RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells

[Nicklas Nordborg]

The 'Import RQS scores from Caliper well table file' wizard seems to have stopped working. The Caliper well table files we have tried with seems to be ok, and we also get the same problem with well table files that has already been imported (for example CaliperPlate0035_2014-11-17_1_WellTable.csv).

The problem is that as soon as the well table file is selected it will display a lot of warning (for all wells):

CaliperPlate0035_2014-11-17_1_WellTable.csv: 
No 'RNA Quality Score' value found for '2210834.1.l.r.qc' (A1); using -100 instead

[Nicklas Nordborg]

I think I found the cause of this. The background is that #669 introduced a check that all biomaterial on the caliper plate also had RQS values in the well table file. This was implemented by first setting the status for all extracts to 'missing', and then as each extract was found in the file, remove them from the missing status. As it turned out a critical code line (missingExtracts.remove()) was contained in a debug output line (CaliperPlateImporter line 312​).

This debug line was initially left in the code that was released in Reggie 2.17, but was later removed as part of #699 and released in Reggie 2.17.2.

The solution would be to add the call to missingExtracts.remove() again and this time not as a debug line.

[Nicklas Nordborg]

(In [3061]) Fixes #727: RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells

[Nicklas Nordborg]

(In [3062]) References #727: RNAQC importer says "No 'RNA Quality Score' value found....; using -100 instead" for all wells

[3061] was made in the 2.17-stable branch which is no longer used. This is the same fix in the 2.18-stable branch.