Recent changes to Generating_cluster_lists

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Fri, 07 Jun 2013 12:40:37 -0000

--- v9
+++ v10
@@ -32,7 +32,7 @@

 ~~~~~~~~~~
 :::jsp
-set var="tpb" value="${ontBean.thirdPartyBean}.  This thirdPartyBean has
+set var="tpb" value="${ontBean.thirdPartyBean}.
 ~~~~~~~~~~~

 ### Content of table by column:

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Fri, 07 Jun 2013 12:39:43 -0000

--- v8
+++ v9
@@ -54,7 +54,7 @@

 ~~~~~~~~~~
 :::jsp
- ( ${  }
+ ( ${tpb.sourceName}
 ~~~~~~~~~~

 __Column 3__:  Hyperlinked exemplar thumb + tooltip is generated with 
@@ -75,5 +75,5 @@

 This runs the OWL query:
 ~~~~~~~~~~~
- 'member_of' some ('has_exemplar' value )
+ 'member_of' some ('has_exemplar' value )
 ~~~~~~~~~~~~~

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Fri, 07 Jun 2013 12:37:02 -0000

--- v7
+++ v8
@@ -50,7 +50,7 @@
 _Note the hardwiring of paths in here._

 __Column 2__ Exemplar name and source name + link
-Exemplar name is specified by \$\{ontBean.name\}.  The source name and link are generated with:
+Exemplar name is specified by $\{ontBean.name\}.  The source name and link are generated with:

 ~~~~~~~~~~
 :::jsp

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Fri, 07 Jun 2013 12:36:26 -0000

--- v6
+++ v7
@@ -37,25 +37,17 @@

 ### Content of table by column:

-__Column 1__ (cluster) thumb and hyperlink are specified as 
+__Column 1__ (cluster) thumb and hyperlink are specified as:

 ~~~~~~~~~~
 :::jsp
-http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/${ontBean.name}/thumb_0.333.png
-http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/${ontBean.name}
+http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/$version/<${ontBean.name}>/
+http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/$version/<${ontBean.name}>/thumb_0.333.png
 ~~~~~~~~~~

+_Where $version is the current clustering version number being used on the site.
+
 _Note the hardwiring of paths in here._
-
-_With the move to new clustering, these paths will need to be changed to:
-
-~~~~~~~~~~
-:::jsp
-http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/<$version>/<${ontBean.name}>/
-http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/<$version>/<${ontBean.name}>/thumb_0.333.png
-~~~~~~~~~~
-
-_Where \$version is the current clustering version number being used on the site.  For the next release, this will be '3'_

 __Column 2__ Exemplar name and source name + link
 Exemplar name is specified by \$\{ontBean.name\}.  The source name and link are generated with:

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 13:06:53 -0000

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 13:05:57 -0000

--- v4
+++ v5
@@ -17,15 +17,23 @@
 ('exemplar_of' some 'cluster') and ('neuron' that 'overlaps' some X))
 ~~~~~~~~~~

-The IDs returned by this are used to generate a list of OntBeanIndividuals.  The jsp page then iterates over these.
+The IDs returned by this are used to generate a list of OntBeanIndividuals.
+
+__Iteration__
+
+The JSP page iterates over the list of beans provided:

 ~~~~~~~~~~
 :::jsp
 
 ~~~~~~~~~~

-During each iteration, the ontBean is used to roll thirdPartyBean bean, using:
-set var="tpb" value="${ontBean.thirdPartyBean}.  This thirdPartyBean has paths etc from the VFB DB
+__During each iteration__: the ontBean is used to roll a related thirdPartyBean bean with paths etc from  paths etc from the VFB DB:
+
+~~~~~~~~~~
+:::jsp
+set var="tpb" value="${ontBean.thirdPartyBean}.  This thirdPartyBean has
+~~~~~~~~~~~

 ### Content of table by column:

@@ -37,9 +45,9 @@
 http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/${ontBean.name}
 ~~~~~~~~~~

-__Note the hardwiring of paths in here.__
+_Note the hardwiring of paths in here._

-_With the move to new clustering, these paths will need to be changed to_
+_With the move to new clustering, these paths will need to be changed to:

 ~~~~~~~~~~
 :::jsp
@@ -49,17 +57,24 @@

 _Where \$version is the current clustering version number being used on the site.  For the next release, this will be '3'_

