User: mcpherson

gravatar for mcpherson
mcpherson40
Reputation:
40
Status:
New User
Location:
Los Alamos National Laboratory
Website:
https://bee.lanl.gov/
Last seen:
1 year, 2 months ago
Joined:
1 year, 7 months ago
Email:
m********@lanl.gov

Working to evaluate CWL for large-scale HPC compute/analytics workflows.

Posts by mcpherson

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Parse CWL to graph data structure or database?
... For those arriving via search, I'm going to answer my own question as a summary of what I've found searching and experimenting. Many thanks to Michael for his responses and help. Again, the premise. We (LANL BEE) view a workflow most naturally as a graph. We also favor the "property store" model ov ...
written 14 months ago by mcpherson40
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Answer: A: More examples of parser_v1.0.py usage?
... For those coming here via search, I'm going to wrap up this thread and answer my own question: Other than Michael's (much appreciated) answer above, I was unable to find any examples of using the auto-generated parser in "larger" projects. That doesn't mean that it isn't useful, though. For more co ...
written 14 months ago by mcpherson40
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Comment: C: More examples of parser_v1.0.py usage?
... Thanks for pointing me to that, Michael. Possible naive question: If `parser_v1_0.py` is auto generated from some Schema Salad description, how is it that the `parser_v1_0.py` file is shown as edited in the pull request? Would that not require changes to the Schema Salad description (in another rep ...
written 14 months ago by mcpherson40
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Comment: C: More examples of parser_v1.0.py usage?
... ```python >>> import cwl_utils.parser_v1_0 as cwl >>> help(cwl) ``` is helping. Doh! More examples would still be useful. Another approach that I may look at: export to RDF and use `rdflib` to parse. ...
written 15 months ago by mcpherson40
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More examples of parser_v1.0.py usage?
... Continuing my effort to parse CWL into a Neo4j graph database... Michael pointed me at the automatically generated `parser_v1.0.py` code and some examples in the `cwl-utils` repository. These are pretty simple examples and I'm finding it a bit overwhelming to dig through the generated source and un ...
python cwl parser written 15 months ago by mcpherson40
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Comment: A: Parse CWL to graph data structure or database?
... Michael, Thanks for your prompt response. Honestly, I was hoping my first post would result in a "Hey, we already did that..." reply from the community ;-) We were able to run the `cwltool --print...` versions. They seem to work fine. I probably didn't look hard enough at `cwl-utils`. I need to ...
written 16 months ago by mcpherson40
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Parse CWL to graph data structure or database?
... We're considering building a new "runner". We envision using a graph database (e.g. Neo4j) to describe and control the running workflow. Step one is to convert a CWL file to a graph. Is there any extant software/library to do this? We've looked at extracting parse code from `cwltool` or Toil but tha ...
neo4j cwl written 16 months ago by mcpherson40 • updated 6 months ago by ngsbioinformatics30

Latest awards to mcpherson

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Parse CWL to graph data structure or database?

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