Updates with new Files #77

mavaylon1 · 2024-11-20T00:31:08Z

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mavaylon1 · 2024-11-20T00:33:14Z

@rly You (I believe) have local changes for command_line_interface.py that is somewhat reflected here. Can you make sure to add those in a PR.

for more information, see https://pre-commit.ci

oruebel · 2024-11-20T16:50:47Z

src/nwb_benchmarks/benchmarks/time_remote_slicing.py

        ),
-        object_name="ElectricalSeriesAp",
+        object_name="ElectricalSeries",  # TODO


Is this still a TODO item or can the comment be removed?

oruebel

Looks good to me. I added a few additional minor changes, so I'll let @rly review and approve

oruebel · 2024-11-21T01:07:23Z

It looks like one of the configuations may have an error. I'm seeing:

For parameters: 'https://dandi-api-staging-dandisets.s3.amazonaws.com/blobs/914/6aa/9146aa46-9c01-45be-9d2a-693e6a7bb778', 'ElectricalSeries', (slice(0, 30000, None), slice(0, 384, None))
             Traceback (most recent call last):
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/server.py", line 179, in _run_server
                 _run(run_args)
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/run.py", line 65, in _run
                 skip = benchmark.do_setup()
                        ^^^^^^^^^^^^^^^^^^^^
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 80, in do_setup
                 result = Benchmark.do_setup(self)
                          ^^^^^^^^^^^^^^^^^^^^^^^^
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/_base.py", line 632, in do_setup
                 setup(*self._current_params)
               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/benchmarks/time_remote_slicing.py", line 186, in setup
                 self.neurodata_object = get_object_by_name(nwbfile=self.nwbfile, object_name=object_name)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/core/_nwb_helpers.py", line 20, in get_object_by_name
                 raise ValueError(f"The specified object name ({object_name}) is not in the NWBFile.")
             ValueError: The specified object name (ElectricalSeries) is not in the NWBFile.

mavaylon1 · 2024-11-21T01:14:23Z

Another error that I am seeing is for Zarr:


[62.50%] ··· time_remote_file_reading.NWBZarrFileReadBenchmark.time_read_zarr_nwbfile                                                                                                                                                                                       failed

[62.50%] ··· ============================================================== ========

                                         s3_url                                     

             -------------------------------------------------------------- --------

              s3://dandiarchive/zarr/2e8d0cb4-c5d4-4abc-88d8-2581c3cf7f5a/   failed 

              s3://dandiarchive/zarr/c8c6b848-fbc6-4f58-85ff-e3f2618ee983/   failed 

             ============================================================== ========

             For parameters: 's3://dandiarchive/zarr/2e8d0cb4-c5d4-4abc-88d8-2581c3cf7f5a/'

             Traceback (most recent call last):

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/server.py", line 179, in _run_server

                 _run(run_args)

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/run.py", line 72, in _run

                 result = benchmark.do_run()

                          ^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run

                 return self.run(*self._current_params)

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 165, in run

                 samples, number = self.benchmark_timing(

                                   ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 258, in benchmark_timing

                 timing = timer.timeit(number)

                          ^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/timeit.py", line 180, in timeit

                 timing = self.inner(it, self.timer)

                          ^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "<timeit-src>", line 6, in inner

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 90, in func

                 self.func(*param)

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/benchmarks/time_remote_file_reading.py", line 273, in time_read_zarr_nwbfile

                 self.nwbfile, self.io = read_zarr_nwbfile(s3_url=s3_url, mode="r")

                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py", line 264, in read_zarr_nwbfile

                 nwbfile = io.read()

                           ^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call

                 return func(args[0], **pargs)

                        ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/backends/io.py", line 56, in read

                 f_builder = self.read_builder()

                             ^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call

                 return func(args[0], **pargs)

                        ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1335, in read_builder

                 f_builder = self.__read_group(self.__file, ROOT_NAME)

                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1400, in __read_group

                 sub_builder = self.__read_group(sub_group, sub_name)

                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1400, in __read_group

                 sub_builder = self.__read_group(sub_group, sub_name)

                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1409, in __read_group

                 self.__read_links(zarr_obj=zarr_obj, parent=ret)

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1428, in __read_links

                 target_name, target_zarr_obj = self.resolve_ref(link)

                                                ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 734, in resolve_ref

                 target_zarr_obj = self.__open_file_consolidated(store=source_file,

                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 496, in __open_file_consolidated

                 return zarr.open_consolidated(store=store,

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/convenience.py", line 1334, in open_consolidated

                 store = normalize_store_arg(

                         ^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/storage.py", line 197, in normalize_store_arg

                 return normalize_store(store, storage_options, mode)

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/storage.py", line 169, in _normalize_store_arg_v2

                 raise ValueError("storage_options passed with non-fsspec path")

             ValueError: storage_options passed with non-fsspec path

             

             For parameters: 's3://dandiarchive/zarr/c8c6b848-fbc6-4f58-85ff-e3f2618ee983/'

             Traceback (most recent call last):

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/server.py", line 179, in _run_server

                 _run(run_args)

