fixes #291 : Fix parsing of quantitation files #317
Merged
Conversation
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
… easier to read
…ml so we can catch this error? Something like this to the end of the tests: labman & LABMAN_PID=$! sleep 5 # or 10? kill $LABMAN_PID "
# Conflicts: # .travis.yml
Prevent parsing exception caused by CR newlines Interpret any values listed as "<0.00" as 0.00 Interpret any values listed as ">(some numeric value)" as "(some numeric value)" Interpret any values listed as a bunch of question marks (when you overflow the sensor; usually sample being too concentrated) as the highest quantification value in that particular file Raise an error if, after these fixes, there are any concentration values that are still NaN
AmandaBirmingham
requested review from
ElDeveloper and
antgonza
and removed request for
ElDeveloper
wasade
approved these changes
Aug 9, 2018
antgonza
approved these changes
Aug 10, 2018
| # if there are any NaN concentrations left, there's a problem with the | ||
| # parsing, so throw an error | ||
| if pico_df[conc_col_name].isnull().any(): | ||
| raise ValueError("Some concentrations in pico green quantitation " |
There was a problem hiding this comment.
Is this actually reported to user in the GUI? In other words, when you do this via the GUI and leave NaNs do you see this error?
----- As this is not part of this PR, if the answer is no; let's just open an issue.
There was a problem hiding this comment.
@antgonza Finally hunted this down :) The error is reported to the user in the web browser, albeit in a totally unpolished way:
Would you like me to open an issue to have it reported within the Labman page chrome, like the example below is?
There was a problem hiding this comment.
Thanks. Let's open an issue but make it the least priority possible.
There was a problem hiding this comment.
Will do ;)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
Prevent parsing exception caused by CR newlines
Interpret any values listed as "<0.00" as 0.00
Interpret any values listed as ">some numeric value" as some numeric value
Interpret any concentrations listed as a bunch of question marks (when you overflow the sensor; usually sample being too concentrated) as the highest concentration value in that particular file
Raise an error if, after these fixes, there are any concentration values that are still NaN