dataset¶
Dataset management operations
Usage¶
Usage: nemar dataset [options] [command]
Dataset management
Options:
-h, --help display help for command
Commands:
ci [dataset-id] Check BIDS validation CI status for the
current dataset
clone [options] <dataset-id> Clone a dataset from NEMAR
collaborators [options] <dataset-id> List collaborators for a dataset
commit [options] Stage and commit changes in the current
dataset
download [options] <dataset-id> Download a dataset from NEMAR or
OpenNeuro
drop [files...] Free local copies of annexed files
(keeps remote copies)
get [options] [files...] Download annexed data files for the
current dataset
help [command] display help for command
invite <username> <dataset-id> Invite a user as collaborator to your
dataset
list [options] List datasets on NEMAR (full catalog)
manifest [options] [version] View version manifests for a dataset
publish Publication workflow management
push [options] Push commits and data to remotes
release [options] <dataset-id> Create a version bump PR for a dataset
request-access <dataset-id> Request collaborator access to a
dataset
save [options] Stage and commit changes (alias for
commit)
search [options] <query> Search datasets using semantic matching
status [options] <dataset-id> Check status of a dataset
update [options] [path] Push local changes to a dataset via PR
upload [options] <path> Upload a BIDS dataset to NEMAR
validate [options] [path] Validate a BIDS dataset using the
official BIDS validator (requires Deno)
Run with --help-all for examples and detailed descriptions.
Subcommands¶
dataset validate¶
Usage: nemar dataset validate [options] [path]
Validate a BIDS dataset using the official BIDS validator (requires Deno)
Arguments:
path Path to BIDS dataset directory (default: ".")
Options:
--ignore-warnings Only report errors, not warnings
-c, --config <file> Validation config file (.bidsvalidatorrc)
-r, --recursive Validate derivatives subdirectories
--prune Skip sourcedata and derivatives for faster validation
-v, --verbose Show verbose output
--json Output results as JSON (for scripting)
--version-info Show BIDS validator version info
--update Force update the BIDS validator to the latest version
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset upload¶
Usage: nemar dataset upload [options] <path>
Upload a BIDS dataset to NEMAR
Arguments:
path Path to BIDS dataset directory
Options:
-n, --name <name> Dataset name (defaults to BIDS Name, then directory
name)
-d, --description <desc> Dataset description
--skip-validation Skip BIDS validation (not recommended)
--skip-orcid Skip co-author ORCID collection
--dry-run Show what would be uploaded without doing it
-j, --jobs <number> Parallel upload streams (default: 4) (default: "4")
-y, --yes Skip confirmation and proceed
--restart Clear upload progress and re-upload all files
--no Skip confirmation and decline
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset download¶
Usage: nemar dataset download [options] <dataset-id>
Download a dataset from NEMAR or OpenNeuro
Arguments:
dataset-id Dataset ID (e.g., nm000104 or OpenNeuro ds000248)
Options:
-o, --output <path> Output directory (default: ./<dataset-id>)
-j, --jobs <number> Parallel download streams (default: 4) (default: "4")
--no-data Download metadata only (skip large data files)
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset status¶
Usage: nemar dataset status [options] <dataset-id>
Check status of a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
--json Output as JSON for scripting
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset list¶
Usage: nemar dataset list [options]
List datasets on NEMAR (full catalog)
Options:
--mine List only your datasets (both private and public)
--owner <username> List datasets owned by a specific user
--search <query> Search by name, description, authors, or tasks
--modality <type> Filter by modality (eeg, emg, meg, etc.)
--author <name> Filter by author name
--task <name> Filter by task name
--doi Show only datasets with DOIs
--recent [days] Show recently published datasets
--sort <order> Sort: newest, oldest, name, participants, size (default:
"newest")
--json Output as JSON for scripting
-n, --limit <n> Results per page (default: 20, max: 200) (default: "20")
--page <n> Page number (starts at 1)
--offset <n> Skip this many results (alternative to --page)
--all Show all results (up to 200)
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset release¶
Usage: nemar dataset release [options] <dataset-id>
Create a version bump PR for a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
--type <type> Bump type: patch, minor, or major
--version <version> Explicit version (e.g., 2.0.0)
--dir <path> Use existing local clone instead of cloning
--monitor Watch CI checks and offer to merge
-y, --yes Skip confirmation and proceed
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset update¶
Usage: nemar dataset update [options] [path]
Push local changes to a dataset via PR
Arguments:
path Path to local dataset clone (default: current directory)
Options:
--bump <type> Version bump type: patch, minor, or major (default:
"patch")
--branch <name> Custom branch name
-m, --message <msg> Commit message
--monitor Watch CI checks and offer to merge
-y, --yes Skip confirmation and proceed
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset request-access¶
Usage: nemar dataset request-access [options] <dataset-id>
Request collaborator access to a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset invite¶
Usage: nemar dataset invite [options] <username> <dataset-id>
Invite a user as collaborator to your dataset
Arguments:
username Username to invite
dataset-id Dataset ID (e.g., nm000104)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset collaborators¶
Usage: nemar dataset collaborators [options] <dataset-id>
List collaborators for a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
--json Output as JSON for scripting
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset publish request¶
Usage: nemar dataset publish request [options] <dataset-id>
Request publication of a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset publish status¶
Usage: nemar dataset publish status [options] <dataset-id>
Check publication status of a dataset
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset publish resend¶
Usage: nemar dataset publish resend [options] <dataset-id>
Resend publication request notification to admins
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset clone¶
Usage: nemar dataset clone [options] <dataset-id>
Clone a dataset from NEMAR
Arguments:
dataset-id Dataset ID (e.g., nm000104)
Options:
-o, --output <path> Output directory (default: ./<dataset-id>)
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset get¶
Usage: nemar dataset get [options] [files...]
Download annexed data files for the current dataset
Arguments:
files Specific files/paths to get (default: all)
Options:
-j, --jobs <number> Parallel download streams (default: "4")
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset save¶
Usage: nemar dataset save [options]
Stage and commit changes (alias for commit)
Options:
-m, --message <msg> Commit message (default: "Save changes")
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset push¶
Usage: nemar dataset push [options]
Push commits and data to remotes
Options:
-j, --jobs <number> Parallel upload streams for S3 (default: "4")
--no-s3 Skip pushing data to S3 remote
--pr Create a pull request after pushing
-t, --title <title> Pull request title (with --pr)
-b, --body <body> Pull request body (with --pr)
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset drop¶
Usage: nemar dataset drop [options] [files...]
Free local copies of annexed files (keeps remote copies)
Arguments:
files Specific files to drop (default: all)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset ci¶
Usage: nemar dataset ci [options] [dataset-id]
Check BIDS validation CI status for the current dataset
Arguments:
dataset-id Dataset ID (auto-detected from git remote if omitted)
Options:
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.
dataset manifest¶
Usage: nemar dataset manifest [options] [version]
View version manifests for a dataset
Arguments:
version Version to view (lists available if omitted)
Options:
-d, --dataset <id> Dataset ID (auto-detected from git remote if omitted)
--json Output raw JSON
-h, --help display help for command
Run with --help-all for examples and detailed descriptions.