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Please add technical replicate to proteomics measurement metadata #747

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KochTobi opened this issue Jul 30, 2024 · 2 comments · Fixed by #832
Closed

Please add technical replicate to proteomics measurement metadata #747

KochTobi opened this issue Jul 30, 2024 · 2 comments · Fixed by #832
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@KochTobi
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core Feature or fix task considered to be in the core product simple Implementation effort

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@KochTobi
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Is your feature request related to a problem? Please describe.
As the proteomics labs switched their process and do always do technical replicates now, we want this information in the measurement metadata. The technical replicate column can be optional and freetext but should be one of the first columns so measurements can easily be identified.

Describe the solution you'd like
Add technical replicates to the proteomics measurement metadata.

Describe alternatives you've considered
Add information on technical replicates to the comment column. As this column is one of the last columns, it is not very helpful if I want to identify my measurement as a lab person.
@sven1103 sven1103 added simple Implementation effort triage An issue that is in discussion to be either scheduled for implepmentation or denied labels Aug 1, 2024
@sven1103 sven1103 added the needs clarification Unclear issue where more information needs to be provided by the issuer label Aug 12, 2024
@sven1103
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@FraBarSol
Before we can consider this issue, can you tell us how you would expect handling of technical metadata for sample pools?

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Ok, so together with @oquendoM , @FraBarSol , @Shraddha0903 ,

we agree to include it as simple property for measurement and in the case of samples, we agree to regard the future biological replicate property with equal names and conditions as technical replicate.

see also #735

@sven1103 sven1103 added core Feature or fix task considered to be in the core product and removed triage An issue that is in discussion to be either scheduled for implepmentation or denied labels Aug 19, 2024
@sven1103 sven1103 removed the needs clarification Unclear issue where more information needs to be provided by the issuer label Sep 3, 2024
@KochTobi KochTobi self-assigned this Sep 16, 2024
KochTobi added a commit that referenced this issue Sep 16, 2024
@KochTobi
solves #747 add technical replicate
4c5bccd
@KochTobi KochTobi linked a pull request Sep 16, 2024 that will close this issue
Edit templates for measurement registration #832
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@KochTobi KochTobi mentioned this issue Sep 16, 2024
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KochTobi added a commit that referenced this issue Sep 17, 2024
@KochTobi @Steffengreiner
Edit templates for measurement registration (#832)
f99ebc2 
* WIP

* wip

* make it work

* Extract behaviour

* remove unused method

* Adapt proteomics template

Fixes the edit case and renames instrument to MS device

fixes #786

* Make ngs row creation simpler

Uses the enum and enhanced switch to make sure all columns are covered and removes complexity.

* remove duplicate row creation for ngs

* Rename `Instrument` to `MS Device` in template

* Fix column name

* Fix sheet locking

Excel protected the visible sheet. I do not know why and can only speculate that some reordering was not complete. Creating the hidden sheet second solves the issue.

* replace instrument by ms device for proteomics

* correct spelling

* fix jpa access

* solves #747 add technical replicate

* fix constructors in tests

* use correct methods

* Fix wrong imports

Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

* move test

Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

* Add QBIC_SAMPLE_ID

Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>

---------

Co-authored-by: steffengreiner <steffen.greiner@qbic.uni-tuebingen.de>
@KochTobi KochTobi closed this as completed by moving to Done in Sprint Planning Sep 17, 2024
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core Feature or fix task considered to be in the core product simple Implementation effort
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Edit templates for measurement registration qbicsoftware/data-manager-app
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@sven1103 @KochTobi