search

sys-bio / temp-biomodels

Temporary place for coordination of updating existing Biomodels
Creative Commons Zero v1.0 Universal
2 stars 2 forks source link

Remove invalid XPP files #23

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

6% of the XPP files appear to be invalid.

jonrkarr commented 3 years ago

From the comments in the XPP files, it appears that they were all autogenerated by the System Biology Format Converter (http://sbfc.sourceforge.net/) from SBML files.

In the interest of providing the community working files, I will remove XPP files that are invalid.

In addition, I'll file a bug report for the System Biology Format Converter with examples of invalid files.

luciansmith commented 3 years ago

I would make sure that the latest version of the SBFC also generates invalid XPP before filing a bug report--most of the XPP files were generated years ago, and the converter could have been fixed since then.

jonrkarr commented 3 years ago

Good point. I'll try that first.

Seeing as SBML files may have been modified, shall we generate the XPP files to they are consistent?

jonrkarr commented 3 years ago

Spot checking, sbfc-1.3.7 (latest) creates the same invalid XPP.

luciansmith commented 3 years ago

Hmm. If it's not too much trouble, then yes, let's regenerate the XPP files. (If they're actually useful for people, we could go ahead and generate them all, if we wanted? I wouldn't spend too much effort on this, though.)

I suppose the basic script could be:

Sounds like a bug report is indeed in order!

jonrkarr commented 3 years ago

Just pushed this to #31

jonrkarr commented 3 years ago

SBFC bug report: https://sourceforge.net/p/sbfc/bugs/16/

hsauro commented 3 years ago

I'd remove them, or get them fixed. Also are the models special in that they need XPP support? It would probably be better to only have SBML/SEDML files and update the XPP converter so that users can create the XPP themselves if they need it,

Herbert

On Thu, Apr 22, 2021 at 11:34 PM Jonathan Karr @.***> wrote:

6% of the XPP files appear to be invalid.

  • Should we recommend removing them?
  • How are they being generated? Can someone be pushed to fix the program which is generating this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sys-bio/temp-biomodels/issues/23, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDUXXWCXZRTEM22ZBO3TKEIEXANCNFSM43OAGIPQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org @.*** Books: http://books.analogmachine.org/

jonrkarr commented 3 years ago

Users can download the use the converter themselves. Only took me a couple minutes to set it up.

Mainly, I want to remove bad files so users don't run into problems. Also, I'd like to see the files be consistent with the SBML.

I'd also prefer to see the XPP files removed because I doubt many people want them. But, I don't have a strong preference.

luciansmith commented 3 years ago

I also don't have a strong feeling about the files, though I agree that biomodels should never provide an invalid file of any type.

I suppose it makes the most sense to just ask the Biomodels team what they want. @ntung and @rsmsheriff, opinions?

Our options are:

  1. Keep the valid XPP files, and remove the invalid ones
  2. Generate XPP files for everything (removing the invalid ones)
  3. Remove all XPP files.
jonrkarr commented 3 years ago

Right now (2) is set up.