JSON and raw FASTQ files that are submitted from external lab should be removed if the consent is retracted

[Nicklas Nordborg]

Currently, the JSON file is linked with the Specimen item as remote File. The FASTQ files are placed in the ImportArchive directory and their names are recorded in the RawFASTQ annotation on the associated DemuxedSequences item.

The retraction wizard only finds the JSON file and claims that it will be removed, but in the end it will not remove it. The FASTQ files are not detected at all by the wziard.

[Nicklas Nordborg]

In 7049:

References #1465: JSON and raw FASTQ files that are submitted from external lab should be removed if the consent is retracted

Added support for handling files that are located outside of the normal secondary analysis directory. This fixes the case with the JSON file.

[Nicklas Nordborg]

In 7050:

References #1465: JSON and raw FASTQ files that are submitted from external lab should be removed if the consent is retracted

The raw FASTQ files are linked as external files via the ImportGateway file server by the JSON importer. The retraction servlet should now be able to find and delete those files files as well.

The files need to be re-linked by the FASTQ importer since it moves them to the ImportArchive directory. This is not yet implemented.

[Nicklas Nordborg]

In 7051:

References #1465: JSON and raw FASTQ files that are submitted from external lab should be removed if the consent is retracted

The FASTQ importer now changes the location of the raw FASTQ files.

[Nicklas Nordborg]

In 7053:

References #1465: JSON and raw FASTQ files that are submitted from external lab should be removed if the consent is retracted

Added FASTQ as a possible file type for DemuxedSequences.