Is your feature request related to a problem? Please describe.
Is is possible to open URLs instead of file paths? and if this is complicated what about using file-like objects?

Describe the solution you'd like
Packages like fsspec allows us to open remote file as they were local and it would be very useful if this library could accept a file-like object to visualize HDF e.g.

with open("file.hdf5") as f:
    H5Web(f)

one of the advantages is that we could use fsspec to open a remote file that's compressed and cache it locally so potentially we won't need to download the whole content.

Describe alternatives you've considered

Additional context

To reproduce:

1. Open in the notebook a file with a long name (>18 characters in my case but can be width-dependent)
2. Select an entry with a visualization (ex: root for NeXus file)
3. (Optional?) Try to reduce the width of the explorer panel: on mouse release, the panel will take its width back and the visualisation panel width will increase without bounds.

Describe the bug

Good Day. I check on my jupyter lab version "4.1.4" where the jupyter serverextension key word returns Jupyter command jupyter-serverextension not found. This is same as the StackOverflow issue https://stackoverflow.com/questions/77711472/jupyter-command-jupyter-serverextension-not-found and can be solved accordingly by changing the command to jupyter server extension list .

To Reproduce

go type jupyter serverextension list and you'll get the error message

Expected behaviour

as above.

Screenshots

Context

• OS: Linux version 3.10.0-1160.92.1.el7.x86_64
• Browser: No
• JupyterLab version: 4.1.4

Paste the output from running `jupyter labextension list` and `jupyter serverextension list` from the command line here.
You may want to sanitize the paths in the output.--- also this template should be changed
`jupyter labextension list`
JupyterLab v4.1.4
/xxx/jupyter/labextensions
        ipyparallel-labextension v8.7.0 enabled OK
        jupyterlab-h5web v12.0.0 enabled OK (python, jupyterlab_h5web)
        @jupyter-notebook/lab-extension v7.1.1 enabled OK
        @jupyter-widgets/jupyterlab-manager v5.0.10 enabled OK (python, jupyterlab_widgets)
        @pyviz/jupyterlab_pyviz v3.0.1 enabled OK
jupyter server extension list
Config dir: /xxx/.jupyter
Config dir: /xxx/etc/jupyter

ipyparallel enabled

- Validating ipyparallel...

Package ipyparallel took 0.2808s to import

A _jupyter_server_extension_points function was not found in ipyparallel. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.

ipyparallel 8.7.0 OK

jupyter_lsp enabled

- Validating jupyter_lsp...

Package jupyter_lsp took 0.0087s to import

A _jupyter_server_extension_points function was not found in jupyter_lsp. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.

jupyter_lsp 2.2.0 OK

jupyter_server_terminals enabled

- Validating jupyter_server_terminals...

Package jupyter_server_terminals took 0.0038s to import

jupyter_server_terminals 0.4.4 OK

jupyterlab enabled

- Validating jupyterlab...

Package jupyterlab took 0.0464s to import

jupyterlab 4.1.4 OK

jupyterlab_h5web enabled

- Validating jupyterlab_h5web...

Package jupyterlab_h5web took 0.0011s to import

jupyterlab_h5web 12.0.0 OK

notebook enabled

- Validating notebook...

Package notebook took 0.0000s to import

notebook 7.1.1 OK

notebook_shim enabled

- Validating notebook_shim...

Package notebook_shim took 0.0000s to import

A _jupyter_server_extension_points function was not found in notebook_shim. Instead, a _jupyter_server_extension_paths function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.

notebook_shim  OK

panel.io.jupyter_server_extension enabled

- Validating panel.io.jupyter_server_extension...

Package panel.io.jupyter_server_extension took 0.6868s to import

panel.io.jupyter_server_extension  OK
Config dir: /usr/local/etc/jupyter

Hello,

I've been trying to install the extension on my mac (Catalina) and I'm facing the following problem. I can't open a Nexus file, and this error message appears in the background :

[W 14:58:51.029 LabApp] 404 GET /hdf/meta/Documents/Recherche/Depository/JupyLabBook/recording/SIRIUS_Isotherm_2019_02_17_01544.nxs?uri=/ (::1) 5.790000ms referer=http://localhost:8889/lab

It seems like it is searching the file in a folder called /hdf/meta/while it does not exist on my machine.

