small update but not all fixed

Former-commit-id: 9a544d3f4e0d6988be142678c41e287e4e669685 [formerly a54f02195d5fcb8eaae8a961cd91e5dc5a2305d5]
Former-commit-id: 7afc43bd1da646344f8fea1e0e6a3702c4995c72

Dockerfile

@@ -27,7 +27,6 @@ COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
 COPY ./python_nedrex/ /usr/src/drugstone/python_nedrex/
 RUN pip install /usr/src/drugstone/python_nedrex/
 
-RUN mkdir store
 COPY . /usr/src/drugstone/
 
 

docker-compose.yml

@@ -14,7 +14,6 @@ services:
     volumes:
       - drugstone_db_schema_volume:/usr/src/drugstone/drugstone/migrations
       - drugstone_data_volume:/usr/src/drugstone/data
-      - drugstone_store_volume:/usr/src/drugstone/store
     ports:
       - 8001:8000
     networks:
@@ -102,5 +101,4 @@ volumes:
   drugstone_db_schema_volume:
 #    external: true
   drugstone_data_volume:
-#    external: true
-  drugstone_store_volume:
+#    external: true
\ No newline at end of file
\ No newline at end of file

drugstone/management/commands/import_from_nedrex.py

@@ -198,7 +198,7 @@ class NedrexImporter:
                 e = models.ProteinDrugInteraction(pdi_dataset=dataset, drug=drug, protein=protein)
                 if not update or e.__hash__() not in existing:
                     bulk.add(e)
-                    for source in edge['databases']:
+                    for source in edge['dataSources']:
                         bulk.add(models.ProteinDrugInteraction(pdi_dataset=source_datasets[source], drug=drug, protein=protein))
             except KeyError:
                 pass
@@ -237,7 +237,7 @@ class NedrexImporter:
                 e = models.ProteinProteinInteraction(ppi_dataset=dataset, from_protein=protein1, to_protein=protein2)
                 if not update or e.__hash__() not in existing:
                     bulk.append(e)
-                    for source in edge['assertedBy']:
+                    for source in edge['dataSources']:
                         bulk.append(
                             models.ProteinProteinInteraction(ppi_dataset=source_datasets[source], from_protein=protein1,
                                                              to_protein=protein2))
@@ -268,7 +268,7 @@ class NedrexImporter:
                                                           score=edge['score'])
                     if not update or e.__hash__() not in existing:
                         bulk.add(e)
-                        for source in edge['assertedBy']:
+                        for source in edge['dataSources']:
                             bulk.add(
                                 models.ProteinDisorderAssociation(pdis_dataset=source_datasets[source], protein=protein, disorder=disorder,
                                                           score=edge['score']))
@@ -298,7 +298,7 @@ class NedrexImporter:
                 e = models.DrugDisorderIndication(drdi_dataset=dataset, drug=drug, disorder=disorder)
                 if not update or e.__hash__() not in existing:
                     bulk.add(e)
-                    for source in edge['assertedBy']:
+                    for source in edge['dataSources']:
                         bulk.add(
                             models.DrugDisorderIndication(drdi_dataset=source_datasets[source], drug=drug, disorder=disorder))
             except KeyError:

drugstone/management/includes/DatasetLoader.py

+from requests.exceptions import RetryError
+
 from drugstone import models
 from python_nedrex.static import get_metadata
 
@@ -23,28 +25,46 @@ def get_ppi_apid():
 
 
 def get_ppi_nedrex_biogrid(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['biogrid']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PPIDataset.objects.get_or_create(
         name='BioGRID',
         link=url,
-        version=get_metadata()['source_databases']['biogrid']['date']
+        version=version
     )
     return dataset
 
 
 def get_ppi_nedrex_iid(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['iid']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PPIDataset.objects.get_or_create(
         name='IID',
         link=url,
-        version=get_metadata()['source_databases']['iid']['date']
+        version=version
     )
     return dataset
 
 
 def get_ppi_nedrex_intact(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['intact']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PPIDataset.objects.get_or_create(
         name='IntAct',
         link=url,
-        version=get_metadata()['source_databases']['intact']['date']
+        version=version
     )
     return dataset
 
