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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
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<meta name="generator" content="Asciidoctor 2.0.23">
<meta name="description" content="Fairspace documentation.">
<meta name="author" content="The Hyve">
<title>Fairspace</title>
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<div id="header">
<div class="details">
<span id="author" class="author">The Hyve</span><br>
<span id="revnumber">version 2.0.1,</span>
<span id="revdate">2024-09-09</span>
</div>
<div id="toc" class="toc2">
<div id="toctitle">Fairspace</div>
<ul class="sectlevel1">
<li><a href="#_usage">Usage</a>
<ul class="sectlevel2">
<li><a href="#_user_interface">User interface</a>
<ul class="sectlevel3">
<li><a href="#_login">Login</a></li>
<li><a href="#_workspaces">Workspaces</a></li>
<li><a href="#_collections">Collections</a></li>
<li><a href="#_metadata">Metadata</a></li>
</ul>
</li>
<li><a href="#_interfaces_for_accessing_and_querying_data_api">Interfaces for accessing and querying data (API)</a>
<ul class="sectlevel3">
<li><a href="#_authentication">Authentication</a></li>
<li><a href="#_webdav">WebDAV</a></li>
<li><a href="#_sparql">SPARQL</a></li>
<li><a href="#_rdf_metadata">RDF metadata</a></li>
<li><a href="#_metadata_views">Metadata views</a></li>
<li><a href="#_text_search">Text search</a></li>
<li><a href="#_workspace_management">Workspace management</a></li>
<li><a href="#_users_and_permissions">Users and permissions</a></li>
<li><a href="#_configuration_endpoints">Configuration endpoints</a></li>
</ul>
</li>
<li><a href="#_external_file_system_integration">External file system integration</a>
<ul class="sectlevel3">
<li><a href="#_access_policy">Access policy</a></li>
<li><a href="#_api_specification_and_supported_parameters">API specification and supported parameters</a></li>
<li><a href="#_text_search_in_external_storages">Text search in external storages</a></li>
<li><a href="#_configuration">Configuration</a></li>
</ul>
</li>
<li><a href="#_multi_fairspace_metadata_views_integration">Multi-Fairspace metadata views integration</a>
<ul class="sectlevel3">
<li><a href="#_access_policy_2">Access policy</a></li>
<li><a href="#_configuration_2">Configuration</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_structure_and_terminology">Structure and terminology</a>
<ul class="sectlevel2">
<li><a href="#_workflow_and_access_modes">Workflow and access modes</a></li>
<li><a href="#_roles_and_permissions">Roles and permissions</a></li>
</ul>
</li>
<li><a href="#_data_model_and_view_configuration">Data model and view configuration</a>
<ul class="sectlevel2">
<li><a href="#_metadata_2">Metadata</a>
<ul class="sectlevel3">
<li><a href="#_types_of_metadata">Types of metadata</a></li>
<li><a href="#_purpose">Purpose</a></li>
</ul>
</li>
<li><a href="#_data_model">Data model</a>
<ul class="sectlevel3">
<li><a href="#_data_domains">Data domains</a></li>
</ul>
</li>
<li><a href="#_data_model_configuration">Data model configuration</a>
<ul class="sectlevel3">
<li><a href="#_limitations">Limitations</a></li>
<li><a href="#_changing_existing_data_model">Changing existing data model</a></li>
<li><a href="#_controlled_vocabularies_2">Controlled vocabularies</a></li>
</ul>
</li>
<li><a href="#_view_configuration">View configuration</a></li>
</ul>
</li>
<li><a href="#_installation_and_configuration">Installation and configuration</a>
<ul class="sectlevel2">
<li><a href="#_local_development">Local development</a></li>
<li><a href="#_kubernetes_and_helm">Kubernetes and helm</a>
<ul class="sectlevel3">
<li><a href="#_instructions_for_deploying_to_google_cloud">Instructions for deploying to Google Cloud</a></li>
</ul>
</li>
<li><a href="#_logging">Logging</a>
<ul class="sectlevel3">
<li><a href="#_configuration_3">Configuration</a></li>
<li><a href="#_audit_log">Audit log</a></li>
<li><a href="#_data_recovery_using_transaction_log">Data recovery using transaction log</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#_architecture">Architecture</a>
<ul class="sectlevel2">
<li><a href="#_mercury">Mercury</a></li>
<li><a href="#_pluto">Pluto</a></li>
<li><a href="#_saturn">Saturn</a></li>
<li><a href="#_storages">Storages</a>
<ul class="sectlevel3">
<li><a href="#_primary_data_storage">Primary data storage</a></li>
<li><a href="#_secondary_data_storage_for_efficient_data_retrieval">Secondary data storage for efficient data retrieval</a></li>
<li><a href="#_extra_file_storage">Extra file storage</a></li>
</ul>
</li>
<li><a href="#_deployment_architecture">Deployment architecture</a></li>
</ul>
</li>
<li><a href="#_acknowledgement">Acknowledgement</a></li>
<li><a href="#_license">License</a></li>
</ul>
</div>
</div>
<div id="content">
<div id="preamble">
<div class="sectionbody">
<div class="paragraph">
<p><span class="image"><img src="docs/images/Fairspace.png" alt="Fairspace"></span></p>
</div>
<div class="paragraph">
<p>Fairspace is a secure place for managing research data.
