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Cast exceptions to string using unicodify #150

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Merged
mvdbeek merged 2 commits into from
Oct 26, 2019
Merged

Cast exceptions to string using unicodify #150

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e2cbc54
Cast exceptions to string using unicodify
mvdbeek Oct 26, 2019
381c0a5
Don't bail out if individual repositories don't install
mvdbeek Oct 26, 2019
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12 changes: 7 additions & 5 deletions src/ephemeris/shed_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
GalaxyInteractorApi,
verify_tool,
)
from galaxy.util import unicodify

from . import get_galaxy_connection, load_yaml_file
from .ephemeris_log import disable_external_library_logging, setup_global_logger
Expand Down Expand Up @@ -141,9 +142,10 @@ def install_repositories(self,
default_install_repository_dependencies=default_install_repository_dependencies,
force_latest_revision=force_latest_revision)
repository_list.append(complete_repo)
except (LookupError, KeyError) as e:
except Exception as e:
# We'll run through the loop come whatever may, we log the errored repositories at the end anyway.
if log:
log_repository_install_error(repository, start, str(e), log)
log_repository_install_error(repository, start, unicodify(e), log)
errored_repositories.append(repository)

# Filter out already installed repos
Expand Down Expand Up @@ -382,13 +384,13 @@ def install_repository_revision(self, repository, log):
log=log)
return "installed"
except (ConnectionError, requests.exceptions.ConnectionError) as e:
if default_err_msg in str(e):
if default_err_msg in unicodify(e):
# THIS SHOULD NOT HAPPEN DUE TO THE CHECKS EARLIER
if log:
log.debug("\tRepository %s already installed (at revision %s)" %
(repository['name'], repository['changeset_revision']))
return "skipped"
elif "504" in str(e) or 'Connection aborted' in str(e):
elif "504" in unicodify(e) or 'Connection aborted' in unicodify(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)
Expand Down Expand Up @@ -437,7 +439,7 @@ def wait_for_install(self, repository, log=None, timeout=3600):
time.sleep(10)
except ConnectionError as e:
if log:
log.warning('Failed to get repositories list: %s', str(e))
log.warning('Failed to get repositories list: %s', unicodify(e))
time.sleep(10)
return False

Expand Down
3 changes: 2 additions & 1 deletion src/ephemeris/sleep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from argparse import ArgumentParser

import requests
from galaxy.util import unicodify

from .common_parser import get_common_args

Expand Down Expand Up @@ -52,7 +53,7 @@ def galaxy_wait(galaxy_url, timeout=600, verbose=False):
sys.stdout.flush()
except requests.exceptions.ConnectionError as e:
if verbose:
sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, str(e)[0:100]))
sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[0:100]))
sys.stdout.flush()
count += 1

Expand Down
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