diff --git a/.gitignore b/.gitignore index 026356d..dde4b69 100644 --- 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 index 41ae680..8384f87 100755 --- 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 index 44b8d62..5464217 100644 --- a/gotrack/pom.xml +++ b/gotrack/pom.xml @@ -4,9 +4,9 @@ ubc.pavlab gotrack war - 1.6.1 + 1.7 gotrack - http://maven.apache.org + https://maven.apache.org @@ -19,7 +19,7 @@ 3.1.0 2.3.3 - 3.0.0.Final + 3.1.7.SP1 2.17.0 @@ -50,10 +50,11 @@ provided - javax.servlet - jstl - 1.2 - + jakarta.servlet.jsp.jstl + jakarta.servlet.jsp.jstl-api + 1.2.7 + runtime + org.glassfish javax.json @@ -91,7 +92,7 @@ org.glassfish.jersey.media jersey-media-json-jackson - 2.21.1 + 3.0.2 @@ -117,7 +118,7 @@ org.primefaces primefaces - 6.1 + 6.2 @@ -129,21 +130,21 @@ org.primefaces.extensions primefaces-extensions - 6.1.1 + 6.2.10 - com.lowagie - itext - 4.2.1 + com.itextpdf + itextpdf + 5.5.13.2 org.apache.poi poi - 3.11 + 5.0.0 @@ -193,8 +194,8 @@ mysql mysql-connector-java - 5.1.35 - provided + 8.0.25 + runtime @@ -221,7 +222,7 @@ com.google.guava guava - 23.0 + 30.1.1-jre @@ -237,7 +238,7 @@ org.mindrot jbcrypt - 0.3m + 0.4