Merge pull request #367 from nanglo123/add_graph_to_docker

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()