Merge branch 'release-1.2.7'

PavlidisLab · Mar 25, 2019 · 099b89e · 099b89e
2 parents e2ec226 + 1dbb77a
commit 099b89e
Show file tree

Hide file tree

Showing 14 changed files with 77,815 additions and 54,368 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.2.6</version>
+    <version>1.2.7</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>

diff --git a/src/main/java/ubc/pavlab/rdp/controllers/MainController.java b/src/main/java/ubc/pavlab/rdp/controllers/MainController.java
@@ -3,8 +3,11 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
@@ -17,6 +20,7 @@
 import ubc.pavlab.rdp.settings.ApplicationSettings;
 
 import javax.mail.MessagingException;
+import javax.servlet.http.Cookie;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
@@ -197,6 +201,41 @@ public ModelAndView supportPost( HttpServletRequest request, @RequestParam("name
         return modelAndView;
     }
 
+
+    @RequestMapping(value="/gettimeout", method = RequestMethod.GET, produces = "application/json")
+    @ResponseBody
+    public ModelAndView getTimeout(HttpServletRequest servletRequest, HttpServletResponse servletResponse) {
+    // public ResponseEntity<Object> getTimeout(HttpServletRequest servletRequest, HttpServletResponse servletResponse) {
+	// Set cookie
+	addTimeoutCookies(servletRequest, servletResponse);
+
+	ModelAndView modelAndView = new ModelAndView();
+	modelAndView.addObject( "message", "Session timeout refreshed." );
+
+	//return new ResponseEntity<Object>(HttpStatus.OK);
+	return modelAndView;
+    }
+
+    private void addTimeoutCookies(HttpServletRequest servletRequest, HttpServletResponse servletResponse) {
+        User user = userService.findCurrentUser();
+	if ( user != null ) {
+	    // Only set timeout cookie if the user is authenticated.	    
+	    long currTime = System.currentTimeMillis();	    
+	    int TIMEOUT_IN_SECONDS = servletRequest.getSession().getMaxInactiveInterval() - 60; // Subtracting by 60s to give an extra minute client-side.
+	    long expiryTime = currTime + TIMEOUT_IN_SECONDS * 1000;
+
+	    // Get cookie for server current time.
+	    Cookie serverTimeCookie = new Cookie("serverTime", "" + currTime);
+	    serverTimeCookie.setPath("/");
+	    servletResponse.addCookie(serverTimeCookie);
+
+	    // Get cookie for expiration time (consistent with serverTime cookie).
+	    Cookie expiryCookie = new Cookie("sessionExpiry", "" + expiryTime);
+	    expiryCookie.setPath("/");
+	    servletResponse.addCookie(expiryCookie);
+	}
+    }
+
     private boolean searchAuthorized(User user){
         if(adminRole == null) {
             adminRole = roleRepository.findByRole( "ROLE_ADMIN" );

diff --git a/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java b/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java
@@ -3,9 +3,12 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;    
+import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.servlet.ModelAndView;
@@ -19,6 +22,14 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedList;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.List;
+import java.util.ArrayList;
+
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
 
 /**
  * Created by mjacobson on 05/02/18.
@@ -227,15 +238,61 @@ public ModelAndView searchUsersByGeneView( @RequestParam String symbol, @Request
             modelAndView.setViewName( "fragments/error :: message" );
             modelAndView.addObject( "errorMessage", String.format( ERR_NO_ORTHOLOGS, symbol ) );
         } else {
-            modelAndView.addObject( "usergenes", handleGeneSearch( gene, tier, orthologs ) );
+	    modelAndView.addObject( "usergenes", handleGeneSearch( gene, tier, orthologs ) );
             modelAndView.setViewName( "fragments/user-table :: usergenes-table" );
         }
 
