From 5e88470c36e25340e1435bf1ba9f1deccee64173 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Feb 2018 08:44:46 +0100
Subject: [PATCH] unnecessary files removed
---
.../WEB-INF/components/admin/header.xhtml | 14 -
.../WEB-INF/components/admin/menu.xhtml | 56 --
.../WEB-INF/components/admin/template.xhtml | 48 --
web/src/main/webapp/admin/comments.xhtml | 72 ---
web/src/main/webapp/admin/configuration.xhtml | 71 ---
web/src/main/webapp/admin/genomes.xhtml | 204 -------
web/src/main/webapp/admin/miriam.xhtml | 48 --
web/src/main/webapp/admin/projects.xhtml | 574 ------------------
web/src/main/webapp/admin/status.xhtml | 51 --
web/src/main/webapp/admin/users.xhtml | 174 ------
10 files changed, 1312 deletions(-)
delete mode 100644 web/src/main/webapp/WEB-INF/components/admin/header.xhtml
delete mode 100644 web/src/main/webapp/WEB-INF/components/admin/menu.xhtml
delete mode 100644 web/src/main/webapp/WEB-INF/components/admin/template.xhtml
delete mode 100644 web/src/main/webapp/admin/comments.xhtml
delete mode 100644 web/src/main/webapp/admin/configuration.xhtml
delete mode 100644 web/src/main/webapp/admin/genomes.xhtml
delete mode 100644 web/src/main/webapp/admin/miriam.xhtml
delete mode 100644 web/src/main/webapp/admin/projects.xhtml
delete mode 100644 web/src/main/webapp/admin/status.xhtml
delete mode 100644 web/src/main/webapp/admin/users.xhtml
diff --git a/web/src/main/webapp/WEB-INF/components/admin/header.xhtml b/web/src/main/webapp/WEB-INF/components/admin/header.xhtml
deleted file mode 100644
index 3f4bf95ce2..0000000000
--- a/web/src/main/webapp/WEB-INF/components/admin/header.xhtml
+++ /dev/null
@@ -1,14 +0,0 @@
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- xmlns:p="http://primefaces.org/ui">
-
- <h:outputStylesheet library="css" name="minerva.css" />
-
- <div class="minerva-header">
- <a href="#{request.contextPath}/?id=#{mapMB.currentMapId}" class="mainTitle"><i class="fa fa-home" style="font-size:17px"></i> #{mapMB.currentProject.name}</a>
- </div>
-
-</html>
-
diff --git a/web/src/main/webapp/WEB-INF/components/admin/menu.xhtml b/web/src/main/webapp/WEB-INF/components/admin/menu.xhtml
deleted file mode 100644
index 1314c0e9df..0000000000
--- a/web/src/main/webapp/WEB-INF/components/admin/menu.xhtml
+++ /dev/null
@@ -1,56 +0,0 @@
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:ui="http://java.sun.com/jsf/facelets"
- xmlns:p="http://primefaces.org/ui">
-
-<ui:include src="/WEB-INF/components/admin/header.xhtml" />
-<h:form id="menuForm">
- <p:menubar >
- <p:menuitem value="Comments"
- url="/admin/comments.xhtml?id=#{mapMB.currentMapId}"/>
- <p:menuitem value="Map manager"
- url="/admin/projects.xhtml?id=#{mapMB.currentMapId}"/>
- <p:menuitem value="User manager"
- url="/admin/users.xhtml?id=#{mapMB.currentMapId}"/>
- <p:menuitem value="Service status"
- url="/admin/status.xhtml?id=#{mapMB.currentMapId}"/>
- <p:menuitem value="Configuration"
- url="/admin/configuration.xhtml?id=#{mapMB.currentMapId}"/>
- <p:menuitem value="Miriam"
- url="/admin/miriam.xhtml?id=#{mapMB.currentMapId}"/>
-<!-- <p:menuitem value="Genome"
- url="/admin/genomes.xhtml?id=#{mapMB.currentMapId}"/> -->
- <p:menuitem value="Manual"
- onclick="window.open('#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other','_admin_manual_');"/>
- <p:menuitem value="Logout" actionListener="#{userMB.doLogout}"
- oncomplete="location.reload();"
- style="position: absolute; right: 6px; color:#ffffff; "/>
- </p:menubar>
-</h:form>
-
-<script type="text/javascript">
-$(window).load(function(){
-var url=$(location).attr('href');
-var active=-1;
-if(url.indexOf('comments.xhtml')>0) active=0;
-if(url.indexOf('projects.xhtml')>0) active=1;
-if(url.indexOf('users.xhtml')>0) active=2;
-if(url.indexOf('status.xhtml')>0) active=3;
-if(url.indexOf('configuration.xhtml')>0) active=4;
-if(url.indexOf('miriam.xhtml')>0) active=5;
-
-if(active>-1){
-var counter=0;
- var tabs = $("a.ui-menuitem-link").each(function(){
- if (counter==active) $(this).attr('class', 'ui-menuitem-link ui-corner-all ui-state-active');
- counter++;
- });
-}
-
-});
-</script>
-
-</html>
-
-
diff --git a/web/src/main/webapp/WEB-INF/components/admin/template.xhtml b/web/src/main/webapp/WEB-INF/components/admin/template.xhtml
deleted file mode 100644
index 97fa8b13c8..0000000000
--- a/web/src/main/webapp/WEB-INF/components/admin/template.xhtml
+++ /dev/null
@@ -1,48 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:p="http://primefaces.org/ui"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <h:head>
- <link rel="shortcut icon" href="../resources/images/favicon.png" type="image/png" />
-
- <ui:include src="/WEB-INF/components/admin/statistics.xhtml" />
-
- <ui:insert name="css"></ui:insert>
-
- <title>#{mapMB.currentProject.name} - <ui:insert name="title">Default title</ui:insert></title>
-
- </h:head>
-
- <h:body>
- <h:outputStylesheet library="css" name="style.css"/>
- <h:outputStylesheet library="css" name="admin.css"/>
-
- <p:layout fullPage="true" resizeTitle="resize">
- <p:layoutUnit styleClass="layoutUnitCenter" position="center" border="0">
-
- <!-- menu -->
- <ui:include src="/WEB-INF/components/admin/menu.xhtml" />
-
- <!-- content -->
- <h:panelGroup layout="block" id="content" rendered="#{access}">
- <ui:insert name="content">Default content</ui:insert>
- </h:panelGroup>
- <h:panelGroup layout="block" id="no-content" rendered="#{not access}">
- <center><h1>Access denied</h1></center>
- </h:panelGroup>
- </p:layoutUnit>
-
- <p:layoutUnit position="south" resizable="true" id="south" size="95">
- <!-- footer -->
- <ui:include src="/WEB-INF/components/admin/footer.xhtml" />
- </p:layoutUnit>
- </p:layout>
-
- <div id="dialog"><ui:insert name="dialog"></ui:insert></div>
- </h:body>
-</html>
diff --git a/web/src/main/webapp/admin/comments.xhtml b/web/src/main/webapp/admin/comments.xhtml
deleted file mode 100644
index e589f05e12..0000000000
--- a/web/src/main/webapp/admin/comments.xhtml
+++ /dev/null
@@ -1,72 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Comments
- </ui:define>
-
- <ui:param name="access" value="#{feedbackMB.userHasCommentPrivilege}"/>
-
- <ui:define name="content">
-
- <h1>COMMENTS</h1>
-
- <h:form id="commentForm">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
-
- <p:panelGrid columns="2" style="width:100%;height:100%;" >
- <p:dataTable id="commentsDataTable" var="comment" value="#{feedbackMB.commentList}" paginator="true" rows="20" styleClass="paginated" paginatorAlwaysVisible="false">
- <p:column sortBy="idObject" headerText="Id">
- <h:outputText id="commentId" value="#{comment.idObject}" />
- </p:column>
-
- <p:column sortBy="title" headerText="Title">
- <h:link value="#{comment.title}"
- outcome="/index.xhtml?id=#{mapMB.currentMapId}&x=#{comment.xCoord}&y=#{comment.yCoord}&zoom=#{comment.zoom}&comments=on&submap=#{comment.submap}"
- target="_map"/>
- </p:column>
-
- <p:column sortBy="author" headerText="Author">
- <h:outputText value="#{comment.author}" />
- </p:column>
-
- <p:column sortBy="email" headerText="Email">