I've installed the extension with:

pip install jupyterlab_h5web
jupyter lab build

Here is what I get when I do jupyter serverextension list

config dir: /Users/arnaudhemmerle/.jupyter
    jupyter_nbextensions_configurator  enabled 
    - Validating...
      jupyter_nbextensions_configurator 0.4.1 OK
config dir: /Users/arnaudhemmerle/anaconda3/etc/jupyter
    jupyterlab  enabled 
    - Validating...
      jupyterlab 2.2.9 OK
    jupyterlab_git  enabled 
    - Validating...
      jupyterlab_git 0.20.0 OK
    nbdime  enabled 
    - Validating...
      nbdime 2.1.0 OK
    voila.server_extension  enabled 
    - Validating...
      voila.server_extension  OK
    jupyter_nbextensions_configurator  enabled 
    - Validating...
      jupyter_nbextensions_configurator 0.4.1 OK

When I do jupyter labextension list:

JupyterLab v2.2.9
Known labextensions:
   app dir: /Users/arnaudhemmerle/.local/share/jupyter/lab
        jupyterlab-h5web v0.0.5  enabled  OK

I've already tried to clean and build jupyterlab several times.

Thanks !

Attempting to open a dataset with a region reference attribute results in the following error:

TypeError: Object of type RegionReference is not JSON serializable

Steps to reproduce

Create the following HDF5 file:

import h5py
import numpy as np

with h5py.File("region_bug.h5", "w") as h5:
    data = h5.create_dataset("data", data=np.ones((3,3)))
    h5.attrs["dataref"] = data.regionref[0]

Attempt to open region_bug.h5 in Jupyter Lab

Describe the bug

Hi, as a user who started testing the H5Web Jupyter Lab plugin yesterday, I'm quite confused by forcing the 400px height on the cell output cell size. This leads IMHO to breaking the Jupyter lab behavior in setting the cell either as scrolling or full-size (in this case it will be always scrolling regardless of the Jupyter settings) - that's why I decided to file this as a bug instead of a feature in the end.

To Reproduce

1. Just use your own guide:

from jupyterlab_h5web import H5Web
h5_path = "<path to hdf5 file>"
​
H5Web(h5_path)

Expected behaviour

When working with bigger files (and bigger screens than tablet), I would expect the default height to be much higher, say half of the screen at least, but setting the responsible style .h5web-in-cell height to 100% would also do it quite elegantly. This might become a little annoying, as it resizes the visualization canvas on the right each time I expand a group on the left, but at least I don't need to stare through a tank viewport at my data.

Screenshots

1. As-is behaviour with Jupyter cell settings to "not scrolling":
   

2. Expected behaviour with the same settings:
   

Context

• OS: Linux
• Browser: Tested in Chrome and Opera
• Version: Latest
• JupyterLab version: 3.x

Thanks for looking into this!

Cheers,

Jiri

I knew that #53 was going to cause problems.

When renaming a file in JupyterLab filebrowser, one usually presses Enter to confirm the new name. However, the code in #53 intercepts the event and triggers the opening of the selected file instead, preventing the renaming.

Same thing when deleting a file: a dialog appears to ask the user to confirm the deletion and pressing Enter to confirm does not work. Confirmation by clicking works fine.

Hi, I use the H5Web VScode extension, witch is very similar to this one. With the VScode extension, I am able to open loom files directly (a HDF5 file format for genetic data, see https://loompy.org/ ), would it be possible to add .loom to the supported file format ?

Thanks !

Link to the VScode extension : https://marketplace.visualstudio.com/items?itemName=h5web.vscode-h5web

Describe the bug

When running your example.ipynb, I get the following error:

from jupyterlab_h5web import H5Web

H5Web('simple.h5')

Request failed with status code 500

To Reproduce

1. run jupyter lab
2. open the notebook example.ipynb
3. run the first two cells

Expected behaviour

It should present the widget

Context

• OS: LinuxMint
• Browser: Firefox
• Version: 110 64bits
• JupyterLab version: 3.5.3
• Python: 3.10
• conda environment

Extension lists

> jupyter labextension list
JupyterLab v3.5.3
/home/nitrosx71/miniconda3/envs/SE/share/jupyter/labextensions
        jupyterlab-h5web v7.0.0 enabled OK (python, jupyterlab_h5web)

> jupyter serverextension list
config dir: /home/nitrosx71/miniconda3/envs/SE/etc/jupyter
    jupyterlab  enabled 
    - Validating...
      jupyterlab 3.5.3 OK
    jupyterlab_h5web  enabled 
    - Validating...
      jupyterlab_h5web 7.0.0 OK

Just an idea, but it's probably useful to provide a h5py.File as parameter to H5Web.

related to #37

JupyterLab v4 was released on May 15th: https://github.com/jupyterlab/jupyterlab/releases/tag/v4.0.0

I tested with release candidates before and it seems that there are issues arising in the back-end (front-end looks fine). This is perhaps due to updates in jupyter-server.

Can the access token fix in #133 please be applied retroactively on 8.x? The same issue arises on JupyterLab 3.

