cmbi · mhekkel · Oct 2, 2019 · Oct 2, 2019 · Oct 4, 2019 · Oct 4, 2019
diff --git a/.gitignore b/.gitignore
@@ -40,3 +40,9 @@ obj/
 obj.dbg/
 test/
 unit_test_*
+log/mrs.log
+.gdb_history
+.vscode/c_cpp_properties.json
+.vscode/launch.json
+.vscode/settings.json
+.vscode/tasks.json
diff --git a/GNUmakefile b/GNUmakefile
@@ -23,32 +23,33 @@ MRS_BASE_URL		?= http://chelonium.cmbi.umcn.nl:$(MRS_PORT)/
 MRS_USER			?= $(shell whoami)
 
 PERL				?= $(shell which perl)
+PERL				:= LANG=C $(PERL)
 
 DEFINES				+= MRS_ETC_DIR='"$(MRS_ETC_DIR)"' \
 					   MRS_USER='"$(MRS_USER)"' \
 						MRS_CURRENT_VERSION='"$(VERSION)"'
 
 BOOST_LIBS			= system thread filesystem regex math_c99 math_c99f program_options date_time iostreams timer random chrono
 BOOST_LIBS			:= $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX))
-LIBS				= m pthread rt z bz2 zeep
+LIBS				= m pthread rt z bz2 zeep $(BOOST_LIBS)
 
 CXX					?= c++
 
-CXXFLAGS			+= -std=c++11
+CXXFLAGS			+= -std=c++14
 CFLAGS				+= $(INCLUDE_DIR:%=-I%) -I. -pthread
 CFLAGS				+= -Wno-deprecated -Wno-multichar
 CFLAGS				+= $(shell $(PERL) -MExtUtils::Embed -e perl_inc)
 CFLAGS				+= $(DEFINES:%=-D%)
 
-LDFLAGS				+= $(LIBRARY_DIR:%=-L %) $(LIBS:%=-l%) $(BOOST_LIBS:%=-l%) -g
+LDFLAGS				+= $(LIBRARY_DIR:%=-L %) $(LIBS:%=-l%) -g
 LDFLAGS				+= $(shell $(PERL) -MExtUtils::Embed -e ldopts)
 
 OBJDIR				= obj
 
 ifneq ($(DEBUG),1)
 CFLAGS				+= -O3 -DNDEBUG -g
 else
-CFLAGS				+= -g -DDEBUG 
+CFLAGS				+= -g
 OBJDIR				:= $(OBJDIR).dbg
 endif
 
@@ -151,7 +152,7 @@ $(OBJDIR)/M6Config.o: make.config
 unicode/M6UnicodeTables.h src/../unicode/M6UnicodeTables.h:
 	cd unicode; $(PERL) unicode-table-creator.pl > $(@F)
 
-include $(OBJECTS:%.o=%.d)
+-include $(OBJECTS:%.o=%.d)
 
 $(OBJECTS:.o=.d):
 

diff --git a/configure b/configure
@@ -323,6 +323,7 @@ END
 	push @libs, "boost_thread";
 	push @libs, "boost_filesystem";
 	push @libs, "boost_math_c99";
+	push @libs, "boost_random";
 	push @libs, "rt";
 
 	if (not CheckLib("zeep", $header_check, $lib_check))
@@ -380,13 +381,15 @@ END
 	$cxxflags =~ s/\s+/ /g;
 
 	$header_check =<<END;
+#define PERL_NO_INLINE_FUNCTIONS	1
 #include "EXTERN.h"
 #include "XSUB.h"
 #include <iostream>
 int main() { std::cout << 1 << '\t' << 0; return 0; }
 END
 
 	$lib_check =<<END;
+#define PERL_NO_INLINE_FUNCTIONS	1
 #include "EXTERN.h"
 #include "perl.h"
 #include "XSUB.h"

diff --git a/docroot/admin.html b/docroot/admin.html
@@ -1,5 +1,6 @@
 <html xmlns="http://www.w3.org/1999/xhtml"
 	xmlns:mrs="https://mrs.cmbi.ru.nl/mrs-web/ml"
+	xmlns:z2="http://www.hekkelman.com/libzeep/m2"
 	xml:lang="en" lang="en">
 <head>
     <title>MRS Administration</title>
@@ -22,17 +23,17 @@
 
