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" %>
 
 
 <%@ 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>
 
     <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
                     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>
 
                 </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" %>
 
 
 <%@ 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>
 
     <c:param name="title">Documentation</c:param>
 </c:import>
 

@@ -152,4 +152,4 @@ MTADGPRELLQLRAAV</pre>
     </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_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" %>
 
 
 <%@ 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>
 
   <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>
 
   </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" %>
 
 
 <%@ 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>
 
        <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
 }
 </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>
                                </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>
 
        </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" %>
 
 
 <%@ 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>
 
     <c:param name="title">Documentation</c:param>
 </c:import>
 

@@ -157,4 +157,4 @@
     </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_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" %>
 
 
 <%@ 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>
 
        <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">
                                <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>
                                <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>
 
        </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" %>
 
 
 <%@ 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>
 
        <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>
                                        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>
 
                                                 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>
                                        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>
                                                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
                                                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>
 
        </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" %>
 
 
 <%@ 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>
 
     <c:param name="title">Documentation</c:param>
 </c:import>
 

@@ -492,4 +492,4 @@ Service ProbconsWS IS NOT FUNCTIONAL</code></pre>
     </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_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" %>
 
 
 <%@ 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>
 
     <c:param name="title">Documentation</c:param>
 </c:import>
 

@@ -66,7 +66,7 @@
                         application server</a> section for further details.
                 </p>
 
                         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">
                         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>
                     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
                         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>
                     <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>
                 <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">
             </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
                          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>
 
     </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/static/img/folder-small.png b/website/static/img/folder-small.png
new file mode 100644 (file)
index 0000000..1933f17
Binary files /dev/null and b/website/static/img/folder-small.png differ