Using the Whyis command-line interface

If you’re using a Docker container:

docker exec -it <container name> bash

In Docker, the whyis command is available at /opt/venv/bin/whyis.

Running the Server

Commands to run or initialize the server. Run them in an empty directory to create a new kgapp (knowledge graph application).

whyis

Runs the command run

usage: whyis [-?] [backup,createuser,load,init,restore,retire,run,test,runagent,updateuser]

-?, –help:

show this help message and exit

whyis run

Runs the Flask development server i.e. app.run():

usage: whyis run [-?] [-h HOST] [-p PORT] [--threaded]
                 [--processes PROCESSES] [--passthrough-errors] [-d]
                 [-D] [-r] [-R] [--ssl-crt SSL_CRT] [--ssl-key SSL_KEY]
                 [--watch]

-?, –help:

show this help message and exit

-h, –host:

The host IP to serve on.

-p, –port:

The port to serve on.

–threaded:

Use threading to serve multiple requests.

–processes:

The size of the process pool.

–passthrough-errors:

-d, –debug:

enable the Werkzeug debugger (DO NOT use in production code)

-D, –no-debug:

disable the Werkzeug debugger

-r, –reload:

monitor Python files for changes (not 100% safe for production use)

-R, –no-reload:

do not monitor Python files for changes

–ssl-crt:

Path to ssl certificate

–ssl-key:

Path to ssl key

whyis init

Initialize fuseki.

usage: whyis init [-?]

-?, –help:

show this help message and exit

Knowledge operations

whyis load

Add a nanopublication to the knowledge graph.

usage: whyis load [-?] -i INPUT_FILE [-f FILE_FORMAT]
                  [-r WAS_REVISION_OF] [--temp-store TEMP_STORE]

-?, –help:

show this help message and exit

-i, –input:

Path to file containing nanopub

-f, –format:

File format (default: trig; also turtle, json-ld, xml, nquads, nt, rdfa)

-r, –revises:

URI of nanopublication that this is a revision of

–temp-store:

backing store type to use for temporary graphs; deprecated

whyis retire

Retire a nanopublication from the knowledge graph.

usage: whyis retire [-?] -n NANOPUB_URI

-?, –help:

show this help message and exit

-n, –nanopub_uri:

URI of the nanopub to retire

Backup/Restore

These operations can also be used to export knowledge graphs to other systems.

whyis backup

Backup the graph to an archive. Synchronizes against previously saved backups.

usage: whyis backup [-?] -a OUTPUT_DIRECTORY

-?, –help:

show help message and exit

-a, –archive:

Backup path

whyis restore

Restores a knowledge graph from an archive.

usage: whyis restore [-?] -a INPUT_DIRECTORY

-?, –help:

show this help message and exit

-a, –archive:

Backup path

Code Operations

whyis test

Run tests

usage: whyis test [-?] [-v VERBOSITY] [--failfast] [--test TESTS]
                  [--ci] [--apponly]

-?, –help:

show this help message and exit

-v , –verbosity:

verbosity level of output, between 0 and 2 (default 2)

–failfast:

Stop the test after the first failure

–test:

Name of python file (without extension) to run tests from, or glob pattern

–ci:

Analyze coverage and store all results as XML (for CI server)

–apponly:

Runs the app tests only

whyis runagent

Runs a specified inference agent.

usage: whyis runagent [-?] -a AGENT_PATH [-e ENTITY_URI] [-d]

-?, –help:

show this help message and exit

-a, –agent:

Python path (dotted) of agent to use

-e, –entity:

Entity URI to run against

-d, –dry-run:

Do not store agent output

Accounts

whyis updateuser

Update a user in Whyis

usage: whyis updateuser [-?] [-e EMAIL] [-p PASSWORD] [-f NAME]
                        [-l NAME] -u IDENTIFIER [--add-roles ADD_ROLES]
                        [--remove-roles REMOVE_ROLES]

-?, –help:

show this help message and exit

-e , –email:

Email address for this user

-p, –password:

Password for this user

-f, –fn:

First name of this user

-l, –ln:

Last name of this user

-u, –username:

Username for this user

–add-roles:

Comma-delimited list of roles to add

–remove-roles:

Comma-delimited list of roles to remove

whyis createuser

Add a user to Whyis

usage: whyis createuser [-?] [-e EMAIL] [-p PASSWORD] [-f FN] [-l LN]
                         -u IDENTIFIER [--roles ROLES]

-?, –help:

show this help message and exit

-e, –email:

Email address for this user

-p, –password:

Password for this user

-f, –fn:

First name of this user

-l, –ln:

Last name of this user

-u, –username:

Username for this user

–roles:

Comma-delimited list of role names