 </head>
 <body>
-	<mrs:include file="header.html" />
+	<div z2:replace="header :: #header" />
 	<div id="main">
 		<div class="nav">
 			<ul>
-				<li><a href="#" id="global">Main</a></li>
-				<li><a href="#" id="server">Server</a></li>
-				<li><a href="#" id="parsers">Parsers</a></li>
-				<li><a href="#" id="formats">Formats</a></li>
-				<li><a href="#" id="databanks">Databanks</a></li>
-				<li><a href="#" id="scheduler">Scheduler</a></li>
-				<li><a href="#" id="blast">Blast Queue</a></li>
+				<li><a href="#" data-id="global">Main</a></li>
+				<li><a href="#" data-id="server">Server</a></li>
+				<li><a href="#" data-id="parsers">Parsers</a></li>
+				<li><a href="#" data-id="formats">Formats</a></li>
+				<li><a href="#" data-id="databanks">Databanks</a></li>
+				<li><a href="#" data-id="scheduler">Scheduler</a></li>
+				<li><a href="#" data-id="blast">Blast Queue</a></li>
 			</ul>
 		</div>
 
@@ -99,7 +100,7 @@ <h3>Web Service Locations</h3>
 						<table cellspacing="0" cellpadding="0" class="select_form">
 							<caption>Parsers</caption>
 							<mrs:iterate collection="parsers" var="parser">
-								<tr><td>${parser.id}</td></tr>
+								<tr data-target="parser-${parser.id}"><td>${parser.id}</td></tr>
 							</mrs:iterate>
 						</table>
 					</div>
@@ -113,7 +114,7 @@ <h3>Web Service Locations</h3>
 
 				<div class="admin-right">
 					<mrs:iterate collection="parsers" var="parser">
-					<form id="${parser.id}" class="admin_form" method="post" style="display:none">
+					<form data-id="${parser.id}" class="admin_form" method="post" style="display:none">
 						<input type='hidden' name='submit' value='parsers'/>
 						<fieldset>
 							<h3>Parser configuration</h3>
@@ -138,7 +139,7 @@ <h3>Parser configuration</h3>
 						<table cellspacing="0" cellpadding="0" class="select_form">
 							<caption>Formats</caption>
 							<mrs:iterate collection="formats" var="format">
-								<tr><td>${format.id}</td></tr>
+								<tr data-target="format-${format.id}"><td>${format.id}</td></tr>
 							</mrs:iterate>
 						</table>
 					</div>
@@ -152,13 +153,13 @@ <h3>Parser configuration</h3>
 
 				<div class="admin-right">
 				<mrs:iterate collection="formats" var="format">
-					<form id="${format.id}" class="admin_form" method="POST" style="display:none">
+					<form data-id="format-${format.id}" class="admin_form" method="POST" style="display:none">
 						<fieldset>
 							<h3>Format specification</h3>
 							<input type='hidden' name='submit' value='formats'/>
 							<input type='hidden' name='original-id' value='${format.id}'/>
 
-							<div><label>ID</label><input type="text" name="id" value="${format.id}"/></div>
+							<div><label>ID</label><input type="text" name="format-id" value="${format.id}"/></div>
 
 							<h3>Document layout</h3>
 
@@ -173,7 +174,7 @@ <h3>Document layout</h3>
 							<h3>Links</h3>
 							<p>Create 'live' links in documents based on a regular expression. You can reference captures in the
 							regular expression using the variable names $1 for the first capture, $2 for the second, etc.</p>
-							<table cellspacing="0" cellpadding="0" style="${empty format.links ? 'display:none' : ''}">
+							<table id="format-link-table-${format.id}" cellspacing="0" cellpadding="0" style="${empty format.links ? 'display:none' : ''}">
 								<tr>
 									<th>Regular Expression</th>
 									<th>Target Databank</th>
@@ -201,8 +202,8 @@ <h3>Links</h3>
 									<td><div class="delete">Delete</div></td>
 								</tr>
 							</table>
-							<button onclick='Admin.addLinkToFormat("${format.id}"); return false;'>Add link</button>
-							
+							<button class="add-link" data-format="${format.id}">Add link</button>
+
 							<hr/>
 							<input type='submit' value='Submit'/><input type='reset' value='Reset'/>
 						</fieldset>
@@ -220,7 +221,7 @@ <h3>Links</h3>
 						<table cellspacing="0" cellpadding="0" class="select_form">
 							<caption>Databanks</caption>
 							<mrs:iterate collection="config-databanks" var="db">
-								<tr><td><mrs:if test="${db.enabled}">${db.id}</mrs:if><mrs:if test="${not db.enabled}"><em>${db.id}</em></mrs:if></td></tr>
+								<tr data-target="db-${db.id}"><td><mrs:if test="${db.enabled}">${db.id}</mrs:if><mrs:if test="${not db.enabled}"><em>${db.id}</em></mrs:if></td></tr>
 							</mrs:iterate>
 						</table>
 					</div>
@@ -234,7 +235,7 @@ <h3>Links</h3>
 
