 |
Page History
| Wiki Markup |
|---|
{scrollbar:icons=false}
h1. { |
| Page info |
|---|
...
|
| Panel | ||||
|---|---|---|---|---|
| ||||
|
| Include Page | ||||
|---|---|---|---|---|
|
Revision History
Content changes to this document from the previous to the current level are indicated by revision bars (|) unless a complete rewrite is indicated.
Date | Version | Description | Author |
|---|---|---|---|
07/29/2008 | 1.0 | Initial document | Kevin Peterson |
8/30/2008 | 1.1 | Revised for Security and Exception Handling | Kevin Peterson |
| Info | ||
|---|---|---|
| ||
If this document has been inspected, please indicate the inspection date that each version is based on in the "Change Description and Explanation" area. Entries in this log must be maintained for at least 3 years. |
Document Purpose
This document provides the detailed design and implementation of LexBIG Enterprise Vocabulary Service (LexEVS) caGrid Service. It should be noted that the LexEVS Grid Service is no longer part of the caGrid 1.1 infrastructure and will be deployed as a separate unit. This is a change from the previous release of the LexEVS Grid Service.
The LexEVS caGrid service will allow programs to utilize the caGrid 1.2 infrastructure to access LexEVS information that is currently being produced by NCICB.
Implementation Overview
Team Members
The following table lists team members.
Role | Name |
|---|---|
Development Lead | Kevin Peterson |
Documentation Lead | Kevin Peterson |
Project Manager | Tom Johnson |
Description
The LexEVS grid service will be used to obtain data accessible via the EVS API 4.2 service, specifically, the Distributed LexBIG services. Please refer to the caCORE EVS API 4.0 technical guide for details on the EVS API 4.2 EVS APIs, and the LexBIG 2.3 Technical and Admin guide for details about LexBIG 2.3.
For more Documentation, Build/Deployment instructions and examples, visit the project documentation home on GForge.
Scope
The LexEVS Grid service will provide programmatic access to the LexBIG domain objects that are available via the LexBIG information model.
The LexEVS grid service will be registered in Cancer Data Standards Repository (caDSR) under the following category:
Category | LexEVS Grid Service |
|---|---|
Context | caBIG |
Classification Scheme | LexBIG |
Version | LexBIG_v2_3_rv1 |
Architecture
The LexEVS Grid Service is implemented to expose the API and Model of LexBIG 2.3. For more information on LexBIG, see http://informatics.mayo.edu.
...
LexEVS
...
Grid
...
Service
...
is
...
deployed
...
in
...
a
...
...
Application
...
Server,
...
inside
...
of
...
a
...
...
Web
...
|Application
...
installation.
...
LexEVS
...
Grid
...
Service
...
depends
...
on
...
...
,
...
which
...
is
...
also
...
deployed
...
to
...
a
...
JBoss
...
container.
...
For
...
more
...
information
...
on
...
the
...
deployment
...
of
...
EVSAPI,
...
see:
| Code Block |
|---|
}http://gforge.nci.nih.gov/docman/index.php?group_id=366&selected_doc_group_id=1914&language_id=1{code} |
EVSAPI
...
itself
...
depends
...
on
...
an
...
installation
...
of
...
The diagram below shows the various components of the LexEVS Grid Service System and how they interact.
LexEVS Grid Service and EVSAPI need not be deployed to physically separate servers, but it is recommended that if they are co-located on the same server, they should be deployed to separate JBoss containers.
Below is the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container. For more information on how Service Contexts and Resources are used, see the section, Service Contexts and State below.
LexEVS Grid Service Class Diagram
The LexEVS Grid Service is built on the LexGrid/LexBIG model and implementation. For more information about this model, visit:
| Code Block |
|---|
|http://informatics.mayo.edu]. The diagram below shows the various components of the LexEVS Grid Service System and how they interact. !LexEVS_GridService_System_Components.jpg|alt="diagram that shows the various components of the LexEVS Grid Service System and how they interact"! LexEVS Grid Service and EVSAPI need not be deployed to physically separate servers, but it is recommended that if they are co-located on the same server, they should be deployed to separate JBoss containers. Below is the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container. For more information on how Service Contexts and Resources are used, see the section, [Service Contexts and State|#Service Contexts and State] below. !LexEVS_GridService_Architecture.jpg|alt="diagram showing the LexEVS Grid Service Architecture, viewed from inside of the Web Service Container"! h4. LexEVS Grid Service Class Diagram The LexEVS Grid Service is built on the LexGrid/LexBIG model and implementation. For more information about this model, visit: {code}https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lexbig/lbModel/?root=lexevs{code} and |
and
| Code Block |
|---|
{code}https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lgModel/?root=lexevs{code} |
Also,
...
visit
...
...
for
...
background
...
information
...
as
...
well
...
as
...
Class
...
Diagrams,
...
examples,
...
and
...
other
...
information.
...
For
...
information
...
specific
...
to
...
the
...
LexEVS
...
Grid
...
Service,
...
visit:
| Code Block |
|---|
}https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/LexBIG_Core_Services/LexBIG-2.3/lexbig/lbModel.cagrid/?root=lexevs{code} |
This
...
link
...
contains
...
Class
...
Diagrams
...
and
...
descriptions
...
for
...
input/output
...
parameters,
...
as
...
well
...
as
...
other
...
information
...
concerning
...
the
...
Silver
...
Level
...
Compliance
...
submission
...
package.
...
LexEVS
...
Grid
...
Service
...
Sequence
...
Diagram
...
The
...
sequence
...
diagram
...
for
...
the
...
operation
...
"getSupportedCodingSchemes"
...
is
...
described
...
below:
The following diagram shows a General Call Sequence from the client, through the caGrid Service, to the Distributed LexBIG and the returned results:
Assumptions
- The LexEVS service will be based on the latest EVSAPI 4.2 patch release built by NCICB.
- The LexBIG 2.3 domain model will be loaded in the GME and caDSR.
