Opened 18 months ago

Closed 15 months ago

Last modified 13 months ago

#1130 closed task (fixed)

Import wizard for MIPs aliquot plates

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by 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...

Change History (26)

comment:1 Changed 17 months ago by 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.

comment:2 Changed 17 months ago by Nicklas Nordborg

Description: modified (diff)
Status: newaccepted
Summary: External RNA/DNA import wizardImport wizard for MIPs aliquot plates

comment:3 Changed 17 months ago by 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.

comment:4 Changed 17 months ago by 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.

comment:5 Changed 17 months ago by Nicklas Nordborg

In 5400:

References #1130: Import wizard for MIPs aliquot plates

Implemented registration.

comment:6 Changed 17 months ago by 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.

comment:7 Changed 17 months ago by Nicklas Nordborg

In 5402:

References #1130: Import wizard for MIPs aliquot plates

Added support for BEDFile and Target columns.

comment:8 Changed 17 months ago by Nicklas Nordborg

In 5403:

References #1130: Import wizard for MIPs aliquot plates

Added a summary section above the plate view.

comment:9 Changed 17 months ago by Nicklas Nordborg

In 5405:

References #1130: Import wizard for MIPs aliquot plates

Added MIPsPlateDesigner and MIPsLibraryPrep roles.

comment:10 Changed 17 months ago by 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.

comment:11 Changed 17 months ago by 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.

comment:12 Changed 17 months ago by 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.

comment:13 Changed 16 months ago by 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.

comment:14 Changed 16 months ago by 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.

comment:15 Changed 16 months ago by Nicklas Nordborg

In 5461:

References #1130: Import wizard for MIPs aliquot plates

Changed the PoolVolumn annotation to a numeric annotation.

comment:16 Changed 16 months ago by Nicklas Nordborg

In 5464:

References #1130: Import wizard for MIPs aliquot plates

The importer should trim white-space from data values.

comment:17 Changed 16 months ago by 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.

comment:18 Changed 16 months ago by 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.

comment:19 Changed 16 months ago by 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.

comment:20 Changed 15 months ago by 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.

comment:21 Changed 15 months ago by 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.

comment:22 Changed 15 months ago by Nicklas Nordborg

In 5526:

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

comment:23 Changed 15 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed

comment:24 Changed 13 months ago by Nicklas Nordborg

In 5599:

References #1130: Import wizard for MIPs aliquot plates

Changed pre-defined pool colors.

comment:25 Changed 13 months ago by Nicklas Nordborg

In 5600:

References #1130: Import wizard for MIPs aliquot plates

Changed the MIPSpool column header to MIPS_Panel.

comment:26 Changed 13 months ago by Nicklas Nordborg

In 5601:

References #1130: Import wizard for MIPs aliquot plates

Changed the MIPS_Pool annotation to MIPS_Panel.

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