JWS-116 Moved the boostrap’ed manual pages to a temporary dir. The documentation...

diff --git a/website/man_about.jsp b/website/man_pages_old/man_about.jsp
similarity index 99%
rename from website/man_about.jsp
rename to website/man_pages_old/man_about.jsp
index 62edca5..8f246cc 100644 (file)
--- a/website/man_about.jsp
+++ b/website/man_pages_old/man_about.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
     <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -296,11 +296,11 @@
                     is the Java tool for creating web service bindings. In addition, this offers some
                     additional methods that simplify
                     working with JABAWS. For more information please refer to the
-                    <a href="dm_javadoc/index.html">data model javadoc</a>.
+                    <a href="../dm_javadoc/index.html">data model javadoc</a>.
                 </p>
             </div>
         </div>
     </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_client.jsp b/website/man_pages_old/man_client.jsp
similarity index 98%
rename from website/man_client.jsp
rename to website/man_pages_old/man_client.jsp
index 69a71e8..ff334c9 100644 (file)
--- a/website/man_client.jsp
+++ b/website/man_pages_old/man_client.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
     <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -152,4 +152,4 @@ MTADGPRELLQLRAAV</pre>
     </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_configuration.jsp b/website/man_pages_old/man_configuration.jsp
similarity index 99%
rename from website/man_configuration.jsp
rename to website/man_pages_old/man_configuration.jsp
index 9d8680f..e3c2abd 100644 (file)
--- a/website/man_configuration.jsp
+++ b/website/man_pages_old/man_configuration.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
   <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -657,4 +657,4 @@ mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000
   </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_dev.jsp b/website/man_pages_old/man_dev.jsp
similarity index 99%
rename from website/man_dev.jsp
rename to website/man_pages_old/man_dev.jsp
index 217b850..58c84d5 100644 (file)
--- a/website/man_dev.jsp
+++ b/website/man_pages_old/man_dev.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
        <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -527,7 +527,7 @@ public static void main(String[] args) throws UnsupportedRuntimeException,
 }
 </code></pre>
                                <p>For a more detailed description of all available types and their functions please
-                                       refer to the <a href="dm_javadoc/index.html">Data Model JavaDoc</a>.
+                                       refer to the <a href="../dm_javadoc/index.html">Data Model JavaDoc</a>.
                                </p>
                                <p class="text-right">
                                        <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
@@ -558,4 +558,4 @@ public static void main(String[] args) throws UnsupportedRuntimeException,
        </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_docs.jsp b/website/man_pages_old/man_docs.jsp
similarity index 99%
rename from website/man_docs.jsp
rename to website/man_pages_old/man_docs.jsp
index a571f5e..93a879e 100644 (file)
--- a/website/man_docs.jsp
+++ b/website/man_pages_old/man_docs.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
     <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -157,4 +157,4 @@
     </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_server_dev.jsp b/website/man_pages_old/man_server_dev.jsp
similarity index 98%
rename from website/man_server_dev.jsp
rename to website/man_pages_old/man_server_dev.jsp
index eea2e0c..9d7b776 100644 (file)
--- a/website/man_server_dev.jsp
+++ b/website/man_pages_old/man_server_dev.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
        <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -123,8 +123,8 @@
                                <h1 class="panel-title">The code structure</h1>
                        </div>
                        <div class="panel-body">
-                               <img src="static/img/ws-structure.png" alt="JABAWS Code Structure"
-                                        width="260" height="300" align="left" style="padding-right: 2em;" />
+                               <img src="../static/img/ws-structure.png" alt="JABAWS Code Structure"
+                     width="260" height="300" align="left" style="padding-right: 2em;" />
                                <ul>
                                        <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> datamodel</span> contains the JABAWS datamodel </li>
                                        <li><span class="directory"><i class="fa fa-folder-o" aria-hidden="true"></i> engine</span> contains the JABAWS engine - the code that abstract the execution environment and executes native binaries</li>
@@ -428,4 +428,4 @@
        </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_servervm.jsp b/website/man_pages_old/man_servervm.jsp
similarity index 97%
rename from website/man_servervm.jsp
rename to website/man_pages_old/man_servervm.jsp
index bf5c439..f895a21 100644 (file)
--- a/website/man_servervm.jsp
+++ b/website/man_pages_old/man_servervm.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
        <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -169,7 +169,7 @@
                                        The VMware Player screen shot below displays JABAWS VM CPU settings.
                                </p>
                                <p>
-                                       <img src="static/img/VMware_cpu.png" alt="vmware cpu settings" width="708"
+                                       <img src="../static/img/VMware_cpu.png" alt="vmware cpu settings" width="708"
                                                 height="267" style="border: solid black 1px" />
                                </p>
 
