diff --git a/pom.xml b/pom.xml index 430cf40d..e78c35cd 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 pom SEquence DAtaset builder diff --git a/seda-docker/Dockerfile b/seda-docker/Dockerfile index eabe460d..c9709ee3 100644 --- a/seda-docker/Dockerfile +++ b/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 diff --git a/seda-docker/Dockerfile.local b/seda-docker/Dockerfile.local index 7843051a..af17620c 100644 --- a/seda-docker/Dockerfile.local +++ b/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 diff --git a/seda-docker/docker-compose.yml b/seda-docker/docker-compose.yml index f722a254..ff756275 100644 --- a/seda-docker/docker-compose.yml +++ b/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 diff --git a/seda-docs/source/conf.py b/seda-docs/source/conf.py index c620a1c9..f9e5ac81 100644 --- a/seda-docs/source/conf.py +++ b/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. diff --git a/seda-plugin-bedtools/pom.xml b/seda-plugin-bedtools/pom.xml index 4e283484..b72c4a7c 100644 --- a/seda-plugin-bedtools/pom.xml +++ b/seda-plugin-bedtools/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-blast/pom.xml b/seda-plugin-blast/pom.xml index ac4e9211..bc952fa5 100644 --- a/seda-plugin-blast/pom.xml +++ b/seda-plugin-blast/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-cga/pom.xml b/seda-plugin-cga/pom.xml index f8cac193..c6223fe9 100644 --- a/seda-plugin-cga/pom.xml +++ b/seda-plugin-cga/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-clustalomega/pom.xml b/seda-plugin-clustalomega/pom.xml index db790770..ceaa1b10 100644 --- a/seda-plugin-clustalomega/pom.xml +++ b/seda-plugin-clustalomega/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-emboss/pom.xml b/seda-plugin-emboss/pom.xml index 6debb28b..a77fa520 100644 --- a/seda-plugin-emboss/pom.xml +++ b/seda-plugin-emboss/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-pfam/pom.xml b/seda-plugin-pfam/pom.xml index 7903ecc5..3efd720e 100644 --- a/seda-plugin-pfam/pom.xml +++ b/seda-plugin-pfam/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-prosplign-procompart/pom.xml b/seda-plugin-prosplign-procompart/pom.xml index acae7491..3da4673c 100644 --- a/seda-plugin-prosplign-procompart/pom.xml +++ b/seda-plugin-prosplign-procompart/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-sapp/pom.xml b/seda-plugin-sapp/pom.xml index 606a82f3..06c4ba0c 100644 --- a/seda-plugin-sapp/pom.xml +++ b/seda-plugin-sapp/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda-plugin-splign-compart/pom.xml b/seda-plugin-splign-compart/pom.xml index 91a1f8e5..edca36d3 100644 --- a/seda-plugin-splign-compart/pom.xml +++ b/seda-plugin-splign-compart/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda/pom.xml b/seda/pom.xml index 17f56871..1949714e 100644 --- a/seda/pom.xml +++ b/seda/pom.xml @@ -6,7 +6,7 @@ org.sing_group seda-all - 1.7.1 + 1.7.2 ../pom.xml diff --git a/seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiDatasetProcessor.java b/seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiDatasetProcessor.java index 3796e2e1..a72174eb 100644 --- a/seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiDatasetProcessor.java +++ b/seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiDatasetProcessor.java @@ -81,7 +81,11 @@ public List 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); } } diff --git a/seda/src/main/java/org/sing_group/seda/gui/PathSelectionPanel.java b/seda/src/main/java/org/sing_group/seda/gui/PathSelectionPanel.java index 4479cbd1..246df514 100644 --- a/seda/src/main/java/org/sing_group/seda/gui/PathSelectionPanel.java +++ b/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() {