Uncaught (in promise) TypeError: Path must be a string, received "undefined" #3523
Description
What went wrong?
I'm trying to upload a dataset with the deno cli, but it's encountering an error. Though, I'm not sure whether this is an issue with the cli (the error message says that it's deno, itself 🤷🏻 ).
Expected behavior
I expected the dataset to be created on OpenNeuro and my local files uploaded.
How to reproduce
$ deno run -A jsr:@openneuro/cli --version
openneuro 4.37.0
$ deno run -A jsr:@openneuro/cli upload --ignoreWarnings --affirmDefaced --new /dcs07/smart/data/SpatialTopology/ds005256-mriqc
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
2 Files, 3.78 kB
0 - Subjects 1 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
Validation complete, preparing upload.
error: Uncaught (in promise) TypeError: Path must be a string, received "undefined"
throw new TypeError(
^
at assertPath (https://jsr.io/@std/path/1.1.1/_common/assert_path.ts:6:11)
at https://jsr.io/@std/path/1.1.1/posix/join.ts:43:27
at Array.forEach (<anonymous>)
at join (https://jsr.io/@std/path/1.1.1/posix/join.ts:43:9)
at join (https://jsr.io/@std/path/1.1.1/join.ts:30:52)
at Command.uploadAction [as actionHandler] (https://jsr.io/@openneuro/cli/4.37.0/src/commands/upload.ts:119:20)
at eventLoopTick (ext:core/01_core.js:178:7)
at async Command.execute (https://jsr.io/@effigies/cliffy-command/1.0.0-dev.8/command.ts:1940:7)
at async Command.parseCommand (https://jsr.io/@effigies/cliffy-command/1.0.0-dev.8/command.ts:1772:14)
at async commandLine (https://jsr.io/@openneuro/cli/4.37.0/src/options.ts:46:29)
============================================================
Deno has panicked. This is a bug in Deno. Please report this
at https://github.com/denoland/deno/issues/new.
If you can reliably reproduce this panic, include the
reproduction steps and re-run with the RUST_BACKTRACE=1 env
var set and include the backtrace in your report.
Platform: linux x86_64
Version: 2.3.3
Args: ["deno", "run", "-A", "jsr:@openneuro/cli", "upload", "--ignoreWarnings", "--affirmDefaced", "--new", "/dcs07/smart/data/SpatialTopology/ds005256-mriqc"]
thread 'main' panicked at /home/conda/feedstock_root/build_artifacts/deno_1748619837309/_build_env/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/deno_unsync-0.4.3/src/tokio/task.rs:76:16:
there is no reactor running, must be called from the context of a Tokio 1.x runtime
note: run with `RUST_BACKTRACE=1` environment variable to display a backtraceDesktop
- OS: linux x86_64
- Browser: n/a
- Version: n/a
Phone
n/a
Additional information
The dataset contains derivatives for MRIQC, so almost all files are covered in the .bidsignore.
