Register library processing results

[Nicklas Nordborg]

This wizard is the last step in #423. In the lab, the library preparation first needs a number of test rounds for finding the correct parameters (eg. depending on humidity, etc.) and quality control. After that a complete plate is processed.

The wizard should be able to register each test round with at least a PDF file and a comment.

The complete plate (if successful) registration need to provide data files from the Caliper and Qubit runs. Details need to be investigated, but we'll need at least a PDF and a CSV file to parse for annotations.

(It should be possible to mark specific positions as failed and their parent RNA should then be flagged for re-processing -- TODO in a later release)

The wizard should also have support for a completely failed plate which also results in all parent RNA being flagged.

[Nicklas Nordborg]

(In [1895]) References #473: Register library processing results

Started with the QC part of the registration.

[Nicklas Nordborg]

(In [1902]) References #473: Register library processing results

Added annotations for storing concentration from Qubit measurements (QubitConc) and fragment sizes from Caliper (CA_SIZE).

[Nicklas Nordborg]

(In [1903]) References #473: Register library processing results

Added two test data files that matches the data in the 'mrna.txt' file that can be used to create a new Mrna plate. The test files should work if this is the first plate that is created and the wells with errors (duplicates, not-found, etc.) are cleared.

• LibPlate0001_Caliper_out.csv: Data from the Caliper run on the entire plate, but not for the Stratagene extracts.
• LibPlate0001_Qubit_out.csv: The file is created by Reggie and the operator enter concentration values for each extract. This is how the final file would look like and it is then uploaded to BASE again.

[Nicklas Nordborg]

(In [1904]) References #473: Register library processing results

Prepared the CaliperPlateImporter implementation for importing data to other plate types (eg. with different prefix than CaliperPlate).

Added possibility to provide external lookup for setting more annotations for each sample. The idea is to pre-parse the Qubit data file and then for each sample in the Caliper file lookup the corresponding concentration in the Qubit file. This way we don't have to duplicate lots of error checking in a QubitPlateImporter class.

[Nicklas Nordborg]

(In [1905]) References #473: Register library processing results

Add possibility in the LookupConverter to throw an exception if a value is not found.

[Nicklas Nordborg]

(In [1906]) References #473: Register library processing results

Added functionality to import Caliper (size) and Qubit (concentration) data. The original quantity of the library is calculated assuming that the final volume is 10µl after the aliquots have been taken for Caliper and Qubit.

Also added the CA_Molarity annotation which is calculated using the formula: 1000 * 1000 * (1/649) * QubitConc * (1/CA_Size)

Removed ng/µg from Qubit file since it may cause issues if opened in programs not automatically using UTF-8.

[Nicklas Nordborg]

(In [1908]) References #473: Register library processing results

It should now be possible to register all three types of library plate processing results:

• QC checks (can be done several times)
• Full plate - success
• Full plate - failed

Removed the "Assign barcode" event since it is no longer needed when the library plate is pre-created without date.