[Bug]: Inspect using DANDI settings

mavaylon1 commented 1 year ago

What happened?

(NWB2) MacBook-Pro:docs mavaylon$ nwbinspector /Users/mavaylon/Research/NWB/ndx-multichannel-volume/docs/test_plane_extend.nwb --config DANDI Traceback (most recent call last): File "/Users/mavaylon/opt/anaconda3/envs/NWB2/bin/nwbinspector", line 8, in sys.exit(inspect_all_cli()) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(args, **kwargs) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/nwbinspector/nwbinspector.py", line 257, in inspect_all_cli config = load_config(filepath_or_keyword=config) File "/Users/mavaylon/opt/anaconda3/envs/NWB2/lib/python3.10/site-packages/nwbinspector/nwbinspector.py", line 99, in load_config with open(file=file, mode="r") as stream: FileNotFoundError: [Errno 2] No such file or directory: 'DANDI' (NWB2) MacBook-Pro:docs mavaylon$

Operating System

macOS

Python Version

3.10

Were you streaming with ROS3?

No

Package Versions

Package Version Editable project location

aiohttp 3.8.5 aiosignal 1.3.1 airium 0.2.5 alabaster 0.7.13 antlr4-python3-runtime 4.9.3 anyio 3.7.1 appdirs 1.4.4 appnope 0.1.3 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 arrow 1.2.3 asciitree 0.3.3 asttokens 2.2.1 async-timeout 4.0.3 attrs 23.1.0 Babel 2.12.1 backcall 0.2.0 bcp47 0.0.4 beautifulsoup4 4.12.2 bidsschematools 0.7.1 bioregistry 0.6.108 black 23.3.0 bleach 6.0.0 blessed 1.20.0 boto3 1.28.0 botocore 1.31.0 cachetools 5.3.1 cattrs 23.1.2 certifi 2023.5.7 cffi 1.15.1 CFGraph 0.2.1 cfgv 3.3.1 chardet 5.1.0 charset-normalizer 3.1.0 ci-info 0.3.0 class-resolver 0.4.2 click 8.1.3 click-didyoumean 0.3.0 codespell 2.2.4 colorama 0.4.6 comm 0.1.3 contourpy 1.1.0 coverage 7.2.5 cssutils 2.7.1 curies 0.5.7 cycler 0.11.0 daff 1.3.46 dandi 0.55.1 dandischema 0.8.4 dataframe-image 0.1.12 debugpy 1.6.7 decorator 5.1.1 defusedxml 0.7.1 Deprecated 1.2.14 deprecation 2.1.0 distlib 0.3.6 dnspython 2.3.0 docutils 0.18.1 EditorConfig 0.12.3 email-validator 2.0.0.post2 entrypoints 0.4 et-xmlfile 1.1.0 etelemetry 0.3.0 eutils 0.6.0 exceptiongroup 1.1.1 executing 1.2.0 fasteners 0.18 fastjsonschema 2.17.1 fastobo 0.12.2 filelock 3.12.2 flake8 6.0.0 fonttools 4.40.0 fparse 1.20.1 fqdn 1.5.1 frozenlist 1.4.0 fscacher 0.3.0 funowl 0.1.13 ghp-import 2.1.0 google 3.0.0 google-api-core 2.11.1 google-api-python-client 2.95.0 google-auth 2.22.0 google-auth-httplib2 0.1.0 google-auth-oauthlib 1.0.0 googleapis-common-protos 1.59.1 graphviz 0.20.1 greenlet 2.0.1 gspread 5.10.0 gspread-formatting 1.1.2 h5py 3.8.0 hbreader 0.9.1 hdmf 3.9.1 /Users/mavaylon/Research/NWB/hdmf2/hdmf hdmf-docutils 0.4.5 hdmf-zarr 0.3.0.post0.dev2 /Users/mavaylon/Research/NWB/hdmf-zarr html2image 2.0.4.3 httplib2 0.22.0 humanize 4.7.0 identify 2.5.24 idna 3.4 ijson 3.2.3 imageio 2.31.3 imagesize 1.4.1 importlib-metadata 6.7.0 iniconfig 2.0.0 interleave 0.2.1 ipykernel 6.24.0 ipython 8.14.0 ipython-genutils 0.2.0 ipywidgets 8.0.7 isodate 0.6.1 isoduration 20.11.0 jaraco.classes 3.2.3 jedi 0.18.2 Jinja2 3.1.2 jmespath 1.0.1 joblib 1.3.1 jsbeautifier 1.14.9 json-flattener 0.1.9 jsonasobj 1.3.1 jsonasobj2 1.0.4 jsonpatch 1.33 jsonpath-ng 1.5.3 jsonpointer 2.4 jsonschema 4.17.3 jupyter 1.0.0 jupyter_client 8.3.0 jupyter-console 6.6.3 jupyter_core 5.3.1 jupyter-events 0.6.3 jupyter_server 2.7.0 jupyter_server_terminals 0.4.4 jupyterlab-pygments 0.2.2 jupyterlab-widgets 3.0.8 keyring 24.2.0 keyrings.alt 4.2.0 kgcl-rdflib 0.5.0 kgcl-schema 0.5.0 kiwisolver 1.4.4 lark 1.1.7 lazy_loader 0.3 linkml 1.5.6 linkml-dataops 0.1.0 linkml-renderer 0.2.0 linkml-runtime 1.5.5 lxml 4.9.3 Markdown 3.4.4 MarkupSafe 2.1.3 matplotlib 3.7.1 matplotlib-inline 0.1.6 mccabe 0.7.0 mergedeep 1.3.4 mistune 3.0.1 mkdocs 1.5.0 mkdocs-material 9.1.20 