[pull] develop from SouthGreenPlatform:master

README.md

@@ -4,9 +4,10 @@ Gigwa aims at managing genomic and genotyping data from NGS analyses. It is a to
 
 Try Gigwa online with public datasets at https://gigwa.southgreen.fr/
 
-## Latest webapp and bundles are now available for download on Gigwa homepage: https://www.southgreen.fr/content/gigwa
+## Check more information about Gigwa on the project homepage:
+[https://www.southgreen.fr/gigwa](https://www.southgreen.fr/gigwa)
 
-## Check the wiki:
+## Check the wiki for changelog:
 https://github.com/SouthGreenPlatform/Gigwa2/wiki
 
 ## Developer instructions

docker-compose.yml

@@ -7,7 +7,7 @@ services:
   tomcat:
     depends_on:
       - mongo
-    image: guilhemsempere/gigwa:2.11-RELEASE
+    image: guilhemsempere/gigwa:2.12-RELEASE
     ports:
       - 8080:8080 # You may amend the external port only (left hand side). By default, webapp URL will be http://host.ip:8080/gigwa
     restart: always

misc/linux_bundle.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Variables
-project_version="2.11-RELEASE"
+project_version="2.12-RELEASE"
 tomcat_version="9.0.113"
 mongodb_linux_file="linux-x86_64-ubuntu1804-4.2.25"
 path_to_ubuntu_jre="zulu17.40.19-ca-jre17.0.6-linux_x64.tar.gz"

misc/macos_bundle.command

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Variables
-project_version="2.11-RELEASE"
+project_version="2.12-RELEASE"
 tomcat_version="9.0.113"
 mongodb_osx_file="macos-x86_64-4.2.25"
 path_to_osx_jre="zulu17.40.19-ca-jre17.0.6-macosx_x64.tar.gz"

misc/win_bundle.ps1

@@ -1,5 +1,5 @@
 # Variables
-$project_version = "2.11-RELEASE"
+$project_version = "2.12-RELEASE"
 $tomcat_version = "9.0.113"
 $mongodb_windows_file = "win32-x86_64-2012plus-4.2.25"
 $path_to_windows_jre = "zulu17.40.19-ca-jre17.0.6-win_x64"

pom.xml

@@ -4,7 +4,7 @@
 
 	<modelVersion>4.0.0</modelVersion>
 	<properties>
-        <project.version>2.11-RELEASE</project.version>
+        <project.version>2.12-RELEASE</project.version>
 		<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<bundle.dir>${project.build.directory}/bundles</bundle.dir>
@@ -52,7 +52,7 @@
    		<dependency>
 		    <groupId>fr.cirad</groupId>
 		    <artifactId>Mgdb2BrapiV2Impl</artifactId>
-		    <version>2.1.1-RELEASE</version>
+		    <version>2.1.2-RELEASE</version>
 		    <exclusions>
 		    	<exclusion>
 				    <groupId>org.slf4j</groupId>
@@ -77,7 +77,7 @@
 		<dependency>
 			<groupId>fr.cirad</groupId>
 			<artifactId>Gigwa2ServiceImpl</artifactId>
-			<version>2.11-RELEASE</version>
+			<version>2.12-RELEASE</version>
 			<exclusions>
 				<exclusion>
 					<groupId>com.fasterxml.jackson.core</groupId>