- The LexEVS Grid Service will not have any method level security. All security requirements will be handled by the actual deployment of the underlying EVSAPI 4.2 service. Please see the "Security" section below for more information on how the LexEVS Grid Service utilizes this security.
- The LexEVS Grid Service will not be deployed as a "core" service by caGrid at NCICB as was previously done, but rather will now be deployed as a standalone service.
- The LexEVS Grid Service release schedule will no longer be coupled to the caGrid deployment schedule as previously done.
- Multiple version of LexEVS Grid Service may be active at the same instance in time depending solely on the availability of the underlining EVSAPI service.
Dependencies
- EVSAPI 4.2 service needs to be available and running correctly.
- The LexBIG 2.3 domain model needs to be registered in caDSR.
- The LexEVS service and operations will use the Introduce toolkit to generate the appropriate structure for registering the service into caDSR.
Issues
- None
Third Party Tools
- Introduce Toolkit
- Globus Toolkit (4.0.3) or appropriate version supported by caGrid 1.2
- caGrid 1.2 core infrastructure
Implementation Contents
Server
The LexEVS Grid Service will be deployed as a "stand alone" grid service at NCICB.
Algorithms
None
Batch Processes
None
APIs
The main Service API exposed by the LexEVS Grid service will be the http://informatics.mayo.edu/LexGrid/downloads/javadocGrid/org/LexGrid/LexBIG/cagrid/interfaces/LexBIGServiceGrid.html
...
Interface.
...
All
...
other
...
APIs
...
will
...
not
...
be
...
directly
...
exposed,
...
but
...
will
...
be
...
made
...
available
...
through
...
Service
...
Contexts.
...
In
...
General,
...
API
...
calls
...
will
...
follow
...
the
...
sequence
...
which
...
is
...
shown
...
in
...
the
...
following
...
diagram:
...
- Client
...
- invokes
...
- caGrid
...
- service
...
- .
...
- caGrid
...
- Service
...
- uses
...
- Distributed
...
- LexBIG
...
- to
...
- implement
...
- call.
...
- Distributed
...
- LexBIG
...
- returns
...
- requested
...
- info
...
- to
...
- caGrid
...
- service
...
- .
- caGrid service sends response to client.
Main Service API
...
Using
...
the
...
API
...
To
...
use
...
the
...
LexEVS
...
Grid
...
Services,
...
either
...
org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter
...
or
...
org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter
...
objects
...
may
...
be
...
instantiated.
...
These
...
are
...
two
...
different
...
Interfaces
...
for
...
accessing
...
the
...
Grid
...
Services.
...
- org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceAdapter
...
- -
...
- An
...
- Interface
...
- for
...
- interacting
...
- with
...
- the
...
- LexEVS
...
- Grid
...
- Services.
...
- This
...
- Interface
...
- is
...
- intended
...
- to
...
- mirror
...
- the
...
- existing
...
- LexBIG
...
- API
...
- as
...
- much
...
- as
...
- possible.
...
- There
...
- is
...
- no
...
- object
...
- wrapping
...
- for
...
- semantic
...
- purposes
...
- on
...
- this
...
- interface.
...
- This
...
- allows
...
- existing
...
- applications
...
- using
...
- the
...
- LexBIG
...
- API
...
- to
...
- used
...
- Grid
...
- Services
...
- without
...
- code
...
- changes.
...
- This
...
- Interface
...
- may
...
- be
...
- acquired
...
- by
...
- instantiating
...
- LexBIGServiceAdapter
...
- with
...
- the
...
- Grid
...
- Service
...
- URL
...
- as
...
- a
...
- parameter.
...
Code Block
...
LexBIGService lbs = new LexBIGServiceAdapter("http://...");
...
- org.LexGrid.LexBIG.cagrid.adapters.LexBIGServiceGridAdapter
...
- -
...
- An
...
- Interface
...
- for
...
- interacting
...
- with
...
- the
...
- LexEVS
...
- Grid
...
- Services.
...
- This
...
- Interfaces
...
- is
...
- the
...
- Semantically
...
- defined
...
- interface.
...
- All
...
- method
...
- parameters
...
- and
...
- return
...
- values
...
- are
...
- defined
...
- and
...
- annotated
...
- as
...
- CDEs
...
- to
...
- be
...
- loaded
...
- into
...
- CADSR.
...
- This
...
- Interface
...
- is
...
- intended
...
- to
...
- be
...
- caGrid
...
- Silver
...
- Level
...
- Compliant.
...
- This
...
- Interface
...
- may
...
- be
...
- acquired
...
- by
...
- instantiating
...
- LexBIGServiceGridAdapter
...
- with
...
- the
...
- Grid
...
- Service
...
- URL
...
- as
...
- a
...
- parameter.
...
Code Block
...
LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter("http://...");
...
getCodingSchemeConcepts
getCodingSchemeConcepts(String,
...
CodingSchemeVersionOrTag)
...
Description | Returns the set of all (or all active) concepts in the specified coding scheme. |
|---|---|
Input | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, |
...
org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag |
...
Output | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.stubs.types.CodedNodeSetReference |
|---|
...
Exception | RemoteException |
|---|---|
Implementation Details |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call: |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getFilter
getFilter(ExtensionIdentification)
...
Description | Returns an instance of the filter extension registered with the given name. |
|---|---|
Input | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
...
Output: |
|---|
...
org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.stubs.types.FilterReference |
...
Exception | RemoteException |
|---|---|
Implementation Details |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getSortAlgorithm
getSortAlgorithm(ExtensionIdentification)
...
Description | Returns an instance of the filter extension registered with the given name. |
|---|---|
Input | org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
...
Output: |
|---|
...
org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort. |
...
|
...
Exception | RemoteException |
|---|---|
Implementation Details |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getFilterExtensions
getFilterExtensions()
...
Description | Returns a description of all registered extensions used to provide additional filtering of query results. |
|---|---|
Input | none |
Output | org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList |
...
Exception | RemoteException |
|---|---|
Implementation Details | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getServiceMetadata
getServiceMetadata()
...
