Opened 13 years ago

Closed 13 years ago

#1138 closed defect (invalid)

SMART option for feature mismatch in rawbioassay import does not work

Reported by: Jari Häkkinen Owned by: everyone
Priority: major Milestone:
Component: coreplugins Version: 2.8.2
Keywords: Cc:

Description

We have problems with the SMART option for feature mismatch error treatment when importing the associated GPR file. The importer aborts for feature that are missing in the array design but name "no well" in the GPR file. I expected a smart skip of these lines.

Change History (3)

comment:1 Changed 13 years ago by Nicklas Nordborg

This works as expected in our test cases. Are you sure that the feature is really missing or that it has a NULL reporter? To check this go to the "Features" tab of the array design. Try to locate the feature that the plug-in reports a mismatch for. If you can find the feature check that the '[Rep] Name' and '[Rep] ID' both have the text '- none -' (in italic style).

If the feature exits and have other values for the name/id then the mismatch is real. If not, can you please provide example files for the array design and raw data that we can use to check this.

comment:2 in reply to:  1 Changed 13 years ago by Jari Häkkinen

Replying to nicklas:

This works as expected in our test cases. Are you sure that the feature is really missing or that it has a NULL reporter? To check this go to the "Features" tab of the array design. Try to locate the feature that the plug-in reports a mismatch for. If you can find the feature check that the '[Rep] Name' and '[Rep] ID' both have the text '- none -' (in italic style).

If the feature exits and have other values for the name/id then the mismatch is real. If not, can you please provide example files for the array design and raw data that we can use to check this.

You are right, the feature exists in the database, with a string N/A for reporter name and empty string for the reporter ID. So, is there an easy way to transform these to become - none -? Can these entries be deleted?

comment:3 Changed 13 years ago by Nicklas Nordborg

Resolution: invalid
Status: newclosed

It is more or less impossible to delete the entries since there are references to them from other tables. The best shot is probably to try to update the entries so they get a "NULL" reporter instead. But this has to be done for a lot of tables:

  • All raw data tables
  • The 'Features' table
  • The 'Wells' table
  • All table in the dynamic database that have a name ending with 'Pos'.

When all references to the reporter has been deleted it should be possible to delete the reporter entry to avoid the same problem from popping up again.

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