Rerun flag reimplementation

[sylvinite]

Description

The features of this PR primarily concerns bioinformaticians

• Rerun flag no longer collides with Reports table
• QC report: Unavailable Application Tag is now displayed in red
• QC report: Unavailable date now shows 'Okänd' instead of date.min
• Reports: Translated Unknown to Okänd for novel alleles in report
• Trimmed the warning message for data already existing in database
• Removed legacy value date_received (date of LIMS project opening), superseeded by date_arrival

Samples containing the new organism S. pneumoniae was incorrectly labelled as containing K. pneumoniae due to lax string comparison, and a lack of databases for the former. Upon using the rerun flag, the automatic version management disallowed the rerun flag to delete old entries.

In addition to this, multiple minor visual elements were improved based on feedback.

Primary function of PR

• [ ] Hotfix
• [X] Patch
• [ ] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

• Copy the production database.
• Create a development version of microSALT, with associated configuration (see github readme) and the copied production database
• Run microSALT analyse project ACC5807
• Run microSALT analyse project ACC5746
• Evaluate that ACC5807 receives an application tag for all samples
• Evaluate that ACC5746 receives the organism S. pneumoniae for all samples

Test results

• ACC5807 receives an application tag for all samples
• ACC5746 receives the organism S. pneumoniae for all samples
• 'Okänt' is in the report for all date.min values (Ankomstdatum, Date sekvensering for ACC5807; Datum sekvensering for ACC5746)
• The old 'Hindered insertion ...' message is now replaced instances of 'WARNING - Record [CG_ID_sample]=[ACC5807A11] in table Samples already exists'
• ACC5807A7 and ACC5807A11 now have the sequence type Okänd (Novel ST, Novel allele[s]) and Okänd (1 alleles) respectively

Sign-offs

• [X] Code reviewed by @sylvinite
• [X] Code tested by @sylvinite
• [x] Approved to run at Clinical-Genomics by @ingkebil