Updates to registration of specimen handled by external lab

[Nicklas Nordborg]

There is a new test file with some changes that should take us a bit closer to a final working implementation. Details will follow in commit messages.

See also tickets #1360, #1349, #1347 and #1295.

[Nicklas Nordborg]

In 6701:

References #1388: Updates to registration of specimen handled by external lab

If the top-level element in the JSON-file is a single element we descend into that element instead.

[Nicklas Nordborg]

In 6702:

References #1388: Updates to registration of specimen handled by external lab

Added option to convert enum values to upper case.

[Nicklas Nordborg]

In 6703:

References #1388: Updates to registration of specimen handled by external lab

"Sample Name" field has been renamed to "PAD" (in the Specimen section).

[Nicklas Nordborg]

In 6704:

References #1388: Updates to registration of specimen handled by external lab

Specimen sampling date and RNA later date support dates without time.

[Nicklas Nordborg]

In 6709:

References #1388: Updates to registration of specimen handled by external lab

Read Specimen-ID values for Specimen, Lysate, RNA, DNA and FlowThroug which should be the text that is found on tubes in storage boxes. The Specimen-ID have a common prefix (which is the same as the Clarity ID on the specimen item) and an item-specific suffix: -Lys, -RNA, -DNA, -Prot.

[Nicklas Nordborg]

In 6710:

References #1388: Updates to registration of specimen handled by external lab

Minor fixes for some validator patterns.

[Nicklas Nordborg]

In 6711:

References #1388: Updates to registration of specimen handled by external lab

Added TubeLabel annotation type intended to store the text on the label on storage tubes if this is different from the name.

[Nicklas Nordborg]

In 6714:

References #1388: Updates to registration of specimen handled by external lab

Original, remaining and used quantities/volumes for Specimen, Lysate, RNA, DNA, Flowthrough and Library.

[Nicklas Nordborg]

In 6715:

References #1388: Updates to registration of specimen handled by external lab

Implemented the "Multiple pieces" annotation on Lysate items. In the JSON file this is stored as "Used number of pieces" so we simply check if the value is set and >1.

[Nicklas Nordborg]

In 6716:

References #1388: Updates to registration of specimen handled by external lab

Fixed formatting of null values to display '-' instead. Found the same problem in some other places and fixed it there as well.

[Nicklas Nordborg]

In 6717:

References #1388: Updates to registration of specimen handled by external lab

Changed "Specimen-ID" to optional entries.

[Nicklas Nordborg]

In 6718:

References #1388: Updates to registration of specimen handled by external lab

The used volume from Lysate was only calculated if no volume had been taken.

[Nicklas Nordborg]

In 6719:

References #1388: Updates to registration of specimen handled by external lab

Fixed incorrect names of JSON keys:

• Sample type --> Sample Type
• Sample comment --> Sample comments

[Nicklas Nordborg]

In 6732:

References #1388: Updates to registration of specimen handled by external lab

Changed "Specimen-ID" to optional entries with warnings if they are missing. See also [6717].

[Nicklas Nordborg]

In 6733:

References #1388: Updates to registration of specimen handled by external lab

We don't have to repeat the name of the source item.

[Nicklas Nordborg]

In 6734:

References #1388: Updates to registration of specimen handled by external lab

Implemented support for importing partial processing from JSON files. For example, if the library preparation failed for some reason and no sequencing could be performed. This assumes that the JSON file then contains sections with data from "Specimen" down to "Library", but no sections for "Pool", "FlowCell", etc. The importer will then accept the JSON (with a warning) and import as much as it can.

There is currently no flagging or marking items with an error so it may be that in some cases, the created items will show up in some of the regular Reggie wizards. This will of course need to be fixed, but it may also be useful to, for example, flag an RNA item to make it possible to schedule a re-extraction in the future.

[Nicklas Nordborg]

In 6736:

References #1388: Updates to registration of specimen handled by external lab

When the end-point is a SequencingRun and there is no demux information or FASTQ files, the sequencing run is annotated as "Failed" and auto-processing is "Disable". This will prevent the sequencing run from showing up in the "Start demux and merge" wizard.

Implemented an option to flag the RNA item since it may be possible to start a re-process from some level.

[Nicklas Nordborg]

In 6737:

References #1388: Updates to registration of specimen handled by external lab

Always set auto-processing to "Disable" on pools. We will never want to process pools in our lab, and without the "Disable" flag the pool will show up in the "Create flow cell" wizard if the pool is the end-point.

Always set the destroyed flag and auto-processing to "Disable" on library plates since we never want to process library plates in our lab.

[Nicklas Nordborg]

In 6738:

References #1388: Updates to registration of specimen handled by external lab

Set auto-processing to "Disable" also on RNA and Lysate items.

[Nicklas Nordborg]

In 6739:

References #1388: Updates to registration of specimen handled by external lab

Fixes some potential issues with null values.