From ebdf1a47d6e48a5e2e487ab499dd9eeb1c623ae5 Mon Sep 17 00:00:00 2001 From: "Jeremy R. Easton-Marks" Date: Fri, 9 Sep 2016 11:06:21 -0400 Subject: [PATCH 1/2] JavaDocs, 1.2.1, and Error Pages - Added Javadocs - Updated to 1.2.1 - Added JSON error pages - Changed default error message to local one --- javadoc/allclasses-frame.html | 29 - javadoc/allclasses-noframe.html | 29 - javadoc/constant-values.html | 4 +- javadoc/deprecated-list.html | 4 +- .../bd2k/irct/cl/filter/SessionFilter.html | 4 +- .../cl/filter/class-use/SessionFilter.html | 4 +- .../bd2k/irct/cl/filter/package-frame.html | 4 +- .../bd2k/irct/cl/filter/package-summary.html | 4 +- .../bd2k/irct/cl/filter/package-tree.html | 4 +- .../dbmi/bd2k/irct/cl/filter/package-use.html | 4 +- .../bd2k/irct/cl/rest/JaxRsActivator.html | 4 +- .../bd2k/irct/cl/rest/ProcessRESTService.html | 335 ---------- .../bd2k/irct/cl/rest/ProcessService.html | 4 +- .../bd2k/irct/cl/rest/QueryRESTService.html | 486 --------------- .../dbmi/bd2k/irct/cl/rest/QueryService.html | 31 +- .../irct/cl/rest/ResourceRESTService.html | 371 ----------- .../bd2k/irct/cl/rest/ResourceService.html | 47 +- .../bd2k/irct/cl/rest/ResultRESTService.html | 493 --------------- .../dbmi/bd2k/irct/cl/rest/ResultService.html | 4 +- .../bd2k/irct/cl/rest/SecurityService.html | 23 +- .../dbmi/bd2k/irct/cl/rest/SystemService.html | 4 +- .../cl/rest/class-use/JaxRsActivator.html | 4 +- .../cl/rest/class-use/ProcessRESTService.html | 124 ---- .../cl/rest/class-use/ProcessService.html | 4 +- .../cl/rest/class-use/QueryRESTService.html | 124 ---- .../irct/cl/rest/class-use/QueryService.html | 4 +- .../rest/class-use/ResourceRESTService.html | 124 ---- .../cl/rest/class-use/ResourceService.html | 4 +- .../cl/rest/class-use/ResultRESTService.html | 124 ---- .../irct/cl/rest/class-use/ResultService.html | 4 +- .../cl/rest/class-use/SecurityService.html | 4 +- .../irct/cl/rest/class-use/SystemService.html | 4 +- .../dbmi/bd2k/irct/cl/rest/package-frame.html | 4 +- .../bd2k/irct/cl/rest/package-summary.html | 4 +- .../dbmi/bd2k/irct/cl/rest/package-tree.html | 4 +- .../dbmi/bd2k/irct/cl/rest/package-use.html | 4 +- .../hms/dbmi/bd2k/irct/cl/util/AdminBean.html | 4 +- .../hms/dbmi/bd2k/irct/cl/util/Constants.html | 395 ------------ .../hms/dbmi/bd2k/irct/cl/util/Resources.html | 4 +- .../hms/dbmi/bd2k/irct/cl/util/Utilities.html | 4 +- .../irct/cl/util/class-use/AdminBean.html | 4 +- .../irct/cl/util/class-use/Constants.html | 124 ---- .../irct/cl/util/class-use/Resources.html | 4 +- .../irct/cl/util/class-use/Utilities.html | 4 +- .../dbmi/bd2k/irct/cl/util/package-frame.html | 4 +- .../bd2k/irct/cl/util/package-summary.html | 4 +- .../dbmi/bd2k/irct/cl/util/package-tree.html | 4 +- .../dbmi/bd2k/irct/cl/util/package-use.html | 4 +- javadoc/help-doc.html | 229 ------- javadoc/index-files/index-1.html | 8 +- javadoc/index-files/index-10.html | 36 +- javadoc/index-files/index-11.html | 60 +- javadoc/index-files/index-12.html | 68 +-- javadoc/index-files/index-13.html | 71 ++- javadoc/index-files/index-14.html | 134 ++++ javadoc/index-files/index-2.html | 8 +- javadoc/index-files/index-3.html | 8 +- javadoc/index-files/index-4.html | 8 +- javadoc/index-files/index-5.html | 25 +- javadoc/index-files/index-6.html | 25 +- javadoc/index-files/index-7.html | 24 +- javadoc/index-files/index-8.html | 24 +- javadoc/index-files/index-9.html | 36 +- javadoc/index.html | 74 --- javadoc/overview-frame.html | 23 - javadoc/overview-summary.html | 4 +- javadoc/overview-tree.html | 153 ----- javadoc/package-list | 3 - javadoc/script.js | 30 - javadoc/serialized-form.html | 272 --------- javadoc/stylesheet.css | 574 ------------------ pom.xml | 8 +- .../dbmi/bd2k/irct/cl/rest/ResultService.java | 3 + src/main/webapp/WEB-INF/web.xml | 11 + src/main/webapp/error.json | 5 + src/main/webapp/unknown.json | 5 + 76 files changed, 488 insertions(+), 4432 deletions(-) delete mode 100644 javadoc/allclasses-frame.html delete mode 100644 javadoc/allclasses-noframe.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ProcessRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/QueryRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResultRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/class-use/ProcessRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/class-use/QueryRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/class-use/ResourceRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/class-use/ResultRESTService.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/util/Constants.html delete mode 100644 javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/util/class-use/Constants.html delete mode 100644 javadoc/help-doc.html create mode 100644 javadoc/index-files/index-14.html delete mode 100644 javadoc/index.html delete mode 100644 javadoc/overview-frame.html delete mode 100644 javadoc/overview-tree.html delete mode 100644 javadoc/package-list delete mode 100644 javadoc/script.js delete mode 100644 javadoc/serialized-form.html delete mode 100644 javadoc/stylesheet.css create mode 100644 src/main/webapp/error.json create mode 100644 src/main/webapp/unknown.json diff --git a/javadoc/allclasses-frame.html b/javadoc/allclasses-frame.html deleted file mode 100644 index ad5b731..0000000 --- a/javadoc/allclasses-frame.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - -All Classes - - - - - -

