--- /dev/null
+package compbio.cassandra;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.dao.DataIntegrityViolationException;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.exceptions.QueryExecutionException;
+import com.datastax.driver.core.exceptions.QueryValidationException;
+
+import compbio.proteocache.users.User;
+import compbio.proteocache.users.UserManager;
+
+public class CassandraUserManager implements UserManager {
+ private Session session;
+ private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+ public CassandraUserManager() {
+ Session inis = CassandraNativeConnector.getSession();
+ setSession(inis);
+ }
+
+ private void setSession(Session s) {
+ assert s != null;
+ session = s;
+ }
+
+ public boolean addUser(User user) throws DataIntegrityViolationException {
+ String chkcom = "SELECT * FROM Users WHERE email = '" + user.getEmail() + "';";
+ try {
+ ResultSet users = session.execute(chkcom);
+ if (0 < users.all().size()) {
+ throw new DataIntegrityViolationException("A user with email " + user.getEmail() + " exists");
+ }
+
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query validation exception... Command: " + chkcom;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ }
+
+ long id = user.getId().longValue();
+ if (id < 1) {
+ String com = "SELECT * FROM MainParameters WHERE Name = 'MaxUserId';";
+ try {
+ ResultSet values = session.execute(com);
+ List<Row> list = values.all();
+ /*
+ if (1 != list.size()) {
+ return false;
+ }
+ */
+ String test = list.get(0).getString("Value");
+ id = Long.parseLong(test, 10);
+ id++;
+ com = "INSERT INTO MainParameters (name,value) VALUES ('MaxUserId','" + id + "');";
+ session.execute(com);
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ }
+ }
+
+ String incom = "INSERT INTO Users (name, id, email, password, organisation, position, signedtolist, registrationdate) VALUES ('"
+ + user.getFullName() + "'," + id + ",'" + user.getEmail() + "','" + user.getPassword() + "','"
+ + user.getOrganisation() + "','" + user.getPosition() + "'," + user.isUpdateByEmail() + ","
+ + user.getRegistrationDate().getTime() + ");";
+ try {
+ session.execute(incom);
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query validation exception... Command: " + incom;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ }
+ return true;
+ }
+
+ public boolean saveUser(User user) {
+ boolean isSaved = false;
+ String com = "SELECT * FROM Users WHERE id = " + user.getId() + ";";
+ try {
+ ResultSet users = session.execute(com);
+ if (1 < users.all().size()) {
+ return false;
+ }
+ isSaved = addUser(user);
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.saveUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.saveUser: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ }
+ return isSaved;
+ }
+
+ public boolean deleteUser(long id) {
+ String com = "DELETE FROM Users WHERE id = " + id + ";";
+ try {
+ session.execute(com);
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.deleteUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.deleteUser: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return false;
+ }
+ return true;
+ }
+
+ public User getUserById(long id) {
+ String com = "SELECT * FROM Users WHERE Id = " + id + ";";
+ User user = new User();
+ try {
+ ResultSet users = session.execute(com);
+ if (1 != users.all().size()) {
+ return null;
+ }
+ user = buildUser(users.one());
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.addUser: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ }
+ return user;
+ }
+
+ public User getUserByEmail(String email) {
+ String com = "SELECT * FROM Users WHERE Email = '" + email + "';";
+ User user = new User();
+ try {
+ ResultSet users = session.execute(com);
+ if (1 != users.all().size()) {
+ return null;
+ }
+ user = buildUser(users.one());
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.getUserByEmail: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.getUserByEmail: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ }
+ return user;
+ }
+
+ public List<User> findAllUsers() {
+ List<User> list = new ArrayList<User>();
+ String com = "SELECT * FROM Users;";
+ try {
+ ResultSet results = session.execute(com);
+ List<Row> rows = results.all();
+ for (Row r : rows) {
+ list.add(buildUser(r));
+ }
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraUserManagerImpl.findAllUsers: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraUserManagerImpl.findAllUsers: query validation exception... Command: " + com;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ }
+ return list;
+ }
+
+ private User buildUser(Row r) {
+ User u = new User();
+ u.setFullName(r.getString("Name"));
+ u.setId(new Long(r.getLong("Id")));
+ u.setEmail(r.getString("Email"));
+ u.setPassword(r.getString("Password"));
+ u.setOrganisation(r.getString("Organisation"));
+ u.setPosition(r.getString("Position"));
+ u.setUpdateByEmail(r.getBool("SignedToList"));
+ u.setRegistrationDate(new Date(r.getLong("RegistrationDate")));
+ return u;
+ }
+}
--- /dev/null
+package compbio.engine;
+
+import java.util.Set;
+
+/**
+ * List of all posible final job statuses
+ *
+ */
+public enum JobStatus {
+ OK, TIMEDOUT, STOPPED, JPREDERROR;
+
+ public static JobStatus getJobStatus(String status) {
+ status = status.trim().toLowerCase();
+ for (JobStatus st : JobStatus.values()) {
+ if (st.toString().equalsIgnoreCase(status)) {
+ return st;
+ }
+ }
+ return null;
+ }
+
+ public static String toString(Set<JobStatus> statuses) {
+ if (statuses == null || statuses.isEmpty()) {
+ return "No known services...\n";
+ }
+ String value = "";
+ for (JobStatus st : statuses) {
+ if (null != st) {
+ value += st + "\n";
+ } else {
+ value += "Unknown Job Status\n";
+ }
+ }
+ return value;
+ }
+
+ public static void main(String[] args) {
+ System.out.println(OK);
+ }
+}
--- /dev/null
+package compbio.proteocache.users;\r
+\r
+import java.io.Serializable;\r
+import java.util.Date;\r
+\r
+import org.springframework.format.annotation.DateTimeFormat;\r
+\r
+import static org.apache.commons.lang.builder.EqualsBuilder.*;\r
+import static org.apache.commons.lang.builder.HashCodeBuilder.*;\r
+import static org.apache.commons.lang.builder.ToStringBuilder.*;\r
+\r
+public class User implements Serializable {\r
+\r
+ /**\r
+ * \r
+ */\r
+ private static final long serialVersionUID = 1L;\r
+\r
+ private Long id = -1L;\r
+ private String email;\r
+ private String password;\r
+ private String fullName;\r
+ private boolean updateByEmail;\r
+ private String position;\r
+ private String organisation;\r
+\r
+ @DateTimeFormat(pattern = "hh:mma MMM d, YYYY")\r
+ private Date registrationDate;\r
+\r
+ public Long getId() {\r
+ return id;\r
+ }\r
+\r
+ public void setId(Long id) {\r
+ this.id = id;\r
+ }\r
+\r
+ public void setEmail(String email) {\r
+ this.email = email;\r
+ }\r
+\r
+ public String getEmail() {\r
+ return email;\r
+ }\r
+\r
+ public String getPassword() {\r
+ return this.password;\r
+ }\r
+\r
+ public void setPassword(String password) {\r
+ this.password = password;\r
+ }\r
+\r
+ public void setFullName(String fullName) {\r
+ this.fullName = fullName;\r
+ }\r
+\r
+ public String getFullName() {\r
+ return fullName;\r
+ }\r
+\r
+ public String getPosition() {\r
+ return position;\r
+ }\r
+\r
+ public void setPosition(String position) {\r
+ this.position = position;\r
+ }\r
+\r
+ public void setOrganisation(String organisation) {\r
+ this.organisation = organisation;\r
+ }\r
+\r
+ private String checkNoUTFsymbols(String s) {\r
+ if (null != s) {\r
+ if (3 < s.length())\r
+ if (s.substring(0, 2).matches("^&#")) {\r
+ return "Unknown organization";\r
+ }\r
+ }\r
+ return s;\r
+ }\r
+\r
+ public String getOrganisation() {\r
+ return checkNoUTFsymbols(organisation);\r
+ }\r
+\r
+ public void setUpdateByEmail(boolean updateByEmail) {\r
+ this.updateByEmail = updateByEmail;\r
+ }\r
+\r
+ public boolean isUpdateByEmail() {\r
+ return updateByEmail;\r
+ }\r
+\r
