    105 Mappings can be defined for:
     105Mappings can be defined for the following entites:
    106106
    107107* Patients, including mappings
    … …  
    109109* Observations
    110110
    111 Currently mappings are not available for other i2b2 types such as concepts and observers.
     111Currently mappings are not available for other i2b2 entities such as concepts and observers.
    112112
    113 === Observation Mappings
     113=== Data Fields
    114114
    115 ==== Data Fields
    116 The types available for observation mappings are:
     115The following data fields are available for mapping entities:
    117116
    118117* !BooleanTrueField
    … …  
    125124* !DataSourceTextField
    126125* !LiteralTextField
    127 
    128 ==== Date Fields
    129 Observation dates are defined as a list of dates that can be used if they are defined.  If the first field in the list is not defined, then next one on the list will be tried and so on.
    130 
    131 The types of date field available are:
    132 
    133126* !DataSourceDateField
    134127* !YearOnlyDateField
    135128
     129===== Observation Fields
     130
     131These fields can be used to create a observations. An observation will only be create if a non-NULL value is returned.
     132
     133Some observation fields create an observation with a text value, others a numeric value, and others an enumeration value (actually just a text value).  Other observations create an observation without a value of any kind.  These are called ''Existence'' fields.
     134
     135===== Date Fields
     136
     137Most dates in entities are defined as a list of date fields instead of a single date field.  If the first date in the list does not yield a date, the next date field in the list is checked and so on.  Only if all dates are undefined will the date be set to NULL.  In some cases this will cause an error.
     138
     139===== Datasource Fields
     140
     141These fields take their data from the patient row (etc) from the data source.  The {{{source}}} attributes of these fields define how the value is located.
     142
     143===== Literal Fields
     144
     145These fields take their values from the mapping definition itself.  In these fields the value is either defined by the {{{source}}} attribute or by the field type itself.
     146
     147==== The Fields
     148
     149===== !BooleanTrueField
     150
     151Always set the value to true.
     152
     153====== Mapping
     154
     155* {{{type}}}: {{{uk.org.briccs.onyxmappedexport2pdo.fields.!BooleanTrueField}}}
     156
     157=== !DataSourceConditionalExistenceField
     158
     159''' A N D   T H E   R E S T'''
     160
     161=== Patient Entity
     162
     163=== Observation Entity
     164
     165=== Event / Visit Entity
     166
     167
    136168== Extensions
    137