- <h:outputText value="#{comment.email}"/>
- </p:column>
-
- <p:column sortBy="content" headerText="Content">
- <h:outputText value="#{comment.content}" />
- </p:column>
-
- <p:column sortBy="removed" headerText="Removed">
- <h:outputText value="#{comment.removed}"/>
- <p:commandButton actionListener="#{feedbackMB.removeComment(comment)}" icon="ui-icon-closethick" update="commentsDataTable" rendered="#{comment.removed=='NO'}" value="remove"/>
- </p:column>
-
- <p:column sortBy="pinned" headerText="Pinned">
- <h:outputText value="#{comment.pinned}"/>
- </p:column>
- </p:dataTable>
-
- <p:dataList value="#{projectMB.projects}" var="project" type="unordered" itemType="none" paginator="true" rows="10" styleClass="paginated" paginatorAlwaysVisible="false">
- <f:facet name="header">
- Projects
- </f:facet>
- <p:commandButton id="selectButton" icon="ui-icon-search" title="View" onclick="window.location.href='#{request.contextPath}/admin/comments.xhtml?id=#{project.projectId}';"/>
- <h:link value="#{project.projectName} (#{project.projectId})" outcome="/index.xhtml?id=#{project.projectId}" target="_map_#{project.idObject}" style="#{project.projectId ==mapMB.currentMapId? 'background-color:#2DCAFF;':''}"/>
- </p:dataList>
- </p:panelGrid>
- <center>
- <p:commandButton id="refreshCommentButton" actionListener="#{feedbackMB.refreshCommentList}" icon="ui-icon-refresh" update="commentsDataTable"/>
- </center>
- </h:form>
- </ui:define>
-</ui:composition>
diff --git a/web/src/main/webapp/admin/configuration.xhtml b/web/src/main/webapp/admin/configuration.xhtml
deleted file mode 100644
index 7c63080fca..0000000000
--- a/web/src/main/webapp/admin/configuration.xhtml
+++ /dev/null
@@ -1,71 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Configuration
- </ui:define>
-
- <ui:param name="access" value="#{configurationMB.userHasConfigurationView}"/>
-
- <ui:define name="content">
- <cc:helpButton style="float:right" helpText='Configuration tab provides a summary of the current version of your MINERVA instance. Moreover, it allows privileged users to configure
-global parameters of the MINERVA instance. More information can be found in the <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h1>CONFIGURATION</h1>
-
- <h:form id="configurationForm">
- <h:outputText value="System version: " class="text"/>
- <h:outputText value="#{configurationMB.version.version}" class="text"/>
- <br/>
- <h:outputText value="Git build version: " />
- <h:outputText value="#{configurationMB.version.gitVersion}" class="bold"/>
- <br/>
- <h:outputText value="Build date: " />
- <h:outputText value="#{configurationMB.version.time}" class="bold"/>
- <br/>
- <br/>
- <h:outputText value="PrimeFaces version: " />
- <h:outputText value="#{configurationMB.primefacesVersion}" class="bold"/>
- <br/>
- <br/>
- <h:outputText value="Memory usage: " />
- <h:outputText value="#{configurationMB.memoryUsage}" class="bold"/>
- <br/>
- <h:outputText value="Max memory available: " />
- <h:outputText value="#{configurationMB.maxMemory}" class="bold"/>
- <br/>
- <br/>
-
- <h:outputText value="System parameters: " class="textLighter"/>
- <p:dataTable id="configurationDataTable" var="configuration" value="#{configurationMB.values}">
- <p:column sortBy="idObject" headerText="Id">
- <h:outputText id="configurationId" value="#{configuration.idObject}" />
- </p:column>
-
- <p:column sortBy="title" headerText="Title">
- <h:outputText value="#{configuration.type.commonName}" />
- </p:column>
-
- <p:column sortBy="value" headerText="Value">
- <p:inputText value="#{configuration.value}" />
- <p:colorPicker value="#{configuration.value}" rendered="#{configuration.type.editType == 'COLOR'}"/>
- </p:column>
-
- </p:dataTable>
- <center>
- <p:commandButton id="refreshConfigurationButton" actionListener="#{configurationMB.refreshValues}"
- icon="ui-icon-refresh" update="configurationDataTable"/>
- <p:commandButton id="saveConfigurationButton" actionListener="#{configurationMB.saveValues}"
- icon="ui-icon-disk" update="configurationDataTable"/>
- </center>
- </h:form>
- </ui:define>
-</ui:composition>
diff --git a/web/src/main/webapp/admin/genomes.xhtml b/web/src/main/webapp/admin/genomes.xhtml
deleted file mode 100644
index ec62f1b842..0000000000
--- a/web/src/main/webapp/admin/genomes.xhtml
+++ /dev/null
@@ -1,204 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- <h:outputStylesheet library="css" name="genomes.css"/>
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Reference genomes
- </ui:define>
-
- <ui:param name="access" value="#{referenceGenomeMB.userHasManageGenomesPrivilege}"/>
-
- <ui:define name="content">
-
- <h1>Configured reference genomes</h1>
-
- <h:form id="genomesForm">
- <h:panelGroup layout="block" id="referenceGenomes">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
- <p:dataTable id="referenceGenomesTable" var="genome" value="#{referenceGenomeMB.downloadedGenomes}">
- <p:column sortBy="name" headerText="Genome type">
- <h:outputText id="name" value="#{genome.type}" />
- </p:column>
-
- <p:column headerText="organism">
- <h:outputText id="organism" value="#{referenceGenomeMB.getOrganismName(genome.organism)}" />
- </p:column>
-
- <p:column headerText="version">
- <h:outputText id="version" value="#{genome.version}" />
- </p:column>
-
- <p:column headerText="progress">
- <h:outputText value="Downloading " rendered="#{genome.downloadProgress < 100.0}"/>
- <h:outputText id="progressBar" value="#{genome.downloadProgress}" rendered="#{genome.downloadProgress < 100.0}">
- <f:convertNumber pattern="#0.00" />
- </h:outputText>
- <h:outputText value="%" rendered="#{genome.downloadProgress < 100.0}"/>
- <h:outputText id="progressReady" value="READY" rendered="#{genome.downloadProgress >= 100.0}" />
- </p:column>
-
- <p:column headerText="source">
- <h:outputText id="source" value="#{genome.sourceUrl}" />
- </p:column>
- <p:column style="width:4%">
- <p:commandButton update=":#{p:component('genomeDlg')}" id="selectButton" oncomplete="PF('genomeDialog').show()" icon="ui-icon-search" title="View">
- <f:setPropertyActionListener value="#{genome}" target="#{referenceGenomeMB.editedReferenceGenome}" />
- </p:commandButton>
- </p:column>
-
- </p:dataTable>
- <center>
- <p:commandButton id="refreshGenomesButton" actionListener="#{referenceGenomeMB.refreshDownloadedGenomes}"
- icon="ui-icon-refresh" update="referenceGenomesTable"/>
- </center>
- </h:panelGroup>
- </h:form>
-
- <h2>Add reference genome</h2>
- <h:form id="addGenomeForm">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
- <h:panelGrid id="addPanelGrid" columns="2" cellpadding="1">
- <h:outputText value="Type: " />
- <h:selectOneMenu value="#{referenceGenomeMB.selectedReferenceGenomeType}">
- <f:selectItems value="#{referenceGenomeMB.genomeTypes}" var="genome"
- itemLabel="#{genome}" itemValue="#{genome}" />
- <f:ajax event="change" execute="@this" render="organismMenu"/>
- <f:ajax event="change" execute="@this" render="versionMenu"/>
- <f:ajax event="change" execute="@this" render="urlText"/>
