From 4329012dd43c3bf6dcb6ac63f2453480ee547ed9 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Wed, 27 Jul 2022 14:14:13 +0200
Subject: [PATCH] handled issues with kpm results
---
tasks/keypathwayminer_task.py | 26 +++++++++++++++++---------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/tasks/keypathwayminer_task.py b/tasks/keypathwayminer_task.py
index 3e5099a..4036466 100755
--- a/tasks/keypathwayminer_task.py
+++ b/tasks/keypathwayminer_task.py
@@ -198,10 +198,16 @@ def kpm_task(task_hook: TaskHook):
network = {'nodes': nodes, 'edges': edges}
# Remapping everything from UniProt Accession numbers to internal IDs
- result_nodes = Protein.objects.filter(uniprot_code__in=network["nodes"])
+ flat_map = lambda f, xs: (y for ys in xs for y in f(ys))
+ uniprote_nodes = []
+ uniprote_nodes.extend(network["nodes"])
+ uniprote_nodes.extend(set(flat_map(lambda l: [l['from'], l['to']], network['edges'])))
+
+ result_nodes = Protein.objects.filter(uniprot_code__in=uniprote_nodes)
node_map = {}
node_map_for_edges = {}
+
for node in result_nodes:
node_map_for_edges[node.uniprot_code] = node.id
if id_space == 'symbol':
@@ -213,19 +219,21 @@ def kpm_task(task_hook: TaskHook):
if id_space == 'ensembl':
node_map[node.uniprot_code] = [ensg.name for ensg in EnsemblGene.objects.filter(protein_id=node.id)]
- flat_map = lambda f, xs: (y for ys in xs for y in f(ys))
- network["nodes"] = flat_map(lambda uniprot: node_map[uniprot], network["nodes"])
- network["edges"] = list(map(
- lambda uniprot_edge: {"from": "p" + str(node_map_for_edges[uniprot_edge["from"]]),
- "to": "p" + str(node_map_for_edges[uniprot_edge["to"]])},
- network["edges"]))
+
+ network["nodes"] = list(flat_map(lambda uniprot: node_map[uniprot], network["nodes"]))
+ drugstone_edges = []
+ for uniprot_edge in network['edges']:
+ from_node = f'p{node_map_for_edges[uniprot_edge["from"]]}' if uniprot_edge['from'] in node_map_for_edges else uniprot_edge['from']
+ to_node = f'p{node_map_for_edges[uniprot_edge["to"]]}' if uniprot_edge['to'] in node_map_for_edges else uniprot_edge['to']
+ drugstone_edges.append({"from": from_node,"to": to_node})
+ network['edges']=drugstone_edges
node_types = {node: "protein" for node in network["nodes"]}
- is_seed = {node: node in set(map(lambda p: "p"+str(p),protein_backend_ids)) for node in network["nodes"]}
+ is_seed = {node: node in set(map(lambda p: "p" + str(p), protein_backend_ids)) for node in network["nodes"]}
result_dict = {
"network": network,
- "target_nodes":[node for node in network["nodes"] if node not in task_hook.seeds],
+ "target_nodes": [node for node in network["nodes"] if node not in task_hook.seeds],
"node_attributes": {"node_types": node_types, "is_seed": is_seed}
}
task_hook.set_results(results=result_dict)
--
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