Describe the bug

A 500 Error gets returned when a 3D array is passed to the framework. The screenshots below contain an image with a large number of the 0th dim, and another with only 67. The error log is as follows:

[E 2022-02-21 14:13:55.396 ServerApp] Uncaught exception GET /lab/api/settings?1645470835248 (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/lab/api/settings?1645470835248', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/tornado/web.py", line 1704, in _execute
        result = await result
    tornado.iostream.StreamClosedError: Stream is closed
[I 2022-02-21 14:13:57.204 LabApp] Build is up to date
[E 2022-02-21 14:14:26.122 ServerApp] Uncaught exception GET /h5web/data/?file=MUSAN_FSD50K%2Fmusan_fsd50k_nooverlap_2s.h5&path=%2F40_mels%2Ftrain%2Ffeatures&selection=0,:,:&flatten=true (127.0.0.1)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/h5web/data/?file=MUSAN_FSD50K%2Fmusan_fsd50k_nooverlap_2s.h5&path=%2F40_mels%2Ftrain%2Ffeatures&selection=0,:,:&flatten=true', version='HTTP/1.1', remote_ip='127.0.0.1')
    Traceback (most recent call last):
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/tornado/web.py", line 1702, in _execute
        result = method(*self.path_args, **self.path_kwargs)
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/tornado/web.py", line 3173, in wrapper
        return method(self, *args, **kwargs)
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/jupyterlab_h5web/handlers.py", line 28, in get
        response = encode(content, format_arg)
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/h5grove/encoders.py", line 109, in encode
        orjson_encode(content),
      File "/home/nickshu/anaconda3/envs/h5web/lib/python3.8/site-packages/h5grove/encoders.py", line 48, in orjson_encode
        return orjson.dumps(content, default=default, option=orjson.OPT_SERIALIZE_NUMPY)
    TypeError: default serializer exceeds recursion limit
[W 2022-02-21 14:14:26.123 ServerApp] Unhandled error
[E 2022-02-21 14:14:26.123 ServerApp] {
      "Host": "localhost:8888",
      "User-Agent": "Mozilla/5.0 (X11; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0",
      "Accept": "application/json, text/plain, */*",
      "Accept-Language": "en-US,en;q=0.5",
      "Accept-Encoding": "gzip, deflate",
      "Connection": "keep-alive",
      "Referer": "http://localhost:8888/lab/workspaces/auto-x/tree/MUSAN_FSD50K",
      "Cookie": "username-localhost-8888=\"2|1:0|10:1645470865|23:username-localhost-8888|44:MTBmODU5YWVjN2QwNGM3OWI0ZGIyYTg3Mzg5NDBhMDc=|71d4f38e3541a61543b4765a12ca598a1413794e587db212ad204ec9317ff226\"; _xsrf=2|be7cd264|72c37ad1b680654d763a713d31046056|1643138022",
      "Sec-Fetch-Dest": "empty",
      "Sec-Fetch-Mode": "cors",
      "Sec-Fetch-Site": "same-origin"
    }
[E 2022-02-21 14:14:26.123 ServerApp] 500 GET /h5web/data/?file=MUSAN_FSD50K%2Fmusan_fsd50k_nooverlap_2s.h5&path=%2F40_mels%2Ftrain%2Ffeatures&selection=0,:,:&flatten=true (127.0.0.1) 5.62ms referer=http://localhost:8888/lab/workspaces/auto-x/tree/MUSAN_FSD50K

To Reproduce

Create an .h5 file which contains a 3D array, and use the latest Jupyter Lab, and Jupyterlab H5web

Expected behaviour

The expected behavior was to be able to see a slide heatmap of a 3D array

Screenshots

Context

• OS: Arch Linux
• Browser: Firefox
• Version:
• JupyterLab version:

jupyterlab==3.2.9
jupyterlab-h5web==2.0.0
jupyterlab-pygments==0.1.2
jupyterlab-server==2.10.3

$ jupyter labextension list
JupyterLab v3.2.9
/home/user/anaconda3/envs/h5web/share/jupyter/labextensions
        jupyterlab-h5web v2.0.0 enabled OK (python, jupyterlab_h5web)

$ jupyter serverextension list
config dir: /home/user/anaconda3/envs/h5web/etc/jupyter
    jupyterlab  enabled
    - Validating...
      jupyterlab 3.2.9 OK
    jupyterlab_h5web  enabled
    - Validating...
      jupyterlab_h5web 2.0.0 OK

When using Jupyter Lab's dark mode, the text in the 'inspect' view is black and almost invisible:

Similarly for the matrix view:

When I run the example for your package the object: <jupyterlab_h5web.widget.H5Web object> is displayed instead of the graphical interface- what am I doing wrong:).

H5Web allows customizing the colors in 2D plots, which is done in the css. It would be great to have a way to be able to inject this to invoking these widgets in Jupyter lab.

