YellowLabel tracking wizard

[Nicklas Nordborg]

See #771.

Implement a new wizard for tracking and summarize the progress of specimen marked with YellowLabel.

The wizard should display information about active specimen (=specimen that has been annotated with the YellowLabel annotation but no report has been sent).

We need new annotations on the specimen level to track what to report and if a report has been sent or not.

• ReportsToSend: Enumerated annotation for specifying which reports to send. Currently PilotReport is the only value. It is possible for yellow specimen to have no value for this annotation.
• CompletedDate: Date when processing this specimen has been completed including sending the requested reports (if any). It is assumed that all requested reports are sent at the same time.
• CompletedStatus: Enumerated annotation that is set when a yellow specimen is considered complete. No value indicates a specimen that is in progress. Possible values need to be defined.

For each active yellow specimen the wizard should display:

• Name
• Arrival date
• Sampling date
• RNA extraction date (Qiacube date)
• Flagged RNA
• Some info about library...
• Some info about sequencing...
• Some info about reports...

If the logged in user has enough permissions (PatientCurator?) it should be possible to perform actions on the specimen.

• Generate and package the reports in a zip file
• Mark specimen as completed
• More...?

This specification is not yet complete...

[Nicklas Nordborg]

(In [3779]) References #861: YellowLabel tracking wizard

Added the main list page with a few data columns about the specimen items. It is not possible to do anything with them yet.

The list currently includes all specimen with the YellowLabel annotation since the CompletedDate or CompletedStatus has not yet been defined.

[Nicklas Nordborg]

(In [3780]) References #861: YellowLabel tracking wizard

Added columns for RNA extraction date and Library creation date.

[Nicklas Nordborg]

(In [3782]) References #861: YellowLabel tracking wizard

Added columns for Raw bioassay and Pilot report.

[Nicklas Nordborg]

(In [3783]) References #861: YellowLabel tracking wizard

Adding counter for number of active YellowLabel specimen.

[Nicklas Nordborg]

(In [3784]) References #861: YellowLabel tracking wizard

Added CompletedDate annotation. The counter service has been updated to filter on this annotation.

The "Yellow label tracking" wizard load some of the most recently completed (within 48 hours) specimen. They are listed for informational purposes only and can't be selected for actions.

[Nicklas Nordborg]

(In [3785]) References #861: YellowLabel tracking wizard

Fixes filtering problems with the completed yellow label specimen.

[Nicklas Nordborg]

(In [3787]) References #861: YellowLabel tracking wizard

Added "Mark as completed" action. The toolbar is no only visible if the logged in user is an Administrator or PatientCurator.

Minor improvements in filtering. The site list include the number of specimen per site.

[Nicklas Nordborg]

(In [3788]) References #861: YellowLabel tracking wizard

Moved code from the GeneReportsCombinerPlugin to external classes so that it should be possible to use the functionality without using the plug-in API.

[Nicklas Nordborg]

(In [3789]) References #861: YellowLabel tracking wizard

Added "Create Pilot report ZIP file" action. IT currently uses "testing" as hard-coded password. The wizard need some redesign to be able to ask for other parameters. Maybe it should be possible to also mark the specimen as completed at the same time.

[Nicklas Nordborg]

(In [3790]) References #861: YellowLabel tracking wizard

Moved yellow label files to it's own directory.

[Nicklas Nordborg]

(In [3791]) References #861: YellowLabel tracking wizard

The "Create Pilot report ZIP file" action now creates a popup dialog asking for a encryption password to use in the ZIP file.

[Nicklas Nordborg]

(In [3800]) References #861: YellowLabel tracking wizard

Gray background for completed specimen. Highlight specimen that has a pilot report.

[Nicklas Nordborg]

(In [3810]) References #861: YellowLabel tracking wizard

The "Pilot report" column now show the last updated date.

[Nicklas Nordborg]

(In [3811]) References #861: YellowLabel tracking wizard

Added linked icons to the regular BASE view/edit pages for "RNA", "Library" and "Raw bioassay".

[Nicklas Nordborg]

(In [3812]) References #861: YellowLabel tracking wizard

Added column for "Completed date".

[Nicklas Nordborg]

(In [3813]) References #861: YellowLabel tracking wizard

The "PilotReportExists" filter (was removed by [3810]) is needed by the "Create pilot report ZIP" functionality.

[Nicklas Nordborg]

(In [3814]) References #861: YellowLabel tracking wizard

When filtering on the "Completed date" column a new database request is made to load items matching the filter.

[Nicklas Nordborg]

(In [3815]) References #861: YellowLabel tracking wizard

Load sites and permissions in a separate request so that it doesn't have to be redone when updating the specimen list due to a change in the "Completed date" filter.

[Nicklas Nordborg]

(In [3821]) References #861: YellowLabel tracking wizard

Added Completed date field in the "Create ZIP" dialog to make it possible to mark the specimen as completed at the same time as the ZIP file is created.

[Nicklas Nordborg]

(In [3822]) References #861: YellowLabel tracking wizard

Added flag icon to RNA that has been flagged. Re-designed the table so that the icons have separate columns in order to keep the dates aligned when the number of icons are not the same.

[Nicklas Nordborg]

(In [3823]) References #861: YellowLabel tracking wizard

Include the site name in the ZIP filename when creating a ZIP file when all reports are from the same site.

Include the current date in the ZIP filename.

[Nicklas Nordborg]

(In [3824]) References #861: YellowLabel tracking wizard

Added dialog for setting the "Completed date" when using the "Mark completed" action.

[Nicklas Nordborg]

(In [3825]) References #861: YellowLabel tracking wizard

Added Re-create report PDF functionality to make easier to create new versions of the pilot report in case not all information (eg. RNAQC) was available when the first version was created.

[Nicklas Nordborg]

(In [3826]) References #861: YellowLabel tracking wizard

Added Consent date column.

Som minor changes to text messages.

[Nicklas Nordborg]

(In [3827]) References #861: YellowLabel tracking wizard

Added RQS/RIN column.

[Nicklas Nordborg]

(In [3828]) References #861: YellowLabel tracking wizard

Display 'In progress' for items that exists but doesn't yet have a date (which typically means they are working with this in the lab).

Display 'Missing' in bold red text if there is no registered consent for a specimen.