admin

Administrative operations (requires admin privileges).

Note

This page is generated from nemar admin --help. Run generate-commands.ts to refresh it.

admin

Usage: nemar admin [options] [command]

Admin commands (requires admin privileges)

Options:
  -h, --help                                  display help for command

Commands:
  approve [options] <username>                Approve a pending user
  bulk-delete [options] <dataset-ids>         Delete multiple phantom/orphaned datasets at once (owner only)
  ci                                          CI workflow management
  delete-dataset [options] <dataset-id>       Delete a dataset and all associated resources (GitHub, S3, D1)
  doi                                         DOI management
  e2e-test [options]                          Run end-to-end test against nm099999 (admin only)
  email-preferences                           Manage email notification preferences
  help [command]                              display help for command
  import-openneuro [options] <openneuro-ids>  Import an OpenNeuro dataset into NEMAR
  make-public <dataset-id>                    Publish a dataset (make repository and data public) - PERMANENT
  notice                                      Manage system notices displayed to CLI users
  notify [options]                            Send an email to a group or a single user
  publish                                     Publication workflow management
  reindex [options] [dataset-id]              Refresh dataset metadata: enrichment + nemar.org sync + first-class D1 columns
  repo                                        Repository visibility management
  revert [options] <dataset-id> [version]     Revert a dataset to a previous version (creates PR for review)
  revoke [options] <username>                 Revoke user access
  role [options] <username> <role>            Change a user's role (owner only)
  s3                                          S3 and IAM credential management
  summary                                     summary.json coverage across published dataset versions
  sync                                        Sync dataset metadata to nemar.org datapipeline
  users [options]                             List NEMAR users

  Run with --help-all for examples and detailed descriptions.

admin approve

Usage: nemar admin approve [options] <username>

Approve a pending user

Arguments:
  username    Username to approve

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin bulk-delete

Usage: nemar admin bulk-delete [options] <dataset-ids>

Delete multiple phantom/orphaned datasets at once (owner only)

Arguments:
  dataset-ids  Comma-separated dataset IDs (e.g., nm000153,nm000154,nm000155)

Options:
  --yes        Skip confirmation prompt
  -h, --help   display help for command

admin ci

Usage: nemar admin ci [options] [command]

CI workflow management

Options:
  -h, --help                   display help for command

Commands:
  add [options] [dataset-id]   Deploy CI workflows to a dataset repository (or
                               all with --all)
  check <dataset-id>           Check CI workflow status for a dataset
  help [command]               display help for command
  sync [options] [dataset-id]  Sync deployed CI workflows to current templates
                               (only writes drifted/missing files)
  validate <dataset-id>        Check whether GitHub Actions can parse the
                               deployed CI workflows

admin ci add

Usage: nemar admin ci add [options] [dataset-id]

Deploy CI workflows to a dataset repository (or all with --all)

Arguments:
  dataset-id     Dataset ID (e.g., nm000104)

Options:
  --all          Deploy to all dataset repositories
  --no-validate  Skip the post-deploy parseability poll on the single-dataset
                 path. No-op for --all (fleet deploys always skip the poll).
  -y, --yes      Skip confirmation and proceed
  -n, --no       Skip confirmation and decline
  -h, --help     display help for command

admin ci check

Usage: nemar admin ci check [options] <dataset-id>

Check CI workflow status for a dataset

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -h, --help  display help for command

admin ci sync

Usage: nemar admin ci sync [options] [dataset-id]

Sync deployed CI workflows to current templates (only writes drifted/missing
files)

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  --all       Sync across all dataset repositories
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin ci validate

Usage: nemar admin ci validate [options] <dataset-id>

Check whether GitHub Actions can parse the deployed CI workflows

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -h, --help  display help for command

admin delete-dataset

Usage: nemar admin delete-dataset [options] <dataset-id>

Delete a dataset and all associated resources (GitHub, S3, D1)

Arguments:
  dataset-id  Dataset ID (e.g., nm000108)

Options:
  --force     Force deletion of published datasets with DOIs (owner only)
  -h, --help  display help for command

admin doi

Usage: nemar admin doi [options] [command]

