Adding variant track does not work

[tirohia]

Bug report

unable to add a variant track to an existing browser

Bug summary

Create browser in previous code block.
Create track dict for a variant, taking structure from here, though have converted all the field names to strings so as to form a legitimate dictionary.
Code block fails with :

TraitError: The 'tracks' trait of an IgvBrowser instance contains which expected <traitlets.traitlets.List object at 0x2aaae2818a90>, not the str 'The "type" trait is read-only.'.

from ipyigv import IgvBrowser as Browser, PUBLIC_GENOMES
from ipyigv.options import Track, ReferenceGenome

genomeToUse = ReferenceGenome(**PUBLIC_GENOMES.hg38)
browser = Browser(genome=genomeToUse)
browser


###################### New code block ####################

trackDict = {
  'type': "variant",
  'format': "vcf",
  'url': "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",
  'indexURL': "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi",
  'name': "1KG variants (chr22)",
  'squishedCallHeight': 1,
  'expandedCallHeight': 4,
  'displayMode': "squished",
  'visibilityWindow': 1000
}

Actual outcome

---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-25-2f6618847406> in <module>
     11 }
     12 
---> 13 browser.add_track(trackDict)

~/.local/lib/python3.8/site-packages/ipyigv/ipyigv.py in add_track(self, track)
     72         # List subscript does not work for empty List, so handling this case manually.
     73         if len(self.tracks) == 0:
---> 74             self.tracks = [track]
     75         else:
     76             self.tracks = self.tracks[:] + [track]

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in __set__(self, obj, value)
    602             raise TraitError('The "%s" trait is read-only.' % self.name)
    603         else:
--> 604             self.set(obj, value)
    605 
    606     def _validate(self, obj, value):

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in set(self, obj, value)
    576 
    577     def set(self, obj, value):
--> 578         new_value = self._validate(obj, value)
    579         try:
    580             old_value = obj._trait_values[self.name]

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
    608             return value
    609         if hasattr(self, 'validate'):
--> 610             value = self.validate(obj, value)
    611         if obj._cross_validation_lock is False:
    612             value = self._cross_validate(obj, value)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate(self, obj, value)
   2498             return value
   2499 
-> 2500         value = self.validate_elements(obj, value)
   2501 
   2502         return value

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2637             self.length_error(obj, value)
   2638 
-> 2639         return super(List, self).validate_elements(obj, value)
   2640 
   2641 

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2510                 v = self._trait._validate(obj, v)
   2511             except TraitError as error:
-> 2512                 self.error(obj, v, error)
   2513             else:
   2514                 validated.append(v)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in error(self, obj, value, error, info)
    674                         "expected %s, not %s." % (self.name, chain,
    675                         error.args[1], describe("the", error.args[0])),)
--> 676             raise error
    677         else:
    678             # this trait caused an error

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2508         for v in value:
   2509             try:
-> 2510                 v = self._trait._validate(obj, v)
   2511             except TraitError as error:
   2512                 self.error(obj, v, error)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
    608             return value
    609         if hasattr(self, 'validate'):
--> 610             value = self.validate(obj, value)
    611         if obj._cross_validation_lock is False:
    612             value = self._cross_validate(obj, value)

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/trait_types.py in validate(self, obj, value)
    161     def validate(self, obj, value):
    162         if isinstance(value, dict):
--> 163             return super(InstanceDict, self).validate(obj, self.klass(**value))
    164         else:
    165             return super(InstanceDict, self).validate(obj, value)

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/widget.py in __init__(self, **kwargs)
    410         """Public constructor"""
    411         self._model_id = kwargs.pop('model_id', None)
--> 412         super(Widget, self).__init__(**kwargs)
    413 
    414         Widget._call_widget_constructed(self)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in __init__(self, *args, **kwargs)
   1075             for key, value in kwargs.items():
   1076                 if self.has_trait(key):
-> 1077                     setattr(self, key, value)
   1078                 else:
   1079                     # passthrough args that don't set traits to super

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in __set__(self, obj, value)
    600         """
    601         if self.read_only:
--> 602             raise TraitError('The "%s" trait is read-only.' % self.name)
    603         else:
    604             self.set(obj, value)

TraitError: The 'tracks' trait of an IgvBrowser instance contains  which expected <traitlets.traitlets.List object at 0x2aaae2818a90>, not the str 'The "type" trait is read-only.'.

Expected outcome

A track added to the browser

Version Info
jupyter lab 2.2.4
python 3.8.1

[tirohia]

As an addendum, if one removes the trait entry from the dict, then the error changes to:

TraitError: The 'tracks' trait of an IgvBrowser instance contains which expected <traitlets.traitlets.List object at 0x2aaae2814520>, not the str "The 'color' trait of a VariantTrack instance expected a valid HTML color, not the Sentinel traitlets.Undefined.".

