First step for building the mermaid flow chart is to parse all the resources and add them as nodes to the flow chart #555
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
…sources and add them as nodes to the flow chart
ch-kr
reviewed
Feb 14, 2024
Comment on lines
+22
to
+23
| REPOSITORY_ROOT_PATH = str(pathlib.Path(os.path.abspath(__file__)).parent.parent) | ||
| sys.path.insert(0, REPOSITORY_ROOT_PATH) |
There was a problem hiding this comment.
cool -- is this to fix the module import errors? asking because I always run something like this
export PYTHONPATH=/Users/kchao/code/gnomad_methods/:/Users/kchao/code/gnomad_qc/
to fix module imports when running scripts locally (so interested in learning about alternatives)
| ) | ||
|
|
||
| for p in paths: | ||
| if check_file_exists_raise_error(p, error_if_exists=False): |
There was a problem hiding this comment.
should this have error_if_not_exists=True?
| bind_kwargs=bind_kwargs, | ||
| ) | ||
| except (ValueError, DataException, KeyError): | ||
| continue |
There was a problem hiding this comment.
should this have a warning message (since it's currently a silent failure)? or are you expecting that some resources will fail
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Outdated suggestions cannot be applied.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 just the first step for building the flow chart. It adds all of the nodes that refer to resources. It also adds helpful node attributes like a link to the gnomad_qc resource function in the sphinx documentation, node type, node color, node display name, node id to put in the flowchart code.
There is a very basic outline for the QCFlowchart class that will be filled in more as I add things to this