Import wizard for MIPs aliquot plates

[Nicklas Nordborg]

We need a wizard for importing external DNA aliquot items that should go into the MIPs pipeline. While this can already be done with regular batch item importers a specific wizard can improve this.

• Check that items with the same name doesn't already exists
• Automatically check that a prefix is used on names
• Create storage boxes/plates if needed

The importer need at least the following information:

• Name of DNA aliquot
• Box/plate name and location
• more to come...

[Nicklas Nordborg]

In 5389:

References #1133: Re-organize the Reggie front page

Added lots of wizards to the "MIPs library preparation and analysis" section. The wizards will be implemented in other tickets. See #1130, #1135, #1136, #1137, #1138 and more to come.

[Nicklas Nordborg]

In 5397:

References #1130: Import wizard for MIPs aliquot plates

Started to work on the importer. It can parse and read date from CSV or Excel files. The information will be displayed in a plate-like preview.

Error checking and error handling is almost non-existing so far. Registration is not possible.

[Nicklas Nordborg]

In 5399:

References #1130: Import wizard for MIPs aliquot plates

Implemented error checking and error handling. For aliquots we require that:

• A name is given
• The name must not already exist in the database
• The name must be unique within the file
• A plate and location must be specified
• The location must be within A1 to H12
• The same location must not be used by more than one aliquot

For plates we require that:

• The name must not already exist in the database

Registration is not yet implemented.

[Nicklas Nordborg]

In 5400:

References #1130: Import wizard for MIPs aliquot plates

Implemented registration.

[Nicklas Nordborg]

In 5401:

References #1130: Import wizard for MIPs aliquot plates

Added support for Quantity and NDConc columns. A warning is generated if the columns are missing. Warnings are also generated on aliquots that has a missing value if the columns exists. Invalid values are reported as errors.

[Nicklas Nordborg]

In 5402:

References #1130: Import wizard for MIPs aliquot plates

Added support for BEDFile and Target columns.

[Nicklas Nordborg]

In 5403:

References #1130: Import wizard for MIPs aliquot plates

Added a summary section above the plate view.

[Nicklas Nordborg]

In 5405:

References #1130: Import wizard for MIPs aliquot plates

Added MIPsPlateDesigner and MIPsLibraryPrep roles.

[Nicklas Nordborg]

In 5406:

References #1130: Import wizard for MIPs aliquot plates

Added functionality for saving and re-using the last used prefix for aliquots. If no old prefix is present it is automatically generated from the name of the current user.

[Nicklas Nordborg]

In 5408:

References #1130: Import wizard for MIPs aliquot plates

Added DesignMIPs to the PlateProcessing annotation. This value is used by the import wizard to indicate that imported plates are ready to be used by the MIPs plate design wizard.

[Nicklas Nordborg]

In 5420:

References #1130: Import wizard for MIPs aliquot plates

Updated the importer to use new features from ​http://base.thep.lu.se/ticket/2174 which means we don't have to check for and handle Excel files in our own code, but can delegate that to the FlatFileParser.

[Nicklas Nordborg]

In 5444:

References #1130: Import wizard for MIPs aliquot plates

Implemented functionality for checking BEDFile values in a column. Normally, all aliquots in a column should have the same BED. If not, a warning is displayed.

Consecutive columns that all have the same BED are grouped into pool-like display in the plate preview.

Empty positions in columns are now handled better even if they are not last. Empty columns in the middle of the plate are handled better.

[Nicklas Nordborg]

In 5447:

References #1130: Import wizard for MIPs aliquot plates

Added more data columns to the importer, removed some columns and renamed some.

• MIPS_BEDFile has been renamed to MIPS_Pool
• MIPS_PoolVolume, MIPS_NormalTumor and MIPS_Form are new columns that are also displayed in the preview.
• MIPS_Variant, MIPS_VariantList and MIPS_Screening are new but not displayed.
• Quantity, NDConc and MIPS_Target columns have been removed

The pool volume is also check column-wise for values that are different. If any values are found a warning is displayed.

[Nicklas Nordborg]

In 5461:

References #1130: Import wizard for MIPs aliquot plates

Changed the PoolVolumn annotation to a numeric annotation.

[Nicklas Nordborg]

In 5464:

References #1130: Import wizard for MIPs aliquot plates

The importer should trim white-space from data values.

[Nicklas Nordborg]

In 5481:

References #1130, #1135, #1136. Introduced soft line-breaks in sample names. This should make it possible to print the lab protocol on a single sheet even if the sample names are a bit longer.

[Nicklas Nordborg]

In 5483:

References #1130, #1135, #1136. Synchronized some missing styles and remove the prefix from external sample names in the plate view lab protocol in order to save space.

[Nicklas Nordborg]

In 5495:

References #1130: Import wizard for MIPs aliquot plates

Added a check for number of aliquots and report an error message if there was no aliquots in an otherwise acceptable file.

[Nicklas Nordborg]

In 5518:

References #1130: Import wizard for MIPs aliquot plates

Implemented color-coding for MIPs pools. With this we do not need to issue warnings if a column has more than one MIPs pool since it easy to see. On the other hand, the color coding can clash with other warnings so cells with a warning are now displayed with a yellow outline instead of a yellow background color. Errors are still displayed with a red background color, so we should not use red for pools.

So far, we are only using the 3 different colors we already have for barcode layouts in the RNA-seq pipeline.

[Nicklas Nordborg]

In 5519:

References #1130: Import wizard for MIPs aliquot plates

Added more colors and implemented support for using pre-defined colors for some MIPs pool names. For example, MIPS_ID=bg-green.

[Nicklas Nordborg]

In 5526:

References #1130, #1135, #1142, #1146. Fixing and getting rid of some 'TODO' entries in the code.

[Nicklas Nordborg]

In 5599:

References #1130: Import wizard for MIPs aliquot plates

Changed pre-defined pool colors.

[Nicklas Nordborg]

In 5600:

References #1130: Import wizard for MIPs aliquot plates

Changed the MIPSpool column header to MIPS_Panel.

[Nicklas Nordborg]

In 5601:

References #1130: Import wizard for MIPs aliquot plates

Changed the MIPS_Pool annotation to MIPS_Panel.