- </h:selectOneMenu>
-
- <h:outputText value="Organism: " />
- <h:selectOneMenu id="organismMenu" value="#{referenceGenomeMB.selectedOrganism}"
- converter="miriamTypeConverter">
- <f:selectItems value="#{referenceGenomeMB.availableOrganisms}" var="organism"
- itemLabel="#{referenceGenomeMB.getOrganismName(organism)}" itemValue="#{organism}" />
- <f:ajax event="change" execute="@this" render="versionMenu"/>
- <f:ajax event="change" execute="@this" render="urlText"/>
- </h:selectOneMenu>
-
- <h:outputText value="Version: " />
- <h:selectOneMenu id="versionMenu" value="#{referenceGenomeMB.selectedVersion}">
- <f:selectItems value="#{referenceGenomeMB.availableVersions}" var="version"
- itemLabel="#{version}" itemValue="#{version}" />
- <f:ajax event="change" execute="@this" render="urlText"/>
- </h:selectOneMenu>
-
- <h:outputText value="Url to file (2bit): " />
- <p:inputText id="urlText" value="#{referenceGenomeMB.selectedUrl}" style="width:400px !important;" />
- </h:panelGrid>
- <center>
- <p:commandButton id="downloadGenomeButton" actionListener="#{referenceGenomeMB.downloadGenome}" value="Download" update=":genomesForm:referenceGenomesTable"
- icon="ui-icon-save" />
- </center>
- </h:form>
-
-</ui:define>
-<ui:define name="dialog">
-
-<h:form id="genomeDetailForm">
- <p:dialog header="Genome Detail" widgetVar="genomeDialog" resizable="false" id="genomeDlg"
- showEffect="fade" modal="true">
- <p:tabView id="genomeDetailPanel">
- <p:tab title="General">
- <p:panelGrid columns="2">
- <h:outputText value="Type:" />
- <p:inputText value="#{referenceGenomeMB.editedReferenceGenome.type}"
- readonly="true" styleClass="genomeValueField"/>
-
- <h:outputText value="Organism:" />
- <p:inputText value="#{referenceGenomeMB.getOrganismName(referenceGenomeMB.editedReferenceGenome.organism)}"
- readonly="true" styleClass="genomeValueField"/>
-
- <h:outputText value="Version: " />
- <p:inputText value="#{referenceGenomeMB.editedReferenceGenome.version}"
- readonly="true" styleClass="genomeValueField" />
-
- <h:outputText value="Url to file:" />
- <p:inputText value="#{referenceGenomeMB.editedReferenceGenome.sourceUrl}"
- readonly="true" styleClass="genomeValueField" style="width:400px !important;"/>
-
- </p:panelGrid>
-
- <p:separator />
-
- <p:commandButton update=":#{p:component('referenceGenomesTable')}"
- actionListener="#{referenceGenomeMB.removeGenome(referenceGenomeMB.editedReferenceGenome)}"
- id="removeButton" oncomplete="PF('genometDialog').hide()" icon="ui-icon-trash" value="Remove"
- title="Remove"/>
- <p:commandButton update=":#{p:component('referenceGenomesTable')}" id="cancelButton"
- oncomplete="PF('genomeDialog').hide()" icon="ui-icon-close" value="Cancel" title="Cancel"/>
-
- </p:tab>
-
- <p:tab id="layoutTab" title="Gene mapping">
-
- <p:dataTable id="geneMappingDataTable" var="geneMapping" value="#{referenceGenomeMB.editedReferenceGenome.geneMapping}"
- rows="10"
- paginator="true"
- paginatorTemplate="{CurrentPageReport} {FirstPageLink} {PreviousPageLink} {PageLinks} {NextPageLink} {LastPageLink}">
- <p:column sortBy="name" headerText="Name">
- <p:inputText value="#{geneMapping.name}" readonly="true" />
- </p:column>
-
- <p:column sortBy="sourceUrl" headerText="Source">
- <p:inputText value="#{geneMapping.sourceUrl}" readonly="true" />
- </p:column>
-
- <p:column sortBy="downloadProgress" headerText="Progress">
- <h:outputText value="Downloading " rendered="#{geneMapping.downloadProgress < 100.0}"/>
- <h:outputText id="progressBar" value="#{geneMapping.downloadProgress}" rendered="#{geneMapping.downloadProgress < 100.0}">
- <f:convertNumber pattern="#0.00" />
- </h:outputText>
- <h:outputText value="%" rendered="#{geneMapping.downloadProgress < 100.0}"/>
- <h:outputText id="progressReady" value="READY" rendered="#{geneMapping.downloadProgress >= 100.0}" />
- </p:column>
-
- <p:column headerText="Remove">
- <p:commandButton update="geneMappingDataTable" actionListener="#{referenceGenomeMB.removeGeneMapping(geneMapping)}" id="removeGeneMappingButton" icon="ui-icon-trash"/>
- </p:column>
-
- </p:dataTable>
-
- <p:separator />
- <p:commandButton value="Add gene mapping" id="openAddGeneMapingButton" update=":#{p:component('geneMappingDlg')}" oncomplete="PF('geneMappingDialog').show()"/>
-
- </p:tab>
- </p:tabView>
-
- </p:dialog>
-</h:form>
-
-<h:form id="addGeneMappingForm">
- <p:dialog header="Add gene mapping" widgetVar="geneMappingDialog" resizable="false" id="geneMappingDlg"
- showEffect="fade" modal="true" >
-
- <p:panelGrid id="layoutDataTable" columns="2">
-
- <h:outputText value="Name" />
- <p:inputText value="#{referenceGenomeMB.selectedReferenceGenomeGeneMappingName}" />
-
- <h:outputText value="File (url)" />
- <p:inputText value="#{referenceGenomeMB.selectedReferenceGenomeGeneMappingUrl}" />
-
- </p:panelGrid>
- <center>
- <p:commandButton id="addLayoutButton"
- actionListener="#{referenceGenomeMB.addGeneMapping(referenceGenomeMB.editedReferenceGenome)}"
- update=":genomeDetailForm:genomeDetailPanel:geneMappingDataTable" icon="ui-icon-disk"
- value="Save" title="Save" onclick="PF('geneMappingDialog').hide();"/>
- </center>
- </p:dialog>
-
-</h:form>
-
-
- </ui:define>
-</ui:composition>
diff --git a/web/src/main/webapp/admin/miriam.xhtml b/web/src/main/webapp/admin/miriam.xhtml
deleted file mode 100644
index f0083da89b..0000000000
--- a/web/src/main/webapp/admin/miriam.xhtml
+++ /dev/null
@@ -1,48 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Miriam
- </ui:define>
-
- <ui:param name="access" value="true"/>
-
- <ui:define name="content">
-
- <cc:helpButton style="float:right" helpText='The MIRIAM panel lists all MIRIAM-supported resources (<a href="http://www.ebi.ac.uk/miriam/main/mdb?section=intro" target="_miriam_" >http://www.ebi.ac.uk/miriam/main/mdb?section=intro</a>) currently handled by MINERVA platform as shown in the figure below. More information can be found in the <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h1>MIRIAM</h1>
-
- <h:form id="miriamForm">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
-
- <h:outputText value="Supported Miriam types: " class="textLighter"/>
- <p:dataTable id="miriamDataTable" var="type" value="#{miriamMB.miriamTypes}">
- <p:column sortBy="commonName" headerText="Annotation type">
- <a target="_blank" href="#{type.dbHomepage}"><h:outputText value="#{type.commonName}" /></a>
- </p:column>
- <p:column sortBy="registryIdentifier" headerText="Miriam identifier">
- <a target="_blank" href="http://www.ebi.ac.uk/miriam/main/collections/#{type.registryIdentifier}"><h:outputText value="#{type.registryIdentifier}" /></a>
- </p:column>
- <p:column headerText="Valid for elements:">
- <p:dataList value="#{type.validClass}" var="classEl">
- #{classEl.simpleName=="Object" ? "All": (classEl.simpleName=="ComplexSpecies" ? "Complex" : classEl.simpleName)}
- </p:dataList>
- </p:column>
- <p:column headerText="Valid uri:">
- <p:dataList value="#{type.uris}" var="uri" >
- #{uri}
- </p:dataList>
- </p:column>
- </p:dataTable>
- </h:form>
- </ui:define>