+__Column 2__ Exemplar name and source name + link
+Exemplar name is specified by \$\{ontBean.name\}.  The source name and link are generated with:
+
 ~~~~~~~~~~
 :::jsp
-Column 2 (Exemplar name) is specified by ${ontBean.name}.  The source name and link are generated with: ${ }
+ ( ${  }
 ~~~~~~~~~~

-Column 3 Hyperlinked exemplar thumb + tooltip is generated with 
+__Column 3__:  Hyperlinked exemplar thumb + tooltip is generated with 
+
 ~~~~~~~~~~~
 :::jsp
-\\
+
+
+
 ~~~~~~~~~~
-Column 4 
+
+__Column 4__ 

 ~~~~~~~~~~~
 :::jsp

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 13:01:24 -0000

--- v3
+++ v4
@@ -2,11 +2,9 @@

 __Example page:__ http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401 

-__Generated by__ [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)
+__Generated by:__ [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)

-__Triggering query__
-
-It is triggered by this URL in [termMenuNeuropil.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/includes/bits/termMenuNeuropil.jsp)
+__Triggering query:__ From [termMenuNeuropil.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/includes/bits/termMenuNeuropil.jsp)

 ~~~~~~~~~~
 :::jsp

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 12:59:35 -0000

--- v2
+++ v3
@@ -1,11 +1,10 @@
 # Generating cluster lists

-## Example page
+__Example page:__ http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401 

-http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401 
+__Generated by__ [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)

-Generated by [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)
-
+__Triggering query__

 It is triggered by this URL in [termMenuNeuropil.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/includes/bits/termMenuNeuropil.jsp)

Generating_cluster_lists modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 12:58:31 -0000

--- v1
+++ v2
@@ -1,9 +1,13 @@
-# [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)
+# Generating cluster lists

-Generates cluster list pages like this:
+## Example page
+
 http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401 

-It is triggered by this URL in termMenuNeuropil.jsp:
+Generated by [clusterList.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/do/clusterList.jsp)
+
+
+It is triggered by this URL in [termMenuNeuropil.jsp](https://sourceforge.net/p/virtualflybrain/code/HEAD/tree/eAtlasViewer/trunk/eAtlasViewer/WebContent/jsp/includes/bits/termMenuNeuropil.jsp)

 ~~~~~~~~~~
 :::jsp

clusterList.jsp modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 11:43:26 -0000

clusterList.jsp

Generates cluster list pages like this:
http://www.virtualflybrain.org/do/cluster_list.html?action=cluster_found&id=FBbt:00007401

It is triggered by this URL in termMenuNeuropil.jsp:

/do/cluster_list.html?action=cluster_found&id=${param.fbbtId}

This passes the ID of the neuropil being displayed to a DL query, cluster_found, that lives in WebQueryUtils.java and has the form:

('exemplar_of' some 'cluster') and ('neuron' that 'overlaps' some X))

The IDs returned by this are used to generate a list of OntBeanIndividuals. The jsp page then iterates over these.

<c:forEach items="${ontBeanList}" var="ontBean" varStatus="status">

During each iteration, the ontBean is used to roll thirdPartyBean bean, using:
set var="tpb" value="${ontBean.thirdPartyBean}. This thirdPartyBean has paths etc from the VFB DB

Content of table by column:

Column 1 (cluster) thumb and hyperlink are specified as

http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/${ontBean.name}/thumb_0.333.png
http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/${ontBean.name}

Note the hardwiring of paths in here.

With the move to new clustering, these paths will need to be changed to

http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/<$version>/<${ontBean.name}>/
http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusterv/<$version>/<${ontBean.name}>/thumb_0.333.png

Where \$version is the current clustering version number being used on the site. For the next release, this will be '3'

Column 2 (Exemplar name) is specified by ${ontBean.name}.  The source name and link are generated with: <a href="${tpb.baseUrl}${tpb.remoteId}">${  }</a>

Column 3 Hyperlinked exemplar thumb + tooltip is generated with
:::jsp
\<a href="${tpb.baseUrl}${tpb.remoteId}"title="View ${tpb.sourceName} entry">\<img src="${tpb.thumbUrl}" height="100" />
Column 4

/do/individual_list.html?action=neuron_found&id=${tpb.fbId}&region=${ontBean.name}

This runs the OWL query:
'member_of' some ('has_exemplar' value )