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/run.py", line 72, in _run

                 result = benchmark.do_run()

                          ^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run

                 return self.run(*self._current_params)

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 165, in run

                 samples, number = self.benchmark_timing(

                                   ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 258, in benchmark_timing

                 timing = timer.timeit(number)

                          ^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/timeit.py", line 180, in timeit

                 timing = self.inner(it, self.timer)

                          ^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "<timeit-src>", line 6, in inner

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 90, in func

                 self.func(*param)

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/mark.py", line 105, in wrapper

                 return func(*args, **kwargs)

                        ^^^^^^^^^^^^^^^^^^^^^

               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/benchmarks/time_remote_file_reading.py", line 273, in time_read_zarr_nwbfile

                 self.nwbfile, self.io = read_zarr_nwbfile(s3_url=s3_url, mode="r")

                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py", line 264, in read_zarr_nwbfile

                 nwbfile = io.read()

                           ^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call

                 return func(args[0], **pargs)

                        ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/backends/io.py", line 56, in read

                 f_builder = self.read_builder()

                             ^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf/utils.py", line 668, in func_call

                 return func(args[0], **pargs)

                        ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1335, in read_builder

                 f_builder = self.__read_group(self.__file, ROOT_NAME)

                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1400, in __read_group

                 sub_builder = self.__read_group(sub_group, sub_name)

                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1400, in __read_group

                 sub_builder = self.__read_group(sub_group, sub_name)

                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1409, in __read_group

                 self.__read_links(zarr_obj=zarr_obj, parent=ret)

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 1428, in __read_links

                 target_name, target_zarr_obj = self.resolve_ref(link)

                                                ^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 734, in resolve_ref

                 target_zarr_obj = self.__open_file_consolidated(store=source_file,

                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/hdmf_zarr/backend.py", line 496, in __open_file_consolidated

                 return zarr.open_consolidated(store=store,

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/convenience.py", line 1334, in open_consolidated

                 store = normalize_store_arg(

                         ^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/storage.py", line 197, in normalize_store_arg

                 return normalize_store(store, storage_options, mode)

                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

               File "/opt/conda/lib/python3.11/site-packages/zarr/storage.py", line 169, in _normalize_store_arg_v2

                 raise ValueError("storage_options passed with non-fsspec path")

             ValueError: storage_options passed with non-fsspec path

I'll take a look

oruebel · 2024-11-21T01:18:01Z

In HDMF-Zarr, we use the logic:

# determine default storage options to use when opening a file from S3
storage_options = {}
if isinstance(path, str) and path.startswith(("s3://")):
    storage_options = dict(anon=True)

to determine if we need to set the storage options. I think we probably need to add this in these two functions:

nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py

Lines 231 to 265 in 61b361b

    
           def read_zarr(s3_url: str, open_without_consolidated_metadata: bool = False) -> zarr.Group: 
        
               """ 
        
               Open a Zarr file from an S3 URL using the built-in fsspec support in Zarr. 
        
               Returns 
        
               ------- 
        
               file : zarr.Group 
        
                  The zarr.Group object representing the opened file 
        
               """ 
        
               if open_without_consolidated_metadata: 
        
                   zarrfile = zarr.open(store=s3_url, mode="r", storage_options=dict(anon=True)) 
        
               else: 
        
                   zarrfile = zarr.open_consolidated(store=s3_url, mode="r", storage_options=dict(anon=True)) 
        
               return zarrfile 
        
           def read_zarr_nwbfile(s3_url: str, mode: str) -> Tuple[pynwb.NWBFile, hdmf_zarr.NWBZarrIO]: 
        
               """ 
        
               Read a Zarr NWB file from an S3 URL using the built-in fsspec support in Zarr. 
        
               Note: `r-` indicated reading without consolidated metadata, while `r` indicated reading with consolidated. 
        
                     `r` should only be used in a benchmark for files that actually have consolidated metadata available, 
        
                     for files without consolidated metadata, `hdmf_zarr` automatically reads without consolidated 
        
                     metadata if no consolidated metadata is present. 
        
               Returns 
        
               ------- 
        
               NWBFile : pynwb.NWBFile 
        
                   The remote NWBFile object. 
        
               NWBZarrIO : hdmf_zarr.NWBZarrIO 
        
                   The open IO object used to open the file. 
        
               """ 
        
               io = hdmf_zarr.NWBZarrIO(s3_url, mode=mode, storage_options=dict(anon=True)) 
        
               nwbfile = io.read() 
        
               return (nwbfile, io)

mavaylon1 · 2024-11-21T02:04:25Z

In HDMF-Zarr, we use the logic:
# determine default storage options to use when opening a file from S3

storage_options = {}

if isinstance(path, str) and path.startswith(("s3://")):

    storage_options = dict(anon=True)
to determine if we need to set the storage options. I think we probably need to add this in these two functions:

nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py

Lines 231 to 265 in 61b361b

def read_zarr(s3_url: str, open_without_consolidated_metadata: bool = False) -> zarr.Group:

"""

Open a Zarr file from an S3 URL using the built-in fsspec support in Zarr.

