From 8c158d5afb2d9fc8c2d1eb5dc166c42a97f6a15a Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 27 Mar 2024 11:32:41 -0600
Subject: [PATCH 1/4] use systematic id for empty gene names

---
 src/monarch_ingest/ingests/pombase/gene.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/src/monarch_ingest/ingests/pombase/gene.py b/src/monarch_ingest/ingests/pombase/gene.py
index 6aea4a33..dd219988 100644
--- a/src/monarch_ingest/ingests/pombase/gene.py
+++ b/src/monarch_ingest/ingests/pombase/gene.py
@@ -1,29 +1,25 @@
-
-
-from koza.cli_runner import get_koza_app
-
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
+from koza.cli_runner import get_koza_app
+# from loguru import logger
 
-from loguru import logger
 
 koza_app = get_koza_app("pombase_gene")
 taxon_labels = koza_app.get_map("taxon-labels")
 
 while (row := koza_app.get_row()) is not None:
-
     in_taxon = "NCBITaxon:4896"
-    in_taxon_label = taxon_labels[in_taxon]['label'] if in_taxon in taxon_labels else "Schizosaccharomyces pombe"
+    in_taxon_label = taxon_labels[in_taxon]["label"] if in_taxon in taxon_labels else "Schizosaccharomyces pombe"
 
     gene = Gene(
         id=row["gene_systematic_id_with_prefix"],
         symbol=row["gene_name"],
-        name=row["gene_name"],
-        full_name=row["gene_name"],
+        name=row["gene_name"] or row["gene_systematic_id"],
+        full_name=row["gene_name"] or row["gene_systematic_id"],
         # No place in the schema for gene type (SO term) right now
         # type=koza_app.translation_table.resolve_term(row["product type"].replace(' ', '_')),
         in_taxon=[in_taxon],
         in_taxon_label=in_taxon_label,
-        provided_by=["infores:pombase"]
+        provided_by=["infores:pombase"],
     )
 
     if row["uniprot_id"]:

From 16375569bd60d3637c7baa8e13c497040c16d8bc Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 27 Mar 2024 12:18:29 -0600
Subject: [PATCH 2/4] woops, forgot to save

---
 src/monarch_ingest/ingests/pombase/gene.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/monarch_ingest/ingests/pombase/gene.py b/src/monarch_ingest/ingests/pombase/gene.py
index dd219988..7d107854 100644
--- a/src/monarch_ingest/ingests/pombase/gene.py
+++ b/src/monarch_ingest/ingests/pombase/gene.py
@@ -12,7 +12,7 @@
 
     gene = Gene(
         id=row["gene_systematic_id_with_prefix"],
-        symbol=row["gene_name"],
+        symbol=row["gene_name"] or row["gene_systematic_id"],
         name=row["gene_name"] or row["gene_systematic_id"],
         full_name=row["gene_name"] or row["gene_systematic_id"],
         # No place in the schema for gene type (SO term) right now

From c2dfd513a1ad02d12926eabea2021cffce2dd4e8 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 27 Mar 2024 12:31:24 -0600
Subject: [PATCH 3/4] update black (and fix? biolink model in pyproject.toml

---
 poetry.lock    | 424 +++++++++++++++++++++++++++----------------------
 pyproject.toml |   8 +-
 2 files changed, 236 insertions(+), 196 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index bfc3363a..2be0b1d5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -129,38 +129,38 @@ docs = []
 [package.source]
 type = "git"
 url = "https://github.com/biolink/biolink-model"
-reference = "dc87efc"
-resolved_reference = "dc87efcf374cd80a462d62a9087978bee1e73a4c"
+reference = "v4.2.0-rc.2"
+resolved_reference = "16e0e617de6d3217b37f0514a7f74e0f1ef2edf0"
 
 [[package]]
 name = "black"
-version = "23.12.1"
+version = "24.3.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "black-23.12.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c88b3711d12905b74206227109272673edce0cb29f27e1385f33b0163c414bba"},
-    {file = "black-23.12.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a920b569dc6b3472513ba6ddea21f440d4b4c699494d2e972a1753cdc25df7b0"},
-    {file = "black-23.12.1-cp310-cp310-win_amd64.whl", hash = "sha256:3fa4be75ef2a6b96ea8d92b1587dd8cb3a35c7e3d51f0738ced0781c3aa3a5a3"},
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-    {file = "black-23.12.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9c4352800f14be5b4864016882cdba10755bd50805c95f728011bcb47a4afd59"},
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-    {file = "black-23.12.1.tar.gz", hash = "sha256:4ce3ef14ebe8d9509188014d96af1c456a910d5b5cbf434a09fef7e024b3d0d5"},
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+    {file = "black-24.3.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:e19cb1c6365fd6dc38a6eae2dcb691d7d83935c10215aef8e6c38edee3f77abd"},
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+    {file = "black-24.3.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:6905238a754ceb7788a73f02b45637d820b2f5478b20fec82ea865e4f5d4d9f7"},
+    {file = "black-24.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d7de8d330763c66663661a1ffd432274a2f92f07feeddd89ffd085b5744f85e7"},
+    {file = "black-24.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:7bb041dca0d784697af4646d3b62ba4a6b028276ae878e53f6b4f74ddd6db99f"},
+    {file = "black-24.3.0-py3-none-any.whl", hash = "sha256:41622020d7120e01d377f74249e677039d20e6344ff5851de8a10f11f513bf93"},
+    {file = "black-24.3.0.tar.gz", hash = "sha256:a0c9c4a0771afc6919578cec71ce82a3e31e054904e7197deacbc9382671c41f"},
 ]
 
