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Feature/fix phenomenal tool config #249

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merged 4 commits into from
Jul 5, 2018
Merged

Feature/fix phenomenal tool config #249

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af62b0d
correct config
michaelvanvliet Jul 4, 2018
c3cad78
Add log entries when parsing of config fails
michaelvanvliet Jul 4, 2018
566c775
Log k8s destionation config errors through galaxy logger
ilveroluca Jul 5, 2018
2b9a917
whitespace
ilveroluca Jul 5, 2018
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4 changes: 2 additions & 2 deletions config/phenomenal_tools2container.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -527,12 +527,12 @@ assignment:
max_pod_retrials: 1
tools_id:
- fingerprint_clustering
- docker_image_override: fingerprintsubnetwork
docker_owner_override: phnmnl
docker_image_override: fingerprintsubnetwork
docker_tag_override: v1.1_cv1.3.4
max_pod_retrials: 1
docker_repo_override: container-registry.phenomenal-h2020.eu
tools_id:
- docker_repo_override: container-registry.phenomenal-h2020.eu
- fingerprint_subnetwork
- docker_image_override: scp-aspera
docker_owner_override: phnmnl
Expand Down
39 changes: 27 additions & 12 deletions rules/k8s_destinations.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
from galaxy.jobs import JobDestination

import logging
import yaml

from galaxy.jobs import JobDestination

log = logging.getLogger(__name__)

# Sizes for the different set of resources to be used in Kubernetes
# CPU values are in CPU units (0.1 means 100 mili CPUs)
Expand All @@ -12,31 +16,31 @@
'limits_cpu': 0.5,
'requests_memory': 0.3,
'limits_memory': 0.6
}
}

__small = {'requests_cpu': 0.4,
'limits_cpu': 0.8,
'requests_memory': 0.5,
'limits_memory': 0.9
}
}

__medium = {'requests_cpu': 0.7,
'limits_cpu': 2,
'requests_memory': 0.8,
'limits_memory': 2
}
}

__large = {'requests_cpu': 1.5,
'limits_cpu': 4,
'requests_memory': 1.8,
'limits_memory': 5
}
}

__xlarge = {'requests_cpu': 4,
'limits_cpu': 8,
'requests_memory': 8,
'limits_memory': 16
}
}

__path_tool2container = "config/phenomenal_tools2container.yaml"

Expand Down Expand Up @@ -72,12 +76,23 @@ def k8s_wrapper_xlarge(resource_params, tool_id):


def __read_assignments(resource_params, tool_id):
stream = open(__path_tool2container, mode='r')
mappings = yaml.load(stream)
for mapping in mappings['assignment']:
if tool_id in mapping['tools_id']:
resource_params.update(mapping)
break
try:
stream = open(__path_tool2container, mode='r')
mappings = yaml.load(stream)
except:
log.error("Couldn't load %s file!\n", __path_tool2container)
raise

try:
for mapping in mappings['assignment']:
if tool_id in mapping['tools_id']:
resource_params.update(mapping)
break
except StandardError as e:
log.error('Error parsing file: %s\n', __path_tool2container)
log.error(str(e))
log.error("Problem in the following assignment mapping: %s", mapping)
raise


def __setup_resources(resource_params, settings):
Expand Down