Research teams have their own workspaces in which they
can manage research data collections.
Researchers can upload directories and files to data collections.
Data access is organised on data collection level.
Collections can be shared with other teams or individual researchers.
Also, collections can be published for all researchers in the organisation.<br></p>
</div>
<div class="paragraph">
<p>Collections and files can be annotated with descriptive metadata.
The metadata is stored using the <a href="https://en.wikipedia.org/wiki/Resource_Description_Framework">Resource Description Framework (RDF)</a> in
an <a href="https://jena.apache.org/">Apache Jena</a> database.
For the metadata, a data model can be configured that suits
the data management needs of the organisation.
The data model is specified using the <a href="https://www.w3.org/TR/shacl/">Shapes Constraint Language (SHACL)</a>,
see the section on <a href="#_data_model_and_view_configuration">Data model and view configuration</a>.
Descriptive metadata entities (e.g., subjects, projects, samples) should be added to the database by a
careful process, ensuring that duplicates and inconsistencies are avoided and
that all entities have proper unique identifiers.
The application provides overviews of the available metadata entities.
In the collection browser, researchers can link their collections and files to these entities
or add textual descriptions and key words.</p>
</div>
<div class="sidebarblock">
<div class="content">
<div class="title"><strong>Key features</strong></div>
<div class="ulist">
<ul>
<li>
<p>Fairspace is a data repository that enables researchers to securely <strong>store</strong> and <strong>organise</strong> their research data sets,
and <strong>share</strong> the data with collaborators.</p>
</li>
<li>
<p>Fairspace lets researchers annotate their data collections with relevant metadata properties
and link the data to associated metadata entities (subjects, samples, projects, etc.).
This helps researchers find their own data and make it <strong>findable</strong> for others,
contributing to implementation of the <a href="https://www.go-fair.org/fair-principles/">FAIR principles</a>.</p>
</li>
<li>
<p>Fairspace ensures that all metadata entities have a unique identifier and checks
metadata consistency and validity upon data entry.</p>
</li>
<li>
<p>Fairspace allows organisations to <strong>customise</strong> the configured data model,
by specifying custom entity types and constraints.
This enables the adoption of community standards for metadata relevant for the research domain,
which contributes to the <strong>reusability</strong> of the data.</p>
</li>
<li>
<p>Fairspace uses the <a href="https://en.wikipedia.org/wiki/Resource_Description_Framework">Resource Description Framework (RDF)</a> and <a href="https://en.wikipedia.org/wiki/WebDAV">WebDAV</a> standards for data exchange,
and stimulates the use of standard vocabularies,
contributing to <strong>interoperability</strong> of data.</p>
</li>
</ul>
</div>
</div>
</div>
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</div>
</div>
<div class="sect1">
<h2 id="_usage">Usage</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_user_interface">User interface</h3>
<div class="sect3">
<h4 id="_login">Login</h4>
<div class="paragraph">
<p>Users are authenticated using <a href="https://www.keycloak.org/">Keycloak</a>, an open-source identity provider
that provides secure authentication methods and can be configured to integrate
with institutional identity providers using user federation or identity brokering,
see the <a href="https://www.keycloak.org/docs/latest/server_admin/">Keycloak server administration</a> pages.</p>
</div>
<div class="paragraph">
<p>The user either logs in directly using Keycloak or is forwarded to a configured
external login:</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="docs/images/screenshots/Keycloak%20login.png" alt="Keycloak login"></span></p>
</div>
</div>
<div class="sect3">
<h4 id="_workspaces">Workspaces</h4>
<div class="paragraph">
<p>Users enter Fairspace on the workspaces page that lists all workspaces.