Description | Return an interface to perform system-wide |
|---|
...
query |
...
over |
...
metadata |
...
for |
...
loaded |
...
code |
...
systems |
...
and |
...
providers. |
...
Input | none |
|---|---|
Output | org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata. |
...
|
...
Exception | RemoteException |
|---|---|
Implementation Details |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getSupportedCodingSchemes
getSupportedCodingSchemes
Description | Return a list of coding schemes and versions that are supported by this service, along with their status. |
|---|---|
Input | none |
Output | org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList |
...
Exception | RemoteException |
|---|---|
Implementation Details | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getLastUpdateTime
getLastUpdateTime()
...
Description | Return the last time that the content of this service was changed; null if no changes have occurred. Tag assignments do not count as service changes for this purpose. |
|---|---|
Input | none |
Output | java.util.Date |
Exception | RemoteException |
Implementation Details | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
resolveCodingScheme
resolveCodingScheme(CodingSchemeIdentification,
...
CodingSchemeVersionOrTag)
...
Description | Return detailed coding scheme information given a specific tag or version identifier. |
|---|---|
Input | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, |
...
org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag |
...
Output | org.LexGrid.codingSchemes.CodingScheme |
|---|
...
Exception | RemoteException |
|---|---|
Implementation Details | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getNodeGraph
getNodeGraph(CodingSchemeIdentification,
...
CodingSchemeVersionOrTag,
...
RelationContainerIdentification)
...
Description | Returns the node graph as represented in the particular relationship set in the coding scheme. |
|---|---|
Input | org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, |
...
org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag, |
...
|
...
Output | ''org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. |
|---|
...
|
...
Exception | RemoteException |
|---|---|
Implementation Details |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getMatchAlgorithms
getMatchAlgorithms()
...
Description: |
|---|
...
Returns |
...
the |
...
node |
...
graph |
...
as |
...
represented |
...
in |
...
the |
...
particular |
...
relationship |
...
set |
...
in |
...
the |
...
coding |
...
scheme. |
...
Input: |
|---|
...
none | |
Output: | org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList |
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getGenericExtensions
getGenericExtensions()
...
Description: |
|---|
...
Returns |
...
a |
...
description |
...
of |
...
all |
...
registered |
...
extensions |
...
used |
...
to |
...
implement |
...
application-specific |
...
behavior |
...
that |
...
is |
...
centrally |
...
accessible |
...
from |
...
a |
...
LexBIGService. |
...
|
...
that |
...
only |
...
generic |
...
extensions |
...
(base |
...
class |
...
GenericExtension) |
...
will |
...
be |
...
listed |
...
here. |
...
All |
...
other |
...
classes |
...
are |
...
retrievable |
...
at |
...
the |
...
appropriate |
...
interface |
...
point |
...
(filter, |
...
sort, |
...
etc). |
...
Input: |
|---|
...
none | |
Output: | org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList |
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getGenericExtension
getGenericExtensions(ExtensionIdentification)
...
Description: |
|---|
...
Returns |
...
an |
...
instance |
...
of |
...
the |
...
application-specific |
...
extension |
...
registered |
...
with |
...
the |
...
given |
...
name. |
...
Input: |
|---|
...
org.LexGrid.LexBIG.DataModel.cagrid.ExtensionIdentification |
...
Output: |
|---|
...
org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList |
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getHistoryService
getHistoryService(CodingSchemeIdentification)
...
Description: |
|---|
...
Resolve |
...
a |
...
reference |
...
to |
...
the |
...
history |
...
api |
...
servicing |
...
the |
...
given |
...
coding |
...
scheme. |
...
Input: |
|---|
...
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification |
...
Output: |
|---|
...
''org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices. |
...
|
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Sample Call: |
|
|---|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
getSortAlgorithms
getSortAlgorithms(SortContext)
...
Description: |
|---|
...
Returns |
...
a |
...
description |
...
of |
...
all |
...
registered |
...
extensions |
...
used |
...
to |
...
provide |
...
additional |
...
filtering |
...
of |
...
query |
...
results. |
...
Input: |
|---|
...
org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext |
...
Output: |
|---|
...
org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList |
...
Exception: | RemoteException |
|---|---|
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
resolveCodingSchemeCopyright
resolveCodingSchemeCopyright(CodingSchemeIdentification)
...
Description: |
|---|
...
Return |
...
coding |
...
scheme |
...
copyright |
...
given |
...
a |
...
specific |
...
tag |
...
or |
...
version |
...
identifier. |
...
Input: |
|---|
...
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification |
...
Output: |
|---|
...
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeCopyRight |
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
setSecurityToken
setSecurityToken(CodingSchemeIdentification,
...
SecurityToken)
...
Description: |
|---|
...
Sets |
...
the |
...
Security |
...
Token |
...
for |
...
the |
...
given |
...
Coding |
...
Scheme. |
...
Input: |
|---|
...
org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification, |
...
gov.nih.nci.evs.security.SecurityToken |
...
Output: |
|---|
...
''org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types |
...
|
...
Exception: |
|---|
...
RemoteException | |
Implementation Details: | Call this method on the associated LexBIG Service instance (or Distributed LexBIG instance) on the server, and forward the results. |
Sample Call: |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
API Examples
For an example clients, service calls, and SOAP messages, see the LexEVS documentation on GForge.
Example API usage:
Searching for concepts in NCI Thesaurus containing the string "Gene"
| Code Block |
|---|
}} | h3. API Examples For an example clients, service calls, and SOAP messages, see the [LexEVS documentation on GForge|http://gforge.nci.nih.gov/docman/index.php?group_id=491&selected_doc_group_id=3880&language_id=1]. Example API usage: *Searching for concepts in NCI Thesaurus containing the string "Gene"* {code} //Create a Connection to the Grid Service LexBIGServiceGrid lbs = new LexBIGServiceGridAdapter(gridServiceURL); //Set up the CodingSchemeIdentification object to define the Coding Scheme CodingSchemeIdentification csid = new CodingSchemeIdentification(); csid.setName("NCI Thesaurus"); //Get the CodedNodeSet for that CodingScheme (This returns a CodedNodeSet Service Context) CodedNodeSetGrid cnsg = lbs.getCodingSchemeConcepts(csid, null); //getCodingSchemeConcepts is a Grid Service Call //Set the text to match MatchCriteria matchText = new MatchCriteria(); matchText.setText("Gene"); //Define a SearchDesignationOption, if any SearchDesignationOption searchOption = new SearchDesignationOption(); //Choose an algorithm to do the matching ExtensionIdentification matchAlgorithm = new ExtensionIdentification(); matchAlgorithm.setLexBIGExtensionName("contains"); //Chose a language LanguageIdentification language = new LanguageIdentification(); language.setIdentifier("en"); //Restrict the CodedNodeSet cnsg.restrictToMatchingDesignations(matchText, searchOption, matchAlgorithm, language); //restrictToMatchingDesignations is a Grid Service Call //Create a SetResolutionPolicy to handle the details of Resolving the CodedNodeSet //Here, we will set the Maximum number of Concepts returned to 10. SetResolutionPolicy resolvePolicy = new SetResolutionPolicy(); resolvePolicy.setMaximumToReturn(10); //Do the resolve ResolvedConceptReferenceList rcrlist = cnsg.resolveToList(resolvePolicy); //resolveToList is a Grid Service Call //Use the returned ResolvedConceptReferenceList to print some details about the concepts found ResolvedConceptReference[] rcref = rcrlist.getResolvedConceptReference(); for (int i = 0; i < rcref.length; i++) { System.out.println(rcref[i].getConceptCode()); System.out.println(rcref[i].getReferencedEntry(). getPresentation()[0].getText().getContent()); }{code} h3. Service Contexts and State Along with the Main Service (described above), the Server will also host the Service Contexts shown in the following diagram and described in the subsequent sections. These Service Contexts are not meant to be called directly as Grid Services. The main function of these Service Contexts is to provide additional functionality to the Main Service. !Service_Context_Operations_Example.jpg|alt="image showing the service contexts, which are detailed in the subsequent sections"! *Service Context Operations Example in Introduce* {warning:title=Important}Service Contexts are only meant to be called through the Main Service - not directly. Through the Main Service, References to these Service Contexts can be obtained. Calls are made to the Service Contexts through these References.{warning} h4. Obtaining a Service Context Reference In the figure below, two LexEVS Grid Service Calls are highlighted, 'getCodingSchemeConcepts' and 'getNodeGraph'. These two Grid Service Calls have been selected because they return to the user a "Reference" to a Service Context. For 'getCodingSchemeConcepts', the return type is CodedNodeSetReference (which references the CodedNodeSet Service Context). For 'getNodeGraph', the return type is CodedNodeGraphReference (which references the CodedNodeGraph Service Context). !Service_Context_Reference.jpg|alt="image that corresponds to the description in the preceding paragraph"! h4. Resources LexEVS Grid Services use the WS-Resource Framework (WSRF) to allow for stateful calls to the server. When a client requests a Service Context, the client is not only issued a Reference to the Service Context that was requested, but to a unique stateful Resource on the server as well. This Resource is used in the LexEVS Grid Services as a way of statefully holding objects for further use by the client. For more information about how caGrid uses the WS-Resource Framework (WSRF), see |
Service Contexts and State
Along with the Main Service (described above), the Server will also host the Service Contexts shown in the following diagram and described in the subsequent sections. These Service Contexts are not meant to be called directly as Grid Services. The main function of these Service Contexts is to provide additional functionality to the Main Service.
Service Context Operations Example in Introduce
| Warning | ||
|---|---|---|
| ||
Service Contexts are only meant to be called through the Main Service - not directly. Through the Main Service, References to these Service Contexts can be obtained. Calls are made to the Service Contexts through these References. |
Obtaining a Service Context Reference
In the figure below, two LexEVS Grid Service Calls are highlighted, 'getCodingSchemeConcepts' and 'getNodeGraph'. These two Grid Service Calls have been selected because they return to the user a "Reference" to a Service Context. For 'getCodingSchemeConcepts', the return type is CodedNodeSetReference (which references the CodedNodeSet Service Context). For 'getNodeGraph', the return type is CodedNodeGraphReference (which references the CodedNodeGraph Service Context).
Resources
LexEVS Grid Services use the WS-Resource Framework (WSRF) to allow for stateful calls to the server. When a client requests a Service Context, the client is not only issued a Reference to the Service Context that was requested, but to a unique stateful Resource on the server as well. This Resource is used in the LexEVS Grid Services as a way of statefully holding objects for further use by the client. For more information about how caGrid uses the WS-Resource Framework (WSRF), see http://www.cagrid.org/wiki/Metadata:WSRF
...
For
...
more
...
information
...
on
...
how
...
Resources
...
are
...
implemented
...
in
...
the
...
LexEVS
...
Grid
...
Service,
...
refer
...
to
...
this
...
...
...
.
Service Context Sequence
The Service Contexts API calls follow this general process:
- Client Requests a Service Context, such as a CodedNodeSet.
- The Grid Node receives the call and forwards the call to EVSAPI.
- EVSAPI calls getCodingSchemeConcepts on the local LexBIG installation and returns a CodedNodeSetImpl object to the Grid Node.
- The Grid Node then creates a Resource to store this CodedNodeSetImpl object for future use by the Client.
- The Client is then returned a Service Context Client for the CodedNodeSet. This client is associated to the Resource that was created.
Service Context and Resource Assignment
| Info | ||
|---|---|---|
| ||
By default, these services are destroyed 5 minutes after creation. |
Supported Service Contexts.
CodedNodeSet
...
To
...
construct
...
a
...
CodedNodeSet,
...
the
...
user
...
calls
...
getCodingSchemeConcepts
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
CodedNodeSet
...
through
...
the
...
API
...
call
...
getCodingSchemeConcepts,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
CodedNodeSet
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
CodedNodeSet
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- CodedNodeSet
...
- using
...
- getCodingSchemeConcepts.
...
Include Page RequestCodedNodeSet Snippet RequestCodedNodeSet Snippet - The server calls the Distributed LexBIG getCodingSchemeConcepts method, returning to the server an org.LexGrid.LexBIG.Impl.CodedNodeSetImpl
...
- (the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.LexBIGService.CodedNodeSet)
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.service.globus.resource.CodedNodeSetResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- org.LexGrid.LexBIG.Impl.CodedNodeSetImpl,
...
- the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.LexBIGService.CodedNodeSet
...
- that
...
- was
...
- created
...
- above.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeSet.stubs.types.CodedNodeSetReference
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- reference
...
- to
...
- the
...
- CodedNodeSet
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- CodedNodeSetClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- These
...
- restrictions
...
- are
...
- separate
...
- calls
...
- but
...
- statefully
...
- maintained
...
- on
...
- the
...
- server
...
- via
...
- the
...
- Resource.
...
CodedNodeGraph
...
To
...
construct
...
a
...
CodedNodeGraph,
...
the
...
user
...
calls
...
getNodeGraph
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
CodedNodeGraph
...
through
...
the
...
API
...
call
...
getNodeGraph,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
CodedNodeGraph
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
CodedNodeGraph
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- CodedNodeGraph
...
- using
...
- getCodingSchemeConcepts.
...
Include Page RequestCodedNodeGraph Snippet RequestCodedNodeGraph Snippet - The server calls the Distributed LexBIG getNodeGraph method, returning to the server an org.LexGrid.LexBIG.Impl.CodedNodeGraphImpl
...
- (the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph)
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeGraph.service.globus.resource.CodedNodeGraphResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- org.LexGrid.LexBIG.Impl.CodedNodeGraphImpl,
...
- the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph
...
- that
...
- was
...
- created
...
- above.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.CodedNodeGraph.stubs.types.CodedNodeGraphReference
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- reference
...
- to
...
- the
...
- CodedNodeGraph
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- CodedNodeGraphClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- For
...
- example,
...
- the
...
- client
...
- may
...
- add
...
- Restrictions
...
- to
...
- the
...
- CodedNodeGraph
...
- before
...
- a
...
- Resolve:
...
Include Page CodedNodeGraphRestriction Snippet CodedNodeGraphRestriction Snippet - These restrictions are separate calls but statefully maintained on the server via the Resource.
LexBIGServiceConvenienceMethods
...
To
...
construct
...
a
...
LexBIGServiceConvenienceMethods,
...
the
...
user
...
calls
...
getGenericExtensions
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
LexBIGServiceConvenienceMethods
...
through
...
the
...
API
...
call
...
getGenericExtensions,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
LexBIGServiceConvenienceMethods
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
LexBIGServiceConvenienceMethods
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- LexBIGServiceConvenienceMethods
...
- using
...
- getGenericExtensions.
...
Include Page RequestLexBIGServiceConvenienceMethods Snippet RequestLexBIGServiceConvenienceMethods Snippet - The server calls the Distributed LexBIG getGenericExtensions method, returning to the server an org.LexGrid.LexBIG.Impl.Extensions.GenericExtensions.LexBIGServiceConvenienceMethodsImpl
...
- (the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods)
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceConvenienceMethods.service.globus.resource.LexBIGServiceConvenienceMethodsResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- org.LexGrid.LexBIG.Impl.Extensions.GenericExtensions.LexBIGServiceConvenienceMethodsImpl,
...
- the
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods
...
- that
...
- was
...
- created
...
- above.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServicesLexBIGServiceConvenienceMethods.stubs.types.LexBIGServiceConvenienceMethodsReference
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- reference
...
- to
...
- the
...
- LexBIGServiceConvenienceMethods
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- This
...
- LexBIGServiceConvenienceMethodsClient
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- Because
...
- this
...
- LexBIGServiceConvenienceMethods
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods,
...
- API
...
- calls
...
- will
...
- look
...
- to
...
- the
...
- user
...
- as
...
- being
...
- identical
...
- to
...
- direct
...
- LexBIG
...
- API
...
- calls.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- LexBIGServiceConvenienceMethods
...
- Client
...
- and
...
- the
...
- assigned
...
- Resource.
...
- These
...
- API
...
- calls
...
- are
...
- separate
...
- calls
...
- but
...
- statefully
...
- maintained
...
- on
...
- the
...
- server
...
- via
...
- the
...
- Resource.
...
LexBIGServiceMetadata
...
To
...
construct
...
a
...
LexBIGServiceMetadata,
...
the
...
user
...
calls
...
getServiceMetadata
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
LexBIGServiceMetadata
...
through
...
the
...
API
...
call
...
getServiceMetadata
...
,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
LexBIGServiceMetadata
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
LexBIGServiceMetadata
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- LexBIGServiceMetadata
...
- using
...
- getServiceMetadata.
...
Include Page RequestLexBIGServiceMetadata Snippet RequestLexBIGServiceMetadata Snippet - The server calls the Distributed LexBIG getServiceMetadata method, returning to the server an implementation of org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.service.globus.resource.LexBIGServiceMetadataResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata.
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.stubs.types.LexBIGServiceMetadata
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- reference
...
- to
...
- the
...
- LexBIGServiceMetadata
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- LexBIGServiceMetadata
...
- and
...
- the
...
- assigned
...
- Resource.
...
- These
...
- API
...
- calls
...
- are
...
- separate
...
- calls
...
- but
...
- statefully
...
- maintained
...
- on
...
- the
...
- server
...
- via
...
- the
...
- Resource.
...
HistoryService
...
To
...
construct
...
a
...
HistoryService,
...
the
...
user
...
calls
...
getHistoryService
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
HistoryService
...
through
...
the
...
API
...
call
...
getHistoryService,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
HistoryService
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
HistoryService
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- HistoryService
...
- using
...
- getHistoryService
...
- .
...