src/main/java/fr/cirad/web/controller/IGVProxyController.java

@@ -0,0 +1,161 @@
+package fr.cirad.web.controller;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import fr.cirad.tools.AppConfig;
+
+@Controller
+@RequestMapping(IGVProxyController.IGV_PROXY_URL)
+public class IGVProxyController {
+
+	public static final String IGV_PROXY_URL = "/igvProxy";
+
+	@Autowired private AppConfig appConfig;
+
+    private List<String> allowedDomains = null;
+    private List<String> wildcardDomains = null;
+
+    @GetMapping("/**")
+    public void proxyRequest(
+            @RequestParam("url") String targetUrl,
+            HttpServletRequest request,
+            HttpServletResponse response) throws IOException {
+
+    	if (allowedDomains == null) {
+	    	String allowedDomainsConfig = appConfig.get("igvProxiedDomains");
+	        allowedDomains = Arrays.stream(allowedDomainsConfig.split(","))
+	            .map(String::trim)
+	            .filter(d -> !d.startsWith("*."))
+	            .collect(Collectors.toList());
+
+	        wildcardDomains = Arrays.stream(allowedDomainsConfig.split(","))
+	            .map(String::trim)
+	            .filter(d -> d.startsWith("*."))
+	            .map(d -> d.substring(2)) // Remove '*.' prefix
+	            .collect(Collectors.toList());
+    	}
+
+        // Validate the URL against whitelist
+        if (!isUrlAllowed(targetUrl)) {
+            response.setStatus(HttpStatus.FORBIDDEN.value());
+            response.getWriter().write("Domain not allowed for proxying");
+            return;
+        }
+
+        HttpURLConnection connection = null;
+        try {
+            URL url = new URL(targetUrl);
+            connection = (HttpURLConnection) url.openConnection();
+
+            // Set method
+            connection.setRequestMethod(request.getMethod());
+
+            // CRITICAL: Forward the Range header if present
+            String rangeHeader = request.getHeader("Range");
+            if (rangeHeader != null)
+                connection.setRequestProperty("Range", rangeHeader);
+
+            // Forward other headers (selectively)
+            String userAgent = request.getHeader("User-Agent");
+            if (userAgent != null) {
+                connection.setRequestProperty("User-Agent", userAgent);
+            }
+
+            // Connect and get response
+            connection.connect();
+            int responseCode = connection.getResponseCode();
+
+            // CRITICAL: Set proper status for partial content
+            if (responseCode == HttpURLConnection.HTTP_PARTIAL) {
+                response.setStatus(HttpStatus.PARTIAL_CONTENT.value());
+            } else {
+                response.setStatus(responseCode);
+            }
+
+            // CRITICAL: Forward Content-Range header if present
+            String contentRange = connection.getHeaderField("Content-Range");
+            if (contentRange != null) {
+                response.setHeader("Content-Range", contentRange);
+            }
+
+            // Forward Accept-Ranges header if present
+            String acceptRanges = connection.getHeaderField("Accept-Ranges");
+            if (acceptRanges != null) {
+                response.setHeader("Accept-Ranges", acceptRanges);
+            }
+
+            // Forward Content-Length if present
+            String contentLength = connection.getHeaderField("Content-Length");
+            if (contentLength != null) {
+                response.setHeader("Content-Length", contentLength);
+            }
+
+            // Forward Content-Type
+            String contentType = connection.getHeaderField("Content-Type");
+            if (contentType != null) {
+                response.setHeader("Content-Type", contentType);
+            }
+
+            // Copy response body
+            InputStream inputStream;
+            if (responseCode >= 400)
+                inputStream = connection.getErrorStream();
+            else
+                inputStream = connection.getInputStream();
+
+            byte[] buffer = new byte[8192];
+            int bytesRead;
+            while ((bytesRead = inputStream.read(buffer)) != -1) {
+                response.getOutputStream().write(buffer, 0, bytesRead);
+            }
+
+            response.getOutputStream().flush();
+
+        } catch (Exception e) {
+            response.setStatus(HttpStatus.INTERNAL_SERVER_ERROR.value());
+            response.getWriter().write("Proxy error: " + e.getMessage());
+        } finally {
+            if (connection != null) {
+                connection.disconnect();
+            }
+        }
+    }
+
+    private boolean isUrlAllowed(String url) {
+        try {
+            URL targetUrl = new URL(url);
+            String host = targetUrl.getHost();
+
+            if (allowedDomains.contains(host)) {
+                return true;
+            }
+
+            for (String wildcardDomain : wildcardDomains) {
+                if (host.endsWith("." + wildcardDomain) || host.equals(wildcardDomain)) {
+                    return true;
+                }
+            }
+
+            return false;
+        } catch (MalformedURLException e) {
+            return false;
+        }
+    }
+}

src/main/java/fr/cirad/web/controller/gigwa/GigwaRestController.java

@@ -1429,27 +1429,7 @@ public ModelAndView setupImportPage()
 
 		return "";
 	}
-
-//	@ApiIgnore
-//	@ApiOperation(authorizations = { @Authorization(value = "AuthorizationToken") }, value = germplasmWithBrapiMappingURL, notes = "Lists IDs of germplasm with external reference source & ID")
-//	@GetMapping(value = BASE_URL + germplasmWithBrapiMappingURL)
-//	public @ResponseBody Collection<String> germplasmWithBrapiMappingURL(HttpServletRequest request, @RequestParam("module") final String sModule) {
-//        return MgdbDao.getInstance().loadIndividualsWithAllMetadata(sModule, AbstractTokenManager.getUserNameFromAuthentication(tokenManager.getAuthenticationFromToken(tokenManager.readToken(request))), null, null)
-//    		.values().stream()
-//    		.filter(ind -> ind.getAdditionalInfo().get(BrapiService.BRAPI_FIELD_externalReferenceSource) != null && ind.getAdditionalInfo().get(BrapiService.BRAPI_FIELD_externalReferenceId) != null)
-//    		.map(ind -> sModule + Helper.ID_SEPARATOR + ind.getId()).toList();
-//	}
-//	
-//	@ApiIgnore
-//	@ApiOperation(authorizations = { @Authorization(value = "AuthorizationToken") }, value = samplesWithBrapiMappingURL, notes = "Lists IDs of samples with external reference source & ID")
-//	@GetMapping(value = BASE_URL + samplesWithBrapiMappingURL)
-//	public @ResponseBody Collection<String> samplesWithBrapiMappingURL(HttpServletRequest request, @RequestParam("module") final String sModule) {
-//        return MgdbDao.getInstance().loadSamplesWithAllMetadata(sModule, AbstractTokenManager.getUserNameFromAuthentication(tokenManager.getAuthenticationFromToken(tokenManager.readToken(request))), null, null)
-//    		.values().stream()
-//    		.filter(sp -> sp.getAdditionalInfo().get(BrapiService.BRAPI_FIELD_externalReferenceSource) != null && sp.getAdditionalInfo().get(BrapiService.BRAPI_FIELD_externalReferenceId) != null)
-//    		.map(sp -> sModule + Helper.ID_SEPARATOR + sp.getId()).toList();
-//	}
-//	
+
 	private HashMap<String, String> getImportFilesByExtension(Collection<MultipartFile> importFiles, Collection<String> filesSpecifiedByURI) throws Exception{
         HashMap<String, String> filesByExtension = new HashMap<>();
         HashMap<String, String> synonymExtensions = new HashMap() {{ put("csv", "tsv"); put("phenotype", "tsv"); }};	// .phenotype is only synonym with tsv