The raw data is a git submodule
$ cat .gitmodules
[submodule "rawdata"]
path = sourcedata/raw
url = https://github.com/OpenNeuroDatasets/ds005256.git
datalad-id = 2ee2bfa7-6c1b-4cf6-87e9-297e30f42517
datalad-url = https://github.com/OpenNeuroDatasets/ds005256.git
[submodule "sourcedata/templateflow"]
path = sourcedata/templateflow
url = https://datasets.datalad.org/templateflow/.git
datalad-id = c79c47b6-d0fb-11e8-aa11-64006a8a730f
datalad-url = ///templateflowConda Environment
$ conda env export
name: spacetop2
channels:
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- annexremote=1.6.6=py312h7900ff3_0
- anyio=4.9.0=pyh29332c3_0
- attr=2.5.1=h166bdaf_1
- backoff=2.2.1=pyhd8ed1ab_1
- backports=1.0=pyhd8ed1ab_5
- backports.tarfile=1.2.0=pyhd8ed1ab_1
- boto3=1.38.10=pyhd8ed1ab_0
- botocore=1.38.10=pyge310_1234567_0
- brotli-python=1.1.0=py312h2ec8cdc_2
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.34.5=hb9d3cd8_0
- ca-certificates=2025.7.14=hbd8a1cb_0
- certifi=2025.7.14=pyhd8ed1ab_0
- cffi=1.17.1=py312h06ac9bb_0
- chardet=5.2.0=pyhd8ed1ab_3
- charset-normalizer=3.4.2=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_1
- cryptography=44.0.3=py312hda17c39_0
- curl=8.13.0=h332b0f4_0
- datalad=1.1.4=py312h7900ff3_0
- dbus=1.13.6=h5008d03_3
- deno=2.3.4=hbf66b88_0
- distro=1.9.0=pyhd8ed1ab_1
- exceptiongroup=1.2.2=pyhd8ed1ab_1
- exifread=3.3.0=pyhd8ed1ab_0
- expat=2.7.0=h5888daf_0
- fasteners=0.19=pyhd8ed1ab_1
- freetype=2.13.3=ha770c72_1
- git=2.49.0=pl5321h59d505e_0
- git-annex=10.20230626=alldep_h9c70df9_101
- gmp=6.3.0=hac33072_2
- gnupg=2.5.5=h1be56c8_0
- gql=3.5.2=pyhd8ed1ab_0
- graphql-core=3.2.4=pyhd8ed1ab_0
- h2=4.2.0=pyhd8ed1ab_0
- hpack=4.1.0=pyhd8ed1ab_0
- humanize=4.12.3=pyhd8ed1ab_0
- hyperframe=6.1.0=pyhd8ed1ab_0
- idna=3.10=pyhd8ed1ab_1
- importlib-metadata=8.6.1=pyha770c72_0
- importlib_resources=6.5.2=pyhd8ed1ab_0
- iso8601=2.1.0=pyhd8ed1ab_1
- jaraco.classes=3.4.0=pyhd8ed1ab_2
- jaraco.context=6.0.1=pyhd8ed1ab_0
- jaraco.functools=4.1.0=pyhd8ed1ab_0
- jeepney=0.9.0=pyhd8ed1ab_0
- jmespath=1.0.1=pyhd8ed1ab_1
- keyring=25.6.0=pyha804496_0
- keyrings.alt=5.0.2=pyhd8ed1ab_0
- keyutils=1.6.1=h166bdaf_0
- krb5=1.21.3=h659f571_0
- lcms2=2.17=h717163a_0
- ld_impl_linux-64=2.43=h712a8e2_4
- lerc=4.0.0=h0aef613_1
- libassuan=3.0.2=h5888daf_0
- libcap=2.75=h39aace5_0
- libcbor=0.10.2=hcb278e6_0
- libcurl=8.13.0=h332b0f4_0
- libdeflate=1.23=h86f0d12_0
- libedit=3.1.20250104=pl5321h7949ede_0
- libev=4.33=hd590300_2
- libexpat=2.7.0=h5888daf_0
- libffi=3.4.6=h2dba641_1
- libfido2=1.15.0=hdd1f21f_0
- libfreetype=2.13.3=ha770c72_1
- libfreetype6=2.13.3=h48d6fc4_1
- libgcc=14.2.0=h767d61c_2
- libgcc-ng=14.2.0=h69a702a_2
- libgcrypt=1.11.0=ha770c72_2
