Unverified Commit f963b67a authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #11955 from mvdbeek/fix_ipv6_port_parsing 

[20.09] Fix container port parsing if IPv6 hostname is ``::``
parents 306e774a 01cdbd3e

lib/galaxy/jobs/__init__.py

+9 −0
Original line number Diff line number Diff line
@@ -2125,6 +2125,15 @@ class JobWrapper(HasResourceParameters): 
            log.debug("found container runtime %s" % container_runtime)

            self.app.interactivetool_manager.configure_entry_points(job, container_runtime)

            return True

        container_exception_path = os.path.join(working_directory, "container_monitor_exception.txt")

        if os.path.exists(container_exception_path):

            with open(container_exception_path) as fh:

                exception_string = fh.read()

            error_message = "Monitoring interactive tool entry point failed"

            log.error("Monitoring interactive tool entry point for job {} failed: {}".format(self.job_id, exception_string))

            self.fail(error_message)

            # local job runner uses return value to determine if we're done polling

            return True



    def container_monitor_command(self, container, **kwds):

        if not container or not self.tool.produces_entry_points:

lib/galaxy/tool_util/deps/docker_util.py

+6 −1
Original line number Diff line number Diff line
@@ -223,6 +223,7 @@ def parse_port_text(port_text): 
    >>> slurm_ports = parse_port_text("8888/tcp -> 0.0.0.0:32769")

    >>> slurm_ports[8888]['host']

    '0.0.0.0'

    >>> ports = parse_port_text("5432/tcp -> :::5432")

    """

    ports = None

    if port_text is not None:
@@ -231,7 +232,11 @@ def parse_port_text(port_text): 
            if " -> " not in line:

                raise Exception("Cannot parse host and port from line [%s]" % line)

            tool, host = line.split(" -> ", 1)

            hostname, port = host.split(':')

            hostname, port = host.rsplit(':', 1)

            if hostname == '::':

                # 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

            port = int(port)

            tool_p, tool_prot = tool.split("/")

            tool_p = int(tool_p)

lib/galaxy_ext/container_monitor/monitor.py

+8 −3
Original line number Diff line number Diff line
@@ -4,6 +4,7 @@ import subprocess 
import sys

import tempfile

import time

import traceback



# insert *this* galaxy before all others on sys.path

sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
@@ -44,6 +45,7 @@ def main(): 
        raise Exception("Monitoring container type [%s], not yet implemented." % container_type)



    ports_raw = None

    exc_traceback = ""

    for i in range(10):

        try:

            ports_raw = parse_ports(container_name, connection_configuration)
@@ -62,10 +64,13 @@ def main(): 
                break

            else:

                raise Exception("Failed to recover ports...")

        except Exception as e:

            with open("container_monitor_exception.txt", "a") as f:

                f.write(str(e) + "\n\n\n")

        except Exception:

            exc_info = sys.exc_info()

            exc_traceback = "".join(traceback.format_exception(*exc_info))

        time.sleep(i * 2)

    else:

        with open("container_monitor_exception.txt", "w") as f:

            f.write(exc_traceback)





if __name__ == "__main__":

test/integration/test_interactivetools_api.py

+7 −2
Original line number Diff line number Diff line
@@ -69,12 +69,17 @@ class BaseInteractiveToolsIntegrationTestCase(ContainerizedIntegrationTestCase): 
            entry_points = self.entry_points_for_job(job_id)

            if len(entry_points) != expected_num:

                return None

            elif any([not e["active"] for e in entry_points]):

            elif any(not e["active"] for e in entry_points):

                job_json = self._get("jobs/{}?full=true".format(job_id)).json()

                if job_json['state'] == 'error':

                    raise Exception("Interactive tool job {} failed: {}".format(job_id, job_json))

                return None

            else:

                return entry_points



        return wait_on(active_entry_points, "entry points to become active")

        # It currently takes at least 90 seconds until we can be sure the container monitor failed.

        # Can be decreased when galaxy_ext/container_monitor/monitor.py changes

        return wait_on(active_entry_points, "entry points to become active", timeout=120)



    def entry_points_for_job(self, job_id):

        entry_points_response = self._get("entry_points?job_id=%s" % job_id)