Opened 7 years ago

Closed 7 years ago

Last modified 6 years ago

#436 closed task (fixed)

Import mRNA quality control results

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.12
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This wizard is part of #422.

Once the fragmented mRNA plate has been created and quality control measurements have been performed, the results should be uploaded to BASE. Currently, this is a PDF file containing various tables and diagrams.

At the same time, the mRNA plate should be registered with a creation date and an operator should be set. Behind the scenes a cDNA child plate and cDNA extracts are also created to enable the next step to be performed.

Change History (12)

comment:1 Changed 7 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 7 years ago by Nicklas Nordborg

(In [1758]) References #436: Import mRNA quality control results

Implemented a registration that incldues a PDF file, creation date, protocol, operator and comments (for the plate). Need to add a way to add comments per biomaterial if that is needed.

The registration also prepares for the cDNA step by creating the cDNA child plate and biomaterial (without creation date).

comment:3 Changed 7 years ago by Nicklas Nordborg

(In [1792]) References #424, #425 and #436. Added a 'comments' field on the mRNA plate design wizard. The comment is included in the lab protocol and in the final mRNA registration wizard.

comment:4 Changed 7 years ago by Nicklas Nordborg

Milestone: Reggie v2.xReggie v2.12

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [1889]) References #436 and #424.

Added support for registering a mRNA plate as failed. No child cDNA plate is created and the parent RNA are placed in the "Flagged RNA" biomaterial list and annotated with Flag=mRnaPlateFailed. This annotation is now also used by the auto-select RNA wizard to flag RNA with not enough remaining quantity (Flag=NotEnoughRemainingQuantity).

Changed the DisableAutoProcessing annotation to AutoProcessing and it is now also an enumeration (Disable, ReProcess). Items without no value for the AutoProcessing annotation should follow the regular workflow. Other values may be used by wizards to trigger special actions. The Create new mRNA plate wizard has support for the AutoProcessing=ReProcess which should be used for RNA that has been processed once already. The ReProcess annotation override all filter checkes usually done by the auto-select function.

Handling RNA that is flagged is part of ticket #455 and is not sheduled until some later release.

comment:6 Changed 7 years ago by Nicklas Nordborg

(In [1890]) References #436 and #441. Added support for registering a cDNA plate as failed. The parent RNA is placed in the "Flagged RNA" list and annotated with Flag=cDnaPlateFailed.

Since child items to the cDNA plate are never created by this wizard we also introduced the PlateProcessResult annotation which can be either Sucessful or Failed. Downstream wizards should check this annotation before proceeding with the next step. This annotation has also been added to the mRNA step for consistency.

If the 'failed' option is selected, the 'Comments' fields is required.

comment:7 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:8 Changed 6 years ago by Nicklas Nordborg

(In [1988]) References #436: Import mRNA quality control results

Set file description that includes the plate name if no description already exists.

comment:9 Changed 6 years ago by Nicklas Nordborg

(In [1990]) References #436: Import mRNA quality control results

Automatically set the working directory to /home/SCANB/MRnaPlateQC when opening the "Browse" dialog.

comment:10 Changed 6 years ago by Nicklas Nordborg

(In [1992]) References #436 and #473. Added subtypes for 5 different files produced or used by Bioanalyzer, Caliper and Qubit. The wizards use those subtypes as a filter when selecting files so that it should be easier to find the correct files.

comment:11 Changed 6 years ago by Nicklas Nordborg

(In [1998]) References #436: Import mRNA quality control results

Added 4 date and operator fields to the mRNA registration wizard. Already registered plates should be fixed manually.

comment:12 Changed 6 years ago by Nicklas Nordborg

(In [2005]) References #436: Import mRNA quality control results

Clarify the use of 'Select manually' button.

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