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On the EMC's internal galaxy, or UseGalaxy.eu, or another 21.09 server
Use the biomart tool
select ensembl genes 105
select human genes
maybe add filters → gene → limit to external reference (gene names) and symbol BRCA1
results tab at top
send to galaxy
Go!
On the server side I see
Traceback (most recent call last):
File "/srv/galaxy/server/lib/galaxy/tools/__init__.py", line 1760, in handle_single_execution
rval = self.execute(
File "/srv/galaxy/server/lib/galaxy/tools/__init__.py", line 1858, in execute
return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs)
File "/srv/galaxy/server/lib/galaxy/tools/actions/__init__.py", line 552, in execute
self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections)
File "/srv/galaxy/server/lib/galaxy/tools/actions/__init__.py", line 761, in _record_inputs
for name, value in tool.params_to_strings(incoming, trans.app).items():
File "/srv/galaxy/server/lib/galaxy/tools/__init__.py", line 1869, in params_to_strings
return params_to_strings(self.inputs, params, app, nested)
File "/srv/galaxy/server/lib/galaxy/tools/parameters/__init__.py", line 215, in params_to_strings
rval[key] = value if nested or value is None else str(dumps(value, sort_keys=True))
File "/usr/lib/python3.8/json/__init__.py", line 234, in dumps
return cls(
File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
return _iterencode(o, 0)
File "/usr/lib/python3.8/json/encoder.py", line 179, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type bytes is not JSON serializable
The text was updated successfully, but these errors were encountered:
Fix the error reported in galaxyproject#13455 ,
which was due to BioMart sending some binary empty strings as values, e.g. for
the `hsapiens_gene_ensembl__filter.chromosomal_region__file` key.
N.B.: the BioMart tool still doesn't work after this fix (probably BioMart's fault), but
at least Galaxy doesn't fail with the mysterious:
"Error executing tool id 'biomart': Object of type bytes is not JSON serializable"
nsoranzo
added a commit
to nsoranzo/galaxy
that referenced
this issue
Apr 28, 2022
Fix the error reported in galaxyproject#13455 ,
which was due to BioMart sending some binary empty strings as values, e.g. for
the `hsapiens_gene_ensembl__filter.chromosomal_region__file` key.
N.B.: the BioMart tool still doesn't work after this fix (probably BioMart's fault), but
at least Galaxy doesn't fail with the mysterious:
"Error executing tool id 'biomart': Object of type bytes is not JSON serializable"
Steps to reproduce
On the server side I see
The text was updated successfully, but these errors were encountered: