From d0654e511f5409562b117b69a7179a89fb8513bc Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 8 Jul 2022 21:48:48 +0200
Subject: [PATCH] fixing quick and super start options
Former-commit-id: f9b708c980c22a69d8d278b18746fa6e4dc0926f [formerly d723b2b2a56250e28389f51e00aa7b1cf3fec4e4]
Former-commit-id: b8187f101c13fe2852638cf69cf188fd52031b63
---
drugstone/backend_tasks.py | 6 ++++--
scripts/docker-entrypoint.sh | 2 +-
tasks/quick_task.py | 29 +++++++++++++++++++++--------
tasks/util/scores_to_results.py | 1 -
4 files changed, 26 insertions(+), 12 deletions(-)
diff --git a/drugstone/backend_tasks.py b/drugstone/backend_tasks.py
index 01f7827..05101a6 100755
--- a/drugstone/backend_tasks.py
+++ b/drugstone/backend_tasks.py
@@ -1,4 +1,5 @@
import json
+import traceback
from datetime import datetime
import redis
@@ -69,9 +70,10 @@ def run_task(token, algorithm, parameters):
elif algorithm in ['quick', 'super']:
from tasks.quick_task import quick_task
quick_task(task_hook)
- except Exception as e:
- r.set(f'{token}_status', f'{e}')
+ except Exception as ex:
+ r.set(f'{token}_status', f'{ex}')
r.set(f'{token}_failed', '1')
+ print(''.join(traceback.format_exception(etype=type(ex), value=ex, tb=ex.__traceback__)))
def refresh_from_redis(task):
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index db7a2d3..0245a23 100755
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
python3 manage.py migrate
python3 manage.py createfixtures
python3 manage.py cleanuptasks
-#python3 manage.py populate_db --update -a
+python3 manage.py populate_db --update -a
#python3 manage.py make_graphs
/usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"
diff --git a/tasks/quick_task.py b/tasks/quick_task.py
index acedc5e..e4a9c5b 100755
--- a/tasks/quick_task.py
+++ b/tasks/quick_task.py
@@ -31,6 +31,25 @@ def quick_task(task_hook: TaskHook):
# Run closeness centrality
closeness_centrality(closeness_task_hook)
+ def run_trust_rank(parameters, seeds):
+ from .trust_rank import trust_rank
+
+ def progress(progress, status):
+ task_hook.set_progress(2 / 3 + 1 / 3 * progress, status)
+
+ def set_result(result):
+ task_hook.set_results(result)
+
+ parameters.update({
+ "seeds": seeds,
+ "result_size": 20,
+ "include_non_approved_drugs": True,
+ "include_indirect_drugs": False,
+ })
+
+ tr_task_hook = TaskHook(parameters, task_hook.data_directory, progress, set_result)
+ trust_rank(tr_task_hook)
+
def run_multi_steiner(parameters):
from .multi_steiner import multi_steiner
@@ -47,14 +66,8 @@ def quick_task(task_hook: TaskHook):
if len(seeds) == 0:
task_hook.set_results({"network": {"nodes": [], "edges": []}})
return
- closeness_parameters = {
- "seeds": seeds,
- "result_size": 10,
- "hub_penalty": 1,
- "strain_or_drugs": "drugs",
- "include_non_approved_drugs": True,
- }
- run_closeness(closeness_parameters)
+
+ run_trust_rank(parameters, seeds)
parameters["num_trees"] = 1
parameters["hub_penalty"] = 1
diff --git a/tasks/util/scores_to_results.py b/tasks/util/scores_to_results.py
index fccbec2..f09b161 100755
--- a/tasks/util/scores_to_results.py
+++ b/tasks/util/scores_to_results.py
@@ -86,7 +86,6 @@ def scores_to_results(
"nodes": [g.vertex_properties[node_name_attribute][node] for node in returned_nodes],
"edges": [{"from": g.vertex_properties[node_name_attribute][source], "to": g.vertex_properties[node_name_attribute][target]} for source, target in returned_edges],
}
- print(subgraph)
# Compute node attributes.
node_types = {g.vertex_properties[node_name_attribute][node]: g.vertex_properties["type"][node] for node in returned_nodes}
--
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