Opened 4 weeks ago

Closed 3 weeks ago

#1005 closed task (fixed)

External data filtering and mapping wizard

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.13
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by nicklas)

The use case is that we have a text file with some kind of personal data. The file is line-based and the first column is the personal number. TAB is used as separator between columns but we don't have to care about this after the personal number.

For each line in the file, we find the patient record with the given personal number. For that patient we find all specimen items. For each of the specimen items, we output a new line as:

<patient-id>{tab}<case-id>{tab}<specimen-id>{tab}<rest-of-data>

The *-id values are the external IDs. Lines that have no matching patient record are skipped in the output.

The generated data file is intended to be further processed in Relax where lines that are not in a specific data release are filtered out. See #1006.

Change History (5)

comment:1 Changed 4 weeks ago by nicklas

  • Description modified (diff)
  • Summary changed from External data filtering wizard to External data filtering and mapping wizard

comment:2 Changed 3 weeks ago by nicklas

(In [4627]) References #1005: External data filtering and mapping wizard

Added a wizard called "Map external data to releases" to the "Personal information wizards" section. This section was also re-organized to make it more compact. The wizard requires that the logged in user is either a "PatientCurator" or "Administrator".

The "Map external data to releases" takes a single file as input. The file will be uploaded to the server and parsed assuming that it is a tab-separated text file with UTF-8 encoding.

The first line should be a header line and the first column should contain personal numbers as they are stored in BASE.

For each personal number the wizard will try to find a specimen that links to a patient with the given personal number. For each specimen that is found it will print out the external id for the patient, case and specimen followed by the rest of the line from the source file. If no specimen is found the line is skipped.

The resulting file is saved in a temporary location on the server and can be downloaded once the wizard has completed. The file is automatically deleted after 3 minutes.

comment:3 Changed 3 weeks ago by nicklas

  • Milestone changed from Reggie v4.x to Reggie v4.13

comment:4 Changed 3 weeks ago by nicklas

(In [4633]) References #1005: External data filtering and mapping wizard

Cleaning up the progress reporter when the export is done.

comment:5 Changed 3 weeks ago by nicklas

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