Consolidate most of the code about the run folder in npg_tracking::illumina::run::folder role #812
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
mgcam
force-pushed
the
simplify_locations
branch
from
86a6ba5 to
5bb1bc4
Compare
Removed largely outdated npg_tracking::illumina::run::folder::location role. Moved a few updated relevant expressions to npg_tracking::illumina::run::folder role. Simplified the code that infers the run folder path. Excluded provisions for tests from the producton code. Brought 'npg_tracking' configuration test file up-to-date and set the updated unit tests for the npg_tracking::illumina::run::folder role to retrieve the value of the test staging area prefix from this configuration file.
Made npg_tracking::illumina::run::folder role inherit from npg_tracking::illumina::run::short_info role since these two roles are never used separately.
... from npg_tracking::illumina::runfolder to npg_tracking::illumina::run::folder.
Merged the remaining code from npg_tracking::illumina::run::short_info role into the npg_tracking::illumina::run::folder role.
The Config directory does not exist in NovaSeqX run folders.
mgcam
force-pushed
the
simplify_locations
branch
from
5bb1bc4 to
4424adf
Compare
mgcam
added a commit
to mgcam/npg_qc
that referenced
this pull request
Apr 4, 2024
This part contained the code that failed the compilation following the deletion of teh short_info role in wtsi-npg/npg_tracking#812
mgcam
added a commit
to mgcam/npg_seq_pipeline
that referenced
this pull request
Apr 4, 2024
They were testing the ability to infer different paths, which is already tested in npg_tracking GitHub repo. The deleted tests were for some unlikely or old scenarios. Some of the deleted tests started to fail following the reorganisation and simplification of the npg_tracking::illumina::runfolder class and its dependencies in wtsi-npg/npg_tracking#812
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 is a huge simplification of the code we have in the npg_tracking::illumina namespace. We will be left with
lib/npg_tracking/illumina/runfolder.pm
lib/npg_tracking/illumina/run/long_info.pm
lib/npg_tracking/illumina/run/folder.pm
lib/npg_tracking/illumina/run.pm
instead of
lib/npg_tracking/illumina/runfolder.pm
lib/npg_tracking/illumina/run/short_info.pm
lib/npg_tracking/illumina/run/folder/location.pm
lib/npg_tracking/illumina/run/long_info.pm
lib/npg_tracking/illumina/run/folder.pm
lib/npg_tracking/illumina/run.pm