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- - diff --git a/javadoc/constant-values.html b/javadoc/constant-values.html index 1f23cb2..3460a14 100644 --- a/javadoc/constant-values.html +++ b/javadoc/constant-values.html @@ -2,9 +2,9 @@ - + Constant Field Values - + diff --git a/javadoc/deprecated-list.html b/javadoc/deprecated-list.html index 4ca3d57..c2c9066 100644 --- a/javadoc/deprecated-list.html +++ b/javadoc/deprecated-list.html @@ -2,9 +2,9 @@ - + Deprecated List - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/SessionFilter.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/SessionFilter.html index af64b10..0d25f52 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/SessionFilter.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/SessionFilter.html @@ -2,9 +2,9 @@ - + SessionFilter - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/class-use/SessionFilter.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/class-use/SessionFilter.html index ba48f7d..1f9410a 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/class-use/SessionFilter.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/class-use/SessionFilter.html @@ -2,9 +2,9 @@ - + Uses of Class edu.harvard.hms.dbmi.bd2k.irct.cl.filter.SessionFilter - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-frame.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-frame.html index 27e2a18..03f3086 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-frame.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-frame.html @@ -2,9 +2,9 @@ - + edu.harvard.hms.dbmi.bd2k.irct.cl.filter - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-summary.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-summary.html index 4b2daeb..5ce6269 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-summary.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-summary.html @@ -2,9 +2,9 @@ - + edu.harvard.hms.dbmi.bd2k.irct.cl.filter - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-tree.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-tree.html index 48a4c80..2fa4095 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-tree.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-tree.html @@ -2,9 +2,9 @@ - + edu.harvard.hms.dbmi.bd2k.irct.cl.filter Class Hierarchy - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-use.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-use.html index be1319b..b2d2379 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-use.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/filter/package-use.html @@ -2,9 +2,9 @@ - + Uses of Package edu.harvard.hms.dbmi.bd2k.irct.cl.filter - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/JaxRsActivator.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/JaxRsActivator.html index 98ad4ff..91c5e98 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/JaxRsActivator.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/JaxRsActivator.html @@ -2,9 +2,9 @@ - + JaxRsActivator - + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ProcessRESTService.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ProcessRESTService.html deleted file mode 100644 index f120a02..0000000 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ProcessRESTService.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - -ProcessRESTService - - - - - - - - -
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edu.harvard.hms.dbmi.bd2k.irct.cl.rest
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Class ProcessRESTService

