Opened 15 years ago

Closed 15 years ago

Last modified 14 years ago

#469 closed enhancement (fixed)

Improve error handling of invalid values in import plugins

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: BASE 2.4
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by Nicklas Nordborg)

Relates to ticket:573

The following was sent to the BASE mailing list (GPR import plugin error) by david vilanova:

In some cases the "log ratio (...)" field has some values that are named "error". This come from the fact that when the background noise is higher than the intensity of the expressed oligo it is not possible to compute the log ration so genepix will return "error" as value for this specific field. Well, base is returning an error when trying to import such values. Could that be fixed ?? I want to keep this files so the option of ignoring this lines is not a solution since i want to keep all the lines of the GPR file.

We need an option of inserting null values for values that fails and not just skipping the whole line.

Change History (7)

comment:1 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.x+BASE 2.4

comment:2 Changed 15 years ago by Jari Häkkinen

Milestone: BASE 2.4BASE 2.3

Milestone BASE 2.4 deleted

comment:3 Changed 15 years ago by Nicklas Nordborg

Priority: minormajor

comment:4 Changed 15 years ago by Nicklas Nordborg

Description: modified (diff)
Owner: changed from Johan Enell to Nicklas Nordborg
Status: newassigned

comment:5 Changed 15 years ago by Nicklas Nordborg

(In [3468]) References #574, #573 and #469. Created a simple test case with dirty data file.

comment:6 Changed 15 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [3472]) Fixes #469.

comment:7 Changed 14 years ago by Nicklas Nordborg

(In [3666]) References #469: Added negative numbers to test case with dirty data

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