src/main/resources/config.default

@@ -156,4 +156,7 @@ allowedOrigins_/**=*
 maxPcaMatrixSize = 1E9
 
 # Max dimension of the genotyping matrix (#samples x #SNPs) to calculate distance matrix on. Default is 1 billion (1E9)
-maxDistanceMatrixSize = 1E9
+maxDistanceMatrixSize = 1E9
+
+# CSV list of domains (supporting wildcards) for which IGV.js will use a proxy to access genome / track files (workaround for CORS issues)
+igvProxiedDomains = jbrowse.southgreen.fr

src/main/resources/config.properties

@@ -175,3 +175,6 @@ maxPcaMatrixSize = 1E8
 
 # Max dimension of the genotyping matrix (#samples x #SNPs) to calculate distance matrix on. Default is 1 billion (1E9)
 maxDistanceMatrixSize = 1E8
+
+# CSV list of domains (supporting wildcards) for which IGV.js will use a proxy to access genome / track files (workaround for CORS issues)
+igvProxiedDomains = jbrowse.southgreen.fr

src/main/webapp/META-INF/MANIFEST.MF

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Build-Jdk-Spec: 21
 Created-By: Maven Integration for Eclipse
-Implementation-version: 2.11-RELEASE
+Implementation-version: 2.12-RELEASE
 Class-Path: 
 

src/main/webapp/css/main.css

@@ -183,6 +183,22 @@ div#termsOfUse .modal-lg {
     width: 950px;
 }
 
+div#termsOfUse ol {
+  list-style-type: none;
+  padding-left: 0;
+  counter-reset: li-counter;
+}
+
+div#termsOfUse ol > li {
+  counter-increment: li-counter;
+  margin-bottom: 0.5em;
+}
+
+div#termsOfUse ol > li h4::before {
+  content: counter(li-counter) ") ";
+  margin-right: 0.2em;
+}
+
 div#chartDialog .modal-lg, div#individualFiltering .modal-lg, div#manual .modal-lg, div#variantDetailPanel .modal-lg, div#fjBytesPanel .modal-lg, div#genomeBrowserPanel .modal-lg, div#igvPanel .modal-lg {
     width: 99%;
 }

src/main/webapp/docs/gigwa_docs.html

@@ -13,7 +13,7 @@
       <BR>
       <a href="javascript:window.print();" title="Print documentation"><IMG SRC="print.png" BORDER=0 style='float:right; margin-right:10px;'></a>
       <P ALIGN=CENTER STYLE="margin-bottom: 0in; line-height: 100%;">
-         <FONT FACE="Arial, sans-serif"><FONT SIZE=6 class='maintitle'>Gigwa v2.11.x &ndash; Documentation</FONT></FONT>
+         <FONT FACE="Arial, sans-serif"><FONT SIZE=6 class='maintitle'>Gigwa v2.12.x &ndash; Documentation</FONT></FONT>
       </P>
       <p style='float:right; text-align:center; margin-top:20px; margin-right:20px; background-color:#f2f288; padding:15px; border:2px dashed #d5d800; border-radius:15px;'>
          <b>Learn how to use Gigwa like a pro in a few minutes!</b>
@@ -582,6 +582,9 @@
 			   <LI>
 			      <P><B>maxDistanceMatrixSize</B> - Max dimension of the genotyping matrix (#samples x #SNPs) to calculate distance matrix on. Default is 1 billion (1E9)</P>
 			   </LI>
+			   <LI>
+			      <P><B>igvProxiedDomains</B> - CSV list of domains (supporting wildcards) for which IGV.js will use a proxy to access genome / track files (workaround for CORS issues)</P>
+			   </LI>
             </UL>
          </LI>
       </UL>