Liveness check. Echoes back the supplied message (or 'ok') and the running mesa-mcp version. No iRODS access required.

Validate a DataCite 4.x record and write it to an iRODS path as AVUs (canonical and/or CyVerse-template naming), mirrored to DuckLake as one snapshot.

Export DataCite AVUs as a DataCite 4.x XML (for DOI registration) or REST JSON document.

Return the DataCite 4.x field scaffold (field, required?, repeatable?, controlled vocabulary, canonical AVU key) to drive a complete, valid record.

Validate DataCite AVUs against the 4.x kernel: report missing mandatory fields, invalid controlled-vocabulary values, and whether the record is DOI-ready.

Resolve an OLS term, build the canonical AVU triple (.<snake_label>, , ), write it to the iRODS path, and record the change in the project's DuckLake. Composite of mesa_avu_from_term + ds_add_avu, in one call.

Pure transformation: turn an OLS term + user value into the canonical AVU triple (attribute='.<snake_case_label>', value=, unit=) without writing to iRODS.

Generate a SCHEMAS-compatible template (prefix + top-level term fields) for an ontology. This is the function that drives the esiil-portal auto-generated AVU forms.

Fetch metadata for a single OLS ontology (term count, version, homepage, preferred prefix).

Get the full record (label, CURIE, synonyms, definition, parents/children) for a single OLS term by IRI.

List the direct children of an OLS term. Use this to walk an ontology's class hierarchy one level at a time.

List ontologies available in the EMBL-EBI Ontology Lookup Service (OLS4), paginated. Returns 266+ ontologies (ENVO, GO, CHEBI, etc.).

Enable a MESA policy on a project root collection by writing the mesa.policy.<policy_name>=true AVU. Records the change into the project's DuckLake when MESA-enabled.

Disable a MESA policy on a project root collection by removing the mesa.policy.<policy_name> AVU. Records the change into the project's DuckLake when MESA-enabled.

Search OLS terms across all ontologies or scoped to one. Optionally restrict to descendants of a parent IRI (hierarchy walk).

Enroll an iRODS collection as a MESA project. Creates the <irods_path>/.mesa/ducklake/ sub-collection (or the configured ducklake.data_collection), sets the mesa.enabled=true AVU on the project root, and registers the project in the DuckLake catalog. Idempotent — safe to re-run.

Add a new AVU (attribute-value-unit) to a file (data-object), directory (collection), resource, or user.

Add MULTIPLE AVUs to one data-object/collection in a single call and mirror them all into DuckLake as ONE snapshot (efficient bulk tagging).

Copy a file (data-object) or directory (collection) to a new location.

Create a read or write iRODS ticket on a data object or collection. Returns the ticket string plus the restrictions that were applied. Anonymous users may not create tickets.

Delete an AVU (attribute-value-unit) from a file, directory, resource, or user.

Delete a file (data-object) or directory (collection).

Revoke an existing iRODS ticket. Issuer or admin only — the server enforces this. Anonymous callers are rejected at the tool layer.

Get a recursive tree view of files (data-objects) and directories (collections). The specified path must be an iRODS path. The output is in JSON format. The output contains all entries in the given directory (collection) path.

Returns how to download the full contgent of a file (data-object) with the specified path. The specified path must be an iRODS path. Returns how to download the file using WebDAV, GoCommands (gocmd), and iCommands.

Run an iRODS rule. Supply either rule_name (server-installed) or rule_text (inline iRL). Output parameters are returned as a dict; iRODS stdout/stderr are returned when output_parameters includes 'ruleExecOut'. Path-typed input parameters are checked against the caller's accessible paths before the rule fires.

Retrieve detailed metadata about a file or directory.

Fetch the full AVU metadata bundle for an iRODS path (data object or collection). Returns the resolved target type alongside the AVU list.

Return the configuration of a named Policy Composition Framework policy. iRODS does not expose PCF config through PRC; this is a stub that returns config=None and a note documenting the limitation.

Return the source of a named iRODS rule. iRODS does not expose rule sources through PRC; this is a best-effort tool whose definition field is None on most servers.

Get information about a specific iRODS ticket, such as its ID and expiration time, in JSON format. Anonymous users are not allowed to get ticket information.

Get a list of directories (collections) that this server is allowed to access. The output also contains API names that can be requested to each directory (collection).

List AVUs (attribute-value-unit) from a file (data-object), directory (collection), resource, or user.

Get a list of files (data-objects) and directories (collections) in a specified path. The specified path must be an iRODS path. The output is in JSON format. The output contains entries in the given directory (collection) path. Use offset and limit parameters to paginate through large directories.

Get a list of files (data-objects) and directories (collections) in a specified path with full detailed info. The specified path must be an iRODS path. The output is in JSON format. The output contains entries in the given directory (collection) path, and users or groups who can access the files (data-ojects). Files (data-objects) will also have replica information. Use offset and limit parameters to paginate through large directories.

List policies in effect for the Data Store. With project_path, returns the MESA policy AVUs (mesa.policy.*) set on that project root — the policies mesa-mcp itself honours. Always includes the server-side Policy Composition Framework envelope; iRODS does not expose PCF state through PRC, so that part is a documented stub.

List iRODS rules visible to the caller. Returns a best-effort list of delayed rules; the static rule base is not exposed by PRC and the note field documents that limitation.

Get a list of iRODS tickets. Return information about the tickets, such as their IDs and expiration times, in JSON format. Anonymous users are not allowed to list tickets.

Make a new directory (collection).

Modify data access of a user or group to a file (data-object) or directory (collection).

Modify data access inheritance flag of a file or directory.

Modify restrictions on an existing iRODS ticket. Cannot change the ticket's mode — that is set at issuance time. Returns the applied restrictions. Anonymous users are not allowed to modify tickets.

Move a file (data-object) or directory (collection) to a new location.

Read the partial content of a file (data-object) with the specified path and offset. The specified path must be an iRODS path. If the file is too large to be displayed inline, use the WebDAV URI to access it.

Recursively search for files (data-objects) and directories (collections) matching a pattern. The specified search root path must be an iRODS path. Use unix wildcards, such as '?' and '*', for the search pattern. The matching entries are returned in JSON format.

Search for files (data-objects) and directories (collections) matching iRODS AVU (attribute-value-units) using specified attribute and value. The matching entries are returned in JSON format.

Search iRODS by AVU attribute/value/unit. More permissive than ds_search_files_by_avu: any combination of attribute, value, and unit can be supplied and you can restrict the result type to data objects, collections, or both.

Returns how to upload the full contgent of a file (data-object) to the specified path. The specified path must be an iRODS path. Returns how to upload the file using WebDAV, GoCommands (gocmd), and iCommands.

Supply an iRODS ticket to the caller's iRODS session. Subsequent operations by the same caller run with the ticket applied, and their AVU writes record the ticket id in DuckLake's via_ticket column. Other callers' sessions are unaffected.

Write the partial content to a file (data-object) with the specified path and offset. The specified path must be an iRODS path. If the file is too large to be displayed inline, use the WebDAV URI to access it.