A workspace represents a team in the organisation that collaborates on research data collections.</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="docs/images/screenshots/Workspace%20list.png" alt="Workspace list"></span></p>
</div>
<div class="paragraph">
<p>Workspace administrators can edit the workspace overview page and
manage workspace membership. All workspace members can add collections to the workspace.</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="docs/images/screenshots/Workspace%20overview.png" alt="Workspace overview"></span></p>
</div>
</div>
<div class="sect3">
<h4 id="_collections">Collections</h4>
<div class="paragraph">
<p>The contents of collections can be navigated in the collections browser.
It behaves like a regular file browser. Click to select a directory or file
and see its metadata, double click to navigate into directories or
open a file.</p>
</div>
<div class="paragraph">
<p>Access is managed on collection level.
Users with at least <em>write</em> access to a collection can upload files or directories,
rename or delete files, restore old file versions,
and edit the associated metadata.</p>
</div>
<div class="paragraph">
<p>Users with <em>manage</em> access can share collections with other users or workspaces,
and change the default access mode for workspace members.
Collection managers can also change the status of the collection
(<em>Active</em>, <em>Read-only</em> or <em>Archived</em>), change the view mode
(<em>Restricted</em>, <em>Metadata published</em> or <em>Data published</em> — only available in the <em>Read-only</em> status),
delete the collection,
or transfer ownership of the collection to another workspace.</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="docs/images/screenshots/Collection%20browser.png" alt="Collection browser"></span></p>
</div>
<div class="paragraph">
<p>Due to the data loss prevention, data in Fairspace is not removed from the system on deletion.
Deleted collections and files can still be viewed in the application using "Show deleted" switch.
The goal is to prevent deleted data from being overwritten by users (not to create collections or files with the paths
that already existed in the system) and to allow administrators to perform special actions (to be performed only in exceptional special cases),
like undeletion or permanent removal, to revert accidental removal or creation of a collection or a file.</p>
</div>
<div class="sect4">
<h5 id="_metadata_forms">Metadata forms</h5>
<div class="paragraph">
<p>Users with write access to the collection can annotate collections,
directories and files using <em>metadata forms</em>.
Free text fields, like description and key words, can be entered freely,
links to shared entities, like subjects, samples and projects, or
values from a controlled vocabulary, like taxonomy or analysis type,
can be selected from a list:</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="docs/images/screenshots/Metadata%20form.png" alt="Metadata form"></span></p>
</div>
<div class="paragraph">
<p>The shared metadata entities and controlled vocabularies cannot
be added via the user interface.
The <a href="#_rdf_metadata">RDF metadata</a> API should be used for that instead.</p>
</div>
</div>
<div class="sect4">
<h5 id="_metadata_upload">Metadata upload</h5>
<div class="paragraph">
<p>Another way to annotate directories and files is by uploading a comma-separated values (CSV) file with metadata.
This section describes the CSV-based format used for bulk metadata uploads.</p>
</div>
<div class="paragraph">
<p>The file should be a valid CSV-file:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>Records are separated with a <code>,</code>-character.</p>
</li>
<li>
<p>Values may be enclosed in double quotes: <code>"value"</code>.</p>
</li>
<li>
<p>In values that contain a double, the double quotes need to be escaped by replacing them with double double quotes:
<code>Example "quoted" text</code> becomes <code>"Example ""quoted"" text"</code>.</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>In the metadata upload, lines starting with <code>#</code> are ignored. These lines are considered to be comments.</p>
</div>
<div class="paragraph">
<p>The file should have a header row containing the names of the columns.
The mandatory <code>Path</code> column is used for the file path. For the property columns, the name should match exactly the name of the property in the database.</p>
</div>
<div class="paragraph">
<p>The format of the values is as follows:</p>
</div>
<div class="ulist">
<ul>
<li>
<p><em>Path</em>: the relative path to a file or a directory (relative to the collection or directory where the file is uploaded).