-</ui:composition>
diff --git a/web/src/main/webapp/admin/projects.xhtml b/web/src/main/webapp/admin/projects.xhtml
deleted file mode 100644
index 8c93d1fcc2..0000000000
--- a/web/src/main/webapp/admin/projects.xhtml
+++ /dev/null
@@ -1,574 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- <h:outputStylesheet library="css" name="projects.css"/>
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Projects
- </ui:define>
-
- <ui:param name="access" value="#{projectMB.userHasManagePrivileges}"/>
-
- <ui:define name="content">
-
- <h1>PROJECTS</h1>
-
- <h:form id="projectForm">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
- <p:commandButton value="Add project" title="Add project" id="openAddProjectButton"
- update=":#{p:component('addProjectDlg')}" oncomplete="PF('addProjectDialog').show()"
- disabled="#{not projectMB.userHasAddMapPrivileges}" styleClass="addButton"/>
- <p:separator />
-
- <p:dataTable id="projectDataTable" var="project" value="#{projectMB.projects}" >
- <p:column sortBy="projectId" headerText="ProjectId">
- <h:link value="#{project.projectId}" outcome="/index.xhtml?id=#{project.projectId}" target="_map_#{project.idObject}"/>
- </p:column>
-
- <p:column sortBy="projectName" headerText="Name">
- <h:outputText value="#{project.projectName}" />
- </p:column>
-
- <p:column sortBy="projectDisease" headerText="Disease">
- <cc:annotation element="#{project.projectDiseaseLink}" showDbName="false"/>
- </p:column>
-
- <p:column sortBy="organismLink" headerText="Organism">
- <cc:annotation element="#{project.organismLink}"/>
- </p:column>
-
- <p:column sortBy="status" headerText="Status">
- <h:outputText value="#{project.status}" />
- <h:outputText value=" (#{project.progress}%)" />
-
- <p:commandLink update=":#{p:component('warningsDlg')}"
- id="warningButton" oncomplete="PF('warningsDialog').show()"
- title="#{project.warningsPreview}"
- rendered="#{not empty project.warnings}" >
- <h:graphicImage library="images" name="icons/warning.png" width="24px" class="imgMiddle" />
- <f:setPropertyActionListener value="#{project}" target="#{projectMB.selectedProject}" />
- </p:commandLink >
-
- <p:commandLink update=":#{p:component('errorDlg')}"
- id="errorButton" oncomplete="PF('errorDialog').show()"
- title="#{project.errors}"
- rendered="#{not empty project.errors}" >
- <h:graphicImage library="images" name="icons/error.png" width="24px" class="imgMiddle" />
- <f:setPropertyActionListener value="#{project}" target="#{projectMB.selectedProject}" />
- </p:commandLink >
- </p:column>
- <p:column style="width:4%">
- <p:commandButton update=":#{p:component('projectDlg')}" id="selectButton" oncomplete="PF('projectDialog').show()" icon="ui-icon-search" title="View">
- <f:setPropertyActionListener value="#{project}" target="#{projectMB.selectedProject}" />
- </p:commandButton>
- <!-- if the last element in the list is not ok then we will try to refresh the list every 3 seconds -->
- <h:panelGroup layout="block" rendered ="#{(project.idObject==projectMB.projects[projectMB.projects.size()-1].idObject) && (project.status !='Ok')}">
- <p:poll listener="#{projectMB.refreshProjectList(null)}" interval="3" update="projectDataTable"/>
- </h:panelGroup>
- </p:column>
- </p:dataTable>
- <center>
- <p:commandButton id="refreshProjectsButton"
- actionListener="#{projectMB.refreshProjectList}" icon="ui-icon-refresh" update="projectDataTable">
- </p:commandButton>
- </center>
- </h:form>
- </ui:define>
- <ui:define name="dialog">
- <h:form>
- <p:dialog header="Warnings" widgetVar="warningsDialog" id="warningsDlg" modal="true">
- <p:dataTable binding="#{table}" id="warningDataTable" var="warning"
- value="#{projectMB.selectedProject.warnings}" paginator="true" rows="20" >
- <p:column headerText="No">
- <h:outputText value="#{table.rowIndex + SessionsController.firstRow + 1}" />
- </p:column>
- <p:column headerText="Content">
- <h:outputText value="#{warning}" />
- </p:column>
- </p:dataTable>
- <h:commandButton action="#{projectMB.downloadWarnings}" value="Download"/>
- </p:dialog>
-
- <p:dialog header="Error" widgetVar="errorDialog" id="errorDlg" modal="true">
- <h:outputText value="#{projectMB.selectedProject.errors}" />
- </p:dialog>
- </h:form>
-
-<h:form id="addProjectForm" >
- <p:dialog header="Add project" widgetVar="addProjectDialog" resizable="false" id="addProjectDlg" showEffect="fade" modal="true" height="500px">
- <h:panelGrid id="addPanelGrid" columns="3" cellpadding="1">
- <h:outputText value="File: " />
- <p:fileUpload fileUploadListener="#{projectMB.handleFileUpload}" mode="advanced" auto="true" allowTypes="/(\.|\/)(sbgn|xml|zip)$/" onstart="document.getElementById('addProjectForm:addProjectDlg').style.maxWidth=document.getElementById('addProjectForm:addProjectDlg').style.width;document.getElementById('addProjectForm:addProjectDlg').style.height= document.getElementById('addProjectForm:addProjectDlg').style.clientWidth;"
- update=" submodels,layouts,dataMining,images,projectId, projectName, addPanelGrid"/>
- <cc:helpButton helpText='File with the map. For a quick start, CellDesigner files are accepted directly. Available options and
-configurations of the source file are discussed in <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h:outputText value="ProjectId: " />
- <p:inputText id="projectId" value="#{projectMB.newProjectId}" />
- <cc:helpButton helpText="A working name of the uploaded project on the MINERVA platform. Unique in the platform."/>
-
- <h:outputText value="Project name: " />
- <p:inputText id="projectName" value="#{projectMB.newProjectName}" />
- <cc:helpButton helpText="The name of the uploaded project displayed in the top left corner of the Admin and User panels; your official name of the project."/>
-
- <h:outputText value="Project Disease: " />
- <p:inputText id="projectDisease"
- value="#{projectMB.newProjectDisease}" />
- <cc:helpButton helpText="Mesh ID identifying disease connected to this map (ie. for Parkinson's Disease it would be D010300)"/>
-
- <h:outputText value="Organism: " />
- <p:inputText id="organism"
- value="#{projectMB.newProjectOrganism}" />
- <cc:helpButton helpText="Taxonomy ID identifying organism for which project is dedicated (ie. for Human map it would be 9606)"/>
-
- <h:outputText value="Complex: " />
- <p:dataTable id="submodels" var="submodel" value="#{projectMB.modelZipEntries}" editable="true" editMode="cell" widgetVar="cellSubmodels">
- <p:column headerText="Filename">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{submodel.filename}" /></f:facet>
- <f:facet name="input"><p:inputText id="modelInput" value="#{submodel.filename}" style="width:96%" readonly="true"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Name">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{submodel.name}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{submodel.name}" style="width:96%" label="Name"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Root model">
- <p:cellEditor>
- <f:facet name="output"><h:selectBooleanCheckbox value="#{submodel.root}" onclick="return false;" style="width:96%" label="Root model" readonly="true"/></f:facet>
- <f:facet name="input">
- <h:inputHidden value="#{submodel.root}" />
- <h:selectBooleanCheckbox value="#{submodel.root}" onclick="$(this).prev().val(this.checked)" style="width:96%" />
- </f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Mapping file">
- <p:cellEditor>
- <f:facet name="output"><h:selectBooleanCheckbox value="#{submodel.mapping}" onclick="return false;" style="width:96%" label="Root model" readonly="true"/></f:facet>
- <f:facet name="input">
- <h:inputHidden value="#{submodel.mapping}" />
- <h:selectBooleanCheckbox value="#{submodel.mapping}" onclick="$(this).prev().val(this.checked)" style="width:96%" />
- </f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Model type">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{submodel.type}" /></f:facet>
- <f:facet name="input">
- <h:selectOneMenu value="#{submodel.type}" style="width:100%">
- <f:selectItems value="#{projectMB.submodelTypes}" itemLabel="#{commonName}" itemValue="#{commonName}" />
- </h:selectOneMenu>
- </f:facet>
- </p:cellEditor>
- </p:column>
- <p:column headerText="File type">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{submodel.fileType.commonName}" /></f:facet>
- <f:facet name="input">
- <h:selectOneMenu value="#{submodel.fileType}" style="width:100%">
- <f:selectItems value="#{projectMB.fileTypes}" var="typeObject" itemLabel="#{typeObject.commonName}" itemValue="#{typeObject}" />
- </h:selectOneMenu>
- </f:facet>
- </p:cellEditor>
- </p:column>
- </p:dataTable>
- <cc:helpButton helpText='This section describes how main map and uploaded submaps (if any) are related. For more details refer to the <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h:outputText value="Additional overlays: " />
- <p:dataTable id="layouts" var="layout" value="#{projectMB.layoutZipEntries}" editable="true" editMode="cell" widgetVar="cellLayouts">
- <p:column headerText="Filename">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{layout.filename}" /></f:facet>
- <f:facet name="input"><p:inputText id="modelInput" value="#{layout.filename}" style="width:96%" readonly="true"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Name">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{layout.name}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{layout.name}" style="width:96%" label="Name"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Description">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{layout.description}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{layout.description}" style="width:96%" label="Description"/></f:facet>
- </p:cellEditor>
- </p:column>
- </p:dataTable>
- <div/>
-
- <h:outputText value="Data mining: " />
- <p:dataTable id="dataMining" var="dm" value="#{projectMB.dataMiningZipEntries}" editable="true" editMode="cell" widgetVar="cellDataMining">
- <p:column headerText="Filename">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{dm.filename}" /></f:facet>
- <f:facet name="input"><p:inputText id="modelInput" value="#{dm.filename}" style="width:96%" readonly="true"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Name">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{dm.name}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{dm.name}" style="width:96%" label="Name"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Description">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{dm.description}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{dm.description}" style="width:96%" label="Description"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Source">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{dm.source}" /></f:facet>
- <f:facet name="input"><p:inputText value="#{dm.source}" style="width:96%" label="Name"/></f:facet>
- </p:cellEditor>
- </p:column>
-
- <p:column headerText="Type">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{dm.type}" /></f:facet>
- <f:facet name="input">
- <h:selectOneMenu value="#{dm.type}" style="width:100%">
- <f:selectItems value="#{missingConnectionMB.dataMiningTypes}"/>
- </h:selectOneMenu>
- </f:facet>
- </p:cellEditor>
- </p:column>
-
- </p:dataTable>
- <cc:helpButton helpText='This section describes uploaded additional overlays. For more details refer to the <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h:outputText value="Overview images: " />
- <p:dataTable id="images" var="image" value="#{projectMB.imageZipEntries}" editable="true" editMode="cell" widgetVar="cellImages">
- <p:column headerText="Filename">
- <p:cellEditor>
- <f:facet name="output"><h:outputText value="#{image.filename}" /></f:facet>
- <f:facet name="input"><p:inputText id="modelInput" value="#{image.filename}" style="width:96%" readonly="true"/></f:facet>
- </p:cellEditor>
- </p:column>
- </p:dataTable>
- <cc:helpButton helpText='This section describes uploaded overview images and their configuration file. For more details refer to the <a href="#{request.contextPath}/javax.faces.resource/admin_guide.pdf.xhtml?ln=other" target="_admin_manual_" >manual</a>.'/>
-
- <h:outputText value="Version: " />
- <p:inputText value="#{projectMB.newMapVersion}" />
- <cc:helpButton helpText='A text field displayed next to the name of your project in the User panel.'/>
-
- <h:outputText value="Annotate model automatically: " />
- <h:panelGroup layout="block">
- <p:selectBooleanCheckbox value="#{projectMB.annotateModel}" styleClass="projectsAdvancedCheckbox"/>
- <h:outputText value=" " />
- <p:commandButton value="Advanced" oncomplete="PF('annotatorDialog').show()" title="Advanced options"/>
- </h:panelGroup>
- <cc:helpButton helpText='If this checkbox is checked, elements of the uploaded map will be automatically annotated using built in annotators. Behavior of the annotators can be configured by clicking the Advanced button.'/>
-
- <h:outputText value="Verify manual annotations: " />
- <h:panelGroup layout="block">
- <p:selectBooleanCheckbox value="#{projectMB.verifyAnnotationsModel}" styleClass="projectsAdvancedCheckbox"/>
- <h:outputText value=" " />
- <p:commandButton value="Advanced" oncomplete="PF('miriamDialog').show()" title="Advanced options"/>
- </h:panelGroup>
- <cc:helpButton helpText='If this checkbox is checked, elements and interactions of the uploaded map will be scanned for existing annotations; if present these existing annotations will be validated against a set of rules. Verification rules can be configured by clicking the Advanced button.'/>
-
- <h:outputText value="Cache data: " />
- <p:selectBooleanCheckbox value="#{projectMB.cacheModel}"/>
- <cc:helpButton helpText='If this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository (e.g. cross-links to external bioinformatic databases) are resolved and cached'/>
-
- <h:outputText value="Auto margin: " />
- <p:selectBooleanCheckbox value="#{projectMB.newMapAutoResize}"/>
- <cc:helpButton helpText='If this checkbox is checked, upon generation of the graphics, empty spaces surrounding elements and interactions will be cropped'/>
