Opened 2 months ago

Closed 3 weeks ago

#1234 closed task (fixed)

Implement batch importer for followup blood samples

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.27
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Handling of follow up blood has been moved to an external entity. However we still want to get information about the blood that is collected, so we have arranged to get data in an Excel file.

The file will contain a full data dump and it is up to the importer to check if we already have information about a given blood item or if we need to create a new item.

The Excel file contains the following columns:

  • PersonalNumber
  • Name
  • BloodRccidNumber
  • BloodSample
  • BloodSamplingDate
  • BloodSamplingTime
  • BloodFreezerDate
  • BloodFreezerTime
  • OtherPathNote

The 'Name' column is a SCAN-B id which should match some existing entry in our database already.

The other columns should map to already existing annotations that we used for blood items, except that we need to merge the two sets of Date and Time columns.

Also note that we typically copy consent information to new blood items in the old wizard, so this should also be done whenever we create new blood items.

Change History (10)

comment:1 Changed 6 weeks ago by Nicklas Nordborg

Milestone: Reggie v4.26Reggie v4.x

comment:2 Changed 6 weeks ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.27

comment:3 Changed 6 weeks ago by Nicklas Nordborg

In 5910:

References #1234: Implement batch importer for followup blood samples

Started the work on the follow-up blood batch importer. A wizard for selecting the (Excel) file has been added and a structure has been setup to send that file to BASE for parsing. Note that the file is NOT saved in the BASE file system.

The importer has only implemented a few minor checks so far (that the header line is found).

comment:4 Changed 5 weeks ago by Nicklas Nordborg

In 5911:

References #1234: Implement batch importer for followup blood samples

Added mappings for all columns and implemented several checks for sensible values.

comment:5 Changed 5 weeks ago by Nicklas Nordborg

In 5916:

References #1234: Implement batch importer for followup blood samples

Added a query that checks if a given follow-up blood entry exists based on the RCC ID. So far, only counters are updated and reported back in the progress meter.

comment:6 Changed 5 weeks ago by Nicklas Nordborg

In 5917:

References #1234: Implement batch importer for followup blood samples

Implemented support for creating new follow-up blood items when an existing item is not found. A patient item must exist.

The importer is currently implemented to be very strict and the entire import will fail if a single problem is found. If this becomes a problem, it would be possible to change so that entries are skipped and generate warnings instead of errors.

comment:7 Changed 5 weeks ago by Nicklas Nordborg

In 5918:

References #1234: Implement batch importer for followup blood samples

Fixed code that generates external ID so that it will work also if there are several new items.

Implemented code for finding a case or another blood item with a registered consent. The importer will copy the consent to the new follow-up blood item. If there are multiple items it will select the item that matches the case name provided in the imported file.

comment:8 Changed 5 weeks ago by Nicklas Nordborg

In 5919:

References #1234: Implement batch importer for followup blood samples

Implemented an "Abort" button that can be used to abort the importer.

comment:9 Changed 3 weeks ago by Nicklas Nordborg

In 5931:

References #1234: Implement batch importer for followup blood samples

Minor changes and improvments in error handling and reporting.

comment:10 Changed 3 weeks ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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