+ public Date getRegistrationDate() {\r
+ return this.registrationDate;\r
+ }\r
+\r
+ public void setRegistrationDate(Date registrationDate) {\r
+ this.registrationDate = registrationDate;\r
+ }\r
+\r
+ // plumbing\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ return reflectionEquals(this, obj);\r
+ }\r
+\r
+ @Override\r
+ public int hashCode() {\r
+ return reflectionHashCode(this);\r
+ }\r
+\r
+ @Override\r
+ public String toString() {\r
+ return reflectionToString(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+package compbio.proteocache.users;
+
+import java.util.List;
+
+import compbio.proteocache.users.User;
+
+public interface UserManager {
+
+ public boolean addUser(User user);
+
+ public boolean saveUser(User user);
+
+ public boolean deleteUser(long id);
+
+ public User getUserById(long id);
+
+ public User getUserByEmail(String email);
+
+ public List<User> findAllUsers();
+
+}
--- /dev/null
+package compbio.controllers;
+
+import java.security.Principal;
+import java.util.Date;
+import java.util.regex.Pattern;
+
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.mail.SimpleMailMessage;
+import org.springframework.mail.javamail.JavaMailSender;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.Model;
+import org.springframework.ui.ModelMap;
+import org.springframework.validation.BindingResult;
+import org.springframework.validation.FieldError;
+import org.springframework.web.bind.annotation.ModelAttribute;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import compbio.proteocache.users.User;
+import compbio.proteocache.users.UserManager;
+import compbio.cassandra.CassandraUserManager;
+
+@Controller
+public class UserController {
+
+ //@Inject
+ //JavaMailSender mailSender;
+ private final Pattern EMAIL = Pattern.compile("[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\\.[A-Za-z]{2,4}");
+
+ @RequestMapping(value = "/register/query", method = RequestMethod.GET)
+ public String printPublicHome(ModelMap model) {
+ User user = new User();
+ model.addAttribute(user);
+ return "Register";
+ }
+
+ @RequestMapping(value = "/register/do", method = RequestMethod.POST)
+ public String addUser(Model model, @ModelAttribute("user") User user, BindingResult bindingResult) {
+
+ if (bindingResult.hasErrors()) {
+ return "Register";
+ }
+
+ int fullName = user.getFullName().length();
+ if (fullName < 6 || 50 < fullName) {
+ bindingResult.addError(new FieldError("user", "fullName", "Your full name must be between 3 and 50 symbols long!"));
+ model.addAttribute("error", "wrong password");
+ return "Register";
+ }
+
+ if (!EMAIL.matcher(user.getEmail()).find()) {
+ bindingResult.addError(new FieldError("user", "email", "Email is empty or in a wrong form!"));
+ model.addAttribute("error", "wrong email");
+ return "Register";
+ }
+
+ int password = user.getPassword().length();
+ if (password < 6 || 20 < password) {
+ bindingResult.addError(new FieldError("user", "password", "The password must be at least 6 symbols long!"));
+ model.addAttribute("error", "wrong password");
+ return "Register";
+ }
+
+ int organisation = 0;
+ if (null != user.getOrganisation())
+ organisation = user.getOrganisation().length();
+ if (organisation < 3 || 250 < organisation) {
+ bindingResult.addError(new FieldError("user", "organisation", "The organisation must be between 3 and 250 symbols long!"));
+ model.addAttribute("error", "wrong organisation name");
+ return "Register";
+ }
+
+ user.setRegistrationDate(new Date());
+ UserManager cm = new CassandraUserManager();
+ try {
+ cm.addUser(user);
+ } catch (DataIntegrityViolationException e) {
+ bindingResult.addError(new FieldError("user", "email", "This email (username) is already in use!"));
+ model.addAttribute("error", "used email");
+ return "Register";
+ }
+ if (user.isUpdateByEmail()) {
+ subscribeToList(user.getEmail());
+ }
+ /*
+ Account.autoLogin(user, request, authenticationManager);
+ */
+ return "redirect:/index";
+ }
+