         return modelAndView;
     }
 
-    @RequestMapping(value = "/search/view/international", method = RequestMethod.GET, params = { "symbol", "taxonId",
-            "tier" })
+    @RequestMapping(value = "/search/view/orthologs", method = RequestMethod.GET, params = { "symbol", "taxonId", "tier" })
+    public ModelAndView searchOrthologsForGene(@RequestParam String symbol, @RequestParam Integer taxonId,
+					       @RequestParam TierType tier,
+					       @RequestParam(name = "orthologTaxonId", required = false) Integer orthologTaxonId ) {
+        if(!searchAuthorized( userService.findCurrentUser(), false )){
+            return null;
+        }
+
+        // Only look for orthologs when taxon is human
+        if(taxonId != 9606){
+            orthologTaxonId = null;
+        }
+
+        Taxon taxon = taxonService.findById( taxonId );
+        Gene gene = geneService.findBySymbolAndTaxon( symbol, taxon );
+        Collection<Gene> orthologs = getOrthologsIfRequested( orthologTaxonId, gene );
+	Map<String, List<Gene>> orthologMap = null;
+
+        ModelAndView modelAndView = new ModelAndView();
+
+        if ( gene == null ) {
+            modelAndView.setViewName( "fragments/error :: message" );
+            modelAndView.addObject( "errorMessage", String.format( ERR_NO_GENE, symbol ) );
+        } else if (
+		   // Check if there is a ortholog request for a different taxon than the original gene
+		   ( orthologTaxonId != null && !orthologTaxonId.equals( gene.getTaxon().getId() ) )
+		   // Check if we got some ortholog results
+		   && ( orthologs == null || orthologs.isEmpty() ) ) {
+            modelAndView.setViewName( "fragments/error :: message" );
+            modelAndView.addObject( "errorMessage", String.format( ERR_NO_ORTHOLOGS, symbol ) );
+        } else {
+	    orthologMap = new HashMap<>();
+	    for (Gene o : orthologs){
+		String name = o.getTaxon().getCommonName();
+		if (!orthologMap.containsKey(name)) {
+		    orthologMap.put(name, new ArrayList<Gene>());
+		} 
+		orthologMap.get(name).add(o);		
+	    }	    
+            modelAndView.addObject( "orthologs", orthologMap );	 
+            modelAndView.setViewName( "fragments/ortholog-table :: ortholog-table" );
+        }
+        return modelAndView;
+    }
+
+
+
+    @RequestMapping(value = "/search/view/international", method = RequestMethod.GET, params = { "symbol", "taxonId", "tier" })
     public ModelAndView searchItlUsersByGeneView( @RequestParam String symbol, @RequestParam Integer taxonId,
             @RequestParam TierType tier,
             @RequestParam(name = "orthologTaxonId", required = false) Integer orthologTaxonId ) {
@@ -321,16 +378,21 @@ Collection<Gene> getOrthologsIfRequested( Integer orthologTaxonId, Gene gene ) {
         //noinspection unchecked
         return Collections.EMPTY_LIST;
     }
-
+    
     private boolean searchAuthorized( User user, boolean international ) {
+
         if ( adminRole == null ) {
             adminRole = roleRepository.findByRole( "ROLE_ADMIN" );
         }
 
-        return ( applicationSettings.getPrivacy().isPublicSearch() // Search is public
-                || ( applicationSettings.getPrivacy().isRegisteredSearch() && user != null ) // Search is registered and there is user logged
-                || ( user != null && adminRole != null && user.getRoles().contains( adminRole ) ) ) // User is admin
-
+	if ( user == null ){
+	    log.info( "User is null in searchAuthorized(); Non-public search will not be authorized." );
+	}
+
+
+        return ( applicationSettings.getPrivacy().isPublicSearch() // Search is public		 
+		 || ( user != null && applicationSettings.getPrivacy().isRegisteredSearch()  ) // Search is registered and there is user logged
+		 || ( user != null && adminRole != null && user.getRoles().contains( adminRole ) ) ) // User is admin
                 && ( !international || applicationSettings.getIsearch().isEnabled() ); // International search enabled
     }
 

diff --git a/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java
@@ -203,10 +203,11 @@ public String getCurrentEmail() {
 
     @Override
     public User findCurrentUser() {
-        Authentication auth = SecurityContextHolder.getContext().getAuthentication();
+        Authentication auth = SecurityContextHolder.getContext().getAuthentication();	
         if ( auth == null || auth.getPrincipal().equals( "anonymousUser" ) ) {
             return null;
         }
+
         return findUserByIdNoAuth( ( ( UserPrinciple ) auth.getPrincipal() ).getId() );
     }