Opened 3 months ago

Closed 3 months ago

Last modified 2 months ago

#969 closed enhancement (fixed)

Changes to Frozen tissue date import wizard

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.10
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by nicklas)

  • The import should work with the complete TAB-separated file. The first line is a header line with column names. The SCAN-B ID is found in the "ProvID" column. When converting the XLS file to text it should be saved with TAB as separator, UTF-8 as character encoding, and no text delimiter.
  • SCAN-B ID can appear in different forms that should be supported:
    • 1234567
    • 12-34567
    • 1234567C
    • 12-34567C
    • PAD value (=any other format)
  • The importer should check that consent is acceptable (=Yes or missing). It should not import anything to items with "No" or "Not asked". Entries with non-acceptable consent should be reported when the wizard has finished.
  • Duplicates should be reported when the wizard has finished.
  • Entries with no match in BASE should be reported when the wizard has finished.

Attachments (1)

xls2tsv.png (6.0 KB) - added by nicklas 3 months ago.

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Change History (8)

Changed 3 months ago by nicklas

comment:1 Changed 3 months ago by nicklas

  • Description modified (diff)

comment:2 Changed 3 months ago by nicklas

  • Milestone changed from Reggie v4.10 to Reggie v4.9.5
  • Status changed from new to assigned

comment:3 Changed 3 months ago by nicklas

(In [4510]) References #969: Changes to Frozen tissue date import wizard

The importer has now been updated and should support the requested features. The final report is presented as a table with warnings.

One particular issue was that it is not possible (due to limitations in BASE) to read annotations on items that are used with the AnnotationBatcher. Since we need to check the Consent annotation and set the FrozenTissueDate there is a clash. Using the regular API for updating the annotations turned out to be very slow. The final solution was to make a single query to load the id of all cases that has a consent annotation that is not 'Yes' and then check all cases against this list.

comment:4 Changed 3 months ago by nicklas

(In [4511]) References #969: Changes to Frozen tissue date import wizard

Added /home/SCANB/FrozenTissueFiles directory for storing the frozen tissue files.

comment:5 Changed 3 months ago by nicklas

  • Milestone changed from Reggie v4.9.5 to Reggie v4.10

Moving to Reggie 4.10 since it will be released soon.

comment:6 Changed 3 months ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed

comment:7 Changed 2 months ago by nicklas

(In [4523]) References #969: Changes to Frozen tissue date import wizard

Removed reference to non-existing script file.

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