"TypeError: data type 'Float64' not understood" Error in Export

[syncrotron]

I encountered an error when exporting "Export data" button in the UI, where the export would fail with the error:

(bulkvis) shorovatin@TARAS:~/assets$ bulkvis serve /home/shorovatin/assets/data --show
2022-04-29 11:44:13,365 Starting Bokeh server version 2.1.1 (running on Tornado 6.0.4)
2022-04-29 11:44:13,366 User authentication hooks NOT provided (default user enabled)
2022-04-29 11:44:13,367 Bokeh app running at: http://localhost:5006/bulkvis_server
2022-04-29 11:44:13,367 Starting Bokeh server with process id: 276595
2022-04-29 11:44:13,604 Using dir: /home/shorovatin/assets/data
2022-04-29 11:44:13,709 404 GET /favicon.ico (127.0.0.1) 0.36ms
2022-04-29 11:44:13,784 WebSocket connection opened
2022-04-29 11:44:13,784 ServerConnection created
2022-04-29 11:44:26,522 Exporting to /home/shorovatin/assets/data/WIMMER_20220224_1124_FAR92883_MN23001_sequencing_run_HMW1_2210210f_bulkvis-read_0-36000000_ch_390.fast5
2022-04-29 11:44:26,524 error handling message
 message: Message 'PATCH-DOC' content: {'events': [{'kind': 'MessageSent', 'msg_type': 'bokeh_event', 'msg_data': {'event_name': 'button_click', 'event_values': {}}}], 'references': []} 
 error: TypeError("data type 'Float64' not understood")
Traceback (most recent call last):
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/server/protocol_handler.py", line 90, in handle
    work = await handler(message, connection)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/server/session.py", line 67, in _needs_document_lock_wrapper
    result = func(self, *args, **kwargs)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/server/session.py", line 261, in _handle_patch
    message.apply_to_document(self.document, self)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/protocol/messages/patch_doc.py", line 100, in apply_to_document
    doc._with_self_as_curdoc(lambda: doc.apply_json_patch(self.content, setter))
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/document/document.py", line 1150, in _with_self_as_curdoc
    return f()
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/protocol/messages/patch_doc.py", line 100, in <lambda>
    doc._with_self_as_curdoc(lambda: doc.apply_json_patch(self.content, setter))
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/document/document.py", line 398, in apply_json_patch
    self._trigger_on_message(event_json["msg_type"], event_json["msg_data"])
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/document/document.py", line 687, in _trigger_on_message
    cb(msg_data)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/document/document.py", line 354, in apply_json_event
    model._trigger_event(event)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/util/callback_manager.py", line 85, in _trigger_event
    self._document._with_self_as_curdoc(invoke)
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/document/document.py", line 1150, in _with_self_as_curdoc
    return f()
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bokeh/util/callback_manager.py", line 72, in invoke
    callback()
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bulkvis/bulkvis_server/main.py", line 1084, in export_data
    cfg_dr["out"],
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/bulkvis/bulkvis_server/main.py", line 82, in export_read_file
    dtype="Float64",
  File "/home/shorovatin/miniconda3/envs/bulkvis/lib/python3.7/site-packages/h5py/_hl/attrs.py", line 149, in create
    dtype = numpy.dtype(dtype) # In case a string, e.g. 'i8' is passed
TypeError: data type 'Float64' not understood

This appears to be an incompatibility with h5py's named type Float64 and numpy's float64 type. Upon editing all instances of Float64 -> float64 within /bulkvis_server/main.py, the error resolves, with bulkvis being able to export the selected region to a fast5 as expected.

I am creating this issue to document a potential solution to the above error. Any feedback would be appreciated.

I am running on Ubuntu 20.04, using a conda environment outlined in provided yaml in the 2.0 branch.

[KiranQureshi53]

Hey, are you still looking for it resolution?