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How are templates expanded in structured_name? #14

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stain opened this issue Nov 7, 2018 · 2 comments
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How are templates expanded in structured_name? #14

stain opened this issue Nov 7, 2018 · 2 comments
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@stain
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stain commented Nov 7, 2018

structured_name seems to define a simple template system:

This field can refer to other fields within the same or other objects. For example, a string like "HCV1a [taxonomy:$taxonomy] mutation detection"

It is not defined what is the syntax for the $magic variable, neither if this is restricted to looking up direct neighbouring keys of provenance_domain.

The example also seems to imply that adding arbitrary non-namespaced keys like taxonomy is allowed, but nowhere else is this clarified.

This should be clarified or removed.

@stain
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stain commented Nov 7, 2018

JSON Pointer might be one way to do the referencing. Relative JSON pointers might be better for resolving neighbours.

@stain stain added the discuss Discussion/opinions requested label Nov 7, 2018
@HadleyKing
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HadleyKing commented Nov 19, 2018

This field was created to fulfill a function that it is not doing in it's current state. The thought was to have a field that was automatically generated based on the templated info already present in the BCO. I believe at this stage that it is out side the scope of what we need to develop working examples. I think we should re-examine this at a later date. I am going to remove this field for the time being.

Remove structured_name from spec:

  • user_guide.md:201:
  • user_guide.md:435:
  • provenance-domain.md:12:
  • provenance-domain.md:36:
  • provenance-domain.md:41:
  • base_type_BioCompute.json:49:
  • HCV1a.json:8:

HadleyKing added a commit that referenced this issue Nov 19, 2018
This field was created to fulfill a function that it is not doing in it's current state. The thought was to have a field that was automatically generated based on the templated info already present in the BCO. I believe at this stage that it is out side the scope of what we need to develop working examples. I think we should re-examine this at a later date. I am going to remove this field for the time being.

Apply #14
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