Merge branch 'release-1.7'

PavlidisLab · Dec 22, 2021 · 20b25d8 · 20b25d8
2 parents 5fbd0b0 + cb9fe6a
commit 20b25d8
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Showing 3 changed files with 33 additions and 19 deletions.
diff --git a/.gitignore b/.gitignore
@@ -34,3 +34,13 @@ created by https://www.gitignore.io
 
 ### Python ###
 *.py[cod]
+.DS_Store
+gotrack/.DS_Store
+gotrack/etc/.DS_Store
+gotrack/etc/scripts/.DS_Store
+gotrack/src/main/java/ubc/pavlab/gotrack/beans/.DS_Store
+gotrack/src/main/java/ubc/pavlab/gotrack/model/.DS_Store
+gotrack/src/main/webapp/.DS_Store
+gotrack/src/main/webapp/resources/.DS_Store
+gotrack/src/main/webapp/WEB-INF/.DS_Store
+gotrack/src/test/java/ubc/pavlab/gotrack/.DS_Store
diff --git a/gotrack/etc/scripts/update/resources.py b/gotrack/etc/scripts/update/resources.py
@@ -26,7 +26,7 @@ class Resources:
     goa_gpi_template = 'goa_{0}.gpi.{1}.gz'
 
     uniprot_ftp_host = 'ftp.uniprot.org'
-    uniprot_ftp_directory = '/pub/databases/uniprot/knowledgebase/docs/'
+    uniprot_ftp_directory = '/pub/databases/uniprot/current_release/knowledgebase/docs/'
 
     def __init__(self, directory, database_state, check_ftp=True):
         self.directory = directory
@@ -163,6 +163,9 @@ def ftp_list(host, directory):
         except error_perm, reason:
             log.warn("Cannot find directory in FTP site: %s: %s", directory, reason)
             return [];
+        except:
+            log.warn("Unknown FTP error occurred")
+            return [];
         finally:
             if ftp is not None:
                 ftp.close()

diff --git a/gotrack/pom.xml b/gotrack/pom.xml
@@ -4,9 +4,9 @@
     <groupId>ubc.pavlab</groupId>
     <artifactId>gotrack</artifactId>
     <packaging>war</packaging>
-    <version>1.6.1</version>
+    <version>1.7</version>
     <name>gotrack</name>
-    <url>http://maven.apache.org</url>
+    <url>https://maven.apache.org</url>
 
     <properties>
 
@@ -19,7 +19,7 @@
         <!-- Web -->
         <servlet.version>3.1.0</servlet.version>
         <jsf.version>2.3.3</jsf.version>
-        <weld.version>3.0.0.Final</weld.version>
+        <weld.version>3.1.7.SP1</weld.version>
 
         <!-- logging -->
         <log4j.version>2.17.0</log4j.version>
@@ -50,10 +50,11 @@
             <scope>provided</scope>
         </dependency>
         <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>jstl</artifactId>
-            <version>1.2</version>
-        </dependency>
+	    <groupId>jakarta.servlet.jsp.jstl</groupId>
+	    <artifactId>jakarta.servlet.jsp.jstl-api</artifactId>
+	    <version>1.2.7</version>
+	    <scope>runtime</scope>
+	</dependency>
         <dependency> <!-- Optional, only when <f:websocket> is used. -->
             <groupId>org.glassfish</groupId>
             <artifactId>javax.json</artifactId>
@@ -91,7 +92,7 @@
         <dependency>
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-json-jackson</artifactId>
-            <version>2.21.1</version>
+            <version>3.0.2</version>
         </dependency>
 
         <!-- End Rest dependencies-->
@@ -117,7 +118,7 @@
         <dependency>
             <groupId>org.primefaces</groupId>
             <artifactId>primefaces</artifactId>
-            <version>6.1</version>
+            <version>6.2</version>
         </dependency>
 
         <dependency>
@@ -129,21 +130,21 @@
         <dependency>
             <groupId>org.primefaces.extensions</groupId>
             <artifactId>primefaces-extensions</artifactId>
-            <version>6.1.1</version>
+            <version>6.2.10</version>
         </dependency>
 
         <!-- PDF Exporting -->
         <dependency>
-            <groupId>com.lowagie</groupId>
-            <artifactId>itext</artifactId>
-            <version>4.2.1</version>
+            <groupId>com.itextpdf</groupId>
+            <artifactId>itextpdf</artifactId>
+            <version>5.5.13.2</version>
         </dependency>
 
         <!-- XLS Exporting -->
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>3.11</version>
+            <version>5.0.0</version>
         </dependency>
 
         <!-- Omnifaces -->
@@ -193,8 +194,8 @@
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>5.1.35</version>
-            <scope>provided</scope>
+            <version>8.0.25</version>
+            <scope>runtime</scope>
         </dependency>
 
         <dependency>
@@ -221,7 +222,7 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>23.0</version>
+            <version>30.1.1-jre</version>
         </dependency>
 
         <!-- Trove -->
@@ -237,7 +238,7 @@
         <dependency>
             <groupId>org.mindrot</groupId>
             <artifactId>jbcrypt</artifactId>
-            <version>0.3m</version>
+            <version>0.4</version>
         </dependency>
 
         <!-- dom4j Dependency -->