From 848ca96424c9d064b1b9e943d09c45cf9498df65 Mon Sep 17 00:00:00 2001
From: Ismail Ugur Bayindir <ubyndr@gmail.com>
Date: Mon, 1 Jul 2024 19:05:19 +0300
Subject: [PATCH] Refactored CURIE generation logic for annotated_target (#76)

* Refactored annotated_target curie generation

* Updated version to 0.1.18
---
 .../graph_generator/graph_generator.py        |  28 +-
 .../graph_generator/graph_namespaces.py       |   8 +
 poetry.lock                                   | 988 +++++++++---------
 pyproject.toml                                |   2 +-
 4 files changed, 536 insertions(+), 490 deletions(-)
 create mode 100644 pandasaurus_cxg/graph_generator/graph_namespaces.py

diff --git a/pandasaurus_cxg/graph_generator/graph_generator.py b/pandasaurus_cxg/graph_generator/graph_generator.py
index 41c816d..8fba3fb 100644
--- a/pandasaurus_cxg/graph_generator/graph_generator.py
+++ b/pandasaurus_cxg/graph_generator/graph_generator.py
@@ -33,6 +33,7 @@
     HAS_SOURCE,
     SUBCLUSTER_OF,
 )
+from pandasaurus_cxg.graph_generator.graph_namespaces import prefixes
 from pandasaurus_cxg.utils.exceptions import (
     InvalidGraphFormat,
     MissingAnalysisProcess,
@@ -141,7 +142,9 @@ def generate_rdf_graph(self):
                         )
                     )
 
-            self.graph.add((dataset_class, URIRef(self.ns[remove_special_characters(key)]), Literal(value)))
+            self.graph.add(
+                (dataset_class, URIRef(self.ns[remove_special_characters(key)]), Literal(value))
+            )
         has_source = URIRef(HAS_SOURCE["iri"])
         self.graph.add((has_source, RDFS.label, Literal(HAS_SOURCE["label"])))
 
@@ -173,7 +176,7 @@ def generate_rdf_graph(self):
         self.graph = graphgen.apply_transitive_reduction(self.graph, [subcluster.toPython()])
 
         # add cell_type nodes and consists_of relations
-        cl_namespace = Namespace("http://purl.obolibrary.org/obo/CL_")
+        cl_namespace = Namespace(prefixes.get("CL"))
         consist_of = URIRef(CONSIST_OF.get("iri"))
         self.graph.add((consist_of, RDFS.label, Literal(CONSIST_OF.get("label"))))
         for curie, label in self.ea.enricher_manager.seed_dict.items():
@@ -243,14 +246,21 @@ def add_metadata_nodes(self, metadata_fields: List[str]):
                         obs[obs[a_cell_type] == str(literal)][metadata].value_counts(normalize=True)
                         * 100
                     ).loc[lambda x: x != 0.0]
+
+                    # Extract the ontology term ID mapping
+                    ontology_term_id_mapping = (
+                        obs[[metadata, f"{metadata}_ontology_term_id"]]
+                        .drop_duplicates()
+                        .set_index(metadata)
+                        .to_dict()[f"{metadata}_ontology_term_id"]
+                    )
+
                     for label, percentage in percentages.items():
-                        annotated_target = self.graph.value(
-                            predicate=RDFS.label, object=Literal(label)
-                        )
-                        if annotated_target is None:
-                            annotated_target = URIRef(self.ns[str(uuid.uuid4())])
-                            self.graph.add((annotated_target, RDF.type, self.ns[metadata]))
-                            self.graph.add((annotated_target, RDFS.label, Literal(label)))
+                        ontology_term_id = ontology_term_id_mapping.get(label).split(":")
+                        annotated_target = Namespace(prefixes.get(ontology_term_id[0]))[
+                            ontology_term_id[-1]
+                        ]
+                        self.graph.add((annotated_target, RDFS.label, Literal(label)))
                         bnode_axiom = BNode()
                         self.graph.add((bnode_axiom, RDF.type, OWL.Axiom))
                         self.graph.add((bnode_axiom, OWL.annotatedSource, s))
diff --git a/pandasaurus_cxg/graph_generator/graph_namespaces.py b/pandasaurus_cxg/graph_generator/graph_namespaces.py
new file mode 100644
index 0000000..b18ce94
--- /dev/null
+++ b/pandasaurus_cxg/graph_generator/graph_namespaces.py
@@ -0,0 +1,8 @@
+prefixes = {
+    "CL": "http://purl.obolibrary.org/obo/CL_",
+    "UBERON": "http://purl.obolibrary.org/obo/UBERON_",
+    "PATO": "http://purl.obolibrary.org/obo/PATO_",
+    "MONDO": "http://purl.obolibrary.org/obo/MONDO_",
+    "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_",
+    "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_",
+}
diff --git a/poetry.lock b/poetry.lock
index 0a1417b..643e41b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -199,13 +199,13 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.6.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
-    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
+    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
 ]
 