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    @Path(value="/processRESTService")
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-public class ProcessRESTService
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      Constructor and Description
      ProcessRESTService() 
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      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      javax.json.JsonStructureaddProcess(javax.ws.rs.core.UriInfo info) 
      javax.json.JsonStructurecancelProcess() 
      javax.json.JsonStructurerunProcess() 
      javax.json.JsonStructurestartProcess() 
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        -equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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        startProcess

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        @GET
- @Path(value="/startProcess")
- @Produces(value="application/json")
-public javax.json.JsonStructure startProcess()
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        addProcess

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        @GET
- @Path(value="/updateProcess")
- @Produces(value="application/json")
-public javax.json.JsonStructure addProcess(@Context
-                                                                                                                    javax.ws.rs.core.UriInfo info)
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edu.harvard.hms.dbmi.bd2k.irct.cl.rest
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Class QueryRESTService

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-public class QueryRESTService
-extends java.lang.Object
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    Creates the query service for the JAX-RS REST service. This service is - conversation scoped all requests for working with a query must include the - conversation id that represents the query. An end user may have multiple - queries going along the same time.
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    Jeremy R. Easton-Marks
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      Modifier and TypeMethod and Description
      javax.json.JsonStructurecancelQuery() -
      Cancels the given query
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      javax.json.JsonStructuredeleteClause(java.lang.Long clauseId) -
      Deletes a given clause
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      javax.json.JsonStructurejoinClause(javax.ws.rs.core.UriInfo info) -
      Adds a join clause to the query
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      javax.json.JsonStructurerunQuery() -
      Runs the query created by the rest service
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      javax.json.JsonStructureselectClause(java.lang.String sq, - java.lang.String field, - java.lang.String alias) -
      Adds a select clause to the query
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      javax.json.JsonStructurestartQuery() -
      Initiates the creation of a query
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      javax.json.JsonStructurestartSubQuery(java.lang.String resource) -
      Initiates the creation of a subQuery.
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      javax.json.JsonStructurewhereClause(javax.ws.rs.core.UriInfo info) -
      Adds or edits a where clause
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        startQuery

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- @Path(value="/startQuery")
- @Produces(value="application/json")
-public javax.json.JsonStructure startQuery()
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        Initiates the creation of a query
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        startSubQuery

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- @Path(value="/startSubQuery")
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-public javax.json.JsonStructure startSubQuery(@DefaultValue(value="") @QueryParam(value="resource")
-                                                                                                                       java.lang.String resource)
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        Initiates the creation of a subQuery. Each query can have one or more - subQueries. These can be used to combine datasets from multiple - resources. Each subQuery can be associated with one or more resources.
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        @GET
- @Path(value="/selectClause")
- @Produces(value="application/json")
-public javax.json.JsonStructure selectClause(@DefaultValue(value="") @QueryParam(value="sq")
-                                                                                                                     java.lang.String sq,
-                                                                                                                     @DefaultValue(value="") @QueryParam(value="field")
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        Adds a select clause to the query
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        sq - Query ID
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        field - Parameter name
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- @Path(value="/joinClause")
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-public javax.json.JsonStructure joinClause(@Context
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        Adds a join clause to the query
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        info - Request Information
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        whereClause

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        @GET
- @POST
- @Path(value="/whereClause")
- @Produces(value="application/json")
-public javax.json.JsonStructure whereClause(@Context
-                                                                                                                          javax.ws.rs.core.UriInfo info)
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        Adds or edits a where clause
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        info - Information about that request
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        A JSON Object representing the status of that request
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        deleteClause

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        @GET
- @Path(value="/deleteClause")
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-public javax.json.JsonStructure deleteClause(@QueryParam(value="clauseId")
-                                                                                                                     java.lang.Long clauseId)
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        Deletes a given clause
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        clauseId - Clause ID
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        A JSON Object representing the status of that request
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        runQuery

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- @Path(value="/runQuery")
- @Produces(value="application/json")
-public javax.json.JsonStructure runQuery()
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        Runs the query created by the rest service
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        A JSON Object representing the status of that request
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        cancelQuery

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- @Path(value="/cancelQuery")
- @Produces(value="application/json")
-public javax.json.JsonStructure cancelQuery()
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        Cancels the given query
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        A JSON Object representing the status of that request
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- - - diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/QueryService.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/QueryService.html index 7bb30ea..b1a3ef9 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/QueryService.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/QueryService.html @@ -2,9 +2,9 @@ - + QueryService - + @@ -18,7 +18,7 @@ catch(err) { } //--> -var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10}; +var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10}; var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]}; var altColor = "altColor"; var rowColor = "rowColor"; @@ -200,6 +200,12 @@

