Fixes PfamScan operation

pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.sing_group</groupId>
 	<artifactId>seda-all</artifactId>
-	<version>1.5.0</version>
+	<version>1.5.1</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-1.5.0.tar.gz -O /tmp/SEDA.tar.gz && \
+RUN wget https://www.sing-group.org/seda/downloads/releases/seda-linux-64b-1.5.1.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.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-1.5.0.tar.gz /tmp/SEDA.tar.gz
+COPY seda-linux-64b-1.5.1.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:1.5.0
+    image: pegi3s/seda:1.5.1
     build:
       context: ./
       dockerfile: Dockerfile.local

seda-docs/source/conf.py

@@ -46,7 +46,7 @@
 
 # General information about the project.
 project = u'SEDA'
-copyright = u'2017-2021, Jorge Vieira, Cristina Vieira, Noé Vázquez, Miguel Reboiro-Jato and Hugo López-Fernández'
+copyright = u'2017-2023, 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'1.5'
 # The full version, including alpha/beta/rc tags.
-release = u'1.5.0'
+release = u'1.5.1'
 
 # 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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanBatch.java

@@ -63,7 +63,7 @@ public void run() {
             try {
               request.query();
 
-              while (request.getStatus().equals(PfamScanStatus.RUNNING)) {
+              while (request.getStatus().isAlive()) {
                 TimeUnit.SECONDS.sleep(DELAY_STATUS_RETRY);
               }
 

seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequest.java

@@ -96,6 +96,11 @@ private HttpEntity buildMultipartEntity() {
         .addTextBody("email", this.configuration.getEmail())
         .addTextBody("title", this.sequence.getName())
         .addTextBody("sequence", this.sequence.getChain());
+
+    if (this.configuration.getEvalue().isPresent()) {
+      entityBuilder = entityBuilder
+        .addTextBody("evalue", Double.toString(this.configuration.getEvalue().get()));
+    }
 
     return entityBuilder.build();
   }
@@ -105,7 +110,7 @@ public PfamScanStatus getStatus() throws ClientProtocolException, IOException {
       return PfamScanStatus.UNSUBMITED;
     }
 
-    if (this.status == null || this.status == PfamScanStatus.RUNNING) {
+    if (this.status == null || this.status.isAlive()) {
       HttpGet httpGet = new HttpGet(new StringBuilder(URL_STATUS).append(this.requestId).toString());
 
       CloseableHttpClient httpClient = HttpClientBuilder.create().build();

seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequestConfiguration.java

@@ -25,6 +25,8 @@
 
 public class PfamScanRequestConfiguration {
 
+  public static final String DEFAULT_DATABASE = "pfam-a";
+
   private String eMail;
   private String database;
   private boolean activeSitePrediction;
@@ -70,7 +72,7 @@ public boolean isActiveSitePrediction() {
   }
 
   public Optional<Double> getEvalue() {
-    return Optional.of(eValue);
+    return Optional.ofNullable(eValue);
   }
 
   public PfamScanSequenceErrorPolicy getErrorPolicy() {

seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanStatus.java

@@ -22,5 +22,9 @@
 package org.sing_group.seda.pfam;
 
 public enum PfamScanStatus {
-  RUNNING, FINISHED, ERROR, FAILURE, NOT_FOUND, UNSUBMITED
+  RUNNING, FINISHED, ERROR, FAILURE, NOT_FOUND, UNSUBMITED, QUEUED;
+
+  public boolean isAlive() {
+    return this.equals(RUNNING) || this.equals(QUEUED);
+  }
 }

seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/gui/PfamScanTransformationProvider.java

@@ -21,6 +21,7 @@
  */
 package org.sing_group.seda.pfam.gui;
 
+import static org.sing_group.seda.pfam.PfamScanRequestConfiguration.DEFAULT_DATABASE;
 import static org.sing_group.seda.pfam.gui.PfamScanTransformationConfigurationChangeType.ACTIVE_SITE_PREDICTION_CHANGED;
 import static org.sing_group.seda.pfam.gui.PfamScanTransformationConfigurationChangeType.BATCH_DELAY_CHANGED;
 import static org.sing_group.seda.pfam.gui.PfamScanTransformationConfigurationChangeType.EMAIL_CHANGED;
@@ -44,8 +45,6 @@
 @XmlAccessorType(XmlAccessType.FIELD)
 public class PfamScanTransformationProvider extends AbstractTransformationProvider {
 
-  public static final String DEFAULT_DATABASE = "pfam-a";
-
   @XmlElement
   private String eMail;
 

seda-plugin-prosplign-procompart/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-        <version>1.5.0</version>
+        <version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</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>1.5.0</version>
+		<version>1.5.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>1.5.0</version>
+		<version>1.5.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>