kmoad
commented
6 months ago All annotations should work with rdata reports. This is a bug with the following traceback. It looks like one or more of the annotators is generating data that is difficult to convert to R. We'll work on narrowing down which annoator is the culprit.
root@b59eeb8e513a:/mnt/jobs/kmoad@potomacitgroup.com/240112-182300# oc report input.sqlite -t rdata --debug
Generating rdata report... Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/cravat/cravat_report.py", line 1129, in run_reporter
response_t = loop.run_until_complete(reporter.run())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/nest_asyncio.py", line 99, in run_until_complete
return f.result()
^^^^^^^^^^
File "/usr/local/lib/python3.11/asyncio/futures.py", line 203, in result
raise self._exception.with_traceback(self._exception_tb)
File "/usr/local/lib/python3.11/asyncio/tasks.py", line 277, in __step
result = coro.send(None)
^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/cravat/cravat_report.py", line 586, in run
ret = self.end()
^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/cravat/modules/reporters/rdatareporter/rdatareporter.py", line 91, in end
pyreadr.write_rdata(self.filename, level_data, df_name=f'{self.filename_prefix}_{level}')
File "/usr/local/lib/python3.11/site-packages/pyreadr/pyreadr.py", line 155, in write_rdata
writer.write_r(filename_bytes, file_format, df, df_name, dateformat, datetimeformat, compress)
File "/usr/local/lib/python3.11/site-packages/pyreadr/_pyreadr_writer.py", line 226, in write_r
tcol = transform_data(col, pyreadr_types[column], hasmissing[indx], dateformat, datetimeformat)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pyreadr/_pyreadr_writer.py", line 144, in transform_data
if type(pd_series.dtype) is pd.core.dtypes.dtypes.CategoricalDtype:
^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/core/generic.py", line 6204, in __getattr__
return object.__getattribute__(self, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'dtype'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/cravat/oc.py", line 238, in main
args.func(args)
File "/usr/local/lib/python3.11/site-packages/cravat/cravat_report.py", line 1140, in run_reporter
loop.run_until_complete(reporter.cf.close_db())
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'close_db'
On web interface https://run.opencravat.org/ The rdata generation option works for example data with 1 default annotator selected but doesn't work if more/all annotators (155) are selected. It throws an error like this:
I'm assuming only certain annotations are supported for rdata currently. Is there are documentation for same?