-
- <h:outputText value="Display as SBGN: " />
- <p:selectBooleanCheckbox value="#{projectMB.sbgnFormat}" />
- <cc:helpButton helpText='If this checkbox is checked, the uploaded model will be displayed in SBGN format, instead of default CellDesigner format.'/>
-
- <h:outputText value="Default network overlay: " />
- <p:selectBooleanCheckbox value="#{projectMB.networkLayoutAsDefault}" />
- <cc:helpButton helpText='If this checkbox is checked, the default overlay in User panel will present pure network. If the checkbox is unchecked then default overlay will present pathways and compartments view.'/>
-
- <h:outputText value="Semantic zooming: " />
- <p:selectBooleanCheckbox value="#{projectMB.semanticOverlay}" />
- <div/>
-
- </h:panelGrid>
- <center>
- <p:commandButton value="Submit" icon="ui-icon-disk" actionListener="#{projectMB.createProject}" onclick="PF('addProjectDialog').hide();" update=":projectForm:projectDataTable"/>
- <p:commandButton value="Cancel" icon="ui-icon-close" onclick="PF('addProjectDialog').hide();"/>
- </center>
- </p:dialog>
-
-</h:form>
-<h:form id="projectDetailForm">
- <p:dialog header="Project Detail" widgetVar="projectDialog" resizable="false" id="projectDlg"
- showEffect="fade" modal="true">
- <p:tabView id="projectDetailPanel">
- <p:tab title="General">
- <p:panelGrid columns="2">
- <h:outputText value="ProjectId:" />
- <p:inputText value="#{projectMB.selectedProject.projectId}" readonly="true" styleClass="projectValueField"/>
-
- <h:outputText value="Name:" />
- <p:inputText value="#{projectMB.selectedProject.projectName}" styleClass="bold"/>
-
- <h:outputText value="Disease: " />
- <p:inputText value="#{projectMB.selectedProject.newDiseaseName}"
- styleClass="bold" />
-
- <h:outputText value="Organism: " />
- <p:inputText value="#{projectMB.selectedProject.newOrganismName}"
- styleClass="bold" />
-
- <h:outputText value="Version:" />
- <p:inputText value="#{projectMB.selectedProject.version}" styleClass="bold"/>
-
- <h:outputText value="Description:" />
- <p:inputText value="#{projectMB.selectedProject.description}" styleClass="bold"/>
-
- <h:outputText value="Notify email:" />
- <p:inputText value="#{projectMB.selectedProject.notifyEmail}" styleClass="bold"/>
- </p:panelGrid>
-
- <p:separator />
- <p:commandButton update=":#{p:component('projectDataTable')}" actionListener="#{projectMB.updateSelectedProject}" id="saveButton" oncomplete="PF('projectDialog').hide()" icon="ui-icon-disk" value="Save" title="Save"/>
- <p:commandButton update=":#{p:component('projectDataTable')}" actionListener="#{projectMB.removeSelectedProject}" id="removeButton" oncomplete="PF('projectDialog').hide()" icon="ui-icon-trash" value="Remove" title="Remove"/>
- <p:commandButton update=":#{p:component('projectDataTable')}" id="cancelButton" oncomplete="PF('projectDialog').hide()" icon="ui-icon-close" value="Cancel" title="Cancel"/>
-
- </p:tab>
-
- <p:tab id="layoutTab" title="Overlays">
-
- <p:dataTable id="layoutDataTable" var="layout" value="#{projectMB.selectedProject.layouts}"
- rows="10"
- paginator="true"
- paginatorTemplate="{CurrentPageReport} {FirstPageLink} {PreviousPageLink} {PageLinks} {NextPageLink} {LastPageLink}">
- <p:column sortBy="name" headerText="Name">
- <p:inputText value="#{layout.name}" />
- </p:column>
-
- <p:column sortBy="directory" headerText="Directory">
- <p:inputText value="#{layout.directory}" />
- </p:column>
-
- <p:column sortBy="description" headerText="Description">
- <p:inputTextarea value="#{layout.description}" />
- </p:column>
-
- <p:column sortBy="creator" headerText="Owner">
- <h:selectOneMenu value="#{layout.creator}">
-
- <!-- for not defined user -->
- <f:selectItem itemLabel="N/A" itemValue="" />
-
- <f:selectItems value="#{usersMB.userList}" var="user"
- itemLabel="#{user.name} #{user.surname}" itemValue="#{user.name} #{user.surname}" />
- </h:selectOneMenu>
- </p:column>
-
- <p:column headerText="Data">
- <p:commandButton id="downloadLayoutButton" actionListener="#{layoutMB.downloadInputData(layout)}" icon="ui-icon-arrowthickstop-1-s" title='#{layout.inputDataAvailable?"":"Not available"}' disabled="#{not layout.inputDataAvailable}" ajax="false"/>
- </p:column>
- <p:column headerText="Update">
- <p:commandButton update=":#{p:component('layoutDataTable')}" actionListener="#{layoutMB.updateLayout(layout)}" id="updateLayoutButton" icon="ui-icon-disk"/>
- </p:column>
- <p:column headerText="Remove">
- <p:commandButton update=":#{p:component('layoutDataTable')}" actionListener="#{layoutMB.removeLayout(layout)}" id="removeLayoutButton" icon="ui-icon-trash"/>
- </p:column>
-
- </p:dataTable>
-
- <p:separator />
- <p:commandButton value="Add overlay" id="openAddProjectButton" update=":#{p:component('layoutDlg')}" oncomplete="PF('layoutDialog').show()"/>
- </p:tab>
-
- <p:tab id="dmTab" title="Data mining">
-
- <p:dataTable id="dmDataTable" var="dataMiningSet" value="#{projectMB.selectedProject.dataMiningSets}">
- <p:column sortBy="name" headerText="Name">
- <h:outputText value="#{dataMiningSet.name}" />
- </p:column>
-
- <p:column sortBy="description" headerText="Description">
- <h:outputText value="#{dataMiningSet.description}" />
- </p:column>
-
- <p:column sortBy="source" headerText="Source">
- <h:outputLink value="#{dataMiningSet.source}" target="_dms_#{dataMiningSet.idObject}">#{dataMiningSet.source}</h:outputLink>
- </p:column>
-
- <p:column sortBy="type" headerText="Type">
- <h:outputText value="#{dataMiningSet.type.commonName}" />
- </p:column>
-
- <p:column headerText="Data">
- <p:commandButton id="downloadDataMiningButton" actionListener="#{missingConnectionMB.downloadInputData(dataMiningSet)}" icon="ui-icon-arrowthickstop-1-s" ajax="false"/>
- </p:column>
- </p:dataTable>
- </p:tab>
-
- <p:tab id="userTab" title="Users">
- <h:panelGroup layout="block" id="userComponent">
- <p:dataTable id="userDataTable" var="user" value="#{usersMB.userList}"
- rows="10"
- paginator="true"
- paginatorTemplate="{CurrentPageReport} {FirstPageLink} {PreviousPageLink} {PageLinks} {NextPageLink} {LastPageLink}">
- <p:column headerText="User">
- <h:outputText value="#{user.surname} #{user.name} (#{user.login})" />
- </p:column>
-
- <p:columns value="#{usersMB.projectPrivilegeTypes}" var="privilegeType" headerText="#{privilegeType.commonName}">
- <p:selectBooleanCheckbox value="#{user.getProjectPrivilegeByProjectId(projectMB.selectedProject.idObject).getProjectPrivilegeByPrivilegeType(privilegeType).selected}" styleClass="projectsAdvancedCheckbox"/>
- </p:columns>
-
- </p:dataTable>
- <p:commandButton value="Update privileges" id="updatePrivilegesButton" update="userDataTable"
- actionListener="#{usersMB.updateUsers(usersMB.userList)}"
- onclick="PF('updatingDlg').show();" oncomplete="PF('updatingDlg').hide();" onsuccess="PF('confirmDlg').show();" onerror="PF('errorDlg').show();"
- />
- </h:panelGroup>
- </p:tab>
- </p:tabView>
-
- </p:dialog>
-
- <p:dialog header="Updating" widgetVar="updatingDlg" resizable="false" id="updatingDlg"
