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To invoke it you must have the repository's URI namespace defined as a prefix. For example,

 PREFIX repo:<[http://eagle-i.org/ont/repo/1.0/]>
..query text...
 ORDER BYrepo:upperCaseStr(?label) 

Workflow

The repository includes a "workflow" control system that directs the complete life cycle of each resource instance, and mediates access by users at each life cycle stage. The word "workflow" is often used to describe process-management and administration systems, but in this case it is really just a minimal implementation of states and extended access control.

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1. Install the webapp by dropping the WAR file into place, and adding configuration:
   1. Add one system property to the Web server's JVM to indicate the configuration properties.
   2. Create configuration properties file with at least the minimum required properties.
2. Create authentication DB and add the initial Administrator user.
3. Start the servlet container---the repository webapp automatically initializes the following named graphs if they are found to be empty:
   1. The internal Repository ontology (read-only)
   2. Internal Repository administrative metadata (e.g. Roles, Named Graphs, WF Transitions, etc.)
   3. SPARQL Query macros.
4. Create an RDF metadata wrapper for the initial administrator user - this is done automatically by the post-install procedure, finish-install.sh. See the Administrator Guide.
5. Load the eagle-i data model ontology. Although this is not necessary for any of the Repository's internal functions, the eagle-i apps will expect it to be there.
6. Browse to the Admin UI and log in as the Administrator user. You can create user logins and assign roles; modulo any customizations of workflow, workspaces and such. With that, the repository is open for business.

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See the Configuration section in the Administrator Guide for a complete list of configuration properties.

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About HTML dissemination:
When the negotiated format is text/html, and unless either of the forceRDF or forceXML args was given, the dissemination process creates an intermediate XML document and transforms it into XHTML with the configured XSLT stylesheet. See description of the eaglei.repository.instance.xslt in the Repoistory Administrator Guide.

If no XSLT stylesheet is configured, the intermediate XML document is delivered instead, with a media content type of application/xml. Note that this means, to obtain correct XHTML output, you MUST configure an XSLT stylesheet.

The content of the intermediate XML format is described in a W3C XML Schema document that may be downloaded from a running repository at for example,

 [https://localhost:8443/repository/schemas/instance.xsd] 

We provide an example transformation stylesheet that produces very simple HTML, intended to be the basis of custom stylesheets. It is available for download at .:{{https://localhost:8443/repository/styles/example.xsl
}}We manage the transformation within the repository, instead of adding an xml-stylesheet processing instruction to the XML, for compelling reasons:

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• Content-Type---header on the value of the content entity in a POST request. This takes precedence because it allows for different content-types in insert and delete args.
• format---query argument value.

Wiki Markup*URL:* {{/repository/update}} \ [_/instance-ID_\] (POST only)

Args:
uri---optional way to explicitly specify the complete URI, instead of assuming that the URI's namespace matches the hostname, context, and servlet path ("/i") of this webserver.
format---the default expected format for insert and delete graphs. If the args specify a content-type header, that overrides this value. Only recognizes triples even if the format supports quads.
action=(update|create|gettoken)---Update to modify an existing instance, create adds a new one. See below for details about gettoken.
token=uri---When action is update or create, this must be supplied. The value is the URI returned by the last gettoken request.
workspace=uri---choose workspace named graph where new instance is created. Only necessary when action=create. Optional, default is the default workspace. DO NOT specify a workspace when action=update.
delete---graph of statements to remove from the instance; subject must be the instance URI. Deletes are done before inserts. Graph may include wildcard URIs in predicate and/or object to match all values in that part of a statement.
insert---graph of statements to add to instance; subject must be the instance URI.
bypassSanity---(boolean, default false, deprecated) NOTE: It is best if you pretend this option does not exist. When true, it skips some of the sanity tests on the resulting instance graph, mostly the ones checking the integrity of Embedded instances. Requires Administrator privilege. This was added to make the data migration from broken old EI data possible, it should rarely if ever be needed.

The delete wildcard URI is http://eagle-i.org/ont/repo/1.0/MatchAnything

Result:
HTTP status indicates success or failure. Any modifications are transactional; on success the entire change was made, and upon failure nothing gets changed.