DOI management

Options:
  -h, --help                     display help for command

Commands:
  create [options] <dataset-id>  Create concept DOI for a dataset
  enrich [options] <dataset-id>  Enrich DOI metadata with ORCIDs, descriptions,
                                 funding, and more
  help [command]                 display help for command
  info <dataset-id>              Get DOI info for a dataset
  update [options] <dataset-id>  Update EZID DOI metadata or status

admin doi create

Usage: nemar admin doi create [options] <dataset-id>

Create concept DOI for a dataset

Arguments:
  dataset-id             Dataset ID (e.g., nm000104)

Options:
  --title <title>        DOI title (defaults to dataset name)
  --description <desc>   DOI description
  --provider <provider>  DOI provider: ezid (default) or zenodo (default:
                         "ezid")
  --sandbox              Use sandbox/test DOI
  -y, --yes              Skip confirmation and proceed
  -n, --no               Skip confirmation and decline
  -h, --help             display help for command

admin doi enrich

Usage: nemar admin doi enrich [options] <dataset-id>

Enrich DOI metadata with ORCIDs, descriptions, funding, and more

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  --no-llm    Skip LLM-based enrichment from README
  --sandbox   Use sandbox DOI
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin doi info

Usage: nemar admin doi info [options] <dataset-id>

Get DOI info for a dataset

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -h, --help  display help for command

admin doi update

Usage: nemar admin doi update [options] <dataset-id>

Update EZID DOI metadata or status

Arguments:
  dataset-id     Dataset ID (e.g., nm000104)

Options:
  --make-public  Transition DOI from reserved to public (permanent)
  --refresh      Refresh metadata from dataset_description.json and
                 .nemar/metadata.json
  -y, --yes      Skip confirmation and proceed
  -n, --no       Skip confirmation and decline
  -h, --help     display help for command

admin e2e-test

Usage: nemar admin e2e-test [options]

Run end-to-end test against nm099999 (admin only)

Options:
  --verbose       Show detailed output for each step
  --skip-reset    Use existing nm099999 state (skip reset)
  --skip-cleanup  Keep temp directories after test
  -h, --help      display help for command

  Run with --help-all for examples and detailed descriptions.

admin email-preferences

Usage: nemar admin email-preferences [options] [command]

Manage email notification preferences

Options:
  -h, --help        display help for command

Commands:
  help [command]    display help for command
  show              Show current email notification preferences
  update [options]  Update email notification preferences

admin email-preferences show

Usage: nemar admin email-preferences show [options]

Show current email notification preferences

Options:
  -h, --help  display help for command

admin email-preferences update

Usage: nemar admin email-preferences update [options]

Update email notification preferences

Options:
  --user-approval <bool>        Enable/disable user approval notifications
  --publication-request <bool>  Enable/disable publication request
                                notifications
  --announcements <bool>        Enable/disable announcement emails
  --all <bool>                  Enable/disable all notifications
  -h, --help                    display help for command

admin import-openneuro

Usage: nemar admin import-openneuro [options] <openneuro-ids>

Import an OpenNeuro dataset into NEMAR

Arguments:
  openneuro-ids     OpenNeuro dataset ID(s), comma-separated (e.g.,
                    ds007262,ds007263)

Options:
  --local           Run import locally instead of dispatching GitHub Actions
                    workflow
  --dir <path>      Working directory for local clone (requires --local)
  --skip-data       Skip S3 data copy, metadata only (requires --local)
  --trust-upstream  If BIDS validation does not register within the bounded
                    poll, fall back to skip_ci_check=true at approval.
                    OpenNeuro data is pre-validated upstream so this is the
                    recommended setting for OpenNeuro imports (#431).
  -h, --help        display help for command

admin make-public

Usage: nemar admin make-public [options] <dataset-id>

Publish a dataset (make repository and data public) - PERMANENT

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -h, --help  display help for command

  Run with --help-all for examples and detailed descriptions.

admin notice

Usage: nemar admin notice [options] [command]

