ckanext-attribution 1.2.9

A CKAN extension that adds support for complex attribution.

ckanext-attribution

A CKAN extension that adds support for complex attribution.

Overview

This extension standardises author/contributor attribution for datasets, enabling enhanced metadata and greater linkage between datasets. It currently integrates with the ORCID and ROR APIs; contributors ('agents') can be added directly from these databases, or manually.

Contributors can be added and edited via actions or via a Vue app that can be inserted into the package_metadata_fields.html template snippet.

Schema

The schema is (partially) based on the RDA/TDWG recommendations. Three new models are added: Agent (contributors), ContributionActivity, and Affiliation (plus small linking models between these and Package records).

Agent

Defines one agent.

Field	Type	Values	Notes
agent_type	string	'person', 'org', 'other'
family_name	string		only used for 'person' records
given_names	string		only used for 'person' records
given_names_first	bool	True, False	only used for 'person' records; if the given names should be displayed first according to the person's culture/language (default True)
name	string		used for non-'person' records
location	string		used for non-person records, optional; a location to display for the organisation to help differentiate between similar names (e.g. 'Natural History Museum (_

London_)' and 'Natural History Museum (Dublin)') external_id|string||an identifier from an external service like ORCID or ROR external_id_scheme|string|'orcid', 'ror', other|the scheme for the external_id; currently only 'orcid' and 'ror' are fully supported, though basic support for others can be implemented by adding to the attribution_controlled_lists action user_id|string|User.id foreign key|link to a user account on the CKAN instance

ContributionActivity

Defines one activity performed by one agent on one specific dataset.

Field	Type	Values	Notes
activity	string	[controlled vocabulary]	the activity/role the agent is associated with, e.g. 'Editor', 'Methodology'; roles are defined in the attribution_controlled_lists action, which currently lists the Datacite and CRediT role taxonomies (but can be expanded)
scheme	string	[controlled vocabulary]	name of the defined scheme from attribution_controlled_lists
level	string	'Lead', 'Equal', 'Supporting'	optional degree of contribution (from CRediT)
time	datetime		optional date/time of the activity
order	integer		order of the agent within all who are associated with the same activity, e.g. 1st Editor, 3rd DataCollector (optional)

A specialised ContributionActivity entry with a '[citation]' activity is used to define the order in which contributors should be cited (and/or if they should be cited at all).

Affiliation

Defines a relationship between two agents, either as a 'universal' (persistent) affiliation or for a single package (e.g. a project affiliation).

Field	Type	Values	Notes
agent_a_id	string	Agent.id foreign key	one of the two agents (a/b order does not matter)
agent_b_id	string	Agent.id foreign key	one of the two agents (a/b order does not matter)
affiliation_type	string		very short description (1 or 2 words) of affiliation, e.g. 'employment' (optional)
description	string		longer description of affiliation (optional)
start_date	date		date at which the relationship began, e.g. employment start date (optional)
end_date	date		date at which the relationship ended (optional)
package_id	string	Package.id foreign key	links affiliation to a specific package/dataset (optional)

Installation

Path variables used below:

• $INSTALL_FOLDER (i.e. where CKAN is installed), e.g. /usr/lib/ckan/default
• $CONFIG_FILE, e.g. /etc/ckan/default/development.ini

Installing from PyPI

pip install ckanext-attribution

Installing from source

1. Clone the repository into the src folder:

   cd $INSTALL_FOLDER/src
   git clone https://github.com/NaturalHistoryMuseum/ckanext-attribution.git
   

2. Activate the virtual env:

   . $INSTALL_FOLDER/bin/activate
   

3. Install via pip:

   pip install $INSTALL_FOLDER/src/ckanext-attribution
   

Installing in editable mode

Installing from a pyproject.toml in editable mode (i.e. pip install -e) requires setuptools>=64; however, CKAN 2.9 requires setuptools==44.1.0. See our CKAN fork for a version of v2.9 that uses an updated setuptools if this functionality is something you need.

Post-install setup

1. Add 'attribution' to the list of plugins in your $CONFIG_FILE:

   ckan.plugins = ... attribution
   

2. Install lessc globally:

   npm install -g "less@~4.1"
   

3. Add this block to package_metadata_fields.html to show the Vue app:

   {% block package_custom_fields_agent %}
        {{ super() }}
   {% endblock %}
   

4. Change the authors field in your SOLR schema.xml to set up faceting.

   <schema>
       <fields>
           <...>
           <field name="author" type="string" indexed="true" stored="true" multiValued="true"/>
           <...>
       </fields>
       <...>
       <copyField source="author" dest="text"/>
   </schema>
   

   After making the changes, restart SOLR and reindex (ckan -c $CONFIG_FILE search-index rebuild). You will also have to enable the config option (see below) to see this in the UI.

Configuration

These are the options that can be specified in your .ini config file. NB: setting ckanext.attribution.debug to True means that the API accesses sandbox.orcid.org instead of orcid.org. Although both run by the ORCID organisation, these are different websites and you will need a separate account/set of credentials for each. It is also worth noting that you will not have access to the full set of authors on the sandbox.