- showEffect="fade" modal="true" closable="false">
- <p:graphicImage library="images" name="icons/ajax-loader.gif"/>
- </p:dialog>
-
- <p:dialog header="Message" widgetVar="confirmDlg" id="confirmDialog" resizable="false"
- showEffect="fade" modal="true" closable="true">
- <h:outputText id="messageText" value="Data updated successfully."/>
- </p:dialog>
-
- <p:dialog header="Error" widgetVar="errorDlg" id="errorDialog" resizable="false"
- showEffect="fade" modal="true" closable="true">
- <h:outputText id="errorMessageText" value="Unexpected error. More info in logs."/>
- </p:dialog>
-</h:form>
-
-<h:form id="annotationForm">
- <p:dialog header="Annotators Detail" widgetVar="annotatorDialog" resizable="false" id="annotatorDlg"
- showEffect="fade" modal="true">
- <cc:helpButton style="float:right" helpText='By clicking on each element type (Object annotators) in the left panel, an annotator can be assigned in the right panel that will attempt to automatically retrieve information from external bioinformatic databases for each relevant element, and annotate them. There are a number annotators available, utilizing either the name, or existing identifier of an object.'/>
- <h:panelGrid columns="2" cellpadding="1" columnClasses="projectsAnnotatorGridFirstColumn,projectsAnnotatorGridSecondColumn">
-
- <p:treeTable value="#{projectMB.annotatorsTree}" var="row" scrollable="true" scrollHeight="520">
- <p:column headerText="Object Annotators">
- <p:commandLink update=":annotationForm:pickList,:annotationForm:pickListTitle">
- <f:setPropertyActionListener value="#{row}" target="#{projectMB.selectedAnnotatorTreeNodeData}" />
- <h:outputText value="#{row.name}" />
- <h:outputText value=" (#{row.validAnnotators.size()+row.usedAnnotators.size()})" rendered="#{row.validAnnotators.size()+row.usedAnnotators.size()>0}"/>
- </p:commandLink>
- </p:column>
- </p:treeTable>
-
- <h:panelGroup layout="block" styleClass="projectsAnnotatorGrid" class="projectsAnnotatorGrid">
- <h:outputText id="pickListTitle" class="projectsAnnotatorCaption" value="#{projectMB.selectedAnnotatorTreeNodeData.name} annotators:"/>
-
- <p:pickList id="pickList" value="#{projectMB.annotators}" var="annotators" itemLabel="#{annotators}" itemValue="#{annotators}" >
- <f:facet name="sourceCaption">Available</f:facet>
- <f:facet name="targetCaption">In use</f:facet>
-
- <p:ajax event="transfer" listener="#{projectMB.onTransfer}" />
-
- </p:pickList>
- </h:panelGroup>
-
- </h:panelGrid>
-
- </p:dialog>
-
-</h:form>
-
-<h:form id="validationForm">
- <p:dialog header="Miriam validation detail" widgetVar="miriamDialog" resizable="false" id="miriamDlg"
- showEffect="fade" modal="true" >
- <h:panelGrid columns="2" cellpadding="1" columnClasses="projectsAnnotatorGridFirstColumn,projectsAnnotatorGridSecondColumn">
-
- <p:treeTable value="#{projectMB.annotatorsTree}" var="row" scrollable="true" scrollHeight="520">
- <p:column headerText="Classes" style="width:200px;">
- <p:commandLink update=":validationForm:data">
- <f:setPropertyActionListener value="#{row}" target="#{projectMB.selectedAnnotatorTreeNodeData}" />
- <h:outputText value="#{row.name}" />
- </p:commandLink>
- </p:column>
- </p:treeTable>
-
- <h:panelGroup id="data" layout="block" styleClass="projectsAnnotatorGrid" class="projectsAnnotatorGrid">
- <h:outputText id="pickListTitle" class="projectsAnnotatorCaption" value="#{projectMB.selectedAnnotatorTreeNodeData.name}"/>
- <br/>
- <h:panelGroup layout="block">
- <h:outputText class="projectsAnnotatorSubtitle" value="Annotations to be considered as valid:"/>
- <cc:helpButton style="float:right" helpText='By clicking on each element or interaction type (Classes) in the left panel a list of valid MIRIAM identifiers can be assigned. All elements or interactions in the uploaded model, annotated with an identifier outside of the **Valid** list will be flagged as warnings.'/>
- </h:panelGroup>
-
- <p:pickList value="#{projectMB.validMiriam}" var="miriam" itemLabel="#{miriam.commonName}" itemValue="#{miriam}" converter="miriamTypeConverter">
- <f:facet name="sourceCaption">Available</f:facet>
- <f:facet name="targetCaption">Valid</f:facet>
-
- <p:ajax event="transfer" listener="#{projectMB.onTransfer}" />
-
- </p:pickList>
-
- <h:panelGroup layout="block">
- <p:selectBooleanCheckbox value="#{projectMB.selectedAnnotatorTreeNodeData.require}" styleClass="projectsAdvancedCheckbox"/>
- <h:outputText class="projectsAnnotatorSubtitle" value="One of these miriam should be required:"/>
- <cc:helpButton style="float:right" helpText='By clicking on each element or interaction type (Classes) in the left panel a list of mandatory MIRIAM identifiers can be assigned. If checkbox **Require annotations** is checked, all elements or interactions in the uploaded model, annotated without at least one identifier marked as **Required** list will be flagged as warnings.'/>
- </h:panelGroup>
- <br/>
-
- <p:pickList value="#{projectMB.requiredMiriam}" var="miriam" itemLabel="#{miriam.commonName}" itemValue="#{miriam}" converter="miriamTypeConverter" >
- <f:facet name="sourceCaption">Available</f:facet>
- <f:facet name="targetCaption">Required</f:facet>
-
- <p:ajax event="transfer" listener="#{projectMB.onTransfer}" />
-
- </p:pickList>
- </h:panelGroup>
-
- </h:panelGrid>
-
- </p:dialog>
-
-</h:form>
-
-<h:form id="addLayoutProjectForm5">
- <p:dialog header="Add overlay" widgetVar="layoutDialog" resizable="false" id="layoutDlg"
- showEffect="fade" modal="true" >
-
- <p:panelGrid id="layoutDataTable" columns="2">
-
- <h:outputText value="Name" />
- <p:inputText value="#{layoutMB.layoutName}" />
-
- <h:outputText value="File" />
- <p:fileUpload fileUploadListener="#{layoutMB.handleFileUpload}" mode="advanced" auto="true" />
-
- </p:panelGrid>
- <center>
- <p:commandButton id="addLayoutButton" actionListener="#{layoutMB.addAnonymousLayout(projectMB.selectedProject)}" update=":projectDetailForm:projectDetailPanel" icon="ui-icon-disk" disabled="#{not layoutMB.userHasAddLayoutPrivilege}" value="Generate" title="Generate" onclick="PF('layoutDialog').hide();"/>
- </center>
- </p:dialog>
-
-</h:form>
-
- </ui:define>
-</ui:composition>
-
diff --git a/web/src/main/webapp/admin/status.xhtml b/web/src/main/webapp/admin/status.xhtml
deleted file mode 100644
index 11343a8df9..0000000000
--- a/web/src/main/webapp/admin/status.xhtml
+++ /dev/null
@@ -1,51 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- </ui:define>
-
- <ui:define name="title">
- Admin panel - Service status
- </ui:define>
-
- <ui:param name="access" value="#{feedbackMB.userHasCommentPrivilege}"/>
-
- <ui:define name="content">
-
- <cc:helpButton style="float:right" helpText='Service status tab lists all external services and databases cross-linked by MINERVA platform. The left column contains service name hyperlinked to the original website. The right column contains the status of the service. The checkup is invoked by the Refresh button at the bottom of the window.'/>
- <h1>SERVICE STATUS</h1>
-
- <h:form id="serviceForm">