Originally posted by @tomio13 in #34 (comment)

Describe the bug

I am creating a dummy h5 file containing a complex array and a integer array as bellow, but I get an error message saying "Expected complex" (for the complex array) and (Expected Number) for the integer array. The same does not happen for floats; it opens normally using dtype=np.float64.

import numpy as np
import h5py

file = h5py.File('test.h5','a')

name = '1'
data = np.ones((5,5),dtype=np.complex64)

file.create_dataset(name,data=data)

Screenshots

Context

• OS: Ubutun 20.04.4 LTS
• Browser: Chrome Version 112.0.5615.49 (Official Build) (x86_64)
  IPython : 7.29.0
  ipykernel : 6.5.0
  ipywidgets : 7.6.3
  jupyter_client : 7.4.9
  jupyter_core : 5.2.0
  jupyter_server : 1.24.0
  jupyterlab : 3.6.1
  nbclient : 0.5.3
  nbconvert : 7.2.9
  nbformat : 5.7.3
  notebook : 6.4.0
  qtconsole : 5.1.1
  traitlets : 5.9.0

JupyterLab v3.6.1

/.../.local/share/jupyter/labextensions

@jupyter-widgets/jupyterlab-manager v3.1.0 enabled OK (python, jupyterlab_widgets)
/.../apps/modules/python/3.9.2/share/jupyter/labextensions

jupyterlab-plotly v5.1.0 enabled OK

jupyterlab-h5web v7.0.0 enabled OK (python, jupyterlab_h5web)

jupyter-matplotlib v0.11.2 enabled OK
config dir: /...//.local/etc/jupyter

jupyter_server_ydoc  enabled

- Validating...

X is jupyter_server_ydoc importable?

config dir: /.../modules/python/3.9.2/etc/jupyter

jupyter_server_ydoc  enabled

- Validating...

X is jupyter_server_ydoc importable?

jupyterlab  enabled

- Validating...

jupyterlab 3.6.1 OK

jupyterlab_h5web  enabled

- Validating...

jupyterlab_h5web 7.0.0 OK

Console shows an Uncaught TypeError: e.current.gl is undefined

I made a recipe for jupyterlab_h5web in conda-forge: https://github.com/conda-forge/jupyterlab-h5web-feedstock

Therefore, it is installable through conda install -c conda-forge jupyterlab-h5web. It might be good to mention this in the README and other documentation. I would also be happy to add any of the developers as maintainers of the package.

Describe the bug

There seems to be a bug with the data displayed by h5web. The axis positions are not properly placed.

Running on jupyter lab 3.2.9 and jupyterlab-h5web 1.3.0.

The minimum and max values of the y axis (energy) are: −4.000e+0 to 1.000e+0
The minimum and max values of the x axis (delay) are: −2.000e+3 to 6.500e+3

To Reproduce

Expected behaviour

Screenshots

Context

• OS: ubuntu
• Browser: Chrome
• Version: 1.3.0
• JupyterLab version: 3.2.9

jupyter labextension list

JupyterLab v3.2.9

/home/.../jupyter/.py37env/share/jupyter/labextensions

jupyterlab-h5web v1.3.0 enabled OK (python, jupyterlab_h5web)

@jupyter-widgets/jupyterlab-manager v3.0.1 enabled OK (python, jupyterlab_widgets)
jupyter serverextension list

config dir: /home/pepe_marquez/.jupyter

jupyterlab_h5web  enabled

- Validating...

jupyterlab_h5web 1.3.0 OK

config dir: /home/pepe_marquez/jupyter/.py37env/etc/jupyter

jupyterlab  enabled

- Validating...

jupyterlab 3.2.9 OK

jupyterlab_h5web  enabled

- Validating...

jupyterlab_h5web 1.3.0 OK

Describe the bug

Trying to inspect an h5 file with tree structure "/confocal/XY/...something.../raw". On initially opening in h5web under jupyter, left pane shows "/confocal" but opening this gives a blank plane.

Digging into the errors I found the following which seems to suggest the second slash is converted to '\\'

{"message": "Unhandled error", "reason": null, "traceback": "Traceback (most recent call last):\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\tornado\web.py", line 1702, in _execute\n result = method(*self.path_args, **self.path_kwargs)\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\tornado\web.py", line 3173, in wrapper\n return method(self, *args, **kwargs)\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\jupyterlab_h5web\handlers.py", line 26, in get\n content = self.get_content(h5file, path)\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\jupyterlab_h5web\handlers.py", line 59, in get_content\n return content.metadata()\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\h5grove\content.py", line 151, in metadata\n ("children", self._get_child_metadata_content(depth - 1)),\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\h5grove\content.py", line 139, in _get_child_metadata_content\n return [\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\h5grove\content.py", line 140, in \n create_content(self._h5file, os.path.join(self._path, child_path)).metadata(\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\h5grove\content.py", line 160, in create_content\n entity = get_entity_from_file(h5file, path, resolve_links)\n File "C:\Users\u1774090\Anaconda3\envs\h5web\lib\site-packages\h5grove\utils.py", line 34, in get_entity_from_file\n raise PathError(f"{path} is not a valid path in {basename(h5file.filename)}")\nh5grove.utils.PathError: /confocal\\XY is not a valid path in session-20211021-131238.hdf5\n"}