- libgcrypt-devel=1.11.0=hb9d3cd8_2
- libgcrypt-lib=1.11.0=hb9d3cd8_2
- libgcrypt-tools=1.11.0=hb9d3cd8_2
- libglib=2.84.1=h2ff4ddf_0
- libgomp=14.2.0=h767d61c_2
- libgpg-error=1.55=h3f2d84a_0
- libiconv=1.18=h4ce23a2_1
- libjpeg-turbo=3.1.0=hb9d3cd8_0
- libksba=1.6.7=hac33072_0
- liblzma=5.8.1=hb9d3cd8_1
- libmagic=5.46=hadc24fc_0
- libnghttp2=1.64.0=h161d5f1_0
- libnsl=2.0.1=hd590300_0
- libpng=1.6.47=h943b412_0
- libsqlite=3.49.1=hee588c1_2
- libssh2=1.11.1=hcf80075_0
- libstdcxx=14.2.0=h8f9b012_2
- libstdcxx-ng=14.2.0=h4852527_2
- libtiff=4.7.0=hd9ff511_4
- libudev1=257.4=hbe16f8c_1
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.5.0=h851e524_0
- libxcb=1.17.0=h8a09558_0
- libxcrypt=4.4.36=hd590300_1
- libzlib=1.3.1=hb9d3cd8_2
- looseversion=1.3.0=pyhd8ed1ab_0
- lsof=4.99.4=hb9d3cd8_0
- lz4-c=1.10.0=h5888daf_1
- more-itertools=10.7.0=pyhd8ed1ab_0
- msgpack-python=1.1.0=py312h68727a3_0
- multidict=6.4.3=py312h178313f_0
- mutagen=1.47.0=pyhd8ed1ab_1
- ncurses=6.5=h2d0b736_3
- npth=1.8=h5888daf_0
- ntbtls=0.3.2=hfc55251_0
- openjpeg=2.5.3=h5fbd93e_0
- openssh=10.0p1=hc830a30_0
- openssl=3.5.1=h7b32b05_0
- p7zip=16.02=h9c3ff4c_1001
- patool=4.0.1=pyhd8ed1ab_0
- pcre2=10.44=hc749103_2
- perl=5.32.1=7_hd590300_perl5
- pillow=11.1.0=py312h80c1187_0
- pip=25.1.1=pyh8b19718_0
- platformdirs=4.3.7=pyh29332c3_0
- popt=1.16=h0b475e3_2002
- propcache=0.3.1=py312h178313f_0
- psutil=7.0.0=py312h66e93f0_0
- pthread-stubs=0.4=hb9d3cd8_1002
- pycparser=2.22=pyh29332c3_1
- pyperclip=1.9.0=pyha804496_3
- pysocks=1.7.1=pyha55dd90_7
- python=3.12.10=h9e4cc4f_0_cpython
- python-dateutil=2.9.0.post0=pyhff2d567_1
- python-gitlab=5.6.0=pyhff2d567_0
- python_abi=3.12=7_cp312
- readline=8.2=h8c095d6_2
- requests=2.32.3=pyhd8ed1ab_1
- requests-ftp=0.3.1=pyhd8ed1ab_2
- requests-toolbelt=1.0.0=pyhd8ed1ab_1
- rsync=3.4.1=h81c0278_2
- s3transfer=0.12.0=pyhd8ed1ab_0
- secretstorage=3.3.3=py312h7900ff3_3
- setuptools=80.1.0=pyhff2d567_0
- simplejson=3.20.1=py312h66e93f0_0
- six=1.17.0=pyhd8ed1ab_0
- sniffio=1.3.1=pyhd8ed1ab_1
- sqlite=3.49.1=h9eae976_2
- tk=8.6.13=noxft_h4845f30_101
- tqdm=4.67.1=pyhd8ed1ab_1
- typing_extensions=4.13.2=pyh29332c3_0
- tzdata=2025b=h78e105d_0
- urllib3=2.4.0=pyhd8ed1ab_0
- wheel=0.45.1=pyhd8ed1ab_1
- whoosh=2.7.4=py312h7900ff3_9
- xclip=0.13=hb9d3cd8_4
- xorg-libice=1.1.2=hb9d3cd8_0
- xorg-libsm=1.2.6=he73a12e_0
- xorg-libx11=1.8.12=h4f16b4b_0
- xorg-libxau=1.0.12=hb9d3cd8_0
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.6=hb9d3cd8_0
- xorg-libxmu=1.2.1=hb9d3cd8_1
- xorg-libxt=1.3.1=hb9d3cd8_0
- xsel=1.2.1=hb9d3cd8_6
- xxhash=0.8.3=hb47aa4a_0
- yarl=1.20.0=py312h178313f_0
- zipp=3.21.0=pyhd8ed1ab_1
- zlib=1.3.1=hb9d3cd8_2
- zstandard=0.23.0=py312h66e93f0_2
- zstd=1.5.7=hb8e6e7a_2