#1005 closed task (fixed)

External data filtering and mapping wizard

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

Description (last modified by Nicklas Nordborg)

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 22 months ago by Nicklas Nordborg

Description: modified (diff)
Summary: External data filtering wizardExternal data filtering and mapping wizard

comment:2 Changed 22 months ago by Nicklas Nordborg

(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 22 months ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.13

comment:4 Changed 22 months ago by Nicklas Nordborg

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

Cleaning up the progress reporter when the export is done.

comment:5 Changed 22 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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