Error: Circular Reference Detected on Table Display

[JohnOmernik]

So this may appear to be similar to #7935 is is actually different. I was running a Dataframe into a BeakerX table and saw that I had some int64 columns and assumed they were the issue. They were not.

However, I had two columns that were of type bool in df.dtypes. When I converted these two to type object, then the dataframe was displayed correctly. Thus what ever caused an issue with int64 probably needs to be looked at for type bool as well.

This is on Pandas version 0.24.2 and BeakerX 1.4.0

[JohnOmernik]

Example Code:

import pandas as pd
from beakerx import *
from beakerx.object import beakerx
#Display mode: TableDisplay Widget
beakerx.pandas_display_table()
df = pd.DataFrame(data=np.zeros((5,5)), index=pd.Int64Index([0, 1, 2, 3, 4], dtype='int64'))
df # Displays properly

df.dtypes

0 float64 1 float64 2 float64 3 float64 4 float64 dtype: object

df[2] = df[2].astype(bool)
df.dtypes

0 float64 1 float64 2 bool 3 float64 4 float64 dtype: object

df # Errors out

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj)
    916             method = get_real_method(obj, self.print_method)
    917             if method is not None:
--> 918                 method()
    919                 return True
    920 

/opt/conda/lib/python3.7/site-packages/beakerx/runtime.py in f()
    467     def __get__(self, model_instance, model_class):
    468         def f():
--> 469             display_html(TableDisplay(model_instance))
    470 
    471         return f

/opt/conda/lib/python3.7/site-packages/beakerx/tabledisplay/tabledisplay.py in __init__(self, *args, **kwargs)
    211         super(TableDisplay, self).__init__(**kwargs)
    212         self.chart = Table(*args, **kwargs)
--> 213         self.model = self.chart.transform()
    214         self.on_msg(self.handle_msg)
    215         self.details = None

/opt/conda/lib/python3.7/site-packages/beakerx/utils.py in transform(self)
     53 
     54     def transform(self):
---> 55         model = json.dumps(self, cls=ObjectEncoder)
     56         return json.loads(model)
     57 

/opt/conda/lib/python3.7/json/__init__.py in dumps(obj, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, **kw)
    236         check_circular=check_circular, allow_nan=allow_nan, indent=indent,
    237         separators=separators, default=default, sort_keys=sort_keys,
--> 238         **kw).encode(obj)
    239 
    240 

/opt/conda/lib/python3.7/json/encoder.py in encode(self, o)
    197         # exceptions aren't as detailed.  The list call should be roughly
    198         # equivalent to the PySequence_Fast that ''.join() would do.
--> 199         chunks = self.iterencode(o, _one_shot=True)
    200         if not isinstance(chunks, (list, tuple)):
    201             chunks = list(chunks)

/opt/conda/lib/python3.7/json/encoder.py in iterencode(self, o, _one_shot)
    255                 self.key_separator, self.item_separator, self.sort_keys,
    256                 self.skipkeys, _one_shot)
--> 257         return _iterencode(o, 0)
    258 
    259 def _make_iterencode(markers, _default, _encoder, _indent, _floatstr,

ValueError: Circular reference detected

[aolwas]

I just ran into the same problem with Pandas 0.24.2 and BeakerX 1.4.1

[Gerenuk]

Had the same bug with all of float16, float32, int8, int16, int32, ... for TableDisplay(pd.DataFrame(np.array([[1]], dtype="float32")))

[jvivian-atreca]

Confirming I get the same bug using the same versions of pandas and beakerx as the original poster.

[maoserr]

Hi all,

I recently saw this issue, I have been able to fix it for me using the following changes:

In beakerx_base\util.py, Line 188, replace the function with the following code:

class ObjectEncoder(json.JSONEncoder):
    def default(self, obj):
        if isinstance(obj, datetime):
            return date_time_2_millis(obj)
        elif isinstance(obj, Enum):
            return obj.value
        elif isinstance(obj, Color):
            return obj.hex()
        elif isinstance(obj, pd.Series):
            return obj.tolist()
        elif isinstance(obj, np.ndarray):
            return obj.tolist()
        elif isinstance(obj, np.generic):
            return obj.item()
        elif hasattr(obj, "__dict__"):
            d = dict(
                (key, value)
                for key, value in inspect.getmembers(obj)
                if value is not None
                and not key == "Position"
                and not key == "colorProvider"
                and not key == "toolTipBuilder"
                and not key == "parent"
                and not key.startswith("__")
                and not inspect.isabstract(value)
                and not inspect.isbuiltin(value)
                and not inspect.isfunction(value)
                and not inspect.isgenerator(value)
                and not inspect.isgeneratorfunction(value)
                and not inspect.ismethod(value)
                and not inspect.ismethoddescriptor(value)
                and not inspect.isroutine(value)
            )
            return d
        return json.JSONEncoder.default(self,obj)