[validation] some bugs and improvements

[antonylebechec]

Some bugs and improvements:

• Contextual menu fail when no "chr" field in query ([Validation] Contextual menu fail when no "chr" field in query #362)

Traceback (most recent call last):
  File "/Users/lebechea/BIOINFO/git/cutevariant/cutevariant/gui/plugins/validation/widgets.py", line 626, in contextMenuEvent
    self.current_variant["chr"]
KeyError: 'chr'

• Ficon is not defined

Traceback (most recent call last):
  File "/Users/lebechea/BIOINFO/git/cutevariant/cutevariant/gui/plugins/validation/widgets.py", line 187, in data
    return QIcon(Ficon(0xF139A)).toPixmap(20, 20)
NameError: name 'Ficon' is not defined

• Ensure icons are clearly defined

  • icons for Lock/Unlock/Rejected sample
  • icon's colors related to validation on variant

• Ensure than validation is locked for locked samples and no genotype variant

• List of columns not selected and not visible and not checkable (MacOs)

• Select fields to display close to presets, at the right

• Add quick selection of samples/genotype in the main window (only on "sample_has_variant" values?)
  As example :

  • selection of samples with the selected variant associated to specific genotypes (to help user to quickly list samples with genotype)
    

  • selection of samples with the selected variant validated (to help user to quickly list samples with validation)
    

  • selection of samples with the selected variant tagged with a specific tag (to help user to quickly list tagged validation)
    

• Contextual menu > variant validation not locked when no genotype for a variant

• Search samples with pattern
  

• Selection with a list of samples (separated by space or comma, allow both, especially to be able to copy/paste from a spreadsheet)

• Selection with a SampleSheet (Illumina format)

• Selection with tags on samples that are not preset (e.g. added during import)

• Search list with icons (and text?)

• Columns in list of samples more usable

  • Order by on columns
  • Selection of columns (or all columns), such as sex, father, mother, hpo, others...
  

• button "Add to selection" and "remove selection(s)" and "clear all" more visible

• Columns in selected samples

• Contextual menu to open Edit each samples (either in "All samples" and "X Selected sample(s)" tabs)

• List of selected samples at the bottom of the window (after the samples' table and before "Cancel" / "OK" button), for each tabs. The list will be just a non editable text field, with samples separated by a space or comma, with a limitation (no more X samples shown, user can list all of them with details in the "X Selected sample(s)" tab)

• Double click to add samples (one by one)

• Facilitate source creation and selection (PR 395)

• Validation of multiple sample_has_variant at the time (issue [validation] Validate a variant for multiple samples at the time impossible #395)

[dridk]

• add all samples button (select all )
• Add validation source button

[SamuelNicaise]

Ensure than validation is locked for locked samples and no genotype variant

should be avoided in case a biologist wants to validate a variant that was undetected by callers

[antonylebechec]

Most of items are solved