+ @RequestMapping(value = "/register/edit/do", method = RequestMethod.POST)
+ public String editUser(Model model, @ModelAttribute("user") User user, BindingResult bindingResult) {
+
+ if (bindingResult.hasErrors()) {
+ return "Register";
+ }
+
+ user.setRegistrationDate(new Date());
+ UserManager cm = new CassandraUserManager();
+ try {
+ cm.addUser(user);
+ } catch (DataIntegrityViolationException e) {
+ bindingResult.addError(new FieldError("user", "email", "This email (username) is already in use!"));
+ return "Register";
+ }
+ if (user.isUpdateByEmail()) {
+ subscribeToList(user.getEmail());
+ }
+
+ return "redirect:/index";
+ }
+
+ private void subscribeToList(String email) {
+ SimpleMailMessage message = new SimpleMailMessage();
+ message.setFrom(email);
+ message.setTo("proteocache-discuss-subscribe@compbio.dundee.ac.uk");
+ message.setSubject("ProteoCache mailing list subscription");
+ message.setText("testing " + email);
+ //mailSender.send(message);
+ }
+
+}
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core"%>
+<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions"%>
+<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form"%>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/publicmenu.jsp" />
+ <spring:url value="/register/do" var="query"/>
+
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <div style="font-weight:bold;">Create a new user account</div>
+ </div>
+ <div class="panel-body">
+
+ <form:form method="POST" modelAttribute="user" action="${query}">
+ <div class="col-xs-4"><!-- make the field shorter -->
+ <c:choose>
+ <c:when test="${error == null}">
+ <div class="form-group">
+ <form:input class="form-control" type="text" path="fullName" placeholder="Full name (3-50 symbols)" />
+ <p></p>
+ <form:input class="form-control" type="text" path="email" placeholder="Email (used as account name)" />
+ <p></p>
+ <form:input class="form-control" type="password" path="password" placeholder="Password (at least 6 symbols)" />
+ <p></p>
+ <form:input class="form-control" type="text" path="position" placeholder="Your position" />
+ <p></p>
+ <form:input class="form-control" type="text" path="organisation" placeholder="Your organisation (3-250 symbols)" />
+ <p></p>
+ <form:checkbox path="updateByEmail"/>
+ <form:label path="updateByEmail" >Subscribe to ProteoCache mailing list</form:label>
+ <p></p>
+ <button type="submit" class="btn btn-default">Login</button>
+ </div>
+ </c:when>
+ <c:otherwise>
+ <div class="form-group has-error">
+ <form:input class="form-control" type="text" path="fullName" placeholder="Full name" />
+ <form:errors path="fullName" cssClass="error" />
+ <p></p>
+ <form:input class="form-control" type="text" path="email" placeholder="Email, used as account name" />
+ <form:errors path="email" cssClass="error" />
+ <p></p>
+ <form:input class="form-control" type="password" path="password" placeholder="Password" />
+ <form:errors path="password" cssClass="error" />
+ <p></p>
+ <form:input class="form-control" type="text" path="position" placeholder="Your position" />
+ <form:errors path="position" cssClass="error" />
+ <p></p>
+ <form:input class="form-control" type="text" path="organisation" placeholder="Your organisation" />
+ <form:errors path="organisation" cssClass="error" />
+ <p></p>
+ <form:checkbox path="updateByEmail"/>
+ <form:label path="updateByEmail" >Subscribe to ProteoCache mailing list</form:label>
+ <p></p>
+ <button type="submit" class="btn btn-default">Login</button>
+ </div>
+ </c:otherwise>
+ </c:choose>
+ </div>
+ </form:form>
+
+<!--
+ <sf:form method="POST" modelAttribute="user" action="/register/do">
+ <fieldset>
+ <table cellspacing="0">
+ <tr>
+ <td><sf:input path="fullName" size="15"/>
+ <sf:errors path="fullName" cssClass="error" />
+ </td>
+ </tr>
+ <tr>
+ <td><sf:input path="email" size="30"/>
+ <small>the email address is used as your JABAWS download username</small><br/>
+ <sf:errors path="email" cssClass="error" />
+ </td>
+ </tr>
+ <tr>