mkdocs-material-extensions 1.1.1 mkdocs-mermaid2-plugin 0.6.0 more-click 0.1.2 more-itertools 9.1.0 multidict 6.0.4 mypy-extensions 1.0.0 natsort 8.4.0 nbclassic 1.0.0 nbclient 0.8.0 nbconvert 7.6.0 nbformat 5.9.0 ndex2 3.5.1 ndx-beadl 0.1.0 /Users/mavaylon/Research/NWB/ndx-beadl/src/pynwb ndx-multichannel-volume 0.1.8 /Users/mavaylon/Research/NWB/ndx-multichannel-volume/src/pynwb nest-asyncio 1.5.6 networkx 3.1 neuroconv 0.4.1 nodeenv 1.8.0 notebook 6.5.4 notebook_shim 0.2.3 numcodecs 0.11.0 numpy 1.24.3 nwbinspector 0.4.29 oaklib 0.5.12 oauthlib 3.2.2 ols-client 0.1.4 ontodev-cogs 0.3.3 ontoportal-client 0.0.4 openpyxl 3.1.2 overrides 7.3.1 packaging 23.1 pandas 2.0.1 pandocfilters 1.5.0 pansql 0.0.1 parse 1.19.1 parso 0.8.3 pathspec 0.11.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 9.5.0 pip 23.1.2 platformdirs 3.8.0 pluggy 1.2.0 ply 3.11 pre-commit 3.3.1 prefixcommons 0.1.12 prefixmaps 0.1.5 prometheus-client 0.17.0 prompt-toolkit 3.0.39 pronto 2.5.4 protobuf 4.23.4 psutil 5.9.5 ptyprocess 0.7.0 pure-eval 0.2.2 pyasn1 0.5.0 pyasn1-modules 0.3.0 pycodestyle 2.10.0 pycparser 2.21 pycryptodomex 3.18.0 pydantic 1.10.9 pyflakes 3.0.1 Pygments 2.15.1 PyJSG 0.11.10 pymdown-extensions 10.1 pynwb 2.3.3+5.g49a4e694.dirty /Users/mavaylon/Research/NWB/pynwb/src pyout 0.7.3 pyparsing 3.1.0 pyproject-api 1.5.2 pyrsistent 0.19.3 PyShEx 0.8.1 PyShExC 0.9.1 pysolr 3.9.0 pystow 0.5.0 pytest 7.3.1 pytest-cov 4.0.0 pytest-logging 2015.11.4 python-dateutil 2.8.2 python-json-logger 2.0.7 PyTrie 0.4.0 pytz 2023.3 PyWavelets 1.4.1 PyYAML 6.0 pyyaml_env_tag 0.1 pyzmq 25.1.0 qtconsole 5.4.3 QtPy 2.3.1 ratelimit 2.2.1 rdflib 6.2.0 rdflib-jsonld 0.6.1 rdflib-shim 1.0.3 regex 2023.6.3 requests 2.31.0 requests-cache 1.1.0 requests-oauthlib 1.3.1 requests-toolbelt 1.0.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rfc3987 1.3.8 rsa 4.9 ruamel.yaml 0.17.24 ruamel.yaml.clib 0.2.7 ruff 0.0.265 s3transfer 0.6.1 schemasheets 0.1.23 scikit-image 0.21.0 scipy 1.10.1 semantic-version 2.10.0 semsimian 0.1.18 semsql 0.3.2 Send2Trash 1.8.2 setuptools 68.0.0 ShExJSG 0.8.2 six 1.16.0 sniffio 1.3.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 soupsieve 2.4.1 sparqlslurper 0.5.1 SPARQLWrapper 2.0.0 Sphinx 6.2.1 sphinx-copybutton 0.5.2 sphinx-gallery 0.13.0 sphinx-rtd-theme 1.2.2 sphinxcontrib-applehelp 1.0.4 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.1 sphinxcontrib-jquery 4.1 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 SQLAlchemy 2.0.19 SQLAlchemy-Utils 0.38.3 sssom 0.3.32 sssom-schema 0.14.0 stack-data 0.6.2 tabulate 0.9.0 tenacity 8.2.2 termcolor 2.3.0 terminado 0.17.1 tifffile 2023.9.18 tinycss2 1.2.1 tomli 2.0.1 tornado 6.3.2 tox 4.5.1 tqdm 4.65.0 traitlets 5.9.0 typing_extensions 4.6.3 tzdata 2023.3 uri-template 1.3.0 uritemplate 4.1.1 url-normalize 1.4.3 urllib3 1.26.16 validators 0.20.0 virtualenv 20.23.1 watchdog 3.0.0 wcwidth 0.2.6 webcolors 1.13 webencodings 0.5.1 websocket-client 1.6.1 wheel 0.40.0 widgetsnbextension 4.0.8 wrapt 1.15.0 yarl 1.9.2 zarr 2.14.2 zarr-checksum 0.2.9 zipp 3.15.0

Code of Conduct

[X] I agree to follow this project's Code of Conduct
[X] Have you ensured this bug was not already reported?
[X] To the best of your ability, have you ensured this is a bug within the code that checks the NWBFile, rather than a bug in the NWBFile reader (e.g., PyNWB or MatNWB)?

mavaylon1 commented 1 year ago

I installed the inspector and ran: nwbinspector test.nwb --config DANDI

CodyCBakerPhD commented 1 year ago

Following the DANDI upload instructions: https://www.dandiarchive.org/handbook/13_upload/#data-uploadmanagement-workflow

This ought to be --config dandi

Please reopen if still not working after trying that

NeurodataWithoutBorders / nwbinspector