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remove dependency to recipe.xml file #62

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jdcourcol opened this issue Jun 15, 2017 · 9 comments
Open

remove dependency to recipe.xml file #62

jdcourcol opened this issue Jun 15, 2017 · 9 comments

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@jdcourcol
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This file is an internal format to BBP. It is also specific to circuit building. It may also contains information that are useless for this tool (such as connectivity).
The current set of tags is also specific to the neo cortical column (blueColumn) for instance, and layers.

@jdcourcol jdcourcol added this to the Open source milestone Jun 15, 2017
@liesbethvanherpe
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Currently, the recipe is parsed into a list of (layer, m-type, e-type)-tuples.

What is common practice for this type of data? An .xml-tree (layers > m-types > e-types), just without the extra info? A .json-file ({: { : [, , ...], : ... }}), a .yaml-file??

The word "layer" could be replaced by a more general indication for an anatomical region.

@mgeplf
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mgeplf commented Jun 21, 2017

My two cents are:

  • XML is overkill IMO
  • json/yaml aren't great for row-style data, however they're usable. Personally, I would say the choice is between json:
[
  {
    "etype": "etype1", 
    "fullmtype": "mtype1", 
    "layer": "1"
  }, 
  {
    "etype": "etype2", 
    "fullmtype": "mtype1", 
    "layer": "1"
  }, 
  {
    "etype": "etype1", 
    "fullmtype": "mtype2", 
    "layer": "1"
  }, 
  {
    "etype": "etype2", 
    "fullmtype": "mtype1", 
    "layer": "2"
  }
]

or something flat, like CSV:

layer,fullmtype,etype
1,mtype1,etype1
1,mtype1,etype2
1,mtype2,etype1
2,mtype1,etype2
  • Agreed about layer, and agree that region is better

@mgeplf
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mgeplf commented Jun 21, 2017

So, it seems that @jdcourcol / @arsenius7 / @liesbethvanherpe and I think that simple CSV is the way to go.

@wvangeit
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I'd say a json is a bit more readable though, but csv is also kind of ok

@wvangeit
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btw, we should also think about fullmtype vs mtype/submtype. I hope the recipe doesn't specify per mtype (without specifying submtype) ?

@wvangeit
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And shouldn't we keep the percentage data, in case we need to something with it in BluePyMM in the future ?

@jdcourcol
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As long as we don't use percentage, there is no reason to have that.

@wvangeit
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the question is, what does it hurt? and we wouldn't have to change the format afterwards.

btw, talking about, in case we use json we could also easily add a format version string.

@jdcourcol
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it hurts as it is useless information for the time being. keep it simple.

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