First step for building the mermaid flow chart is to parse all the resources and add them as nodes to the flow chart#555
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…sources and add them as nodes to the flow chart
ch-kr
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Feb 14, 2024
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| REPOSITORY_ROOT_PATH = str(pathlib.Path(os.path.abspath(__file__)).parent.parent) | ||
| sys.path.insert(0, REPOSITORY_ROOT_PATH) |
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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)
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| for p in paths: | ||
| if check_file_exists_raise_error(p, error_if_exists=False): |
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should this have error_if_not_exists=True?
| bind_kwargs=bind_kwargs, | ||
| ) | ||
| except (ValueError, DataException, KeyError): | ||
| continue |
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should this have a warning message (since it's currently a silent failure)? or are you expecting that some resources will fail
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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