No further modifications change the error message, which is in full:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in get(self, obj, cls)
    534         try:
--> 535             value = obj._trait_values[self.name]
    536         except KeyError:

KeyError: 'color'

During handling of the above exception, another exception occurred:

TraitError                                Traceback (most recent call last)
<ipython-input-18-4863a6327e30> in <module>
      5 }
      6 
----> 7 browser.add_track(trackDict)

~/.local/lib/python3.8/site-packages/ipyigv/ipyigv.py in add_track(self, track)
     72         # List subscript does not work for empty List, so handling this case manually.
     73         if len(self.tracks) == 0:
---> 74             self.tracks = [track]
     75         else:
     76             self.tracks = self.tracks[:] + [track]

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in __set__(self, obj, value)
    602             raise TraitError('The "%s" trait is read-only.' % self.name)
    603         else:
--> 604             self.set(obj, value)
    605 
    606     def _validate(self, obj, value):

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in set(self, obj, value)
    576 
    577     def set(self, obj, value):
--> 578         new_value = self._validate(obj, value)
    579         try:
    580             old_value = obj._trait_values[self.name]

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
    608             return value
    609         if hasattr(self, 'validate'):
--> 610             value = self.validate(obj, value)
    611         if obj._cross_validation_lock is False:
    612             value = self._cross_validate(obj, value)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate(self, obj, value)
   2498             return value
   2499 
-> 2500         value = self.validate_elements(obj, value)
   2501 
   2502         return value

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2637             self.length_error(obj, value)
   2638 
-> 2639         return super(List, self).validate_elements(obj, value)
   2640 
   2641 

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2510                 v = self._trait._validate(obj, v)
   2511             except TraitError as error:
-> 2512                 self.error(obj, v, error)
   2513             else:
   2514                 validated.append(v)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in error(self, obj, value, error, info)
    674                         "expected %s, not %s." % (self.name, chain,
    675                         error.args[1], describe("the", error.args[0])),)
--> 676             raise error
    677         else:
    678             # this trait caused an error

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value)
   2508         for v in value:
   2509             try:
-> 2510                 v = self._trait._validate(obj, v)
   2511             except TraitError as error:
   2512                 self.error(obj, v, error)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
    608             return value
    609         if hasattr(self, 'validate'):
--> 610             value = self.validate(obj, value)
    611         if obj._cross_validation_lock is False:
    612             value = self._cross_validate(obj, value)

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/trait_types.py in validate(self, obj, value)
    161     def validate(self, obj, value):
    162         if isinstance(value, dict):
--> 163             return super(InstanceDict, self).validate(obj, self.klass(**value))
    164         else:
    165             return super(InstanceDict, self).validate(obj, value)

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/widget.py in __init__(self, **kwargs)
    413 
    414         Widget._call_widget_constructed(self)
--> 415         self.open()
    416 
    417     def __del__(self):

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/widget.py in open(self)
    426         """Open a comm to the frontend if one isn't already open."""
    427         if self.comm is None:
--> 428             state, buffer_paths, buffers = _remove_buffers(self.get_state())
    429 
    430             args = dict(target_name='jupyter.widget',

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/widget.py in get_state(self, key, drop_defaults)
    516         for k in keys:
    517             to_json = self.trait_metadata(k, 'to_json', self._trait_to_json)
--> 518             value = to_json(getattr(self, k), self)
    519             if not PY3 and isinstance(traits[k], Bytes) and isinstance(value, bytes):
    520                 value = memoryview(value)

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in __get__(self, obj, cls)
    573             return self
    574         else:
--> 575             return self.get(obj, cls)
    576 
    577     def set(self, obj, value):

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in get(self, obj, cls)
    546                 )
    547             with obj.cross_validation_lock:
--> 548                 value = self._validate(obj, default)
    549             obj._trait_values[self.name] = value
    550             obj._notify_observers(Bunch(

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
    608             return value
    609         if hasattr(self, 'validate'):
--> 610             value = self.validate(obj, value)
    611         if obj._cross_validation_lock is False:
    612             value = self._cross_validate(obj, value)

~/.local/lib/python3.8/site-packages/ipywidgets/widgets/trait_types.py in validate(self, obj, value)
     50                 return value
     51 
---> 52         self.error(obj, value)
     53 
     54 

~/.local/lib/python3.8/site-packages/traitlets/traitlets.py in error(self, obj, value, error, info)
    688                     e = "The '%s' trait expected %s, not %s." % (
    689                         self.name, self.info(), describe("the", value))
--> 690                 raise TraitError(e)
    691 
    692     def get_metadata(self, key, default=None):

TraitError: The 'tracks' trait of an IgvBrowser instance contains  which expected <traitlets.traitlets.List object at 0x2aaae2814520>, not the str "The 'color' trait of a VariantTrack instance expected a valid HTML color, not the Sentinel traitlets.Undefined.".

[vdauwera]

I just ran into the same error, did you ever find a fix or workaround?

[vdauwera]

Ah! Checked the v1.0 API doc and found that adding 'color': "#000000" to the track dictionary made the track appear!