Use <code>./</code> for the current directory or collection.</p>
</li>
<li>
<p><em>Entity types</em> can be referenced by ID or unique label.</p>
</li>
<li>
<p>Multiple values must be separated by the pipe symbol <code>|</code>, e.g.,
use <code>test|lab</code> to enter the values <code>test</code> and <code>lab</code>.</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>The file can be uploaded to the current directory by dropping the file in the metadata panel of the directory, or by selecting the metadata upload button.<br>
By hovering over the metadata upload button, a link to a <em>metadata template file</em> becomes available:</p>
</div>
<div class="paragraph">
<p><span class="image th"><img src="docs/images/screenshots/Download%20metadata%20template.png" alt="Download metadata template"></span></p>
</div>
<div class="paragraph">
<p>The file describes the format in commented lines and
contains the available properties in the header row.</p>
</div>
<div class="exampleblock">
<div class="title">Example 1. Example metadata file</div>
<div class="content">
<div class="paragraph">
<p>An example comma-separated values file with metadata about the current directory <code>./</code>,
which is annotated with a description and two key words (<code>sample</code> and <code>lab</code>),
and the file <code>test.txt</code> which is linked to Subject 1 by the unique subject label
and to the RNA-seq analysis type by the analysis type identifier (<code>O6-12</code>).</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="rouge highlight"><code data-lang="csv">Path,Is about subject,Type of analysis,Description,Keywords
./,,,Directory with samples,sample|lab,
test.txt,Subject 1,https://institut-curie.org/analysis#O6-12,,</code></pre>
</div>
</div>
<div class="paragraph">
<p>This specifies the table:</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 20%;">
<col style="width: 20%;">
<col style="width: 20%;">
<col style="width: 20%;">
<col style="width: 20%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Path</th>
<th class="tableblock halign-left valign-top">Is about subject</th>
<th class="tableblock halign-left valign-top">Type of analysis</th>
<th class="tableblock halign-left valign-top">Description</th>
<th class="tableblock halign-left valign-top">Keywords</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">./</p></td>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Directory with samples</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">sample|lab</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">test.txt</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Subject 1</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><a href="https://institut-curie.org/analysis#O6-12" class="bare">https://institut-curie.org/analysis#O6-12</a></p></td>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
<div class="sect3">
<h4 id="_metadata">Metadata</h4>
<div class="paragraph">
<p>Explore metadata and find associated collections and files.
<span class="image"><img src="docs/images/screenshots/Metadata%20view.png" alt="Metadata"></span></p>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_interfaces_for_accessing_and_querying_data_api">Interfaces for accessing and querying data (API)</h3>
<div class="paragraph">
<p>The data in Fairspace can be accessed via Application Programming Interfaces (APIs).
The user interfaces application uses those APIs, but also other programs can use them,
e.g., for automated data uploading or for exporting data for further processing
or for synchronisation with other systems.</p>
</div>
<div class="sect3">
<h4 id="_authentication">Authentication</h4>
<div class="paragraph">
<p>All API endpoints require authentication via an authorisation header.
To enable WebDAV clients to connect to Fairspace, also so-called <em>Basic authentication</em> is supported.</p>
</div>
<div class="paragraph">
<p>For secure authentication, it is strongly advised to use the <em>OpenID Connect (OIDC) / OAuth2</em> workflow.
The user interface application also uses this workflow.</p>
</div>
<div class="paragraph">
<p>When using the APIs in automated scripts, ensure that an account is used with only the required
privileges (conform the <em>principle of least privilege</em>). I.e., when an admin account is not needed, use a non-admin account.
For adding shared metadata, an account with
<em>Add shared metadata</em> role is required, see <a href="#_uploading_metadata">Uploading metadata</a>.</p>
</div>
<div class="paragraph">
<p>When an action is done on behalf of a specific user,
do not use a service account or system account for the action directly, but obtain a token for that user first, e.g.,
by using the <a href="https://www.keycloak.org/docs/latest/securing_apps/#impersonation">impersonation</a> feature of Keycloak.
That way the audit logging still captures which user did what.</p>
</div>
<div class="sect4">
<h5 id="_openid_connect_oidc_oauth2_workflow">OpenID Connect (OIDC) / OAuth2 workflow</h5>
<div class="paragraph">
<p>Fairspace supports OpenID Connect authentication via Keycloak.
The workflow for API access is roughly as follows.</p>
</div>
<div class="ulist">
<ul>
<li>
<p>The client authenticates with the token endpoint of the identity provider (Keycloak) and obtains a signed access token</p>
</li>
<li>
<p>The client uses the access token in the request header when connecting to the Fairspace API</p>
</li>
<li>
<p>Fairspace receives the request with the access token and validates if the token is valid,
using the public key of the identity provider.</p>