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Handle timeout gracefully for UWSGI connection #123

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Merged
rhpvorderman merged 3 commits into from
Mar 18, 2019
Merged

Handle timeout gracefully for UWSGI connection #123

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2499ba5
Handle timeout gracefully for UWSGI connection
pcm32 Mar 15, 2019
f7a04b9
Fix install with installed data managers
mvdbeek Mar 15, 2019
59d863e
Point out why get_repo_from_tool may return empty dict
mvdbeek Mar 18, 2019
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4 changes: 3 additions & 1 deletion src/ephemeris/get_tool_list_from_galaxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,9 @@ def record_repo(tool_elem):
if self.get_data_managers:
for tool in self.installed_tool_list:
if tool.get("model_class") == 'DataManagerTool':
repositories.append(get_repo_from_tool(tool))
repo = get_repo_from_tool(tool)
if repo:
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@rhpvorderman rhpvorderman Mar 18, 2019

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This is a good idea if a tool does not have a repo. Could you add a comment here with an example of why this is needed? For the people who read the code in the future and do not know all galaxy specifics by heart.

repositories.append(repo)

if self.get_all_tools:
tools_with_panel = repositories[:]
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2 changes: 1 addition & 1 deletion src/ephemeris/shed_tools.py
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Expand Up @@ -331,7 +331,7 @@ def install_repository_revision(self, repository, log):
log.debug("\tRepository %s already installed (at revision %s)" %
(repository['name'], repository['changeset_revision']))
return "skipped"
elif "504" in str(e):
elif "504" in str(e) or 'Connection aborted' in str(e):
if log:
log.debug("Timeout during install of %s, extending wait to 1h", repository['name'])
success = self.wait_for_install(repository=repository, log=log, timeout=3600)
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