+ <th><sf:label path="password">Enter a password for JABAWS:</sf:label></th>
+ <td><sf:password path="password" size="30" showPassword="true"/>
+ <small>6 characters or more</small><br/>
+
+ </td>
+ </tr>
+ <tr>
+ <th><sf:label path="position">Position:</sf:label></th>
+ <td><sf:input path="position" size="20" maxlength="200" />
+ <small>postdoc, PI, Staff scientists, Industry, etc</small><br/>
+ <sf:errors path="position" cssClass="error" />
+ </td>
+ </tr>
+ <tr>
+ <th><sf:label path="organisation">Organisation:</sf:label></th>
+ <td><sf:input path="organisation" size="20" maxlength="200" />
+ <small>your organisation</small><br/>
+ <sf:errors path="organisation" cssClass="error" />
+ </td>
+ </tr>
+ <tr>
+ <th></th>
+ <td>
+ <sf:checkbox path="updateByEmail"/>
+ <sf:label path="updateByEmail" >Subscribe to ProteoCache mailing list</sf:label>
+ <br/>
+ </td>
+ </tr>
+ <tr>
+ <th></th>
+ <td><input name="commit" type="submit" value="I accept. Create my account." /></td>
+ </tr>
+ </table>
+ </fieldset>
+ </sf:form>
+-->
+
+ </div>
+ </div>
+ <jsp:include page="fragments/footer.jsp"/>
+ </div>
+</body>
+</html>
\ No newline at end of file
+++ /dev/null
-<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
-<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
-
-<jsp:include page="logos.jsp" />
-
-<nav class="navbar navbar-default" role="navigation">
- <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
- <ul class="nav navbar-nav">
- <li style="width: 100px;">
- <a href="<spring:url value="/" htmlEscape="true" />"><span class="glyphicon glyphicon-home"></span> Home</a>
- </li>
- <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-search"></span> Search Servlets <b class="caret"></b></a>
- <ul class="dropdown-menu">
- <li><a href="<spring:url value="/sequence/query1" htmlEscape="true" />">Protein Sequence</a></li>
- <li><a href="<spring:url value="/joblog" htmlEscape="true" />">Job</a></li>
- <li><a href="<spring:url value="/ip" htmlEscape="true" />">IP</a></li>
- </ul>
- </li>
- <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-stats"></span> Statistics Servlets<b class="caret"></b></a>
- <ul class="dropdown-menu">
- <li><a href="<spring:url value="/exectime" htmlEscape="true" />">Job Time Execution</a></li>
- <li><a href="<spring:url value="/stat" htmlEscape="true" />">Daily Job Statistics</a></li>
- <li><a href="<spring:url value="/ip/stat" htmlEscape="true" />">IPs by Job count</a></li>
- <li><a href="<spring:url value="/sequence/query2" htmlEscape="true" />">Proteins by Job count</a></li>
- </ul>
- </li>
- <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-edit"></span> Database Servlets<b class="caret"></b></a>
- <ul class="dropdown-menu">
- <li><a href="<spring:url value="/database/state" htmlEscape="true" />">DB state</a></li>
- <li><a href="<spring:url value="/database/remove" htmlEscape="true" />">Remove records</a></li>
- </ul>
- </li>
- </ul>
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-question-sign"></span> Help<b class="caret"></b></a>
- <ul class="dropdown-menu">
- <li><a href="<spring:url value="/help/overview" htmlEscape="true" />">Overview</a></li>
- <li><a href="<spring:url value="/help/howto" htmlEscape="true" />">How to</a></li>
- <li><a href="<spring:url value="/help/doc" htmlEscape="true" />">Documentation</a></li>
- <li><a href="<spring:url value="/help/javadoc" htmlEscape="true" />">Javadoc</a></li>
- </ul>
- </li>
- </ul>
- </div><!-- /.navbar-collapse -->
-</nav>
--- /dev/null
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+
+<jsp:include page="logos.jsp" />
+
+<nav class="navbar navbar-default">
+ <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="<spring:url value="/" htmlEscape="true" />"><span class="glyphicon glyphicon-home"></span> Home</a>
+ </li>
+ <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-arrow-down"></span> Login<b class="caret"></b></a>
+ <ul class="dropdown-menu">
+ <li><a href="<spring:url value="/login" htmlEscape="true" />">Login</a></li>
