Fixes progress dialog appearance

pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.sing_group</groupId>
 	<artifactId>seda-all</artifactId>
-	<version>1.7.1</version>
+	<version>1.7.2</version>
 	<packaging>pom</packaging>
 
 	<name>SEquence DAtaset builder</name>

seda-docker/Dockerfile

@@ -15,7 +15,7 @@ RUN apt-get update && apt-get install -y \
 		stable" && \
 	apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io
 
-RUN wget https://www.sing-group.org/seda/downloads/releases/seda-linux-64b-1.7.1.tar.gz -O /tmp/SEDA.tar.gz && \
+RUN wget https://www.sing-group.org/seda/downloads/releases/seda-linux-64b-1.7.2.tar.gz -O /tmp/SEDA.tar.gz && \
 	mkdir /opt/SEDA && tar zxvf /tmp/SEDA.tar.gz -C /opt/SEDA && rm /tmp/SEDA.tar.gz
 
 RUN sed -i -e "s#DIR=#if [ -d \"/data\" ]; then D_ARGS='-Dseda.output.directory=/data -Dseda.input.directory=/data'; else D_ARGS='-Dseda.output.directory=/ -Dseda.input.directory=/'; fi\n\nDIR=#g" /opt/SEDA/run-gui.sh

seda-docker/Dockerfile.local

@@ -15,7 +15,7 @@ RUN apt-get update && apt-get install -y \
 		stable" && \
 	apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io
 
-COPY seda-linux-64b-1.7.1.tar.gz /tmp/SEDA.tar.gz
+COPY seda-linux-64b-1.7.2.tar.gz /tmp/SEDA.tar.gz
 
 RUN mkdir /opt/SEDA && tar zxvf /tmp/SEDA.tar.gz -C /opt/SEDA && rm /tmp/SEDA.tar.gz
 

seda-docker/docker-compose.yml

@@ -1,7 +1,7 @@
 version: "3.3"
 services:
   seda:
-    image: pegi3s/seda:1.7.1
+    image: pegi3s/seda:1.7.2
     build:
       context: ./
       dockerfile: Dockerfile.local

seda-docs/source/conf.py

@@ -46,7 +46,7 @@
 
 # General information about the project.
 project = u'SEDA'
-copyright = u'2017-2024, Jorge Vieira, Cristina Vieira, Noé Vázquez, Miguel Reboiro-Jato and Hugo López-Fernández'
+copyright = u'2017-2025, Jorge Vieira, Cristina Vieira, Noé Vázquez, Miguel Reboiro-Jato and Hugo López-Fernández'
 author = u'Jorge Vieira, Cristina Vieira, Noé Vázquez, Miguel Reboiro-Jato and Hugo López-Fernández'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -56,7 +56,7 @@
 # The short X.Y version.
 version = u'1.7'
 # The full version, including alpha/beta/rc tags.
-release = u'1.7.1'
+release = u'1.7.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

seda-plugin-bedtools/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-blast/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-cga/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-clustalomega/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-emboss/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-pfam/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-prosplign-procompart/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-        <version>1.7.1</version>
+        <version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-sapp/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-splign-compart/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.7.1</version>
+		<version>1.7.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiDatasetProcessor.java

@@ -81,7 +81,11 @@ public List<File> process(File outputDirectory) throws IOException {
                         for (File file : files) {
                             // Move and rename each file to output directory
                             File renamedFile = new File(outputDirectory, subDir.getName() + ".fasta");
-                            Files.move(file.toPath(), renamedFile.toPath());
+                            if (!renamedFile.exists()) {
+                                Files.move(file.toPath(), renamedFile.toPath());
+                            } else {
+                                System.out.println("File " + renamedFile.getAbsolutePath() + " already exists. Skipping.");
+                            }
                             extractedFiles.add(renamedFile);
                         }
                     }

seda/src/main/java/org/sing_group/seda/gui/PathSelectionPanel.java

@@ -384,23 +384,25 @@ private void loadNcbiDataset() {
 
     new CustomSwingWorker(() -> {
       showFileChooserAndProcess(
-          JFileChooser.FILES_ONLY, JFileChooser.OPEN_DIALOG, true, zipFile -> {
-            System.out.println(zipFile);
+          JFileChooser.FILES_ONLY, JFileChooser.OPEN_DIALOG, false, zipFile -> {
+            System.out.println("Processing NCBI ZIP file" + zipFile);
             try {
+              SwingUtilities.invokeLater(() -> {
+                dialog.setVisible(true);
+              });
               new NcbiDatasetProcessor(zipFile.toFile())
                   .process(IOUtils.createSedaUserHomeDirectory("SEDA_NCBI_datasets"))
                   .forEach(f -> model.addAvailablePath(f.toPath()));
             } catch (IOException e) {
               e.printStackTrace();
+            } finally {
+              dialog.dispose();
             }
-            dialog.dispose();
           },
           () -> {
             dialog.dispose();
           });
     }).execute();
-
-    dialog.setVisible(true);
   }
 
   private void updateAvailableAndSelectedLabels() {