Add obo pickled graphs to docker build

docker/Dockerfile

@@ -39,6 +39,8 @@ RUN python -m pip install --upgrade pip && \
     python -m pip install --no-dependencies "lxml>=4.6.4" && \
     python -m pip install --no-dependencies --ignore-requires-python sbmlmath
 
+RUN python -m mira.dkg.generate_obo_graphs
+
 # Copy the example json for reconstructing the ode semantics
 RUN wget -O /sw/sir_flux_span.json https://raw.githubusercontent.com/gyorilab/mira/main/tests/sir_flux_span.json
 

mira/dkg/construct.py

@@ -41,10 +41,8 @@
 from pydantic import BaseModel, Field
 from pyobo.struct import part_of, is_a
 from pyobo.sources import ontology_resolver
-from pyobo.getters import _ensure_ontology_path
 from pyobo.api.utils import get_version
 from pyobo.utils.path import prefix_directory_join
-from obonet import read_obo
 from tabulate import tabulate
 from tqdm.auto import tqdm
 from typing_extensions import Literal
@@ -63,6 +61,7 @@
 from mira.dkg.resources.geonames import get_geonames_terms
 from mira.dkg.resources.extract_eiffel_ontology import get_eiffel_ontology_terms
 from mira.dkg.resources.uat import get_uat
+from mira.dkg.generate_obo_graphs import download_convert_ncbitaxon_obo_to_graph
 
 MODULE = pystow.module("mira")
 DEMO_MODULE = MODULE.module("demo", "import")
@@ -434,14 +433,11 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
     under the corresponding entry's subtree in its respective ontology.
     Relation information is also extracted with this option.
 
-    Running this method for the first time for each specific resource will
-    take a long time (minutes) as the obo resource file has to be downloaded,
-    converted to a networkx graph, have their node indices normalized, and
-    pickled.
-
-    Subsequent runs of this method will take a few seconds as the pickled
+    Execution of this method will take a few seconds as the pickled
     graph object has to be loaded.
 
+    Currently we only support the addition of ncbitaxon terms.
+
     Parameters
     ----------
     curie :
@@ -465,19 +461,12 @@ def extract_ontology_subtree(curie: str, add_subtree: bool = False):
         type = "class"
         version = get_version(resource_prefix)
         cached_relabeled_obo_graph_path = prefix_directory_join(resource_prefix,
-                                                   name="relabeled_obo_graph.pkl",
-                                                                 version=version)
+                                                            name="relabeled_obo_graph.pkl",
+                                                            version=version)
         if not cached_relabeled_obo_graph_path.exists():
-            _, obo_path = _ensure_ontology_path(resource_prefix, force=False,
-                                                version=version)
-            obo_graph = read_obo(obo_path)
-            relabeled_graph = networkx.relabel_nodes(obo_graph,
-                                               lambda node_index: node_index.lower())
-            with open(cached_relabeled_obo_graph_path,'wb') as relabeled_graph_file:
-                pickle.dump(relabeled_graph, relabeled_graph_file)
-        else:
-            with open(cached_relabeled_obo_graph_path,'rb') as relabeled_graph_file:
-                relabeled_graph = pickle.load(relabeled_graph_file)
+            download_convert_ncbitaxon_obo_to_graph()
+        with open(cached_relabeled_obo_graph_path,'rb') as relabeled_graph_file:
+            relabeled_graph = pickle.load(relabeled_graph_file)
     else:
         return nodes, edges
 

mira/dkg/generate_obo_graphs.py

@@ -0,0 +1,34 @@
+from pyobo.api.utils import get_version
+from pyobo.getters import _ensure_ontology_path
+from pyobo.utils.path import prefix_directory_join
+from obonet import read_obo
+import networkx
+import pickle
+
+
+def download_convert_ncbitaxon_obo_to_graph():
+    resource_prefix = "ncbitaxon"
+    version = get_version(resource_prefix)
+
+    # Checks to see if the pickled ncbitaxon obo graph exists in the container
+    cached_relabeled_obo_graph_path = prefix_directory_join(resource_prefix,
+                                                            name="relabeled_obo_graph.pkl",
+                                                            version=version)
+    if not cached_relabeled_obo_graph_path.exists():
+        _, obo_path = _ensure_ontology_path(
+            resource_prefix, force=False, version=version
+        )
+        obo_graph = read_obo(obo_path)
+
+        # Normalize node indices
+        relabeled_graph = networkx.relabel_nodes(
+            obo_graph, lambda node_index: node_index.lower()
+        )
+        with open(
+            cached_relabeled_obo_graph_path, "wb"
+        ) as relabeled_graph_file:
+            pickle.dump(relabeled_graph, relabeled_graph_file)
+
+
+if __name__ == "__main__":
+    download_convert_ncbitaxon_obo_to_graph()