 				<div class="admin-right">
 				<mrs:iterate collection="config-databanks" var="db">
-					<form id="${db.id}" class="admin_form" method="POST" style="display:none">
+					<form data-id="db-${db.id}" class="admin_form" method="POST" style="display:none">
 						<fieldset>
 							<h3>Databank information</h3>
 							<input type='hidden' name='submit' value='databanks'/>
@@ -249,7 +250,7 @@ <h3>Databank information</h3>
 							the values found in e.g. db_xref records. The <em>name</em> is used in the blast databank popup menu.</p>
 
 							<div><label>Aliases</label><div class="aliases">
-								<table id="${db.id}-aliases" cellspacing="0" cellpadding="0"
+								<table data-id="${db.id}-aliases" cellspacing="0" cellpadding="0"
 												style="${empty db.aliases ? 'display:none;' : ''}">
 									<tr>
 										<th>ID</th>
@@ -269,7 +270,7 @@ <h3>Databank information</h3>
 										<td><div class="delete">Delete</div></td>
 									</tr>
 								</table>
-								<span class="clickable" onclick='Admin.addAliasToDb("${db.id}"); return false;'>Add alias</span>
+								<span class="clickable add-alias" data-db="${db.id}">Add alias</span>
 							</div>
 							</div>
 
@@ -304,7 +305,7 @@ <h3>Data processing</h3>
 							<p>Formatting can be done with one of the defined formatters, or for XML databanks, with
 							an XML Stylesheet.</p>
 
-							<div><label>Formatter</label><select name="format" onchange="Admin.changeFormat('${db.id}');">
+							<div><label>Formatter</label><select name="format" data-db="${db.id}">
 									<option value="none">No format</option>
 									<mrs:option value="xml" selected="${db.format}">XML Stylesheet</mrs:option>
 									<mrs:options collection="formats" value="id" label="id" selected="${db.format}"/>

diff --git a/docroot/align.html b/docroot/align.html
@@ -1,5 +1,6 @@
 <html xmlns="http://www.w3.org/1999/xhtml"
 	xmlns:mrs="https://mrs.cmbi.ru.nl/mrs-web/ml"
+	xmlns:z2="http://www.hekkelman.com/libzeep/m2"
 	xml:lang="en" lang="en">
 <head>
     <title>M6</title>
@@ -20,7 +21,7 @@
 	</script>
 </head>
 <body>
-	<mrs:include file="header.html" />
+	<div z2:replace="header :: #header" />
 
 	<div id="main">
 		<form id="alignForm" method="POST" action="#" onsubmit="submitAlignJob(); return false;" class="align_form">

diff --git a/docroot/blast.html b/docroot/blast.html
@@ -1,5 +1,6 @@
 <html xmlns="http://www.w3.org/1999/xhtml"
 	xmlns:mrs="https://mrs.cmbi.ru.nl/mrs-web/ml"
+	xmlns:z2="http://www.hekkelman.com/libzeep/m2"
 	xml:lang="en" lang="en">
 <head>
     <title>M6</title>
@@ -25,7 +26,7 @@
 
 </head>
 <body>
-	<mrs:include file="header.html" />
+	<div z2:replace="header :: #header" />
 
 	<div id="main">
 		<div style="margin-bottom: 1em;">
@@ -39,14 +40,14 @@
 					<textarea name="query" rows="5" cols="72">${query}</textarea>
 <!--					<li>Or enter filename: <input type="file" name="queryFile" size="50" maxlength="80" /></li>-->
 					<div>
-						<label>Databank to search</label><select name="db" style="width:10em;">
+						<label for="db">Databank to search</label><select id="db" name="db" style="width:10em;">
 							<mrs:options collection="blastdatabanks" value="id" label="name" selected="${blastdb}" />
 						</select>
 					</div>
 
 					<div id="options">
-<!--						<div><h3>Options</h3></div>-->
-						<div><label>Filter low complexity</label><mrs:checkbox name="filter" checked="${filter}" /></div>
+						<div><label for="filter">Filter low complexity</label><input type="checkbox" id="filter" z2:checked="${filter}" name="filter" />
+						</div>
 						<div><label>E-value cutoff</label><select name="expect"><mrs:options collection="expectRange" selected="${expect}" /></select></div>
 					</div>
 