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Args:
query---the text of the SPARQL query document.
default-graph-uri---add this URI to the list of default graphs in the query dataset, overriding any built-in default. Read access required. Conflicts with other explicit methods of specifying datasets: the *-graph-uri, view, and workspace arguments are all mutually exclusive. Can be specified multiple times to include multiple graphs.
named-graph-uri---add this URI to the list of named graphs in the query dataset, overriding any built-in default. Read access required. NOTE: Sesame's query engine does not seem to pay attention to named graphs, just default graphs, so this argument should be deprecated.
format---explicitly names a result format, overriding the default from HTTP content negotiation. Value must be one of the specified MIME type strings. This is a nonstandard extension to the SPARQL Protocol.
view---symbolic name of a pre-packaged set of named graphs presenting a "view" of the data; see secton on Views in the Concepts section above. Conflicts with other explicit methods of specifying datasets: the *-graph-uri, {{view, and workspace arguments are all mutually exclusive. This is a nonstandard extension to the SPARQL Protocol.
workspace---URI of the workspace named graph to take the place of the default graph. Relevant metadata and ontology graphs are included automatically. Conflicts with other explicit methods of specifying datasets: the *-graph-uri, view, and workspace arguments are all mutually exclusive. This is a nonstandard extension to the SPARQL Protocol.
time---sets an explicit time limit on the query, overriding any built-in default. Value is in seconds. This is a nonstandard extension to the SPARQL Protocol.
inferred---boolean arg.  When false, any inferred statements are excluded from the results. The default is true. This is a nonstandard extension to the SPARQL Protocol.

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Note on File Format and Character Set: The request specifies the file format and/or character set of the serialized RDF data as a Content-Type value, for example:

 text/rdf+n3; charset="ISO-8859-1"

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The value of loaded is the result of this query over the ontology view:

 select * where {<http://purl.obolibrary.org/obo/ero.owl> owl:versionInfo ?loaded} 

URL: /repository/admin/model (POST)

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Loads a new copy of the data model ontology, replacing the entire existing contents (if any) of its named graph. For more details about how the graph name and data model source are determined, see The Data Model Configuration Properties Guide.

When action=update, only load the ontology if the version of the current ontology is different from the version of the available one (also if there is nothing loaded yet). Note that it does not attempt to judge if the available version is later, just different.

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Precise last-modified timestamp: the /harvest service also adds a non-standard HTTP header to its responses to describe the last-modified time in full precision down to the millisecond level. This allows an application to give that precise time as the after argument value on the next incremental harvest to be sure of capturing any changes since that last /harvest call. The header name and date format looks like:

 X-Precise-Last-Modified:Mon, 10 Jan 2011 20:49:10.770 GMT 

Note that the time format is essentially the HTTP time format with ".mmm" appended to the time for milliseconds.  It must be converted to the XML timestamp format to serve as an argument value to "after". By the time it was obvious what a stupid choice this was, it was too late in the development cycle to change easily, but perhaps in the future an XML-format precise timestamp header can be added.

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Sends an email message to the designated contacts for the resource identified by URI. The exact rules for determining that contact address have not been formally specified yet. When a contact cannot be determined, the mail is sent to the configured postmaster for the repository. See the Repository Installation and Administrator Guide for  for details about configuring that and the rest of the e-mail service.

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/repository/admin/updateUser

Method: POST
Args:
username=text---account name to change, only not required for create
only_password=(boolean)---do not process changes to user metadata, just update password
password---new password
password_confirm---must match new password
old_password---current (old) password, required for non-admin user
first---first name of person (metadata)
last---last name of person (metadata)
mailbox---email address of person
role---URI of role to add to user, may be multiple; when specified, this list of roles replaces the user's current roles.

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/repository/admin/updateGrants

Method: POST
Args:
action= add | remove---(keyword)
uri = URI---subject of the access grant
access= URI---access type to be added or removed
agent = URI of person or Role in the grant

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/repository/admin/updateTransition

Method: POST
Args:
action= create | update | delete}}---(keyword)
uri = URI---required except for create, identifies the role
uri=URI--subject to release
label=text---required to create
comment=text---description
initial= URI of initial state (required to create)
final=URI of final state (required to create)
tAction=java class of transition action provider
tActionParameter = text or URI param to pass to action method
order= sorting key, usually a decimal integer

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/repository/admin/updateNamedGraph

Method: POST
Args:
uri*=URI names the graph or context
label=text
type=URI of a NamedGraph Type

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Visit this page for a directory of all administrative UI functions.  Users without superuser privilege will only see a partial list.  It also displays server-status and configuration details.

 http://_hostname_/repository/admin 

Although almost all repository administration is done by manipulating RDF statements in an internal administrative-metadata graph, there is a need for a Web-based UI to make it easier for site administrators to see and change the current state. Except as noted, these pages are only available to users with the Administrator role:

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