+ <li><a href="<spring:url value="/register/query" htmlEscape="true" />">Register</a></li>
+ </ul>
+ </li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown"><span class="glyphicon glyphicon-question-sign"></span> Help<b class="caret"></b></a>
+ <ul class="dropdown-menu">
+ <li><a href="<spring:url value="/help/overview" htmlEscape="true" />">Overview</a></li>
+ <li><a href="<spring:url value="/help/howto" htmlEscape="true" />">How to</a></li>
+ <li><a href="<spring:url value="/help/doc" htmlEscape="true" />">Documentation</a></li>
+ <li><a href="<spring:url value="/help/javadoc" htmlEscape="true" />">Javadoc</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!-- /.navbar-collapse -->
+</nav>
--- /dev/null
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core"%>
+<html>
+<body>
+ <h3>Message : ${message}</h3>
+ <h3>Username : ${username}</h3>
+
+ <a href="<c:url value="/j_spring_security_logout" />"> Logout</a>
+
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core"%>
+<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions"%>
+<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form"%>
+
+<spring:url value="/j_spring_security_check" var="scheck" />
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body onload='document.f.j_username.focus();'>
+ <div class="container">
+ <jsp:include page="fragments/publicmenu.jsp" />
+ <spring:url value="/ip/query" var="query" />
+
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <div style="font-weight: bold;">Enter your username (email used during registration) and password</div>
+ </div>
+ <div class="panel-body">
+ <form name='f' action="${scheck}" method='POST'>
+ <div class="col-xs-3"><!-- make the field shorter -->
+ <c:choose>
+ <c:when test="${error == null}">
+ <div class="form-group">
+ <input class="form-control" type="text" name="j_username" id="UserName" placeholder="Username (email)" />
+ <p></p>
+ <input class="form-control" type="password" name="j_password" id="UserPass" placeholder="Password" />
+ <p></p>
+ <button type="submit" class="btn btn-default">Login</button>
+ </div>
+ </c:when>
+ <c:otherwise>
+ <div class="form-group has-error">
+ <input class="form-control" type="text" name="j_username" id="UserName" placeholder="Username (email)" />
+ <p></p>
+ <input class="form-control" type="password" name="j_password" id="UserPass" placeholder="Password" />
+ <p class="help-block">${error}</p>
+ <button type="submit" class="btn btn-default">Login</button>
+ </div>
+ </c:otherwise>
+ </c:choose>
+ </div>
+ </form>
+ </div>
+ </div>
+ <jsp:include page="fragments/footer.jsp" />
+ </div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/publicmenu.jsp" />
+ <div class="row">
+ <div class="col-md-6">
+ <div class="panel panel-default">
+ <div class="panel-heading">Execution statistics for the last days</div>
+ <div class="panel-body">
+ bla-bla
+ </div>
+ </div>
+ </div>
+ <div class="col-md-6">
+ <div class="panel panel-default">
+ <div class="panel-heading">Overview</div>
+ <div class="panel-body">
+ ProteoCache is as a repository of the result of running all tools in the Dundee Resource on
+ complete proteomes. The data are updated on a regular basis as tools are improved and genomes newly
+ sequenced or updated.
+ </div>
+ </div>
+ </div>
+ </div>
+ <jsp:include page="fragments/footer.jsp"/>
+ </div>
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+ pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@page import="java.util.ArrayList"%>
+
+<html>
+<jsp:include page="../fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="../fragments/mainmenu.jsp" />
+
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <div style="font-weight:bold;">The page is not available...</div>
+ </div>
+ <div class="panel-body">
+ <p>You don'h have enough permissions to view the page</p>
+ </div>
+ </div>
+
+ <jsp:include page="../fragments/footer.jsp" />
+ </div>
+</body>
+</html>
\ No newline at end of file
git://source.jalview.org / proteocache.git / commitdiff