Include Page RequestHistoryService Snippet RequestHistoryService Snippet - The server calls the Distributed LexBIG getHistoryService method, returning to the server an implementation of org.LexGrid.LexBIG.History.HistoryService
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.HistoryService.service.globus.resource.HistoryServiceResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.History.HistoryService.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.LexBIGServiceMetadata.stubs.types.LexBIGServiceMetadata
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- reference
...
- to
...
- the
...
- HistoryService
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- HistoryServiceClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- For
...
- example,
...
- the
...
- client
...
- may
...
- call
...
- any
...
- method
...
- in
...
- org.LexGrid.LexBIG.History.HistoryService.
...
- Example:
...
- history.getLatestBaseline();
...
- These
...
- API
...
- calls
...
- are
...
- separate
...
- calls
...
- but
...
- statefully
...
- maintained
...
- on
...
- the
...
- server
...
- via
...
- the
...
- Resource.
...
Sort
http://informatics.mayo.edu/LexGrid/downloads/javadoc/org/LexGrid/LexBIG/Extensions/Query/Sort.html
...
To
...
construct
...
a
...
Sort,
...
the
...
user
...
calls
...
getSortAlgorithm
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
Sort
...
through
...
the
...
API
...
call
...
getSortAlgorithm,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
Sort
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
Sort
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- Sort
...
- using
...
- getSortAlgorithm
...
- .
...
Include Page :RequestSort Snippet :RequestSort
...
Snippet
...
- The
...
- server
...
- calls
...
- the
...
- Distributed
...
- LexBIG
...
- getSortAlgorithm
...
- method,
...
- returning
...
- to
...
- the
...
- server
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Extensions.Query.Sort)
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Sort
...
- .service.globus.resource.Sort
...
- Resource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Extensions.Query.Sort.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.SortClient
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- client
...
- to
...
- the
...
- Sort
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- This
...
- SortClient
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Query.Sort.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- Because
...
- this
...
- Sort
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Query.Sort,
...
- API
...
- calls
...
- will
...
- look
...
- to
...
- the
...
- user
...
- as
...
- being
...
- identical
...
- to
...
- direct
...
- LexBIG
...
- API
...
- calls.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- SortClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- For
...
- example,
...
- the
...
- client
...
- may
...
- call
...
- any
...
- method
...
- in
...
- org.LexGrid.LexBIG.Extensions.Query.Sort
...
Wiki Markup {Include:RequestSortCompare Snippet}
...
- These
...
- API
...
- calls
...
- are
...
- separate
...
- calls
...
- but
...
- statefully
...
- maintained
...
- on
...
- the
...
- server
...
- via
...
- the
...
- Resource.
...
Filter
http://informatics.mayo.edu/LexGrid/downloads/javadoc/org/LexGrid/LexBIG/Extensions/Query/Filter.htm
...
To
...
construct
...
a
...
Filter,
...
the
...
user
...
calls
...
getFilter
...
as
...
described
...
above.
...
When
...
the
...
user
...
creates
...
a
...
Filter
...
through
...
the
...
API
...
call
...
getFilter,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
Sort
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
Filter
...
Call
...
Sequence:
...
- The
...
- user
...
- requests
...
- a
...
- Filter
...
- using
...
- getFilter
...
Include Page RequestFilter Snippet RequestFilter Snippet - The server calls the Distributed LexBIG getFilter method, returning to the server an implementation of org.LexGrid.LexBIG.Extensions.Query.Filter)
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.Filter.service.globus.resource.FilterResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Extensions.Query.Filter.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.FilterClient
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- client
...
- to
...
- the
...
- Filter
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- This
...
- FilterClient
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Query.Filter.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- Because
...
- this
...
- Filter
...
- implements
...
- org.LexGrid.LexBIG.Extensions.Query.Filter,
...
- API
...
- calls
...
- will
...
- look
...
- to
...
- the
...
- user
...
- as
...
- being
...
- identical
...
- to
...
- direct
...
- LexBIG
...
- API
...
- calls.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- FilterClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- For
...
- example,
...
- the
...
- client
...
- may
...
- call
...
- any
...
- method
...
- in
...
- org.LexGrid.LexBIG.Extensions.Query.Filter
...
Include Page RequestFilterMatch Snippet RequestFilterMatch Snippet - These API calls are separate calls but statefully maintained on the server via the Resource.
ResolvedConceptReferencesIterator
...
A
...
ResolvedConceptReferencesIterator
...
is
...
created
...
when
...
a
...
CodedNodeSet
...
or
...
CodedNodeGraph
...
is
...
resolved.
...
It
...
allows
...
results
...
to
...
be
...
returned
...
from
...
the
...
server
...
incrementally
...
instead
...
of
...
all
...
at
...
once.
...
When
...
the
...
user
...
creates
...
a
...
ResolvedConceptReferencesIterator,
...
the
...
server
...
creates
...
and
...
stores
...
the
...
ResolvedConceptReferencesIterator
...
server-side
...
as
...
a
...
Resource.
...
This
...
Resource
...
is
...
associated
...
with
...
the
...
client
...
and
...
will
...
be
...
accessible
...
only
...
by
...
the
...
client
...
that
...
created
...
it.
...
ResolvedConceptReferencesIterator
...
Call
...
Sequence:
...
- The
...
- user
...
- gets
...
- a
...
- ResolvedConceptReferencesIterator
...
- from
...
- a
...
- Resolve.
...
- The
...
- server
...
- calls
...
- the
...
- Distributed
...
- LexBIG
...
- resolve
...
- method
...
- on
...
- the
...
- CodedNodeSet,
...
- returning
...
- to
...
- the
...
- server
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
...
- object.
...
- The
...
- server
...
- then
...
- creates
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.ResolvedConceptReferencesIterator.service.globus.resource.ResolvedConceptReferencesIteratorResource.
...
- This
...
- Resource
...
- will
...
- be
...
- used
...
- to
...
- hold
...
- the
...
- instance
...
- of
...
- an
...
- implementation
...
- of
...
- org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator.
...
- The
...
- server
...
- returns
...
- an
...