Expected behaviour

Should allow traversal of an h5 tree from root

Screenshots

Context

• OS: Windows 10
• Browser: Edge
• Version: [e.g. 22]
• H5Web context: jupyterlab_h5web + @h5web/lib

Good day,
don't know if this bug is for jyputer-h5web or for jupyter-collaboration

In jupyterlab v4 with collaborative mode got file not found because of adding "RTC:" to filepath - for example "File not found: 'RTC:discharges/2023/202306/20230629/T/1230T 2023-06-29 13:03:54.nx"

H5Web("discharges/2023/202306/20230629/T/1230T 2023-06-29 13:03:54.nx") - works

To Reproduce

Try to open hdf5/nexus file in jupyterlab with jypyter-collaboration enabled

Expected behaviour

Open file without error

Screenshots

For example csv works

but to open from python (with open(..)) "RTC:path" needs to be changed to "path")

Context

• OS: Ubuntu 22.04
• Browser: Chrome
• Version: 114
• JupyterLab version: 4.0.2

Paste the output from running `jupyter labextension list` and `jupyter serverextension list` from the command line here.
You may want to sanitize the paths in the output.
jupyter_lsp  enabled

- Validating...

jupyter_lsp 2.2.0 OK

jupyter_nbextensions_configurator  enabled

- Validating...

jupyter_nbextensions_configurator 0.6.3 OK

jupyter_server_ydoc  enabled

- Validating...

X is jupyter_server_ydoc importable?

jupyterlab  enabled

- Validating...

jupyterlab 4.0.2 OK

jupyterlab_git  enabled

- Validating...

jupyterlab_git 0.41.0 OK

jupyterlab_h5web  enabled

- Validating...

jupyterlab_h5web 10.0.0 OK

nbdime  enabled

- Validating...

nbdime 3.2.1 OK
    jupyter-vuetify v1.8.10 enabled  X
    jupyterlab-h5web v10.0.0 enabled OK (python, jupyterlab_h5web)
    nbdime-jupyterlab v2.2.0 enabled  X
    jupyterlab_pygments v0.2.2 enabled  X (python, jupyterlab_pygments)
    jupyter-vue v1.9.2 enabled OK
    jupyter-matplotlib v0.11.3 enabled OK
    @jupyter-widgets/jupyterlab-manager v5.0.7 enabled  X (python, jupyterlab_widgets)
    @jupyter/collaboration-extension v1.0.1 enabled OK (python, jupyter_collaboration)
    @bokeh/jupyter_bokeh v3.0.7 enabled  X (python, jupyter_bokeh)
    @jupyterlab/git v0.41.0 enabled  X (python, jupyterlab-git)

Also checked on new vm:

jupyterlab-h5web v10.0.0 enabled OK (python, jupyterlab_h5web)

jupyterlab_pygments v0.2.2 enabled  X (python, jupyterlab_pygments)

@jupyter/collaboration-extension v1.0.1 enabled OK (python, jupyter_collaboration)

#108 (comment)

Tasks:

• Update h5grove to 1.3.0
• Use the new get_list_of_paths util to implement the /paths handler

To be done before the 7.1.0 release

Waiting on jupyterlab/jupyterlab#7596

I am assuming this is the project behind the wonderful thing I found yesterday that lets me browse hdf5 files in jupyterlab? It looks fantastic. I wish I could figure out how to select x and y axes for a plot? I always see data versus point number. The rest of the message is a bug report for how I seem to have broke something already (sorry!) :

Describe the bug

jupyterlab crashes when reading large dataset, perhaps an out of memory error?

To Reproduce

1 - Log into jupyter-slurm.esrf.fr with one single core and the lab interface
2 - Navigate to open : /data/id11/nanoscope/blc12407/id11/CeO2_38keV/CeO2_38keV_CeO2_rotation/CeO2_38keV_CeO2_rotation.h5
3 - open dataset /1.1/measurement/eiger : it displays
4 - open dataset /1.1/measurement/fpico6 : it displays
5 - go back to /1.1/measurement/eiger : jupyterlab stops running
6 - all the other tabs and kernels appear to exit when jupyterlab fails

Expected behaviour

In the worst case, a plugin would crash without taking down all of the other kernels. Ideally it would not crash.

Is there a way to use hdf5 slice operations (maybe combined with fast histograms) so you only hold in memory what is going to be displayed on the screen (e.g. maximum data is a 2D image)? Then libhdf5 should manage the memory cache in some sensible way.