 [package.dependencies]
@@ -196,17 +196,17 @@ stringcase = ">=1.2.0,<2.0.0"
 
 [[package]]
 name = "boto3"
-version = "1.34.57"
+version = "1.34.71"
 description = "The AWS SDK for Python"
 optional = false
-python-versions = ">= 3.8"
+python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.34.57-py3-none-any.whl", hash = "sha256:f8046e3e2d1186a49b49f7464c4811c265c86001f404dd1a96c4365c773a4245"},
-    {file = "boto3-1.34.57.tar.gz", hash = "sha256:c26c31ceeeb2bc5d2bb96ba0fdc9a04d7b10e6e0b081c55b9cea9069a0be04dd"},
+    {file = "boto3-1.34.71-py3-none-any.whl", hash = "sha256:7ce8c9a50af2f8a159a0dd86b40011d8dfdaba35005a118e51cd3ac72dc630f1"},
+    {file = "boto3-1.34.71.tar.gz", hash = "sha256:d786e7fbe3c4152866199786468a625dc77b9f27294cd7ad4f63cd2e0c927287"},
 ]
 
 [package.dependencies]
-botocore = ">=1.34.57,<1.35.0"
+botocore = ">=1.34.71,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -215,19 +215,19 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.57"
+version = "1.34.71"
 description = "Low-level, data-driven core of boto 3."
 optional = false
-python-versions = ">= 3.8"
+python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.34.57-py3-none-any.whl", hash = "sha256:c8dafe0ad378a88bcf4153e6972870b03fb5aab406b694202307500709940baf"},
-    {file = "botocore-1.34.57.tar.gz", hash = "sha256:9a5aa2034de9f0c367b4b61a92af0fa827f5c21affa19e0a284838a142e71083"},
+    {file = "botocore-1.34.71-py3-none-any.whl", hash = "sha256:3bc9e23aee73fe6f097823d61f79a8877790436038101a83fa96c7593e8109f8"},
+    {file = "botocore-1.34.71.tar.gz", hash = "sha256:c58f9ed71af2ea53d24146187130541222d7de8c27eb87d23f15457e7b83d88b"},
 ]
 
 [package.dependencies]
 jmespath = ">=0.7.1,<2.0.0"
 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
+urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 
 [package.extras]
 crt = ["awscrt (==0.19.19)"]
@@ -464,13 +464,13 @@ test = ["codacy-coverage", "coveralls", "dict_hash", "pytest", "pytest-cov", "ra
 
 [[package]]
 name = "curies"
-version = "0.7.7"
+version = "0.7.8"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.7.7-py3-none-any.whl", hash = "sha256:609de3e8cdf39f410e8f4d9f06eb7df379465860f4fb441bf0e79672430f8e2a"},
-    {file = "curies-0.7.7.tar.gz", hash = "sha256:a8d674029f906fb9c3564eafa0862ce96725932bd801fa751e076265b111cb34"},
+    {file = "curies-0.7.8-py3-none-any.whl", hash = "sha256:a60b2559f08557176b0a3df1f7c47ec7cd8ae4e0695f23fc6574825d2ccd17eb"},
+    {file = "curies-0.7.8.tar.gz", hash = "sha256:d208ad40b5e40b532285c917f116001f9e887a48dda54e6eedd10e514ea6aa1a"},
 ]
 
 [package.dependencies]
@@ -631,13 +631,13 @@ files = [
 
 [[package]]
 name = "elastic-transport"
-version = "8.12.0"
+version = "8.13.0"
 description = "Transport classes and utilities shared among Python Elastic client libraries"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "elastic-transport-8.12.0.tar.gz", hash = "sha256:48839b942fcce199eece1558ecea6272e116c58da87ca8d495ef12eb61effaf7"},
-    {file = "elastic_transport-8.12.0-py3-none-any.whl", hash = "sha256:87d9dc9dee64a05235e7624ed7e6ab6e5ca16619aa7a6d22e853273b9f1cfbee"},
+    {file = "elastic-transport-8.13.0.tar.gz", hash = "sha256:2410ec1ff51221e8b3a01c0afa9f0d0498e1386a269283801f5c12f98e42dc45"},
+    {file = "elastic_transport-8.13.0-py3-none-any.whl", hash = "sha256:aec890afdddd057762b27ff3553b0be8fa4673ec1a4fd922dfbd00325874bb3d"},
 ]
 
