Changes between Version 15 and Version 16 of Ticket #525, comment 10


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Timestamp:
Mar 11, 2016, 4:43:09 PM (9 years ago)
Author:
olle

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  • Ticket #525, comment 10

    v15 v16  
    44 * The INCA import wizard should perform an initial check of each INCA data file, after which the results are presented to the user:[[BR]][[BR]]a. If critical problems are encountered, import should be blocked.[[BR]]b. If problems with individual headers/data lines are encountered, the corresponding data columns/lines might be skipped during import; it is then the user's decision whether to fix the problems in the data file, or proceed with import of the eligible data.[[BR]]c. Basic results from the file check should be presented in the web form. In addition, it should be possible to open/download a text file with more detailed information from the file check by clicking on a button. The file should include the information presented in the web form, but also optional information on what headers or data lines problems were found with.[[BR]]d. In the report file, due to the sensitive type of information in the INCA data file, temporary patient ID values should be used instead of personal numbers to identify entries in the INCA file.
    55
    6  * The INCA data file check should include three parts:
     6 * The INCA data file check should include four parts:
    77
    88|| '''Check (Information)''' || '''Comment''' ||
    … …  
    1313|| Number of lines with too many columns || None accepted ||
    1414|| Number of lines with too few columns || None accepted ||
    15 || '''B: Internal data check''' || ||
     15|| '''B. Internal data check''' || ||
    1616|| Number of duplicate header columns || None accepted ||
    1717|| Temporary patient ID column index || Column required ||
    … …  
    2525|| Number of data lines with personal no. not in database || Data lines skipped at import ||
    2626|| Number of patient lateralities without database reference || Data lines skipped at import ||
     27|| '''D. Database consistency check II''' || (All files together) ||
     28|| Number of missing INCA headers || INCA headers skipped at import ||
    2729
    2830 * INCA import annotation types:[[BR]][[BR]]a. All annotation types are coupled to `Case` items.[[BR]]b. Data in all columns in the two INCA example files except the temporary patient ID should be imported to annotations.[[BR]]c. The name of the annotation type corresponding to a data column should equal prefix "`INCA_`" plus the name of the header for the column.[[BR]]d. The value type of an annotation type should be one of `Type.DATE`, `Type.STRING`, `Type.INT`, `Type.BOOLEAN`, or `Type.FLOAT`, corresponding to the type of the corresponding column in the INCA data file, according to the description of the variables in the INCA database from 2014-01-01.[[BR]]e. INCA example file two contained two headers, "`BN20_Sida_Beskrivning`" and "`BP20_Sida_Beskrivning`", without the corresponding "value" headers, "`BN20_Sida_Värde`" and "`BP20_Sida_Värde`", respectively. In order to be able to check if some INCA data annotation types are missing in an import session, it was decided not to define annotation types for the latter two "`_Värde`" columns.[[BR]]f. Columns corresponding to list values in the INCA variable description, should be mapped to annotation types with value options set to the available values. However, except for the "`A030Sida_Beskrivning`" column used for laterality mapping, value options should only be set for integer "`_Värde`" columns, since the strings corresponding to these values in the INCA data files are not guaranteed to exactly match the descriptions strings in the INCA variable description.[[BR]]g. All INCA annotation types should belong to a new "INCA" annotation type category.[[BR]]h. Two extra annotation types, not coupled to columns in the INCA data file, should be added, one for the date that the INCA data was exported from the database, and one for the last date an INCA annotation was updated. These two annotation types should not have prefix "`INCA_`", since they do not correspond to INCA import file headers, and should be excluded, when checking if some INCA data annotation types are missing in an import session.[[BR]]i. At import, a data line in the INCA data file should be mapped to the `Case` item corresponding to a patient with the same personal number as in the line, and where the `Case` item has a laterality matching the laterality description in the line.[[BR]]j. An INCA annotation should only be updated if the value from the INCA data file at import differs from the current annotation value. However, annotations for the extra annotation types for the date that the INCA data was exported from the database, and the last date an INCA annotation was updated, should still be updated, to indicate that the INCA annotation values for the case item equals those of the latest INCA data file.