Context

• OS: ubuntu20.04
• Browser: Chrome
• Version: 94.0.4606.81
• JupyterLab version: 2.3.1 (ESRF slurm installation

jupyter-slurm:~ % /scisoft/users/jupyter/jupy38ubuntu/bin/jupyter labextension list
JupyterLab v2.3.1
Known labextensions:
   app dir: /home/esrf/jupyter/jupy38ubuntu/share/jupyter/lab
        @jupyter-widgets/jupyterlab-manager v2.0.0  enabled  OK
        jupyter-matplotlib v0.7.4  enabled  OK
        jupyter-threejs v2.2.0  enabled  OK
        jupyterlab-datawidgets v6.3.0  enabled  OK
        jupyterlab-h5web v0.0.10  enabled  OK
        k3d v2.9.3  enabled  OK
jupyter-slurm:~ % /scisoft/users/jupyter/jupy38ubuntu/bin/jupyter serverextension list
config dir: /home/esrf/jupyter/jupy38ubuntu/etc/jupyter
    jupyterlab_h5web  enabled 
    - Validating...
      jupyterlab_h5web  OK
    jupyterlab  enabled 
    - Validating...
      jupyterlab 2.3.1 OK
    jupyterlab_hdf  enabled 
    - Validating...
      jupyterlab_hdf 0.5.1 OK
    jupyter_nbextensions_configurator  enabled 
    - Validating...
      jupyter_nbextensions_configurator 0.4.1 OK

This would be inline with h5py and h5glance behaviour.

Describe the bug

When the extension was installed in "dev mode", it is not possible to display a R3F visualisation: it freezes the browser.

Displaying scalar values, navigating in the file or inspecting entities do not trigger this freeze.

To Reproduce

1. Install the extension according to https://github.com/silx-kit/jupyterlab-h5web/blob/main/CONTRIBUTING.md#install
2. Run jupyter lab
3. Open a HDF file with nD datasets inside
4. Open a nD dataset
5. The browser will freeze

Interestingly, this does not happen with a regular installation pip install .

Context

• Browser: any
• Version: 1.0.0
• JupyterLab version: 3

Reported in #48

For now, the server extension is a thin wrapper around https://github.com/jupyterlab/jupyterlab-hdf5. It would be better to depend directly on it.

Dear h5web-Team,
I created a h5 file with a virtual dataset. I am following, in general, this example: https://github.com/h5py/h5py/blob/master/examples/eiger_use_case.py
As a result, I get a h5 file, where data contains my 3D stack in '/data/'.
I thought I check the content out in h5web because I work on a jupyterhub. I get "Request failed with status code 500"
What is the minimum requirement to visualize your own created h5 files with h5web, please?
In silx, I am able to see my data.
Thank you.

Hi, I was using jupyterlab-h5web on jupyter-slurm.esrf.fr, and some files are veeeery slow, and I have one that doesn't even open. I am not sure if this is somehow expected/normal, but I recorded a few of this issues so you can check it.

See: https://youtu.be/qSM2JsVVEHY

I open 4 files in the video, respectively:

1. 0:08: an .h5 from the acquisition system at id11
   path: /data/id11/3dxrd/blc12852/id11/bmg_l1/bmg_l1_bmg_dct2/bmg_l1_bmg_dct2.h5
   issue: 0:38: displaying one frame is quite slow

2. 1:15: a "small" .h5 written by my code is quite slow
   path: /data/id11/3dxrd/blc12852/id11/analysis/bmg_l1_bmg_dct2/difspots/000000.h5
   issue: isn't it slow relative to the size of the things inside?

3. 1:33: an .h5 regrouping (external links) about 3300 .h5s like the one above
   path: /data/id11/3dxrd/blc12852/id11/analysis/bmg_l1_bmg_dct2/difspots.h5
   issue: slow to open, then very slow to expand the group with the external links

4. 2:30: an .h5 with only 2 datasets, about the same size of the first one
   path: /data/id11/3dxrd/blc12852/id11/bmg_l1/bmg_l1_bmg_dct2/bmg_l1_bmg_dct2.preprocessed.h5
   issue: veeeeeeeery slow; I kept waiting after the end of the video for several minutes, the entire jupyterlab becomes very slow, and it ends up breaking the page (screenshot below). When I reload the page, the h5web tab (in jupyterlab) is not there anymore.

A few notes (Idk if this might have some influence):

• I am using symbolic links (ln -s) to be able to see those files in jupyter-slurm because they are in /data.
• I am writting my .h5 files with silx.io.dictdump.dicttoh5. I can show you specifically where in my code.
• I saw similar effects on a jupyterlab instances on gpid11-nice and rnice8 nodes. In these cases I launch jupyterlab on those machines, connect to them with ssh -L 8888:localhost:8888 to forward the application's port, then access it using my local browser (my personal computer, not an ESRF one).

