Comparison of models

[lemoncxd]

We are trying to make a model comparison, but the results do not come out, I don't know why。

This is my code：

memote report diff E:/file/latest571_meto.xml E:/file/iHZ565.xml E:/file/iGD1575.xml E:/file/iCC541.xml

This is my result：

Writing diff report to 'index.html'.
Traceback (most recent call last):
  File "e:\software\python35\lib\runpy.py", line 184, in _run_module_as_main
    "__main__", mod_spec)
  File "e:\software\python35\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "E:\software\python35\Scripts\memote.exe\__main__.py", line 7, in <module>
  File "e:\software\python35\lib\site-packages\click\core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "e:\software\python35\lib\site-packages\click\core.py", line 717, in main
    rv = self.invoke(ctx)
  File "e:\software\python35\lib\site-packages\click\core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "e:\software\python35\lib\site-packages\click\core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "e:\software\python35\lib\site-packages\click\core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "e:\software\python35\lib\site-packages\click\core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "e:\software\python35\lib\site-packages\memote\suite\cli\reports.py", line 287, in diff
    file_handle.write(api.diff_report(diff_results, config))
  File "e:\software\python35\lib\site-packages\memote\suite\api.py", line 174, in diff_report
    report = DiffReport(diff_results=diff_results, configuration=config)
  File "e:\software\python35\lib\site-packages\memote\suite\reporting\diff.py", line 45, in __init__
    self.result = self.format_and_score_diff_data(diff_results)
  File "e:\software\python35\lib\site-packages\memote\suite\reporting\diff.py", line 56, in format_and_score_diff_data
    meta = result["meta"]
KeyError: 'meta'

Thanks in advance for your help.

[Midnighter]

Hi, thank you for the report. As suggested in the issue template, can you please paste the output of the following command in the environment where you have memote installed.

python -c "import memote;memote.show_versions()"

[lemoncxd]

Hi, the output is like this

System Information

OS Windows OS-release 10 Python 3.5.2

Package Versions

Jinja2 2.10 click 7.0 click-configfile 0.2.3 click-log 0.3.2 cobra 0.15.3 cookiecutter 1.7.0 depinfo 1.4.0 equilibrator-api 0.1.26 future 0.16.0 gitpython 3.1.0 goodtables 2.4.2 importlib-resources 1.0.2 lxml 4.2.4 memote 0.9.13 numpydoc 0.9.2 pandas 0.23.4 pip 10.0.1 pylru 1.2.0 pytest 5.3.5 requests 2.19.1 ruamel.yaml 0.16.10 setuptools 20.10.1 six 1.11.0 sqlalchemy 1.2.11 sympy 1.2 travis-encrypt 1.1.2

Is it because the version is not right?

[Midnighter]

No, you're up-to-date. I'll dig into it today.

[Midnighter]

Hi @lemoncxd, do you see any other error messages above the traceback that you posted here? I just tried running the diff report with three models and it worked perfectly. (Of course, I don't have the same models as you do.) Also, our continuous testing includes the diff report on Windows and we haven't noticed any problems.

[lemoncxd]

It seems that because of the different versions of our models, we cannot use memote for comparison, because the cobra version required by memote is higher than 0.15.3, but this version of cobra cannot read our model.

[Midnighter]

I see, that is unfortunate. Is it because of GPR annotations in the notes field? In general, it should be possible to "upgrade" an SBML document by loading it and saving it again. Maybe @matthiaskoenig, you have an idea for how to best achieve this?