@@ -229,12 +229,12 @@
                                        New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview
                                        <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.
                                </p>
-                               <p><img src="static/img/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734"
+                               <p><img src="../static/img/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734"
                                                height="461" /></p>
                                <p class="justify">If you click on Advanced Menu, you will see the configuration console,
                                        similar to the one below.
                                </p>
-                               <p><img src="static/img/VMware_booted.png" alt="JABAWS welcome screen" width="735"
+                               <p><img src="../static/img/VMware_booted.png" alt="JABAWS welcome screen" width="735"
                                                height="461" /></p>
                                <p class="justify">
                                        If you need to configure a static IP address the configuration console will
@@ -268,4 +268,4 @@
        </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_serverwar.jsp b/website/man_pages_old/man_serverwar.jsp
similarity index 99%
rename from website/man_serverwar.jsp
rename to website/man_pages_old/man_serverwar.jsp
index 54d943a..be77d97 100644 (file)
--- a/website/man_serverwar.jsp
+++ b/website/man_pages_old/man_serverwar.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
     <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -492,4 +492,4 @@ Service ProbconsWS IS NOT FUNCTIONAL</code></pre>
     </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
\ No newline at end of file
+<jsp:include page="../template_footer.jsp" />
\ No newline at end of file

diff --git a/website/man_stats.jsp b/website/man_pages_old/man_stats.jsp
similarity index 97%
rename from website/man_stats.jsp
rename to website/man_pages_old/man_stats.jsp
index 2ecab15..d162d45 100644 (file)
--- a/website/man_stats.jsp
+++ b/website/man_pages_old/man_stats.jsp
@@ -7,7 +7,7 @@
 <%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
 
 
-<c:import url="template_header.jsp" >
+<c:import url="../template_header.jsp" >
     <c:param name="title">Documentation</c:param>
 </c:import>
 
@@ -66,7 +66,7 @@
                         application server</a> section for further details.
                 </p>
 
-                <p><img src="static/img/usage_statistics_main.gif" alt="JABAWS usage statistics"
+                <p><img src="../static/img/usage_statistics_main.gif" alt="JABAWS usage statistics"
                         width="608" height="318" />
                 </p>
                 <p class="justify">
@@ -125,7 +125,7 @@
                     Detailed execution statistics for each month is available for
                     authenticated users only.
                 </p>
-                <p><img src="static/img/usage_statistics_month.gif" alt="JABAWS one month usage statistics"
+                <p><img src="../static/img/usage_statistics_month.gif" alt="JABAWS one month usage statistics"
                         width="670" height="902" />
                 </p>
                 <p>Each table contains the number of jobs processed by JABAWS during the period of
@@ -163,7 +163,7 @@
                     <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section
                     for further details.
                 </p>
-                <p><img src="static/img/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>
+                <p><img src="../static/img/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>
                 <p>Columns: </p>
                 <ul>
                     <li>JobID - the JABAWS job id, unique for every job</li>
@@ -195,7 +195,7 @@
             </div>
             <div class="panel-body">
                 <p class="justify">
-                    <img src="static/img/usage_statistics_job_details.gif" alt="JABAWS- job details"
+                    <img src="../static/img/usage_statistics_job_details.gif" alt="JABAWS- job details"
                          width="600" height="340" /></p>
                 <p>
                     STARTED and FINISHED files contain Unix timestamp - when the job was started and
@@ -327,4 +327,4 @@ local.stat.maxruntime=6</code></pre>
     </div>
 </div>
 
-<jsp:include page="template_footer.jsp" />
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+<jsp:include page="../template_footer.jsp" />
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diff --git a/website/static/img/folder-small.png b/website/static/img/folder-small.png
new file mode 100644 (file)
index 0000000..1933f17
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