Method Summary

javax.ws.rs.core.Response +saveQuery(java.lang.String payload) +
Saves a query
+ + + +javax.ws.rs.core.Response startQuery()
Starts the creation of a query
@@ -339,6 +345,25 @@

clause

+ + + + diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceRESTService.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceRESTService.html deleted file mode 100644 index aa05834..0000000 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceRESTService.html +++ /dev/null @@ -1,371 +0,0 @@ - - - - - -ResourceRESTService - - - - - - - - -
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edu.harvard.hms.dbmi.bd2k.irct.cl.rest
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Class ResourceRESTService

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    @Path(value="/resourceService")
- @RequestScoped
-public class ResourceRESTService
-extends java.lang.Object
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    Creates the resource service for the JAX-RS REST service
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    Author:
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    Jeremy R. Easton-Marks
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      Method Summary

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      All Methods Instance Methods Concrete Methods 
      Modifier and TypeMethod and Description
      javax.json.JsonStructuregetPath(java.lang.String resourceName, - java.lang.String path, - java.lang.String relationship) -
      Returns a JSON Array of Paths from a given resource, path, and - relationship.
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      javax.json.JsonStructurelistProcessResource() -
      Returns a list of the process resources as a JSON Array
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      javax.json.JsonStructurelistQueryResource() -
      Returns a list of the query resources as a JSON Array
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      javax.json.JsonStructurelistResource() -
      Returns a list of resources as a JSON Array
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        Methods inherited from class java.lang.Object

        -equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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      Constructor Detail

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        ResourceRESTService

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        public ResourceRESTService()
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      Method Detail

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        listResource

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        @GET
- @Path(value="/resources")
- @Produces(value="application/json")
-public javax.json.JsonStructure listResource()
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        Returns a list of resources as a JSON Array
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        Returns:
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        Resources JSON Array
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        listQueryResource

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        @GET
- @Path(value="/queryResources")
- @Produces(value="application/json")
-public javax.json.JsonStructure listQueryResource()
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        Returns a list of the query resources as a JSON Array
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        Returns:
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        Query Resources JSON Array
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        listProcessResource

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        @GET
- @Path(value="/processResources")
- @Produces(value="application/json")
-public javax.json.JsonStructure listProcessResource()
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        Returns a list of the process resources as a JSON Array
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        Returns:
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        Process Resources JSON Array
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        getPath

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        @GET
- @Path(value="/path/{resource}{path:.*}")
- @Produces(value="application/json")
-public javax.json.JsonStructure getPath(@PathParam(value="resource")
-                                                                                                                            java.lang.String resourceName,
-                                                                                                                            @PathParam(value="path")
-                                                                                                                            java.lang.String path,
-                                                                                                                            @DefaultValue(value="CHILD") @QueryParam(value="relationship")
-                                                                                                                            java.lang.String relationship)
        -
        Returns a JSON Array of Paths from a given resource, path, and - relationship. The default relationship type is CHILD. If the path is - empty then it returns the path root of the resource.
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        Parameters:
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        resourceName - Name of Resource
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        path - Initial Path
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        relationship - Relationship Type
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        Returns:
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        JSON Array of Paths
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- - - diff --git a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceService.html b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceService.html index 16dfb36..566936c 100644 --- a/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceService.html +++ b/javadoc/edu/harvard/hms/dbmi/bd2k/irct/cl/rest/ResourceService.html @@ -2,9 +2,9 @@ - + ResourceService - + @@ -18,7 +18,7 @@ catch(err) { } //--> -var methods = {"i0":10,"i1":10,"i2":10,"i3":10}; +var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10}; var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]}; var altColor = "altColor"; var rowColor = "rowColor"; @@ -161,21 +161,23 @@

Method Summary

javax.ws.rs.core.Response -path(java.lang.String path, - java.lang.String relationshipString, - java.lang.String searchTerm, - java.lang.String ontologyType, - java.lang.String ontologyTerm) +find(java.lang.String path, + javax.ws.rs.core.UriInfo info)  + + +javax.ws.rs.core.Response +path(java.lang.String path, + java.lang.String relationshipString)
Returns a list of entities.
- + javax.ws.rs.core.Response resources(java.lang.String type)
Returns a list of all resources.
- + javax.ws.rs.core.Response search(javax.ws.rs.core.UriInfo info)
Searches the resources for ones that match a category
@@ -279,7 +281,22 @@

search

- + + + + +