API credentials [REQUIRED]

Name	Description	Options
ckanext.attribution.orcid_key	Your ORCID API client ID/key
ckanext.attribution.orcid_secret	Your ORCID API client secret

Optional

Name	Description	Options	Default
ckanext.attribution.debug	If true, use sandbox.orcid.org (for testing)	True/False	True
ckanext.attribution.enable_faceting	Enable filtering by contributor name (requires change to SOLR schema)	True/False	False

Usage

Actions

This extension adds numerous new actions. These are primarily CRUD actions for managing models, with inline documentation and predictable interactions. It's probably more helpful to only go over the more "unusual" new actions here.

agent_list

Search for agents by name or external ID, or just list all agents.

data_dict = {
    'q': 'QUERY',  # optional; searches in name, family_name, given_names, and external_id
}

toolkit.get_action('agent_list')({}, data_dict)

package_contributions_show

Show all contribution records for a package, grouped by agent. Optionally provide a limit and offset for pagination.

data_dict = {
    'id': 'PACKAGE_ID',
    'limit': 'PAGE_SIZE',
    'offset': 'OFFSET'
}

toolkit.get_action('package_contributions_show')({}, data_dict)

Returns a dict:

{
    'contributions': [
        {
            'agent': {
                # Agent.as_dict()
            },
            'activities': [
                # list of Activity.as_dict()
            ],
            'affiliations': [
                {
                    'affiliation': {
                        # Affiliation.as_dict()
                    },
                    'other_agent': {
                        # Agent.as_dict()
                    }
                },
                # ...
            ]
        },
        # ...
    ],
    'total': total,
    'offset': offset,
    'page_size': limit or total
}

agent_affiliations

Show all affiliations for a given agent, optionally limited to a specific dataset/package (plus ' global' affiliations).

data_dict = {
    'agent_id': 'AGENT_ID',
    'package_id': 'PACKAGE_ID'  # optional
}

toolkit.get_action('agent_affiliations')({}, data_dict)

Returns a list of records formatted as such:

{
    'affiliation': {
        # Affiliation.as_dict()
    },
    'other_agent': {
        # Agent.as_dict()
    }
}

attribution_controlled_lists

Returns collections of defined values (which can be modified by using @toolkit.chained_action).

data_dict = {
    'lists': ['NAME1', 'NAME2']  # optional; only return these lists
}

toolkit.get_action('attribution_controlled_lists')({}, data_dict)

There are four collections:

1. agent_types describes valid types for agents and adds additional detail;
2. contribution_activity_types contains role/activity taxonomies (i.e. Datacite and CRediT) and lists the available activity values;
3. contribution_activity_levels is a list of contribution levels (i.e. 'lead', 'equal', and ' supporting', from CRediT);
4. agent_external_id_schemes describes valid schemes for external IDs (currently, ORCID and ROR).

These collections are useful for validation and frontend connectivity/standardisation. They are contained within an action to a. enable frontend access via AJAX requests, and b. allow users to override values as needed.

agent_external_search

Search external sources (ORCID and ROR) for agent data. Ignores records that already exist in the database.

data_dict = {
    'q': 'QUERY_STRING',
    'sources': ['SOURCE1', 'SOURCE2']  # optional; only search these sources
}

toolkit.get_action('agent_external_search')({}, data_dict)

Results are returned formatted as such:

{
    'SCHEME_NAME': {
        'records': [
            # list of agent dicts
        ]
        'remaining': 10000  # number of other records found
    }
}

agent_external_read

Read data from an external source like ORCID or ROR, either from an existing record or a new external ID.

# EITHER
data_dict_existing = {
    'agent_id': 'AGENT_ID',
    'diff': False
    # optional; only show values that differ from the record's current values (default False)
}

# OR
data_dict_new = {
    'external_id': 'EXTERNAL_ID',
    'external_id_scheme': 'orcid'  # or 'ror', etc.
}

toolkit.get_action('agent_external_read')({}, data_dict)

Commands

initdb

ckan -c $CONFIG_FILE attribution initdb

Initialise database tables.

sync

ckan -c $CONFIG_FILE attribution sync $OPTIONAL_ID $ANOTHER_OPTIONAL_ID

Retrieve up-to-date information from external APIs for contributors with an external ID set.

refresh-packages

ckan -c $CONFIG_FILE attribution refresh-packages $OPTIONAL_ID $ANOTHER_OPTIONAL_ID

Update the author string for all (or the specified) packages.

agent-external-search

ckan -c $CONFIG_FILE attribution agent-external-search --limit 10 $OPTIONAL_ID $ANOTHER_OPTIONAL_ID

Search external APIs for contributors without an external ID set. Run refresh-packages and rebuild the search index after this command.

merge-agents

ckan -c $CONFIG_FILE attribution merge-agents --q $SEARCH_QUERY --match-threshold 75

Find agents with similar names (optionally matching the search query) and merge them. Run refresh-packages and rebuild the search index after this command.

migratedb

ckan -c $CONFIG_FILE attribution migratedb --limit 10 --dry-run --no-search-api

Attempt to extract names of contributors from author fields and convert them to the new format.

• --limit will only convert a certain number of packages at a time.
• --dry-run prevents saving to the database.
• --no-search-api just extracts the names, without searching external APIs for contributors after.

It is recommended to run merge-agents, refresh-packages, and rebuild the search index after running this command.

Testing

There is a Docker compose configuration available in this repository to make it easier to run tests. The ckan image uses the Dockerfile in the docker/ folder.

To run the tests against ckan 2.9.x on Python3:

1. Build the required images:

   docker-compose build
   

2. Then run the tests. The root of the repository is mounted into the ckan container as a volume by the Docker compose configuration, so you should only need to rebuild the ckan image if you change the extension's dependencies.

   docker-compose run ckan