@@ -59,37 +79,61 @@ def get_ppi_biogrid():
 
 
 def get_drug_target_nedrex(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['version'],
+    except RetryError:
+        pass
+
     dataset, _ = models.PDIDataset.objects.get_or_create(
         name='NeDRex',
         link=url,
-        version=get_metadata()['version'],
+        version=version
     )
     return dataset
 
 
 def get_ppi_nedrex(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['version'],
+    except RetryError:
+        pass
+
     dataset, _ = models.PPIDataset.objects.get_or_create(
         name='NeDRex',
         link=url,
-        version=get_metadata()['version'],
+        version=version
     )
     return dataset
 
 
 def get_protein_disorder_nedrex(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['version'],
+    except RetryError:
+        pass
+
     dataset, _ = models.PDisDataset.objects.get_or_create(
         name='NeDRex',
         link=url,
-        version=get_metadata()['version'],
+        version=version
     )
     return dataset
 
 
 def get_drug_disorder_nedrex(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['version'],
+    except RetryError:
+        pass
+
     dataset, _ = models.DrDiDataset.objects.get_or_create(
         name='NeDRex',
         link=url,
-        version=get_metadata()['version'],
+        version=version
     )
     return dataset
 
@@ -138,62 +182,103 @@ def get_drug_disorder_drugbank():
     )
     return dataset
 
+def get_today_version():
+    import datetime
+    now = datetime.date.today()
+    version = f'{now.year}-{now.month}-{now.day}_temp'
+    return version
 
 def get_dis_prot_nedrex_disgenet(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['disgenet']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PDisDataset.objects.get_or_create(
         name='DisGeNET',
         link=url,
-        version=get_metadata()['source_databases']['disgenet']['date']
+        version=version
     )
     return dataset
 
 
 def get_dis_prot_nedrex_omim(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['omim']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PDisDataset.objects.get_or_create(
         name='OMIM',
         link=url,
-        version=get_metadata()['source_databases']['omim']['date']
+        version=version
     )
     return dataset
 
 
 def get_drdis_nedrex_drugcentral(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['drug_central']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.DrDiDataset.objects.get_or_create(
         name='Drug Central',
         link=url,
-        version=get_metadata()['source_databases']['drug_central']['date']
+        version=version
     )
     return dataset
 
 def get_drdis_nedrex_ctd(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['ctd']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.DrDiDataset.objects.get_or_create(
         name='CTD',
         link=url,
-        version=get_metadata()['source_databases']['ctd']['date']
+        version=version
     )
     return dataset
 
 def get_pdr_nedrex_drugcentral(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['drug_central']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PDIDataset.objects.get_or_create(
         name='Drug Central',
         link=url,
-        version=get_metadata()['source_databases']['drug_central']['date']
+        version=version
     )
     return dataset
 
 def get_pdr_nedrex_drugbank(url):
+    version = get_today_version()
+    try:
+        version = get_metadata()['source_databases']['drugbank']['date']
+    except RetryError:
+        pass
+
     dataset, _ = models.PDIDataset.objects.get_or_create(
         name='DrugBank',
         link=url,
-        version=get_metadata()['source_databases']['drugbank']['date']
+        version=version
     )
     return dataset
 
 def get_pdr_nedrex_datasets(url):
-    return {'DrugBank': get_pdr_nedrex_drugbank(url), 'DrugCentral': get_pdr_nedrex_drugcentral(url)}
+    return {'drugbank': get_pdr_nedrex_drugbank(url), 'drugcentral': get_pdr_nedrex_drugcentral(url)}
 
 def get_drdis_nedrex_datasets(url):
-    return {'ctd':get_drdis_nedrex_ctd(url), 'Drug Central':get_drdis_nedrex_drugcentral(url)}
+    return {'ctd':get_drdis_nedrex_ctd(url), 'drugcentral':get_drdis_nedrex_drugcentral(url)}
 
 def get_ppi_nedrex_datasets(url):
     return {'biogrid':get_ppi_nedrex_biogrid(url), 'iid':get_ppi_nedrex_iid(url), 'intact':get_ppi_nedrex_intact(url)}

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"

tasks/quick_task.py

@@ -45,6 +45,7 @@ def quick_task(task_hook: TaskHook):
             "result_size": 20,
             "include_non_approved_drugs": True,
             "include_indirect_drugs": False,
+            "target":"drug"
         })
 
         tr_task_hook = TaskHook(parameters, task_hook.data_directory, progress, set_result)

tasks/trust_rank.py

@@ -200,8 +200,6 @@ def trust_rank(task_hook: TaskHook):
     task_hook.set_progress(0 / 4.0, "Parsing input.")
     file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
     g, seed_ids, drug_ids = read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
-    print(seed_ids)
-    print(drug_ids)
     task_hook.set_progress(1 / 4.0, "Computing edge weights.")
     weights = edge_weights(g, hub_penalty, inverse=True)
     

tasks/util/read_graph_tool_graph.py

@@ -37,7 +37,7 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
       The graph indices for all drug nodes
     """
     # Read the graph.
-
+    print(f"loading {file_path} for {target}")
     g = gt.load_graph(file_path)
     # g = gtt.extract_largest_component(gg, directed=False, prune=True)   # this line is added since we need to work with the LCC of the graphs for all algorithms
 
@@ -47,16 +47,20 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
     # Delete all nodes that are not contained in the selected datasets and have degrees higher than max_deg
     deleted_nodes = []
     for node in range(g.num_vertices()):
+        #Remove all unconnected nodes TODO probably already skip when creating .gt files
+        if g.vertex(node).out_degree() == 0 and target == 'drug':
+            deleted_nodes.append(node)
         # if not g.vertex_properties["name"][node] in set(seeds) and g.vertex(node).out_degree() > max_deg:
-        if not g.vertex_properties[node_name_attribute][node] in set(seeds) and g.vertex(node).out_degree() > max_deg:
+        elif not g.vertex_properties[node_name_attribute][node] in set(seeds) and (g.vertex(node).out_degree() > max_deg):
             deleted_nodes.append(node)
         # remove all drugs from graph if we are not looking for drugs
         elif target != 'drug' and g.vertex_properties["type"][node] == d_type:
             deleted_nodes.append(node)
     g.remove_vertex(deleted_nodes, fast=True)
 
-    # Retrieve internal IDs of seed_ids and viral_protein_ids.
+    # Retrieve internal IDs of seed_ids
     seeds = set(seeds)
+    print(seeds)
     seed_ids = []
     drug_ids = []
     is_matched = {protein: False for protein in seeds}
@@ -64,7 +68,7 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
         node_type = g.vertex_properties["type"][node]
         if g.vertex_properties[node_name_attribute][node] in seeds:
             seed_ids.append(node)
-            is_matched[g.vertex_properties[node_name_attribute][node]] = True
+            is_matched[g.vertex_properties[node_name_attribute][node]] = node
         if node_type == d_type:
             if include_non_approved_drugs:
                 drug_ids.append(node)
@@ -74,9 +78,11 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
                     drug_ids.append(node)
 
     # Check that all seed seeds have been matched and throw error, otherwise.
+    # print(deleted_nodes)
+    print(seed_ids)
     for protein, found in is_matched.items():
         if not found:
-            raise ValueError("Invaliddd seed protein {}. No node named {} in {}.".format(protein, protein, file_path))
+            raise ValueError("Invalid seed protein {}. No node named {} in {}.".format(protein, protein, file_path))
 
     # Delete edges that should be ignored or are not contained in the selected dataset.
     deleted_edges = []
@@ -87,8 +93,6 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
                 direct_drugs.add(edge.target())
             elif g.vertex_properties["type"][edge.source()] == d_type and edge.target() in seed_ids:
                 direct_drugs.add(edge.source())
-        for drug in direct_drugs:
-            print(int(drug))
         for edge in g.edges():
             if g.edge_properties["type"][edge] == 'drug-protein':
                 if g.vertex_properties["type"][edge.target()] == d_type:
@@ -113,6 +117,17 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
     for edge in deleted_edges:
         g.remove_edge(edge)
     g.set_fast_edge_removal(fast=False)
-
+    print("Drugs")
+    print(drug_ids)
+    print("Vertices")
+    vertices = 0
+    for _ in g.vertices():
+        vertices += 1
+    print(f'\t{vertices}')
+    print("Edges")
+    edges = 0
+    for _ in g.edges():
+        edges+=1
+    print(f'\t{edges}')
     # Return the graph and the indices of the seed_ids and the seeds.
     return g, seed_ids, drug_ids

tasks/util/scores_to_results.py

@@ -23,6 +23,7 @@ def scores_to_results(
     else:
         candidates = [(node, scores[node]) for node in range(g.num_vertices()) if scores[node] > 0 and node not in set(seed_ids)]
     best_candidates = [item[0] for item in sorted(candidates, key=lambda item: item[1], reverse=True)[:result_size]]
+    print(f'Candidate list length: {len(best_candidates)}')
 
     # Concatenate best result candidates with seeds and compute induced subgraph.
     # since the result size filters out nodes, the result network is not complete anymore.
@@ -82,6 +83,7 @@ def scores_to_results(
                 for edge in edges:
                     if ((edge.source(), edge.target()) not in returned_edges) or ((edge.target(), edge.source()) not in returned_edges):
                         returned_edges.add((edge.source(), edge.target()))
+    print(f'Returned nodes number: {len(returned_nodes)}')
     subgraph = {
         "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],