 [[package]]
@@ -434,63 +434,63 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
-version = "7.5.1"
+version = "7.5.4"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -723,53 +723,53 @@ test = ["pytest"]
 
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 optional = false
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+    {file = "SQLAlchemy-2.0.31-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:2fc47dc6185a83c8100b37acda27658fe4dbd33b7d5e7324111f6521008ab4fe"},
+    {file = "SQLAlchemy-2.0.31-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8a41514c1a779e2aa9a19f67aaadeb5cbddf0b2b508843fcd7bafdf4c6864005"},
+    {file = "SQLAlchemy-2.0.31-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:afb6dde6c11ea4525318e279cd93c8734b795ac8bb5dda0eedd9ebaca7fa23f1"},
+    {file = "SQLAlchemy-2.0.31-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:3f9faef422cfbb8fd53716cd14ba95e2ef655400235c3dfad1b5f467ba179c8c"},
+    {file = "SQLAlchemy-2.0.31-cp39-cp39-win32.whl", hash = "sha256:fc6b14e8602f59c6ba893980bea96571dd0ed83d8ebb9c4479d9ed5425d562e9"},
+    {file = "SQLAlchemy-2.0.31-cp39-cp39-win_amd64.whl", hash = "sha256:3cb8a66b167b033ec72c3812ffc8441d4e9f5f78f5e31e54dcd4c90a4ca5bebc"},
+    {file = "SQLAlchemy-2.0.31-py3-none-any.whl", hash = "sha256:69f3e3c08867a8e4856e92d7afb618b95cdee18e0bc1647b77599722c9a28911"},
+    {file = "SQLAlchemy-2.0.31.tar.gz", hash = "sha256:b607489dd4a54de56984a0c7656247504bd5523d9d0ba799aef59d4add009484"},
+]
+
+[package.dependencies]
+greenlet = {version = "!=0.4.17", markers = "python_version < \"3.13\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
 typing-extensions = ">=4.6.0"
 
 [package.extras]
@@ -3310,13 +3335,13 @@ url = ["furl (>=0.4.1)"]
 
 [[package]]
 name = "sssom"
-version = "0.4.9"
+version = "0.4.11"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "sssom-0.4.9-py3-none-any.whl", hash = "sha256:54af580957947175dfcc96e7ce2323ea3b476eb58b6e7a2e95d8c3e10c6393f4"},
-    {file = "sssom-0.4.9.tar.gz", hash = "sha256:16674d58aa37ab82c1f6f69d317c0bdc6eedd59e8d809fcbc87f5f1e1eefdbf1"},
+    {file = "sssom-0.4.11-py3-none-any.whl", hash = "sha256:4642f126a6ec8a4201bef77107a5ac76ed69b8f624014b5b77e56745969c0f76"},
+    {file = "sssom-0.4.11.tar.gz", hash = "sha256:5043390657a396f9e5d064e5788990a52ec19c395c6380514abfe01b85a5eebc"},
 ]
 
 [package.dependencies]
@@ -3382,13 +3407,13 @@ telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
@@ -3418,13 +3443,13 @@ six = "*"
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
+    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
 ]
 
 [package.extras]
@@ -3435,15 +3460,18 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "validators"
-version = "0.28.1"
+version = "0.29.0"
 description = "Python Data Validation for Humans™"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "validators-0.28.1-py3-none-any.whl", hash = "sha256:890c98789ad884037f059af6ea915ec2d667129d509180c2c590b8009a4c4219"},
-    {file = "validators-0.28.1.tar.gz", hash = "sha256:5ac88e7916c3405f0ce38ac2ac82a477fcf4d90dbbeddd04c8193171fc17f7dc"},
+    {file = "validators-0.29.0-py3-none-any.whl", hash = "sha256:31a8285ca8889347babad77cc541f0b88e95b30553ca5f69b1d3ae4351587e3e"},
+    {file = "validators-0.29.0.tar.gz", hash = "sha256:7c8c599ea8128a6425ecb3f0da9ee10dd22b3d41b2f89560383761abf39de4df"},
 ]
 
+[package.extras]
+crypto-eth-addresses = ["eth-hash[pycryptodome] (>=0.7.0)"]
+
 [[package]]
 name = "wrapt"
 version = "1.16.0"
@@ -3525,18 +3553,18 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.18.2"
+version = "3.19.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"},
-    {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"},
+    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
+    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [extras]
 docs = ["sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
diff --git a/pyproject.toml b/pyproject.toml
index 962b72c..8a2902d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pandasaurus-cxg"
-version = "0.1.17"
+version = "0.1.18"
 description = "Ontology enrichment tool for CxG standard AnnData files."
 authors = ["Ugur Bayindir <ugur@ebi.ac.uk>"]
 license = "http://www.apache.org/licenses/LICENSE-2.0"