- org.LexGrid.LexBIG.cagrid.LexBIGCaGridServices.service.ResolvedConceptReferencesIteratorClient
...
- object
...
- to
...
- the
...
- client.
...
- This
...
- is
...
- the
...
- client
...
- to
...
- the
...
- ResolvedConceptReferencesIterator
...
- Service
...
- Context.
...
- This
...
- object
...
- has
...
- a
...
- direct
...
- reference
...
- to
...
- the
...
- Resource
...
- created
...
- above.
...
- This
...
- ResolvedConceptReferencesIteratorClient
...
- implements
...
- org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator.
...
- The
...
- user
...
- now
...
- uses
...
- this
...
- client
...
- to
...
- make
...
- transparent
...
- Grid
...
- calls
...
- through
...
- the
...
- Service
...
- Context.
...
- Because
...
- this
...
- ResolvedConceptReferencesIterator
...
- implements
...
- org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator,
...
- API
...
- calls
...
- will
...
- look
...
- to
...
- the
...
- user
...
- as
...
- being
...
- identical
...
- to
...
- direct
...
- LexBIG
...
- API
...
- calls.
...
- The
...
- client
...
- may
...
- continue
...
- to
...
- make
...
- statefull
...
- calls
...
- to
...
- the
...
- ResolvedConceptReferencesIteratorClient
...
- and
...
- the
...
- assigned
...
- Resource.
...
- For
...
- example,
...
- the
...
- client
...
- may
...
- call
...
- any
...
- method
...
- in
...
- org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator
...
Include Page ResolvedConceptReferencesIterator Snippet ResolvedConceptReferencesIterator Snippet - These API calls are separate calls but statefully maintained on the server via the Resource.
Error Handling
Error Connecting to LexEVS Grid Service
When connecting through the Java Client, java.net.ConnectException
...
and
...
org.apache.axis.types.URI.MalformedURIException
...
may
...
be
...
thrown
...
upon
...
an
...
unsuccessful
...
attempt
...
to
...
connect.
...
A
...
MalformedURIException
...
is
...
thrown
...
in
...
the
...
case
...
if
...
a
...
poorly-formed
...
URL
...
string.
...
In
...
this
...
case,
...
the
...
exception
...
is
...
thrown
...
before
...
an
...
attempt
...
to
...
connect
...
is
...
even
...
made.
...
If
...
the
...
URL
...
is
...
well-formed,
...
proper
...
connection
...
is
...
tested.
...
If
...
the
...
connection
...
attempt
...
fails,
...
a
...
ConnectException
...
is
...
thrown
...
containing
...
the
...
reason
...
for
...
the
...
failure.
...
| Include Page | ||||
|---|---|---|---|---|
|
This example shows a typical connection to the LexEVS Grid Service, with the two potential Exceptions being caught and handled as necessary.
LexBIG Errors
LexBIG errors will be forwarded through the Distributed LexBIG layer and then on to the Grid layer. Input parameters, along with any other LexBIG (or Distributed LexBIG) errors will be detected on the server, not the client, and forwarded. All Generic LexBIG (or Distributed LexBIG) errors will be forwarded via a RemoteException, with the cause of the error and underlying LexBIG error message included.
Invalid Service Context Access
Service Context Services are not meant to be called directly. If the client attempts to do so, an org.LexGrid.LexBIG.cagrid.LexEVSGridService.CodedNodeSet.stubs.types.InvalidServiceContextAccess
...
Exception
...
will
...
be
...
thrown.
...
This
...
indicates
...
a
...
call
...
was
...
made
...
to
...
a
...
Service
...
Context
...
without
...
obtaining
...
a
...
Service
...
Context
...
Reference
...
via
...
the
...
Main
...
Service
...
(see
...
the
...
above
...
section
...
...
...
...
...
for
...
more
...
information).
...
Database
...
Changes
...
None
Client
The Introduce toolkit generates a "client"
...
class
...
that
...
will
...
be
...
provided
...
to
...
the
...
users.
...
JSP/HTML
None
Servlet
None
Security Issues
Security in the LexEVS Grid Service is implemented in the Distributed LexBIG layer. The information in this section explains how the LexEVS Grid Services utilize this security implementation. For more information about the Distributed LexBIG Security Implementation, see this documentation:
| Code Block |
|---|
None h4. Servlet None h3. Security Issues Security in the LexEVS Grid Service is implemented in the Distributed LexBIG layer. The information in this section explains how the LexEVS Grid Services utilize this security implementation. For more information about the Distributed LexBIG Security Implementation, see this documentation: {code}http://gforge.nci.nih.gov/tracker/download.php/366/1462/10884/4060/Distributed_LexBIG_%20AccessTo_Licensed_Vocabulary_implemenation.doc{code} h4. LexEVS Grid Service Security Certain vocabulary content accessible through the LexEVS Grid Service may require extra authorization to access. Each client is required to supply its own access credentials via Security Tokens. These Security Tokens are implemented by a SecurityToken object: * Name: SecurityToken * Namespace: |
LexEVS Grid Service Security
Certain vocabulary content accessible through the LexEVS Grid Service may require extra authorization to access. Each client is required to supply its own access credentials via Security Tokens. These Security Tokens are implemented by a SecurityToken object:
- Name: SecurityToken
- Namespace: gme://caCORE.caCORE/3.2/gov.nih.nci.evs.security
...
- Package:
...
- gov.nih.nci.evs.security
...
Accessing
...
Secure
...
Content
...
A
...
client
...
establishes
...
access
...
to
...
a
...
secured
...
vocabulary
...
via
...
the
...
following
...
Grid
...
Service
...
Calls:
...
- Connect
...
- to
...
- the
...
- LexBIG
...
- caGrid
...
- Service
...
LexBIGServiceGrid
...
lbs
...
=
...
new
...
LexBIGServiceGridAdapter(url);
...
- Build
...
- an
...
- org.LexGrid.LexBIG.DataModel.cagrid.CodingSchemeIdentification
...
- to
...
- hold
...
- the
...
- Coding
...
- Scheme
...
- name.
...
Code Block
...
