diff --git a/pom.xml b/pom.xml
index 74dfb68..429b481 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
pom
SEquence DAtaset builder
diff --git a/seda-docker/Dockerfile b/seda-docker/Dockerfile
index c5b052c..9d44ca5 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-1.5.0.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
diff --git a/seda-docker/Dockerfile.local b/seda-docker/Dockerfile.local
index 03953ca..3da4697 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-1.5.0.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
diff --git a/seda-docker/docker-compose.yml b/seda-docker/docker-compose.yml
index d9cd24c..b487686 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:1.5.0
+ image: pegi3s/seda:1.5.1
build:
context: ./
dockerfile: Dockerfile.local
diff --git a/seda-docs/source/conf.py b/seda-docs/source/conf.py
index e3b0610..5385916 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'2017-2021, 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.
diff --git a/seda-plugin-bedtools/pom.xml b/seda-plugin-bedtools/pom.xml
index 84456c5..723b521 100644
--- a/seda-plugin-bedtools/pom.xml
+++ b/seda-plugin-bedtools/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-blast/pom.xml b/seda-plugin-blast/pom.xml
index 3214368..a124c1d 100644
--- a/seda-plugin-blast/pom.xml
+++ b/seda-plugin-blast/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-cga/pom.xml b/seda-plugin-cga/pom.xml
index ebe84f3..a7d38d7 100644
--- a/seda-plugin-cga/pom.xml
+++ b/seda-plugin-cga/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-clustalomega/pom.xml b/seda-plugin-clustalomega/pom.xml
index 2f005c7..74b9f4e 100644
--- a/seda-plugin-clustalomega/pom.xml
+++ b/seda-plugin-clustalomega/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-emboss/pom.xml b/seda-plugin-emboss/pom.xml
index 5e40e66..2e3a231 100644
--- a/seda-plugin-emboss/pom.xml
+++ b/seda-plugin-emboss/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-pfam/pom.xml b/seda-plugin-pfam/pom.xml
index ce5ac8a..b469e00 100644
--- a/seda-plugin-pfam/pom.xml
+++ b/seda-plugin-pfam/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanBatch.java b/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanBatch.java
index bfc0d30..4eb3c3a 100644
--- a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanBatch.java
+++ b/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);
}
diff --git a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequest.java b/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequest.java
index 3426fc8..ccac3ed 100644
--- a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequest.java
+++ b/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();
diff --git a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequestConfiguration.java b/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequestConfiguration.java
index e9cd0bf..535ab82 100644
--- a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanRequestConfiguration.java
+++ b/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 getEvalue() {
- return Optional.of(eValue);
+ return Optional.ofNullable(eValue);
}
public PfamScanSequenceErrorPolicy getErrorPolicy() {
diff --git a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanStatus.java b/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanStatus.java
index c70fd3a..da2fdbb 100644
--- a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/PfamScanStatus.java
+++ b/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);
+ }
}
diff --git a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/gui/PfamScanTransformationProvider.java b/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/gui/PfamScanTransformationProvider.java
index a093eab..110bfb6 100644
--- a/seda-plugin-pfam/src/main/java/org/sing_group/seda/pfam/gui/PfamScanTransformationProvider.java
+++ b/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;
diff --git a/seda-plugin-prosplign-procompart/pom.xml b/seda-plugin-prosplign-procompart/pom.xml
index b85c1fb..da01992 100644
--- a/seda-plugin-prosplign-procompart/pom.xml
+++ b/seda-plugin-prosplign-procompart/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-sapp/pom.xml b/seda-plugin-sapp/pom.xml
index 95b784a..81c4759 100644
--- a/seda-plugin-sapp/pom.xml
+++ b/seda-plugin-sapp/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda-plugin-splign-compart/pom.xml b/seda-plugin-splign-compart/pom.xml
index e65c2a4..76b6e1c 100644
--- a/seda-plugin-splign-compart/pom.xml
+++ b/seda-plugin-splign-compart/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml
diff --git a/seda/pom.xml b/seda/pom.xml
index 7b00de1..6dfbb30 100644
--- a/seda/pom.xml
+++ b/seda/pom.xml
@@ -6,7 +6,7 @@
org.sing_group
seda-all
- 1.5.0
+ 1.5.1
../pom.xml