Merge pull request #28 from kkaris/extend-subgraph-timeout

Extend subgraph timeout

.github/workflows/tests.yml

@@ -23,7 +23,7 @@ jobs:
         sudo apt-get install libstdc++6 graphviz python3-dev libgraphviz-dev pkg-config
         python -m pip install --upgrade pip
         pip install -e .[tests]
-        pip install termcolor cachetools
+        pip install termcolor cachetools httpx
         git clone https://github.com/indralab/depmap_analysis.git
     - name: Run unit tests
       run: |

indra_network_search/data_models/__init__.py

@@ -20,6 +20,7 @@
 #  - In FilterOptions, set overall weighted based on values of weighted
 #    context weighted. See here for more info:
 #    https://stackoverflow.com/q/54023782/10478812
+#  - Make the is_empty method also look into the children of the object?
 import logging
 from collections import Counter
 from typing import Callable, Dict, Iterable, List, Optional, Set, Tuple, Union
@@ -77,6 +78,7 @@
     "SubgraphResults",
     "MultiInteractorsResults",
     "DEFAULT_TIMEOUT",
+    "MAX_TIMEOUT",
     "WEIGHT_NAME_MAPPING",
     "basemodels_equal",
     "basemodel_in_iterable",
@@ -89,6 +91,7 @@
 
 # Set defaults
 DEFAULT_TIMEOUT = 30
+MAX_TIMEOUT = 590  # Less than timeout on the load balancer and nginx
 WEIGHT_NAME_MAPPING = {
     "belief": "weight",
     "context": "context_weight",
@@ -571,6 +574,7 @@ class SubgraphRestQuery(BaseModel):
     """Subgraph query"""
 
     nodes: conlist(item_type=Node, min_items=1, max_items=4000)
+    timeout: confloat(ge=1, le=MAX_TIMEOUT) = MAX_TIMEOUT
 
 
 class SubgraphOptions(BaseModel):

indra_network_search/frontend/src/views/About.vue

@@ -25,7 +25,7 @@
     </p>
     <p>
       This project's backend is powered by <a href="https://fastapi.tiangolo.com/" target="_blank">FastAPI</a>.
-      The frontend is made 100 % in <a href="https://v3.vuejs.org/" target="_blank">Vue 3</a>.
+      The frontend is made 100 % in <a href="https://vuejs.org/" target="_blank">Vue 3</a>.
     </p>
   </div>
 </template>

indra_network_search/query.py

@@ -671,6 +671,7 @@ def result_options(self) -> Dict[str, Any]:
             "original_nodes": self.query.nodes,
             "nodes_in_graph": self._nodes_in_graph,
             "not_in_graph": self._not_in_graph,
+            "timeout": self.query.timeout
         }
 
 

indra_network_search/rest_api.py

@@ -278,12 +278,12 @@ def startup_event():
     #  - https://www.starlette.io/events/
     if DEBUG:
         from indra_network_search.tests.util import (
-            _setup_graph,
-            _setup_signed_node_graph,
+            unsigned_graph,
+            signed_node_graph,
         )
 
-        dir_graph = _setup_graph()
-        sign_node_graph = _setup_signed_node_graph(False)
+        dir_graph = unsigned_graph
+        sign_node_graph = signed_node_graph
     else:
         # ToDo The file IO has to be done awaited to make this function async
         dir_graph, _, _, sign_node_graph = load_indra_graph(

indra_network_search/result_handler.py

@@ -23,7 +23,7 @@
     Union,
 )
 
-from depmap_analysis.network_functions.famplex_functions import get_identifiers_url
+from indra.databases.identifiers import get_identifiers_url
 from indra.explanation.pathfinding import (
     bfs_search,
     open_dijkstra_search,
@@ -733,7 +733,7 @@ def _get_results(self) -> SharedInteractorsResults:
         target_edges: List[EdgeData] = []
         for (s1, s2), (t1, t2) in self.path_gen:
             if self.timeout and datetime.utcnow() - self.start_time > timedelta(seconds=self.timeout):
-                logger.info(f"Timeout reached ({self.timeout} seconds), " f"breaking results loop")
+                logger.info(f"Timeout reached ({self.timeout} seconds), breaking results loop")
                 self.timed_out = True
                 break
             source_edge = self._get_edge_data(a=s1, b=s2)
@@ -858,12 +858,14 @@ def __init__(
         nodes_in_graph: List[Node],
         not_in_graph: List[Node],
         ev_limit: int = 10,
+        timeout: float = MAX_TIMEOUT,
     ):
         super().__init__(
             path_generator=path_generator,
             graph=graph,
             filter_options=filter_options,
             input_nodes=original_nodes,
+            timeout=timeout
         )
         self.edge_dict: Dict[Tuple[str, str], EdgeDataByHash] = {}
         self._available_nodes: Dict[str, Node] = {n.name: n for n in nodes_in_graph}

indra_network_search/tests/util.py

@@ -1,5 +1,5 @@
 from inspect import signature
-from typing import Any, Callable, Dict, List, Optional, Set, Tuple
+from typing import Any, Callable, Dict, List, Optional, Set, Tuple, Union
 
 from indra.assemblers.indranet.net import default_sign_dict
 from indra.explanation.model_checker.model_checker import signed_edges_to_signed_nodes
@@ -96,6 +96,13 @@ def _setup_signed_node_graph(large: bool) -> DiGraph:
     return signed_edges_to_signed_nodes(graph=seg, copy_edge_data=True, prune_nodes=True)
 
 
+def _add_graph_meta(g: Union[DiGraph, MultiDiGraph]):
+    ns_id_to_nodename = {}
+    for name, data in g.nodes(data=True):
+        ns_id_to_nodename[(data["ns"], data["id"])] = name
+    g.graph["node_by_ns_id"] = ns_id_to_nodename
+
+
 def _setup_api(large: bool) -> IndraNetworkSearchAPI:
     g = expanded_unsigned_graph if large else unsigned_graph
     sg = exp_signed_node_graph if large else signed_node_graph
@@ -346,3 +353,6 @@ def _get_edge_hash(edge: StrEdge, graph: DiGraph, large: bool, signed: bool):
 exp_signed_node_graph = _setup_signed_node_graph(True)
 search_api = _setup_api(False)
 exp_search_api = _setup_api(True)
+
+for graph in [unsigned_graph, expanded_unsigned_graph, signed_node_graph, exp_signed_node_graph]:
+    _add_graph_meta(graph)

setup.cfg

@@ -41,9 +41,13 @@ install_requires =
     fnvhash
     autodoc_pydantic
 
+zip_safe = false
 include_package_data = True
 python_requires = >=3.7
 
+# Where is my code
+packages = find:
+
 [options.extras_require]
 tests =
     nose