Returns

-------

file : zarr.Group

The zarr.Group object representing the opened file

"""

if open_without_consolidated_metadata:

zarrfile = zarr.open(store=s3_url, mode="r", storage_options=dict(anon=True))

else:

zarrfile = zarr.open_consolidated(store=s3_url, mode="r", storage_options=dict(anon=True))

return zarrfile

def read_zarr_nwbfile(s3_url: str, mode: str) -> Tuple[pynwb.NWBFile, hdmf_zarr.NWBZarrIO]:

"""

Read a Zarr NWB file from an S3 URL using the built-in fsspec support in Zarr.

Note: `r-` indicated reading without consolidated metadata, while `r` indicated reading with consolidated.

`r` should only be used in a benchmark for files that actually have consolidated metadata available,

for files without consolidated metadata, `hdmf_zarr` automatically reads without consolidated

metadata if no consolidated metadata is present.

Returns

-------

NWBFile : pynwb.NWBFile

The remote NWBFile object.

NWBZarrIO : hdmf_zarr.NWBZarrIO

The open IO object used to open the file.

"""

io = hdmf_zarr.NWBZarrIO(s3_url, mode=mode, storage_options=dict(anon=True))

nwbfile = io.read()

return (nwbfile, io)

I'm not sure what you mean. Those two functions already have anon=True defined.

mavaylon1 · 2024-11-21T03:14:14Z

It looks like one of the configuations may have an error. I'm seeing:

For parameters: 'https://dandi-api-staging-dandisets.s3.amazonaws.com/blobs/914/6aa/9146aa46-9c01-45be-9d2a-693e6a7bb778', 'ElectricalSeries', (slice(0, 30000, None), slice(0, 384, None))
             Traceback (most recent call last):
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/server.py", line 179, in _run_server
                 _run(run_args)
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/run.py", line 65, in _run
                 skip = benchmark.do_setup()
                        ^^^^^^^^^^^^^^^^^^^^
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/time.py", line 80, in do_setup
                 result = Benchmark.do_setup(self)
                          ^^^^^^^^^^^^^^^^^^^^^^^^
               File "/opt/conda/lib/python3.11/site-packages/asv_runner/benchmarks/_base.py", line 632, in do_setup
                 setup(*self._current_params)
               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/benchmarks/time_remote_slicing.py", line 186, in setup
                 self.neurodata_object = get_object_by_name(nwbfile=self.nwbfile, object_name=object_name)
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
               File "/home/jovyan/nwb_benchmarks/src/nwb_benchmarks/core/_nwb_helpers.py", line 20, in get_object_by_name
                 raise ValueError(f"The specified object name ({object_name}) is not in the NWBFile.")
             ValueError: The specified object name (ElectricalSeries) is not in the NWBFile.

Found the issue. Pushing fix.

for more information, see https://pre-commit.ci

mavaylon1 · 2024-11-21T03:48:13Z

In HDMF-Zarr, we use the logic:
# determine default storage options to use when opening a file from S3
storage_options = {}
if isinstance(path, str) and path.startswith(("s3://")):
    storage_options = dict(anon=True)
to determine if we need to set the storage options. I think we probably need to add this in these two functions:

nwb_benchmarks/src/nwb_benchmarks/core/_streaming.py

Lines 231 to 265 in 61b361b

def read_zarr(s3_url: str, open_without_consolidated_metadata: bool = False) -> zarr.Group:

"""

Open a Zarr file from an S3 URL using the built-in fsspec support in Zarr.

Returns

-------

file : zarr.Group

The zarr.Group object representing the opened file

"""

if open_without_consolidated_metadata:

zarrfile = zarr.open(store=s3_url, mode="r", storage_options=dict(anon=True))

else:

zarrfile = zarr.open_consolidated(store=s3_url, mode="r", storage_options=dict(anon=True))

return zarrfile

def read_zarr_nwbfile(s3_url: str, mode: str) -> Tuple[pynwb.NWBFile, hdmf_zarr.NWBZarrIO]:

"""

Read a Zarr NWB file from an S3 URL using the built-in fsspec support in Zarr.

Note: `r-` indicated reading without consolidated metadata, while `r` indicated reading with consolidated.

`r` should only be used in a benchmark for files that actually have consolidated metadata available,

for files without consolidated metadata, `hdmf_zarr` automatically reads without consolidated

metadata if no consolidated metadata is present.

Returns

-------

NWBFile : pynwb.NWBFile

The remote NWBFile object.

NWBZarrIO : hdmf_zarr.NWBZarrIO

The open IO object used to open the file.

"""

io = hdmf_zarr.NWBZarrIO(s3_url, mode=mode, storage_options=dict(anon=True))

nwbfile = io.read()

return (nwbfile, io)

@oruebel I believe I have a fix. That being said it is in resolve_ref, which we have updated with export that will be merged tomorrow. This "fix" is tape to get the file readable.

mavaylon1 and others added 5 commits November 7, 2024 11:07

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Updates with new Files #77

Updates with new Files #77

mavaylon1 commented Nov 20, 2024

mavaylon1 commented Nov 20, 2024

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Updates with new Files #77

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