CodingSchemeIdentification codingScheme = new CodingSchemeIdentification(); codingScheme.setName("codingScheme");
...
- Build an gov.nih.nci.evs.security.SecurityToken
...
- containing
...
- the
...
- security
...
- information
...
- for
...
- the
...
- desired
...
- Coding
...
- Scheme.
...
Code Block
...
SecurityToken token = new SecurityToken(); token.setAccessToken("securityToken");
...
- Invoke the LexBIG caGrid service as follows: This will return a reference to a new "LexBIGServiceGrid" instance that is associated with the security properties that were passed in.
LexBIGServiceGrid lbsg = lbs.setSecurityToken(codingScheme,
...
token);
...
It
...
is
...
important
...
to
...
note
...
that
...
the
...
Grid
...
Service
...
"setSecurityToken"
...
returns
...
an
...
org.LexGrid.LexBIG.cagrid.LexEVSGridService.stubs.types
...
.LexEVSGridServiceReference.LexEVSGridServiceReference
...
object.
...
This
...
reference
...
must
...
be
...
used
...
to
...
access
...
the
...
secured
...
vocabularies.
...
Implementation
...
of
...
Security
...
Each
...
call
...
to
...
"setSecurityToken"
...
sets
...
up
...
a
...
secured
...
connection
...
to
...
Distributed
...
LexBIG
...
with
...
the
...
access
...
privileges
...
included
...
in
...
the
...
SecurityToken
...
parameter.
...
The
...
LexEVSGridServiceReference
...
that
...
is
...
returned
...
to
...
the
...
client
...
contains
...
a
...
unique
...
key
...
identifier
...
to
...
the
...
secure
...
connection
...
that
...
has
...
been
...
created
...
on
...
the
...
server.
...
All
...
subsequent
...
calls
...
the
...
client
...
makes
...
through
...
this
...
LexEVSGridServiceReference
...
will
...
be
...
made
...
securely.
...
If
...
additional
...
SecurityTokens
...
are
...
passed
...
in
...
through
...
the
...
"setSecurityToken"
...
Grid
...
Service,
...
the
...
additional
...
security
...
will
...
be
...
added
...
and
...
maintained.
...
The
...
"setSecurityToken"
...
Grid
...
Service
...
is
...
a
...
stateful
...
service.
...
This
...
means
...
that
...
after
...
the
...
client
...
sets
...
a
...
SecurityToken,
...
any
...
subsequent
...
call
...
will
...
be
...
applied
...
to
...
that
...
SecurityToken.
...
Secure
...
connections
...
are
...
not
...
maintained
...
on
...
the
...
server
...
indefinitely,
...
but
...
are
...
based
...
on
...
load
...
conditions.
...
The
...
server
...
will
...
allow
...
30
...
unique
...
secure
...
connections
...
to
...
be
...
set
...
up
...
for
...
clients
...
without
...
any
...
time
...
limitations.
...
As
...
additional
...
requests
...
for
...
secure
...
connections
...
are
...
received
...
by
...
the
...
server,
...
connections
...
will
...
be
...
released
...
by
...
the
...
server
...
on
...
an
...
'oldest
...
first'
...
basis.
...
No
...
connection,
...
however,
...
may
...
be
...
released
...
prior
...
to
...
5
...
minutes
...
after
...
its
...
creation.
...
If
...
no
...
SecurityTokens
...
are
...
passed
...
in
...
by
...
the
...
client,
...
a
...
non-secure
...
Distributed
...
LexBIG
...
connection
...
will
...
be
...
used.
...
The
...
server
...
maintains
...
one
...
(and
...
only
...
one)
...
un-secured
...
Distributed
...
LexBIG
...
connection
...
that
...
is
...
shared
...
by
...
any
...
client
...
not
...
requesting
...
security.
| Info | ||||
|---|---|---|---|---|
| =
| |||
| } All non-secured information accessed by the LexEVS Grid Service is publicly available from NCICB and users are expected to follow the licensing requirements currently in place for accessing and using NCI EVS information. {info} h3. Performance The LexEVS service will take advantage of all improvements made to the EVSAPI services with the exception of lazy loading. LexEVS grid service, being in nature a web service is currently not taking advantage of lazy loading since objects are transferred as fully populated objects. However, future releases of LexEVS Grid Service may refractor the interface in such as way as to take advantage of some of the benefits brought about by the inclusion of lazy loading in to EVSAPI service. LexEVS Grid Services utilize the performance enhancements of the LexBIG API. For more information about LexBIG performance (which LexEVS Grid Services are dependent on), see |
Performance
The LexEVS service will take advantage of all improvements made to the EVSAPI services with the exception of lazy loading. LexEVS grid service, being in nature a web service is currently not taking advantage of lazy loading since objects are transferred as fully populated objects. However, future releases of LexEVS Grid Service may refractor the interface in such as way as to take advantage of some of the benefits brought about by the inclusion of lazy loading in to EVSAPI service.
LexEVS Grid Services utilize the performance enhancements of the LexBIG API.
For more information about LexBIG performance (which LexEVS Grid Services are dependent on), see http://informatics.mayo.edu
Internationalization
Not Internationalized
Installation / Packaging
The service will be installed and deployed as a "stand alone" service at NCICB.
Migration
Both the current version of LexEVS grid service and a previous version may be "in service" simultaneously if the corresponding underlying EVSAPI service is also "in service" to manage migration of clients.
System Testing
See LexEVS Grid Service Testing Documentation
| Wiki Markup |
|---|
h3. Internationalization
Not Internationalized
h3. Installation / Packaging
The service will be installed and deployed as a "stand alone" service at NCICB.
h3. Migration
Both the current version of LexEVS grid service and a previous version may be "in service" simultaneously if the corresponding underlying EVSAPI service is also "in service" to manage migration of clients.
h2. System Testing
See [LexEVS Grid Service Testing Documentation|http://gforge.nci.nih.gov/docman/index.php?group_id=491&selected_doc_group_id=3879&language_id=1]
{scrollbar:icons=false} |