Manage system notices displayed to CLI users

Options:
  -h, --help            display help for command

Commands:
  clear [options] <id>  Delete a notice by ID
  help [command]        display help for command
  list                  List all notices (including expired)
  set [options]         Create a new system notice

admin notice clear

Usage: nemar admin notice clear [options] <id>

Delete a notice by ID

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin notice list

Usage: nemar admin notice list [options]

List all notices (including expired)

Options:
  -h, --help  display help for command

admin notice set

Usage: nemar admin notice set [options]

Create a new system notice

Options:
  -m, --message <text>      Notice message text
  -l, --level <level>       Notice level: info, warning, critical (default:
                            "info")
  -s, --scope <scope>       Target scope: all, admins, members (default: "all")
  -e, --expires <datetime>  Expiry datetime (ISO 8601)
  -h, --help                display help for command

admin notify

Usage: nemar admin notify [options]

Send an email to a group or a single user

Options:
  --to <group>        Recipient group: all, admins, members
  --user <username>   Send to a single user by username
  --subject <text>    Email subject line
  --body <text>       Email body (markdown)
  --body-file <path>  Read email body from file (markdown)
  --dry-run           Preview recipients without sending
  -y, --yes           Skip confirmation and proceed
  -n, --no            Skip confirmation and decline
  -h, --help          display help for command

admin publish

Usage: nemar admin publish [options] [command]

Publication workflow management

Options:
  -h, --help                      display help for command

Commands:
  approve [options] <dataset-id>  Approve and publish a dataset (runs
                                  orchestrator)
  deny [options] <dataset-id>     Deny a publication request
  help [command]                  display help for command
  list [options]                  List publication requests

admin publish approve

Usage: nemar admin publish approve [options] <dataset-id>

Approve and publish a dataset (runs orchestrator)

Arguments:
  dataset-id       Dataset ID

Options:
  --resume         Resume from last failed step
  --sandbox        Use Zenodo sandbox for testing
  --skip-ci-check  Skip BIDS validation CI check (admin override)
  -y, --yes        Skip confirmation and proceed
  -n, --no         Skip confirmation and decline
  -h, --help       display help for command

  Run with --help-all for examples and detailed descriptions.

admin publish deny

Usage: nemar admin publish deny [options] <dataset-id>

Deny a publication request

Arguments:
  dataset-id             Dataset ID

Options:
  -r, --reason <reason>  Reason for denial
  -y, --yes              Skip confirmation and proceed
  -n, --no               Skip confirmation and decline
  -h, --help             display help for command

  Run with --help-all for examples and detailed descriptions.

admin publish list

Usage: nemar admin publish list [options]

List publication requests

Options:
  -s, --status <status>  Filter by status (requested, approving, published,
                         denied)
  -h, --help             display help for command

  Run with --help-all for examples and detailed descriptions.

admin reindex

Usage: nemar admin reindex [options] [dataset-id]

Refresh dataset metadata: enrichment + nemar.org sync + first-class D1 columns

Arguments:
  dataset-id           Dataset ID to reindex (e.g., nm000103)

Options:
  --all                Reindex every dataset with a GitHub repo
  --missing-metadata   Reindex only datasets with NULL metadata columns
  --stale              Reindex only datasets whose metadata is older than
                       --older-than days
  --older-than <days>  Threshold in days. Default 30 for --stale, 1 (24h) for
                       --missing-metadata recency guard.
  --skip-enrichment    Skip the LLM enrichment step
  --skip-sync          Skip the nemar.org sync + D1 column refresh step
  --ref <ref>          Ref to enrich from (single-dataset only; default: main)
  --dry-run            List matched datasets without firing the reindex (bulk
                       only)
  -h, --help           display help for command

admin repo

Usage: nemar admin repo [options] [command]

Repository visibility management

Options:
  -h, --help                      display help for command

Commands:
  help [command]                  display help for command
  private [options] <dataset-id>  Make a dataset repository private
  public [options] <dataset-id>   Make a dataset repository public

admin repo private

Usage: nemar admin repo private [options] <dataset-id>

Make a dataset repository private

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin repo public

Usage: nemar admin repo public [options] <dataset-id>

Make a dataset repository public

Arguments:
  dataset-id  Dataset ID (e.g., nm000104)