- <h:panelGroup layout="block" id="statusComponent">
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
- <p:dataTable id="statusesDataTable" var="service" value="#{statusMB.statuses}">
- <p:column sortBy="name" headerText="Name">
- <a href="#{service.page}" class="textBigger" target="_blank">
- <h:outputText id="name" value="#{service.name}" />
- </a>
- </p:column>
-
- <p:column sortBy="status" headerText="status">
- <h:outputText id="status" value="#{service.status}" />
- </p:column>
- </p:dataTable>
- <center>
- <p:commandButton id="refreshStatusButton" actionListener="#{statusMB.refreshStatuses}"
- icon="ui-icon-refresh" update="statusesDataTable" onclick="PF('statusPanelBlock').show()"
- oncomplete="PF('statusPanelBlock').hide()">
- </p:commandButton>
- </center>
- </h:panelGroup>
-
- <p:blockUI block="statusComponent" widgetVar="statusPanelBlock">
- CHECKING<br />
- <p:graphicImage library="images" name="icons/ajax-loader.gif"/>
- </p:blockUI>
- </h:form>
- </ui:define>
-</ui:composition>
diff --git a/web/src/main/webapp/admin/users.xhtml b/web/src/main/webapp/admin/users.xhtml
deleted file mode 100644
index ca235f5ae3..0000000000
--- a/web/src/main/webapp/admin/users.xhtml
+++ /dev/null
@@ -1,174 +0,0 @@
-<ui:composition template="/WEB-INF/components/admin/template.xhtml"
- xmlns="http://www.w3.org/1999/xhtml"
- xmlns:f="http://java.sun.com/jsf/core"
- xmlns:h="http://java.sun.com/jsf/html"
- xmlns:p="http://primefaces.org/ui"
- xmlns:cc="http://java.sun.com/jsf/composite/pfcomp"
- xmlns:ui="http://java.sun.com/jsf/facelets">
-
- <ui:define name="css">
- </ui:define>
-
- <ui:define name="title">
- Admin panel - User management
- </ui:define>
-
- <ui:param name="access" value="#{usersMB.userHasManagePrivileges}"/>
-
- <ui:define name="content">
-
- <h1>USERS</h1>
-
- <h:form id="userForm">
-
- <p:messages id="messages" showDetail="true" autoUpdate="true" closable="true" />
- <p:dataTable id="usersDataTable" var="user" value="#{usersMB.userList}">
- <p:column sortBy="id" headerText="Id">
- <h:outputText value="#{user.idObject}" />
- </p:column>
-
- <p:column sortBy="title" headerText="Name">
- <h:outputText value="#{user.name}" />
- </p:column>
-
- <p:column sortBy="author" headerText="Surname">
- <h:outputText value="#{user.surname}" />
- </p:column>
-
- <p:column sortBy="email" headerText="Email">
- <h:outputText value="#{user.email}"/>
- </p:column>
-
- <p:column sortBy="content" headerText="Login">
- <h:outputText value="#{user.login}" />
- </p:column>
-
- <p:column style="width:4%">
- <p:commandButton update=":#{p:component('userDlg')}" id="selectButton" oncomplete="PF('userDialog').show()" icon="ui-icon-search" title="View">
- <f:setPropertyActionListener value="#{user}" target="#{usersMB.selectedUser}" />
- </p:commandButton>
- </p:column>
-
- </p:dataTable>
- <center>
- <p:commandButton id="refreshUsersButton" actionListener="#{usersMB.refreshUserList}" icon="ui-icon-refresh" update="usersDataTable"/>
- <p:commandButton id="addUserButton" actionListener="#{usersMB.prepareEmptyUser}" icon="ui-icon-document" update=":#{p:component('userDlg')}" oncomplete="PF('userDialog').show()"/>
- </center>
- </h:form>
- </ui:define>
- <ui:define name="dialog">
- <h:form id="userForm2" autocomplete="off">
- <p:dialog header="User Detail" widgetVar="userDialog" resizable="false" id="userDlg"
- showEffect="fade" modal="true">
- <!-- fake fields are a workaround for chrome autofill getting the wrong fields -->
- <input style="display:none" type="text" name="fakeusernameremembered"/>
- <input style="display:none" type="password" name="fakepasswordremembered"/>
-
- <table>
- <tr>
- <td>
- <h:outputText value="Id:" />
- </td>
- <td>
- <h:outputText value="#{usersMB.selectedUser.idObject}" class="bold"/>
- </td>
- </tr>
- <tr>
- <td>
- <h:outputText value="Login:" />
- </td>
- <td>
- <p:inputText value="#{usersMB.selectedUser.login}" styleClass="bold" rendered="#{empty usersMB.selectedUser.login}" validator="loginValidator"/>
- <h:outputText autocomplete="off" value="#{usersMB.selectedUser.login}" class="bold" rendered="#{not empty usersMB.selectedUser.login}"/>
- </td>
- </tr>
- <tr>
- <td>
- <h:outputText value="Password:" />
- </td>
- <td>
- <p:password autocomplete="off" id="nonFeedback" value="#{usersMB.selectedUser.password}" />
- </td>
- </tr>
- <tr>
- <td>
- <h:outputText value="Name:" />
- </td>
- <td>
- <p:inputText value="#{usersMB.selectedUser.name}" styleClass="bold"/>
- </td>
- </tr>
- <tr>
- <td>
- <h:outputText value="Surname:" />
- </td>
- <td>
- <p:inputText value="#{usersMB.selectedUser.surname}" styleClass="bold"/>
- </td>
- </tr>
- <tr>
- <td>
- <h:outputText value="Email:" />
- </td>
- <td>
- <p:inputText value="#{usersMB.selectedUser.email}" styleClass="bold"/>
- </td>
- </tr>
- <tr>
- <td colspan="2">
- <h:outputText value="Privileges:" />
- </td>
- </tr>
- <tr>
- <td colspan="2">
-
- <p:dataTable id="basicPrivilegesDataTable" var="privilege" value="#{usersMB.selectedUser.basicPrivileges}" >
- <p:column>
- <h:outputText value="#{privilege.commonName}"/>
- </p:column>
- <p:column >
- <p:selectBooleanCheckbox styleClass="smallCheckbox" value="#{privilege.selected}" rendered="#{not privilege.numeric}"/>
- <p:inputText value="#{privilege.level}" rendered="#{privilege.numeric}"/>
- </p:column>
- </p:dataTable>
- </td>
- </tr>
- <tr>
- <td >
- <h:outputText value="Project:" />
- <p:dataTable value="#{usersMB.selectedUser.pdm}" selection="#{usersMB.projectPrivilege}" var="project" selectionMode="single" style="height:180px" paginator="true" rows="5" styleClass="paginated" paginatorPosition="bottom">
- <p:ajax event="rowSelect" update=":#{p:component('tmpas')}"/>
- <p:ajax event="rowUnselect" update=":#{p:component('tmpas')}"/>
- <p:column>
- <h:outputText value="#{project.projectId}" />
- </p:column>
- </p:dataTable>
-
- </td>
- <td >
- <h:outputText value="Access:" />
- <h:panelGroup layout="block" id="tmpas" >
- <p:dataTable value="#{usersMB.projectPrivilege.projectPrivileges}" selection="#{usersMB.projectPrivilege}" var="privilege" style="height:180px" >
- <p:column >
- <p:selectBooleanCheckbox styleClass="smallCheckbox" value="#{privilege.selected}"/>
- </p:column>
- <p:column>
- <h:outputText value="#{privilege.commonName}" />
- </p:column>
- </p:dataTable>
- </h:panelGroup>
- </td>
- </tr>
-
-
- </table>
- <br/>
- <center>
- <p:commandButton update=":#{p:component('usersDataTable')}" actionListener="#{usersMB.updateSelectedUser}" id="saveUserButton" oncomplete="PF('userDialog').hide()" icon="ui-icon-disk" value="Save" title="Save"/>
- <p:commandButton update=":#{p:component('usersDataTable')}" actionListener="#{usersMB.removeSelectedUser}" id="removeUserButton" oncomplete="PF('userDialog').hide()" icon="ui-icon-trash" value="Remove" title="Remove"/>
- <p:commandButton update=":#{p:component('usersDataTable')}" id="cancelUserButton" oncomplete="PF('userDialog').hide()" icon="ui-icon-close" value="Cancel" title="Cancel"/>
- </center>
- </p:dialog>
- </h:form>
- </ui:define>
-</ui:composition>
--
GitLab