Running H5Web("new_file+d.h5") from a notebook leads to opening "new_file d.h5" on the server side (its already changed in the GET request).

Logs on the server side:

    Traceback (most recent call last):
      File "lib/python3.8/site-packages/tornado/web.py", line 1702, in _execute
        result = method(*self.path_args, **self.path_kwargs)
      File "lib/python3.8/site-packages/tornado/web.py", line 3173, in wrapper
        return method(self, *args, **kwargs)
      File "lib/python3.8/site-packages/jupyterlab_h5web/handlers.py", line 25, in get
        with h5py.File(as_absolute_path(self.base_dir, Path(file_path)), "r") as h5file:
      File "lib/python3.8/site-packages/h5py/_hl/files.py", line 424, in __init__
        fid = make_fid(name, mode, userblock_size,
      File "lib/python3.8/site-packages/h5py/_hl/files.py", line 190, in make_fid
        fid = h5f.open(name, flags, fapl=fapl)
      File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
      File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
      File "h5py/h5f.pyx", line 96, in h5py.h5f.open
    OSError: Unable to open file (unable to open file: name = '/home/new_file d.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

The display of 2D datasets makes the viewer crash 🙁

Installation fails with:

ERROR: Could not build wheels for jupyterlab-h5web which use PEP 517 and cannot be installed directly

While a potential workaround could have been:

pip install --no-use-pep517 jupyterlab_h5web

this also fails with:

ERROR: Disabling PEP 517 processing is invalid: project specifies a build backend of 
setuptools.build_meta in pyproject.toml

Ideas? Thanks!

Due to the signature change of orjson_encode: https://github.com/silx-kit/h5grove/releases/tag/v0.0.9

We are typically working with files that have a different extension than .h5 or .hdf5. Those can only be opened after renaming them as far as I can tell. Even the 'Open with' menu lists only the editor, not h5web.
It is probably not useful to list all custom extensions that people use. But it would be great if the viewer would not be tied to the file name.

I've been trying to install the extension on ubuntu 20.04 and I'm getting the following conflicting dependency error message

[LabBuildApp] JupyterLab 2.2.9
[LabBuildApp] Building in $HOME/anaconda3/envs/hdf5/share/jupyter/lab
[LabBuildApp] Building jupyterlab assets (build:prod:minimize)
[LabBuildApp] WARNING | 
"[email protected]" is not compatible with the current JupyterLab
Conflicting Dependencies:
JupyterLab                        Extension      Package
>=2.2.6 <2.3.0                    >=2.3.0 <2.4.0||>=3.0.5 <4.0.0@jupyterlab/apputils
>=2.2.4 <2.3.0                    >=2.3.0 <2.4.0||>=3.0.7 <4.0.0@jupyterlab/rendermime
>=2.2.1 <2.3.0                    >=2.3.0 <2.4.0||>=3.0.6 <4.0.0@jupyterlab/rendermime-interfaces


JupyterLab v2.2.9
Known labextensions:
   app dir: $HOME/anaconda3/envs/hdf5/share/jupyter/lab
        @jupyterlab/hdf5 v0.5.1  enabled  OK
        jupyterlab-h5web v0.0.7  enabled   X

Thanks!

Toolbar controls are shared among JupyterLab tabs, even if they display different files.

Hello!

My group is interested to explore an H5 dataset through plotting various dimensions across each other. Your JupyterLab plugin interface is awesome, but we cannot seem select our own dimensions to plot. Can your plugin accommodate selecting data dimensions for plotting, or can the code be expanded to add this functionality?

Andrew

See the discussion at #12

Good day
Looks like that legend color changes with theme switch, but not the lines color. (Incorrect view in dark mode)

Screenshots

Context

• OS: Ubuntu 22.04.2 LTS
• Browser: Chrome
• Version: 7.1.2
• JupyterLab version: 2.5.0

 jupyterlab-h5web v7.1.2 enabled OK (python, jupyterlab_h5web)
jupyterlab_pygments v0.2.2 enabled OK (python, jupyterlab_pygments)
jupyter_server_ydoc  enabled

- Validating...

X is jupyter_server_ydoc importable?

jupyterlab  enabled

- Validating...

jupyterlab 3.6.3 OK

jupyterlab_h5web  enabled

- Validating...

jupyterlab_h5web 7.1.2 OK

The extension cannot be enabled with Jupyter Lab 3.1.x

Expected Result:

$ jupyter labextension list
JupyterLab v3.1.1

Other labextensions (built into JupyterLab)
   app dir: ~/.venv/share/jupyter/lab
        jupyterlab-h5web v0.0.8 enabled  **OK**

Actual Result

$ jupyter labextension list
JupyterLab v3.1.1

Other labextensions (built into JupyterLab)
   app dir: ~/.venv/share/jupyter/lab
        jupyterlab-h5web v0.0.8 enabled  **X**

   The following extension are outdated:
        jupyterlab-h5web

Workaround

I think the last version with which it could be enabled was Jupyter Lab 3.0.16

When opening a hdf5 file, the widget briefly (milliseconds) pops-up, to close again immediately.
Other widgets and interactive elements have no problems.