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin revert

Usage: nemar admin revert [options] <dataset-id> [version]

Revert a dataset to a previous version (creates PR for review)

Arguments:
  dataset-id       Dataset ID (e.g., nm000104)
  version          Target version to revert to (e.g., 1.0.0)

Options:
  --list           List available versions without reverting
  --force          Direct push to main without PR (emergency only)
  --message <msg>  Custom revert commit message
  --dir <path>     Use existing local clone instead of cloning fresh
  -y, --yes        Skip confirmation and proceed
  -n, --no         Skip confirmation and decline
  -h, --help       display help for command

admin revoke

Usage: nemar admin revoke [options] <username>

Revoke user access

Arguments:
  username    Username to revoke

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin role

Usage: nemar admin role [options] <username> <role>

Change a user's role (owner only)

Arguments:
  username    Username to change role for
  role        New role: owner, admin, or member

Options:
  -y, --yes   Skip confirmation prompt
  -h, --help  display help for command

  Run with --help-all for examples and detailed descriptions.

admin s3

Usage: nemar admin s3 [options] [command]

S3 and IAM credential management

Options:
  -h, --help                           display help for command

Commands:
  help [command]                       display help for command
  lock [options] <dataset-id>          Apply S3 Object Lock (Governance mode)
                                       to a dataset
  regenerate-iam [options] <username>  Regenerate AWS IAM credentials for a
                                       user

admin s3 lock

Usage: nemar admin s3 lock [options] <dataset-id>

Apply S3 Object Lock (Governance mode) to a dataset

Arguments:
  dataset-id  Dataset ID to lock

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin s3 regenerate-iam

Usage: nemar admin s3 regenerate-iam [options] <username>

Regenerate AWS IAM credentials for a user

Arguments:
  username    Username to regenerate credentials for

Options:
  -y, --yes   Skip confirmation and proceed
  -n, --no    Skip confirmation and decline
  -h, --help  display help for command

admin summary

Usage: nemar admin summary [options] [command]

summary.json coverage across published dataset versions

Options:
  -h, --help       display help for command

Commands:
  check [options]  Report which (dataset_id, version) pairs have stale or
                   missing summary.json
  help [command]   display help for command

admin summary check

Usage: nemar admin summary check [options]

Report which (dataset_id, version) pairs have stale or missing summary.json

Options:
  --fix           Dispatch generate-manifest for every stale/missing version
  --id <id>       Limit to a single dataset_id (exact match)
  --match <glob>  Limit to dataset_ids matching a glob pattern: `*` matches any
                  run of chars, `?` matches one char. Examples: `on*`,
                  `nm00010?`, `*99999`. Can be combined with --id (id wins if
                  both passed).
  --only-stale    Print only rows that are not ok (suppresses ok rows)
  --json          Emit the full report as JSON instead of a table
  -y, --yes       Skip confirmation and proceed
  -n, --no        Skip confirmation and decline
  -h, --help      display help for command

admin sync

Usage: nemar admin sync [options] [command]

Sync dataset metadata to nemar.org datapipeline

Options:
  -h, --help        display help for command

Commands:
  help [command]    display help for command
  run <dataset-id>  Sync a dataset to nemar.org
  status            Show nemar.org sync status for all published datasets

admin sync run

Usage: nemar admin sync run [options] <dataset-id>

Sync a dataset to nemar.org

Arguments:
  dataset-id  Dataset ID (e.g., nm000103)

Options:
  -h, --help  display help for command

admin sync status

Usage: nemar admin sync status [options]

Show nemar.org sync status for all published datasets

Options:
  -h, --help  display help for command

admin users

Usage: nemar admin users [options]

List NEMAR users

Options:
  --pending      Show only pending approval
  --verified     Show only verified (awaiting approval)
  --approved     Show only approved users
  --revoked      Show only revoked users
  --role <role>  Filter by role: owner, admin, or member
  -h, --help     display help for command

  Run with --help-all for examples and detailed descriptions.