From 3ee6f17a53d312fdda57ba275f4f22f9075439a0 Mon Sep 17 00:00:00 2001 From: "Yakubov, Sergey" Date: Fri, 10 Feb 2023 14:42:38 -0500 Subject: [PATCH 1/2] fix hostname parsing for newer Docker versions newer versions seem to return "[::]" instead "::", we check that as well --- lib/galaxy/tool_util/deps/docker_util.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/deps/docker_util.py b/lib/galaxy/tool_util/deps/docker_util.py index dade02ba898..0c02636e06e 100644 --- a/lib/galaxy/tool_util/deps/docker_util.py +++ b/lib/galaxy/tool_util/deps/docker_util.py @@ -198,6 +198,11 @@ def parse_port_text(port_text): >>> slurm_ports[8888]['host'] '0.0.0.0' >>> ports = parse_port_text("5432/tcp -> :::5432") + >>> len(ports) + 0 + >>> ports_new = parse_port_text("5432/tcp -> [::]:5432") + >>> len(ports_new) + 0 """ ports = None if port_text is not None: @@ -207,7 +212,7 @@ def parse_port_text(port_text): raise Exception(f"Cannot parse host and port from line [{line}]") tool, host = line.split(" -> ", 1) hostname, port = host.rsplit(":", 1) - if hostname == "::": + if hostname in ["::", "[::]"]: # Skip unspecified IPv6 address, which is also specified as 0:0:0:0 in another line. # This is brittle of course, but so is parsing the container ports like this. continue From c0ebe9fdb021e6d3dd7db13f6197d62df8f15fa8 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 15 Mar 2023 12:06:43 +0100 Subject: [PATCH 2/2] Bump tuswsgi middleware The middleware attempts to cleanup files on every upload, this can be a problem if there are many files in the upload directory, especially on NFS. --- lib/galaxy/dependencies/dev-requirements.txt | 2 +- lib/galaxy/dependencies/pinned-requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index d28bada04ad..2de873dbd20 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -227,7 +227,7 @@ tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or pytho trio-websocket==0.9.2; python_version >= "3.7" and python_version < "4.0" trio==0.21.0; python_version >= "3.7" and python_version < "4.0" tuspy==0.2.5 -tuswsgi==0.5.4 +tuswsgi==0.5.5 twill==3.0.2 typed-ast==1.5.4; python_version < "3.8" and implementation_name == "cpython" and python_full_version >= "3.6.2" and python_version >= "3.7" typing-extensions==4.2.0; python_version >= "3.7" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 74f8f510fc7..9e4d35bb5bd 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -159,7 +159,7 @@ tenacity==8.0.1; python_version >= "3.6" tifffile==2021.11.2; python_version >= "3.7" tornado==6.1; python_version >= "3.5" tqdm==4.64.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" -tuswsgi==0.5.4 +tuswsgi==0.5.5 typing-extensions==4.2.0; python_version >= "3.7" tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2