|DAS2 Table of contents||$Id: das2_writeback.html,v 1.7 2008/10/31 09:10:24 gregghelt2 Exp $|
Some annotations servers support curational writeback of a versioned source. Clients POST a writeback document to a URL to create, delete or modify features. The formal schema for the writeback document XML is a RelaxNG schema in .rnc format. The writeback document is also called a delta because it describes the changes to make in the server. The server response to a writeback is a modified features document. Each FEATURE element contains the optional attribute "old_uri". A server may change the FEATURE uri during writeback. If this happens the "old_uri" attibute contains the uri sent in the writeback and the normal "uri" attribute contains the new attribute.
This version of DAS only support feature writeback and does not support type or sequence writeback.
The writeback configuration information is specified in the versioned source record of a sources document using the CAPABILITIES element of type "writeback". At most one writeback CAPABILITIES element is allowed in a versioned source record.
The query_uri attribute of the CAPABILITIES element contains the URL used to POST the writeback delta document.
<CAPABILITY type="writeback" query_uri="http://www.biodas.org/das/h_sapiens/v35/writeback.cgi" />
The writeback document is in XML format with content-type "application/x-das-writeback+xml". All of the DAS writeback elements are in the standard DAS2 namespace http://biodas.org/documents/das2. This namespace is reserved and authors of DAS extensions may not create new XML elements in it.
Here is an example of a writeback document modifying a single feature:
Content-Type: application/x-das-writeback+xml <WRITEBACK xmlns="http://biodas.org/documents/das2" xml:base="http://www.biodas.org/das/h_sapiens/v35/"> <MESSAGE>Moved endpoint by 1; wrong coordinate numbers</MESSAGE> <FEATURE uri="feature/cTel54X" type="type/gene" title="tg-3"> <LOC segment="segment/Chr2" range="1200:2916:1" /> </FEATURE> </WRITEBACK>
Here is a more complicated example. This one deletes a feature named "http://example.com/das2/dasypus/April2006/F001", and changes an existing feature (".../F002") to a different type.
Content-Type: application/x-das-writeback+xml <WRITEBACK xmlns="http://biodas.org/documents/das2" xml:base="http://example.com/das2/dasypus/April2006/"> <MESSAGE>Removed duplicate gene; changed remaining one to a pseudogene</MESSAGE> <DELETES> <DELETE uri="F001" /> </DELETES> <FEATURE uri="F002" type="T981" title="tg-3"> <LOC segment="segment/Chr2" range="1200:2916:1" /> </FEATURE> </WRITEBACK>
The root element is named WRITEBACK. The MESSAGE element contains human-readable text summarizing the changes made by the writeback. After the MESSAGE are zero or more DELETE elements followed by zero or more FEATURE elements.
Each DELETE element has a "uri" attribute with the identifier of the feature to delete. If a feature is deleted then it may not be present as a FEATURE in the same writeback.
The writeback FEATURE element is identical to the FEATURE element used in the features document. The writeback feature replaces an existing feature with the same uri. If the parent/part relationship changes then all modified features must be included in the same writeback. This includes sending DELETE elements when a feature is removed. New features must use the private identifier scheme described below.
The WRITEBACK, DELETE and FEATURE elements include the xml:base attributes. As there is no reasonable retrieval context providing a base url for the POSTed writeback document, all relative URIs must be resolved to absolute URIs inside the document.
Each feature has its own unique URI assigned by the server. To create a new feature record the client temporarily assigns a private id. These URIs have the syntax "das-private:" followed by an alphanumeric string of at least 1 and no more than 20 characters. The legal characters are 0-9, A-Z and a-z. Some examples are: "das-private:0", "das-private:AAAA" and "das-private:ThisIsPrivate007".
When the server receives a feature record with a private identifier it generates a new URI appropriate to the server's namespace and assigns the URI to the feature. The "old_uri" attribute in the writeback response document will include the temporary das-private identifier.
A writeback server may further modify the feature record sent by the client. It will assign a new URI for newly created features and curational servers might add fields for history tracking. Changes to one feature may affect other features. Consider a change to a feature involved in a parent/part relationshop. A versioning server may create new versions of all features in that annotation, with new URIs for the new features. (Such a server might add extra feature filter query terms to support historical queries. XXX make sure the feature filter spec allows this!)
A server is not required to change the feature URI when the feature changes. The decision is left to the server implementer.
The server responds to a writeback document with a modified features document. This contains all of the features that changed as a result of the writeback. The document format is identical to the standard features document except for one addition. The FEATURE element has an optional "old_uri" attribute. If present it is the previous URI for the given object. This may be a relative URI and it resolved as normal through the xml:base and URI resolution mechanism. If the "old_uri" attribute is not present then the URI has not changed.
The server should not reuse feature identifiers which were used for earlier features. Doing so may cause synchronization problems with other clients. The "old_uri" URI may no longer be retrievable and a client should consider it no longer valid.
XXX What about XID tracking, if the XID is an intra-database link. Will those records change? Will a versioning database change them?
Following is an example XXX insert example here XXX.
The writeback document may contain errors. It may reference invalid URIs, delete a feature type while features of that type still exist, introduce features with cycles, include malformed XML, modify locked regions, and more. The server must respond with an HTTP error 400 ("Bad Request") when an error occurs and must implement the writeback atomically and transactionally. That is, writebacks occur in order with no overlap and if there is an error the annotation database is unchanged.
There is a possible loss of synchronization between the client and the server if the writeback is processed but the connection is lost before the mapping document is fully returned to the client. A client must not automatically repost the writeback if this occurs. It should rely on user intervention to determine how to recover in this case.
Because we judge this to be a rare case we have no solution for it. We suggest implementors consider responding with an HTTP code 202 ("Accepted") and a Location header pointing to a URL for status and/or results.
This document does not describe how to lock regions to prevent accidental writeback conflicts. Instead see the locking documentation.Last modified: Tue Feb 27 12:14:25 PST 2007