Merge pull request #18 from geneontology/issue-13-cx2-context-attribute

Add `@context` network attribute to CX2 output

Makefile

@@ -52,7 +52,7 @@ endif
 
 
 # basename of a YAML file in model/
-.PHONY: all clean setup gen-project gen-examples gendoc git-init-add git-init git-add git-commit git-status
+.PHONY: all clean setup gen-project gen-examples gendoc git-init-add git-init git-add git-commit git-status lint lint-python lint-fix-python
 
 # note: "help" MUST be the first target in the file,
 # when the user types "make" they should get help info
@@ -148,6 +148,14 @@ test-python:
 lint:
 	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
 
+lint-python:
+	$(RUN) ruff format --check
+	$(RUN) ruff check
+
+lint-fix-python:
+	$(RUN) ruff check --fix
+	$(RUN) ruff format
+
 check-config:
 ifndef LINKML_SCHEMA_NAME
 	$(error **Project not configured**:\n\n - See '.env.public'\n\n)

pyproject.toml

@@ -12,6 +12,7 @@ python = "^3.9"
 click = "^8"
 linkml-runtime = "^1.1.24"
 ndex2 = "^3.9.0"
+prefixmaps = "^0.2.5"
 pydantic = "^2"
 pyyaml = "^6"
 requests = "^2"
@@ -20,6 +21,7 @@ requests = "^2"
 linkml = "^1.3.5"
 mkdocs-material = "^8.2.8"
 mkdocs-mermaid2-plugin = ">=1.1.1"
+ruff = "^0.6.9"
 schemasheets = "^0.1.14"
 
 [tool.poetry.group.test.dependencies]
@@ -42,3 +44,12 @@ gocam = "gocam.cli:cli"
 markers = [
     "integration"
 ]
+
+[tool.ruff]
+exclude = [
+    "project",
+    "src/gocam/datamodel"
+]
+
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "I"]

src/gocam/__init__.py

@@ -1 +1 @@
-from gocam._version import __version__
+from gocam._version import __version__ as __version__

src/gocam/_version.py

@@ -1,4 +1,4 @@
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version(__package__)

src/gocam/cli.py

@@ -135,7 +135,9 @@ def convert(model, input_format, output_format, output, ndex_upload):
             # Make the network searchable
             client.set_network_system_properties(network_id, {"index_level": "META"})
 
-            click.echo(f"View network at: 'https://www.ndexbio.org/viewer/networks/{network_id}")
+            click.echo(
+                f"View network at: 'https://www.ndexbio.org/viewer/networks/{network_id}"
+            )
         else:
             click.echo(json.dumps(cx2), file=output)
 

src/gocam/translation/__init__.py

@@ -1 +1 @@
-from gocam.translation.minerva_wrapper import MinervaWrapper
+from gocam.translation.minerva_wrapper import MinervaWrapper as MinervaWrapper

src/gocam/translation/cx2/__init__.py

@@ -1 +1 @@
-from gocam.translation.cx2.main import model_to_cx2
+from gocam.translation.cx2.main import model_to_cx2 as model_to_cx2

src/gocam/translation/cx2/main.py

@@ -1,7 +1,10 @@
+import json
 import logging
 import re
+from functools import cache
 from typing import Dict, List, Optional, Union
 
+import prefixmaps
 from ndex2.cx2 import CX2Network
 
 from gocam.datamodel import (
@@ -50,13 +53,17 @@ def _remove_species_code_suffix(label: str) -> str:
     return label
 
 
+@cache
+def _get_context():
+    return prefixmaps.load_context("go").as_dict()
+
+
 # Regex from
 # https://github.com/ndexbio/ndex-enrichment-rest/wiki/Enrichment-network-structure#via-node-attributes-preferred-method
 IQUERY_GENE_SYMBOL_PATTERN = re.compile("(^[A-Z][A-Z0-9-]*$)|(^C[0-9]+orf[0-9]+$)")
 
 
 def model_to_cx2(gocam: Model) -> list:
-
     # Internal state
     input_output_nodes: Dict[str, int] = {}
     activity_nodes: Dict[str, int] = {}
@@ -101,6 +108,7 @@ def _add_input_output_nodes(
     cx2_network = CX2Network()
     cx2_network.set_network_attributes(
         {
+            "@context": json.dumps(_get_context()),
             "name": gocam.title if gocam.title is not None else gocam.id,
             "represents": gocam.id,
         }