@@ -60,7 +61,8 @@
 						<div><label>Scoring matrix</label><select name="matrix" onchange="updateGapValues();">
 							<mrs:options collection="matrices" selected="${matrix}" /></select>
 						</div>
-						<div><label>Perform gapped alignment</label><mrs:checkbox name="gapped" checked="${gapped}" onchange="gappedChanged();" /></div>
+						<div><label for="gapped">Perform gapped alignment</label>
+								<input id="gapped" type="checkbox" name="gapped" z2:checked="${gapped}" onchange="gappedChanged();" /></div>
 						<div><label>Cost to open a gap</label><select name="gapOpen" onchange="gapOpenChanged();">
 							<option value="-1">Default</option>
 							<mrs:options collection="gapOpenRange" selected="${gapOpen}" /></select>

diff --git a/docroot/browse.html b/docroot/browse.html
@@ -1,5 +1,5 @@
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:mrs="https://mrs.cmbi.ru.nl/mrs-web/ml"
+	xmlns:z2="http://www.hekkelman.com/libzeep/m2"
 	xml:lang="en" lang="en">
 <head>
     <title>M6</title>
@@ -18,74 +18,33 @@
 	</script>
 </head>
 <body>
-	<mrs:include file="header.html" />
+	<div z2:replace="header :: #header" />
 
 	<div id="main">
 
 		<div class="nav">
 			<span class="left">
 <!--				Records ${first}-${last} of <mrs:number f="#,##0" n="${keyCount}"/>-->
-				<mrs:if test="${not empty first}">Keys ${first} to ${last} for index ${ix} in ${db}</mrs:if>
-				<mrs:if test="${empty first}">Keys for index ${ix} in ${db}</mrs:if>
+				<span z2:if="${not first.empty}" z2:text="|Keys ${first} to ${last} for index ${ix} in ${db}|"></span>
+				<span z2:if="${first.empty}" z2:text="|Keys for index ${ix} in ${db}|"></span>
 			</span>
 
-			<span class="right">
-				<mrs:if test="${page > 1}">
-					<mrs:url var="url"><mrs:param name="page" value="${page - 1}"/></mrs:url>
-					<a href="${url}">previous</a>
-				</mrs:if>
-				<mrs:for var="p" begin="${page > 4 ? page - 4 : 1}"
-							end="${lastPage > page + 4 ? page + 4 : lastPage}">
-					<mrs:if test="${p != page}">
-						<mrs:url var="url"><mrs:param name="page" value="${p}"/></mrs:url>
-						<a href="${url}">${p}</a>
-					</mrs:if>
-					<mrs:if test="${p = page}">${p}</mrs:if>
-				</mrs:for>
-				<mrs:if test="${lastPage > page}">
-					<mrs:url var="url"><mrs:param name="page" value="${page + 1}"/></mrs:url>
-					<a href="${url}">next</a>
-				</mrs:if>
-			</span>
 			&#x00a0;
 		</div>
 
-		<mrs:if test="${not empty sections}">
-			<div class="wbox">
-
-				<div class="wleft">
-					<ul class="browse">
-						<mrs:for begin="0" end="${(sections.count / 2) - 1}" var="i">
-							<li>
-								<a href="browse?ix=${ix};db=${db};first=${sections[i].first};last=${sections[i].last}">
-									${sections[i].first} .. ${sections[i].last}
-								</a>
-							</li>
-						</mrs:for>
-					</ul>
-				</div>
-				<div class="wright">
-					<ul class="browse">
-						<mrs:for begin="${sections.count / 2}" end="${sections.count - 1}" var="i">
-							<li>
-								<a href="browse?ix=${ix};db=${db};first=${sections[i].first};last=${sections[i].last}">
-									${sections[i].first} .. ${sections[i].last}
-								</a>
-							</li>
-						</mrs:for>
-					</ul>
-				</div>
-				<div class="wclear"/>
-			</div>
-		</mrs:if>
-
-		<mrs:if test="${not empty keys}">
-			<mrs:iterate collection="keys" var="key">
+		<div z2:if="${not sections.empty}" class="wbox">
 			<ul class="browse">
-				<li><a href="link?db=${db}&amp;ix=${ix}&amp;id=${key}">${key}</a></li>
+				<li z2:each="section: ${sections}">
+					<a z2:href="@{browse(ix=${ix},db=${db},first=${section.first},last=${section.last})}"
+						z2:text="|${section.first} .. ${section.last}|">
+					</a>
+				</li>
 			</ul>
-			</mrs:iterate>
-		</mrs:if>
+		</div>
+
+		<ul class="browse">
+			<li z2:each="key: ${keys}"><a z2:href="@{link(db=${db},ix=${ix},id=${key})}" z2:text="${key}"></a></li>
+		</ul>
 	</div>
 </body>
 </html>