fix: AppBio QuantStudio RT-PCR - force calculate data to have the cycle threshold result data source#1128
Open
joshua-benchling wants to merge 9 commits intomainfrom
Conversation
…ld result is missing
nathan-stender
requested changes
Dec 4, 2025
Collaborator
nathan-stender
left a comment
nathan-stender
left a comment
There was a problem hiding this comment.
Code LGTM - looks like there are some test f ailures to fix
james-leinas
requested changes
Dec 18, 2025
Collaborator
james-leinas
left a comment
james-leinas
left a comment
There was a problem hiding this comment.
@joshua-benchling -- left comments for one representative file from the testdata directory.
For Calibration related fields, lets remap those to the Device Control Document
tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.json
Outdated
Show resolved
Hide resolved
tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.json
Outdated
Show resolved
Hide resolved
tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.json
Outdated
Show resolved
Hide resolved
tests/parsers/appbio_quantstudio/testdata/appbio_quantstudio_minimal_test01.json
Outdated
Show resolved
Hide resolved
...udio_designandanalysis/testdata/appbio_quantstudio_design_and_analysis_example15_v1.5.2.json
Show resolved
Hide resolved
joshua-benchling
force-pushed
the
jherna/skip-calc-docs-when-missing-measurement-doc-data-source-reference
branch
from
009f2b1 to
cc29ed0
Compare
joshua-benchling
force-pushed
the
jherna/skip-calc-docs-when-missing-measurement-doc-data-source-reference
branch
from
cc29ed0 to
3f3f1c1
Compare
nathan-stender
previously approved these changes
Jan 12, 2026
james-leinas
requested changes
Jan 14, 2026
Collaborator
james-leinas
left a comment
james-leinas
left a comment
There was a problem hiding this comment.
One note on quantstudio_example_10 example
Collaborator
There was a problem hiding this comment.
@joshua-benchling -- PR generally LGTM but notice that this file specifically has duplicated fields of calculated data documents (Cq, Quantity, Quantity SD) that are also listed as custom information document fields. Lets remove the duplicated custom information fields.
Fields like Quantity, Quantity SD, Ct Mean, Ct SD, Y-Intercept, Slope, Efficiency, and R(superscript 2) are already captured in calculated data documents and should not be duplicated in custom information documents.
- Remove 'Cq Conf' from sample document (duplicated with 'cq confidence' in calculated data) - Remove 'Task', 'Target Name', 'Sample Color', 'Target Color' fields from processed data document (keep only in sample document)
james-leinas
approved these changes
Jan 21, 2026
nathan-stender
approved these changes
Jan 28, 2026
ajcariaga16
approved these changes
Feb 3, 2026
…nt-doc-data-source-reference
…nt-doc-data-source-reference
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.