From c0c0c6f2ee7d140b3a890f4306cc0cf0068ddefa Mon Sep 17 00:00:00 2001
From: "Hartung, Michael" <michael.hartung@uni-hamburg.de>
Date: Mon, 19 Sep 2022 17:27:43 +0200
Subject: [PATCH] first implementation of add edges

Former-commit-id: 7a4b816159343135421f578808fa9ce45dca79fb
---
 docker-compose.yml              |  2 +-
 drugstone/views.py              |  9 +++++----
 tasks/betweenness_centrality.py |  8 ++++++++
 tasks/closeness_centrality.py   |  8 +++++++-
 tasks/degree_centrality.py      |  7 +++++++
 tasks/multi_steiner.py          |  9 +++++++++
 tasks/network_proximity.py      |  8 ++++++++
 tasks/trust_rank.py             |  9 +++++++++
 tasks/util/custom_edges.py      | 18 ++++++++++++++++++
 9 files changed, 72 insertions(+), 6 deletions(-)
 create mode 100644 tasks/util/custom_edges.py

diff --git a/docker-compose.yml b/docker-compose.yml
index 1924f92..3b0d7a3 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -82,7 +82,7 @@ services:
       - db
     networks:
       - drugstone_net
-  flower:  
+  flower:
     image: mher/flower
     container_name: drugstone_flower
     env_file:
diff --git a/drugstone/views.py b/drugstone/views.py
index a18fb48..1b5ae62 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -26,7 +26,6 @@ from drugstone.settings import DEFAULTS
 def get_ppi_ds(source, licenced):
     try:
         ds = models.PPIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
-        ds.id
         return ds
     except:
         if licenced:
@@ -37,7 +36,6 @@ def get_ppi_ds(source, licenced):
 def get_pdi_ds(source, licenced):
     try:
         ds = models.PDIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
-        ds.id
         return ds
     except:
         if licenced:
@@ -48,7 +46,6 @@ def get_pdi_ds(source, licenced):
 def get_pdis_ds(source, licenced):
     try:
         ds = models.PDisDataset.objects.filter(name__iexact=source, licenced=licenced).last()
-        ds.id
         return ds
     except:
         if licenced:
@@ -59,7 +56,6 @@ def get_pdis_ds(source, licenced):
 def get_drdis_ds(source, licenced):
     try:
         ds = models.DrDiDataset.objects.filter(name__iexact=source, licenced=licenced).last()
-        ds.id
         return ds
     except:
         if licenced:
@@ -75,6 +71,11 @@ class TaskView(APIView):
         parameters = request.data['parameters']
         licenced = parameters.get('licenced', False)
 
+        print(models.PDIDataset.objects.all())
+
+        print(get_ppi_ds(parameters.get('ppi_dataset', DEFAULTS['ppi']), licenced))
+        print(get_pdi_ds(parameters.get('pdi_dataset', DEFAULTS['pdi']), licenced))
+
         # find databases based on parameter strings
         parameters['ppi_dataset'] = PPIDatasetSerializer().to_representation(
             get_ppi_ds(parameters.get('ppi_dataset', DEFAULTS['ppi']), licenced))
diff --git a/tasks/betweenness_centrality.py b/tasks/betweenness_centrality.py
index deba027..d4b9e21 100755
--- a/tasks/betweenness_centrality.py
+++ b/tasks/betweenness_centrality.py
@@ -1,3 +1,4 @@
+from tasks.util.custom_edges import add_edges
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
 from tasks.util.scores_to_results import scores_to_results
 from tasks.util.edge_weights import edge_weights
@@ -172,6 +173,8 @@ def betweenness_centrality(task_hook: TaskHook):
 
     id_space = task_hook.parameters["config"].get("identifier","symbol")
 
+    custom_edges = task_hook.parameters.get("custom_edges", False)
+
     # Parsing input file.
     task_hook.set_progress(0 / 3.0, "Parsing input.")
     filename = f"{id_space}_{ppi_dataset['name']}-{pdi_dataset['name']}"
@@ -187,6 +190,11 @@ def betweenness_centrality(task_hook: TaskHook):
         include_non_approved_drugs,
         target=search_target
     )
+
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+
     weights = edge_weights(g, hub_penalty)
 
     # Set number of threads if OpenMP support is enabled.
diff --git a/tasks/closeness_centrality.py b/tasks/closeness_centrality.py
index 1c306ee..3dafc51 100755
--- a/tasks/closeness_centrality.py
+++ b/tasks/closeness_centrality.py
@@ -1,4 +1,5 @@
 import numpy as np
+from tasks.util.custom_edges import add_edges
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
 from tasks.util.scores_to_results import scores_to_results
 from tasks.util.edge_weights import edge_weights
@@ -173,13 +174,18 @@ def closeness_centrality(task_hook: TaskHook):
 
     id_space = task_hook.parameters["config"].get("identifier", "symbol")
 
-    node_name_attribute = "internal_id"
+    custom_edges = task_hook.parameters.get("custom_edges", False)
 
     filename = f"{id_space}_{ppi_dataset['name']}-{pdi_dataset['name']}"
     if ppi_dataset['licenced'] or pdi_dataset['licenced']:
         filename += "_licenced"
     filename = os.path.join(task_hook.data_directory, filename + ".gt")
     g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, id_space, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
+    
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+    
     task_hook.set_progress(1 / 4.0, "Computing edge weights.")
     weights = edge_weights(g, hub_penalty) 
     
diff --git a/tasks/degree_centrality.py b/tasks/degree_centrality.py
index e529c8a..368b5a1 100755
--- a/tasks/degree_centrality.py
+++ b/tasks/degree_centrality.py
@@ -1,5 +1,6 @@
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
 from tasks.util.scores_to_results import scores_to_results
+from tasks.util.custom_edges import add_edges
 from tasks.task_hook import TaskHook
 import graph_tool as gt
 import os.path
@@ -147,6 +148,8 @@ def degree_centrality(task_hook: TaskHook):
     search_target = task_hook.parameters.get("target", "drug-target")
 
     filterPaths = task_hook.parameters.get("filter_paths", True)
+
+    custom_edges = task_hook.parameters.get("custom_edges", False)
     
     # Parsing input file.
     task_hook.set_progress(0 / 3.0, "Parsing input.")
@@ -160,6 +163,10 @@ def degree_centrality(task_hook: TaskHook):
     # g, seed_ids, viral_protein_ids, drug_ids = read_graph_tool_graph(file_path, seeds, datasets, ignored_edge_types, max_deg, ignore_non_seed_baits, False, include_non_approved_drugs)
     g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, id_space, max_deg, False, include_non_approved_drugs, search_target)
     
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+
     # Set number of threads if OpenMP support is enabled.
     if gt.openmp_enabled():
         gt.openmp_set_num_threads(num_threads)
diff --git a/tasks/multi_steiner.py b/tasks/multi_steiner.py
index cc479ad..210b82a 100755
--- a/tasks/multi_steiner.py
+++ b/tasks/multi_steiner.py
@@ -1,4 +1,5 @@
 from tasks.task_hook import TaskHook
+from tasks.util.custom_edges import add_edges
 from tasks.util.steiner_tree import steiner_tree
 from tasks.util.find_bridges import find_bridges
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
@@ -99,6 +100,8 @@ def multi_steiner(task_hook: TaskHook):
 
     node_name_attribute = "internal_id" # nodes in the input network which is created from RepoTrialDB have primaryDomainId as name attribute
 
+    custom_edges = task_hook.parameters.get("custom_edges", False)
+
     # Set number of threads if OpenMP support is enabled.
     if gt.openmp_enabled():
         gt.openmp_set_num_threads(num_threads)
@@ -112,7 +115,13 @@ def multi_steiner(task_hook: TaskHook):
     if ppi_dataset['licenced'] or pdi_dataset['licenced']:
         filename += "_licenced"
     filename = os.path.join(task_hook.data_directory, filename + ".gt")
+    print(filename)
     g, seed_ids, _ = read_graph_tool_graph(filename, seeds, id_space, max_deg, target=search_target)
+
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+
     seed_map = {g.vertex_properties[node_name_attribute][node]: node for node in seed_ids}
     task_hook.set_progress(1 / (float(num_trees + 3)), "Computing edge weights.")
     weights = edge_weights(g, hub_penalty)
diff --git a/tasks/network_proximity.py b/tasks/network_proximity.py
index c07beee..af1ad4a 100755
--- a/tasks/network_proximity.py
+++ b/tasks/network_proximity.py
@@ -1,4 +1,5 @@
 from tasks.task_hook import TaskHook
+from tasks.util.custom_edges import add_edges
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
 from tasks.util.edge_weights import edge_weights
 import os.path
@@ -79,6 +80,8 @@ def network_proximity(task_hook: TaskHook):
 
     filter_paths = task_hook.parameters.get("filter_paths", True)
 
+    custom_edges = task_hook.parameters.get("custom_edges", False)
+
     node_name_attribute = "internal_id"  # nodes in the input network which is created from RepoTrialDB have primaryDomainId as name attribute
     # Set number of threads if OpenMP support is enabled.
     if gt.openmp_enabled():
@@ -95,6 +98,11 @@ def network_proximity(task_hook: TaskHook):
     filename = os.path.join(task_hook.data_directory, filename + ".gt")
     # g, seed_ids, _, drug_ids = read_graph_tool_graph(file_path, seeds, "", "", max_deg, False, True, include_non_approved_drugs)
     g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, id_space, max_deg, True, include_non_approved_drugs, target=search_target)
+    
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+    
     # Computing edge weights.
     task_hook.set_progress(1.0 / 8, "Computing edge weights.")
     weights = edge_weights(g, hub_penalty)
diff --git a/tasks/trust_rank.py b/tasks/trust_rank.py
index 6922fa6..8f5c40c 100755
--- a/tasks/trust_rank.py
+++ b/tasks/trust_rank.py
@@ -1,3 +1,4 @@
+from tasks.util.custom_edges import add_edges
 from tasks.util.read_graph_tool_graph import read_graph_tool_graph
 from tasks.util.scores_to_results import scores_to_results
 from tasks.util.edge_weights import edge_weights
@@ -195,6 +196,8 @@ def trust_rank(task_hook: TaskHook):
     search_target = task_hook.parameters.get("target", "drug-target")
 
     filter_paths = task_hook.parameters.get("filter_paths", True)
+
+    custom_edges = task_hook.parameters.get("custom_edges", False)
     
     # Parsing input file.
     task_hook.set_progress(0 / 4.0, "Parsing input.")
@@ -205,7 +208,13 @@ def trust_rank(task_hook: TaskHook):
     if ppi_dataset['licenced'] or pdi_dataset['licenced']:
         filename += "_licenced"
     filename = os.path.join(task_hook.data_directory, filename+".gt")
+    print(filename)
     g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, id_space, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
+    
+    if custom_edges:
+      edges = task_hook.parameters.get("input_network")['edges']
+      g = add_edges(g, edges)
+    
     task_hook.set_progress(1 / 4.0, "Computing edge weights.")
     weights = edge_weights(g, hub_penalty, inverse=True)
     
diff --git a/tasks/util/custom_edges.py b/tasks/util/custom_edges.py
new file mode 100644
index 0000000..d0b8ea2
--- /dev/null
+++ b/tasks/util/custom_edges.py
@@ -0,0 +1,18 @@
+def make_node_id_map(g):
+    mapping = {}
+    for node in range(g.num_vertices()):
+        mapping[g.vertex_properties['internal_id'][node]] = node
+    return mapping
+
+def add_edges(g, edge_list):
+    """
+    edge list is [{"fom":..., "to":...}, ...]
+    """
+    mapping = make_node_id_map(g)
+    edge_id_list = []
+    for edge in edge_list:
+        a = mapping[edge['from']]
+        b = mapping[edge['to']]
+        edge_id_list.append((a, b))
+    g.add_edge_list(edge_list)
+    return g
\ No newline at end of file
-- 
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