I just used the sample notebook to replicate the issue.
Tried multiple browsers: FF, Edge, Chrome on Win10.
Tried versions v0.0.10, 9 and 8.
Using jupyterlab v3.0.16

Settings > JupyterLab Theme > JupyterLab Light

All is well.

Settings > JupyterLab Theme > JupyterLab Dark

Heatmap, color map and color bar are inverted.

In its current implementation, the extension basically merges H5Web's CSS and JS code into Jupyer Lab's:

• H5Web's global styles (normalize.css and .btn-clean, variables, etc.) are merged with Jupyter Lab's styles, which leads to unexpected results - e.g. H5Web's built-in support for system dark mode (prefers-color-scheme: dark) applies filter: invert() to JupyterLab as a whole, even when JLab is configured with a light theme.
• H5Web's JS bundle is executed on launch of JLab, which means any global state is shared between JLab tabs. This is what led us to switching from global zustand stores to context-injected stores.

All of these issues, and likely future issues, would be avoided if every instance of H5Web (tab or cell) were completely self-contained. The easiest way to achieve JS/CSS containment is to use an iframe.

The way I see it, the extension could take the form of a little create-react-app that renders H5Web's App component (wrapped in a JupyterProvider) on a simple HTML page. Building the extension would generate all the static assets (index.html + JS/CSS bundles). On JLab start-up, the extension would start a static file server (or use JLab's) to serve those static assets at https://jlab.url/h5web/?file=some-file.h5. When opening an HDF5 file in a JLab tab or cell, the extension would then render an iframe with its src attribute set to that URL.

I have no idea how feasible this solution is...

Is your feature request related to a problem? Please describe.

I think this plugin can handle netcdf files as they are CF compliant HDF files, I tested changing the file extension to some .nc files and it worked fine.

Describe the solution you'd like A clear and concise description of what you
want to happen.

Would it be possible to include netcdf in the list of supported formats?

Describe alternatives you've considered A clear and concise description of
any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature
request here.

When the top-level HDF5 groups are external links (BLISS proposal and sample collection files), the entire file doesn't show up and this traceback is printed:

[E 2021-06-16 23:54:31.907 ServerApp] Found and opened file, error getting contents from object specified by the uri.
    Error: Traceback (most recent call last):
      File "/users/denolf/virtualenvs/jupyter/ubuntu_20_04/lib/python3.9/site-packages/jupyterlab_hdf/baseHandler.py", line 72, in get
        out = self._get(fpath, uri, **kwargs)
      File "/users/denolf/virtualenvs/jupyter/ubuntu_20_04/lib/python3.9/site-packages/jupyterlab_hdf/baseHandler.py", line 90, in _get
        return self._getFromFile(f, uri, **kwargs)
      File "/users/denolf/virtualenvs/jupyter/ubuntu_20_04/lib/python3.9/site-packages/jupyterlab_hdf/meta.py", line 16, in _getFromFile
        return jsonize(hobjMetaDict(f[uri], ixstr=ixstr, min_ndim=min_ndim))
      File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
      File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
      File "/users/denolf/virtualenvs/jupyter/ubuntu_20_04/lib/python3.9/site-packages/h5py/_hl/group.py", line 288, in __getitem__
        oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
      File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
      File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
      File "h5py/h5o.pyx", line 190, in h5py.h5o.open
    KeyError: "Unable to open object (object '8.1' doesn't exist)"
    
    relfpath: data/inhouse/id002106/id00/id002106_id00.h5, uri: /8.1, min_ndim: None, ixstr: None, subixstr: None

The HDF5 group of the link destination is indeed /8.1 but the relfpath is the path of the file that contains the link, not the path of the file of the link destination.

>>> import os, h5py
>>> os.getcwd()
'/tmp/data/inhouse/id002106/id00'

>>> f = h5py.File("id002106_id00.h5")
>>> f.filename
'id002106_id00.h5'

>>> f["sample_0005_8.1"].file.filename
'/tmp/data/inhouse/id002106/id00/sample/sample_0005/sample_0005.h5'
>>> f["sample_0005_8.1"].name
'/8.1'

>>> link = f.get("sample_0005_8.1", getlink=True)
>>> link.filename
'sample/sample_0005/sample_0005.h5'
>>> link.path
'/8.1'

The jupyterlab working directory was /tmp