Fix for nested params with the same name #2485
Merged
Conversation
This file contains 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
jacarey
force-pushed
the
fix-nested-params
branch
5 times, most recently
from
ce82477 to
7d39b2a
Compare
nh13
approved these changes
Dec 7, 2021
modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy
Show resolved
Hide resolved
…th the same names at different levels of nesting. Create a deepMerge for command line params to avoid deleting values at the same level on override. Signed-off-by: jay Carey <jay@fulcrumgenomics.com>
jacarey
force-pushed
the
fix-nested-params
branch
from
e849217 to
6f2a8ce
Compare
pditommaso
requested changes
Dec 8, 2021
Signed-off-by: jay Carey <jay@fulcrumgenomics.com>
|
Released along with version 21.12.1-edge |
phue
pushed a commit
to phue/nextflow
that referenced
this pull request
Jan 25, 2022
- Clone `scope` if found for current key to avoid overwriting params with the same names at different levels of nesting. - Create a deepMerge for command line params to avoid deleting values at the same level on override. Signed-off-by: jay Carey <jay@fulcrumgenomics.com>
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Outdated suggestions cannot be applied.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.
This fixes #1982, #2166, #2247 and #2358
The first three issues were caused by a lack of cloning which allowed mutability of values where they should have been immutable.
The last issue required a deep merge vs a
putAllto avoid overwriting multiple values at the same level when you are overriding them on the command line.