Even more functionality in the Flagged alignment wizard

[Nicklas Nordborg]

See #1050.

• [Done] Implement possibility to flag and add/modify comments when scheduling re-extractions. Since it takes about a week or more to get the result it is good to be able keep some information about why the re-extraction was made in the first place.

• [Done] Introduce a DoNotUse flag that should be set on the top-most item that is considered incorrect. The top-most item is typically a Specimen, Lysate, RNA, PreNormalizedRNA or Library. The flag should then be copied downstreams to all child items. A DoNotUseComment that goes along with the flag is probably also a good idea.

• [Done] Alignments that are flagged as DoNotUse should be removed from the Flagged alignments list and disabled for future genotype checks. (Update) Disabling is the default, but there should also be an option to keep them available for genotype checks. Remaining items in the list should be checked again and items that no longer get any genotype warning should also be removed.

• A lot of other wizards need to be updated to check the DoNotUse flag. For example:
  • When manually selecting RNA for library preparation a warning should be displayed.
  • Demuxing should skip flagged libraries. The rules for generating warnings, etc. need to be updated.
  • and more...

[Nicklas Nordborg]

Copied to ticket description.

[Nicklas Nordborg]

(In [4970]) References #1054: Even more functionality in the Flagged alignment wizard

Extended the "Schedule re-processing" functionality with the ability to add or modify comments (QC_GENOTYPE_COMMENT) and flag more alignments. The functionality is available when a filter has been selected.

[Nicklas Nordborg]

(In [4972]) References #1054: Even more functionality in the Flagged alignment wizard

Added two new annotation types: DoNotUse and DoNotUseComment.

They should be set on any item (from Specimen all the way down to RawBioassay) to indicate that it should not be used in the future for some reason (as indicated by the comment). The DoNotUse is a string enumeration with possible values: Specimen, Lysate, RNA, Library. The value should reflect the top-most item where there is a problem. For example, if an RNA is contaminated, then DoNotUse=RNA for the RNA and all items downstreams.

[Nicklas Nordborg]

(In [4973]) References #1054: Even more functionality in the Flagged alignment wizard

Adding 'debug'-level messages from servlets that are displayed in the regular result list after the registration. Messages should be prefixed with [Debug].

[Nicklas Nordborg]

(In [4974]) References #1054: Even more functionality in the Flagged alignment wizard

Preparing the template HTML with support for the "resolve" mode by adding some more CSS rules and a "Register" button.

[Nicklas Nordborg]

(In [4975]) References #1054: Even more functionality in the Flagged alignment wizard

Implemented functionality for marking items as "Ok to use" or "Do not use". The selection can be done on Specimen, Lysate, RNA or Library level and will affect all downstream child items.

The functionality is only available if a filter is active. If the filter is a Qiacube or Libplate filter it is a requirement that an option is selected for all flagged items. If the "Do not use" option is used a comment is required.

[Nicklas Nordborg]

(In [4976]) References #1054: Even more functionality in the Flagged alignment wizard

Added an indicator for re-processing that is enabled if there is no other alignment for the same specimen. Alignments from the same RNA (if a Qiacube filter is active) or library (if HET filter or libplate filter is active) are not counted as a separate alignment.

When the High HET filter is active there is also an indicator for DoNotUse that is active if there is another alignement without an "error" condition.

[Nicklas Nordborg]

(In [4977]) References #1054: Even more functionality in the Flagged alignment wizard

Messages are registration now reports number of specimen, lysates, rna and libraries instead of total number. Also fixed so that messages are correct for "one" and "multiple" items.

[Nicklas Nordborg]

(In [4978]) References #1054: Even more functionality in the Flagged alignment wizard

Sorting items in order from Specimen->Lysate->RNA->Library to make results predictable in the case that two or more items from the same parent-child chain are selected.

[Nicklas Nordborg]

(In [4979]) References #1054: Even more functionality in the Flagged alignment wizard

When a RNA is selected for DoNotUse we should also find the corresponding DNA and FlowThrough. This is done by looking for the other items that have the same Lysate parent and same Qiacube date and run number.

[Nicklas Nordborg]

(In [4980]) References #1054: Even more functionality in the Flagged alignment wizard

Display existing DoNotUse information for alignments. If a re-process option is selected from an item marked as DoNotUse a warning icon is displayed. In the "Resolve" mode alignments marked as DoNotUse can't be modified.

[Nicklas Nordborg]

(In [4981]) References #1054: Even more functionality in the Flagged alignment wizard

Added an option to keep an alignment that was marked as DoNotUse available for future genotype checks (eg. QC_GENOTYPE_STATUS=Checked instead of QC_GENOTYPE_STATUS=Disabled).

For example, if we have a QiaCube shift on positions 8-12, a verified RNA on position 6 but no information about the RNA at position 7 (and no remaining specimen) we can mark it as DoNotUse but keep it enabled for genotype checks in case we get a second sample from the same patient in the future.

Note that there is no possibility yet to change the DoNotUse to OkToUse if the second sample confirms that the original sample was correct.

[Nicklas Nordborg]

(In [4982]) References #1054: Even more functionality in the Flagged alignment wizard

Added PreNormalizedRNA as an option for the DoNotUse annotation. The options is of course only available if the alignment has a pre-normalied RNA item in the parent chain.

A minor complication is present when filtering on a QiaCube. It is possible that alignments from both a pre-normalized and a regular RNA exists and that there is a mixup that only affects the pre-normalized RNA. But the "Resolve" options are grouped by QiaCube positions so there is only one set of options for the two alignments. If the PreNormalizedRNA option is selected, only the pre-normalized RNA is marked as DoNotUse and we rely on the auto-unflag option to fix the regular RNA as if the Ok checkbox had been selected.