Opened 2 months ago

Closed 2 weeks ago

#1388 closed enhancement (fixed)

Updates to registration of specimen handled by external lab

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.39
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

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.

Change History (21)

comment:1 Changed 2 months ago by 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.

comment:2 Changed 2 months ago by Nicklas Nordborg

In 6702:

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

Added option to convert enum values to upper case.

comment:3 Changed 2 months ago by 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).

comment:4 Changed 2 months ago by 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.

comment:5 Changed 2 months ago by 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.

comment:6 Changed 2 months ago by Nicklas Nordborg

In 6710:

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

Minor fixes for some validator patterns.

comment:7 Changed 2 months ago by 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.

comment:8 Changed 2 months ago by 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.

comment:9 Changed 2 months ago by 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.

comment:10 Changed 8 weeks ago by 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.

comment:11 Changed 8 weeks ago by Nicklas Nordborg

In 6717:

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

Changed "Specimen-ID" to optional entries.

comment:12 Changed 8 weeks ago by 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.

comment:13 Changed 8 weeks ago by 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

comment:14 Changed 7 weeks ago by 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].

comment:15 Changed 7 weeks ago by 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.

comment:16 Changed 7 weeks ago by 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.

comment:17 Changed 7 weeks ago by 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.

comment:18 Changed 7 weeks ago by 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.

comment:19 Changed 7 weeks ago by 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.

comment:20 Changed 7 weeks ago by Nicklas Nordborg

In 6739:

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

Fixes some potential issues with null values.

comment:21 Changed 2 weeks ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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