 [package.dependencies]
@@ -645,24 +645,25 @@ certifi = "*"
 urllib3 = ">=1.26.2,<3"
 
 [package.extras]
-develop = ["aiohttp", "furo", "mock", "pytest", "pytest-asyncio", "pytest-cov", "pytest-httpserver", "pytest-mock", "requests", "sphinx (>2)", "sphinx-autodoc-typehints", "trustme"]
+develop = ["aiohttp", "furo", "httpx", "mock", "opentelemetry-api", "opentelemetry-sdk", "orjson", "pytest", "pytest-asyncio", "pytest-cov", "pytest-httpserver", "pytest-mock", "requests", "respx", "sphinx (>2)", "sphinx-autodoc-typehints", "trustme"]
 
 [[package]]
 name = "elasticsearch"
-version = "8.12.1"
+version = "8.13.0"
 description = "Python client for Elasticsearch"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "elasticsearch-8.12.1-py3-none-any.whl", hash = "sha256:cc459b7e0fb88dc85b43b9d7d254cffad552b0063a3e0a12290c8fa5f138c038"},
-    {file = "elasticsearch-8.12.1.tar.gz", hash = "sha256:00c997720fbd0f2afe5417c8193cf65d116817a0250de0521e30c3e81f00b8ac"},
+    {file = "elasticsearch-8.13.0-py3-none-any.whl", hash = "sha256:4aaf49253e974eb500f01136a487bdd0f09d3cafd37a0456eff6acfff0c9199b"},
+    {file = "elasticsearch-8.13.0.tar.gz", hash = "sha256:e4ebebb22d09f0ef839c26b6aa98e19ccd636bcb77f08c12b562b02cacd5e744"},
 ]
 
 [package.dependencies]
-elastic-transport = ">=8,<9"
+elastic-transport = ">=8.13,<9"
 
 [package.extras]
 async = ["aiohttp (>=3,<4)"]
+orjson = ["orjson (>=3)"]
 requests = ["requests (>=2.4.0,<3.0.0)"]
 
 [[package]]
@@ -692,18 +693,18 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.13.1"
+version = "3.13.3"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
-    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
+    {file = "filelock-3.13.3-py3-none-any.whl", hash = "sha256:5ffa845303983e7a0b7ae17636509bc97997d58afeafa72fb141a17b152284cb"},
+    {file = "filelock-3.13.3.tar.gz", hash = "sha256:a79895a25bbefdf55d1a2a0a80968f7dbb28edcd6d4234a0afb3f37ecde4b546"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
 typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
@@ -756,18 +757,19 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "google-api-core"
-version = "2.17.1"
+version = "2.18.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.17.1.tar.gz", hash = "sha256:9df18a1f87ee0df0bc4eea2770ebc4228392d8cc4066655b320e2cfccb15db95"},
-    {file = "google_api_core-2.17.1-py3-none-any.whl", hash = "sha256:610c5b90092c360736baccf17bd3efbcb30dd380e7a6dc28a71059edb8bd0d8e"},
+    {file = "google-api-core-2.18.0.tar.gz", hash = "sha256:62d97417bfc674d6cef251e5c4d639a9655e00c45528c4364fbfebb478ce72a9"},
+    {file = "google_api_core-2.18.0-py3-none-any.whl", hash = "sha256:5a63aa102e0049abe85b5b88cb9409234c1f70afcda21ce1e40b285b9629c1d6"},
 ]
 
 [package.dependencies]
 google-auth = ">=2.14.1,<3.0.dev0"
 googleapis-common-protos = ">=1.56.2,<2.0.dev0"
+proto-plus = ">=1.22.3,<2.0.0dev"
 protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0.dev0"
 requests = ">=2.18.0,<3.0.0.dev0"
 
@@ -778,13 +780,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-auth"
-version = "2.28.1"
+version = "2.29.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-auth-2.28.1.tar.gz", hash = "sha256:34fc3046c257cedcf1622fc4b31fc2be7923d9b4d44973d481125ecc50d83885"},
-    {file = "google_auth-2.28.1-py2.py3-none-any.whl", hash = "sha256:25141e2d7a14bfcba945f5e9827f98092716e99482562f15306e5b026e21aa72"},
+    {file = "google-auth-2.29.0.tar.gz", hash = "sha256:672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360"},
+    {file = "google_auth-2.29.0-py2.py3-none-any.whl", hash = "sha256:d452ad095688cd52bae0ad6fafe027f6a6d6f560e810fec20914e17a09526415"},
 ]
 
 [package.dependencies]
@@ -819,13 +821,13 @@ grpc = ["grpcio (>=1.38.0,<2.0dev)", "grpcio-status (>=1.38.0,<2.0.dev0)"]
 
 [[package]]
 name = "google-cloud-storage"
-version = "2.15.0"
+version = "2.16.0"
 description = "Google Cloud Storage API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-cloud-storage-2.15.0.tar.gz", hash = "sha256:7560a3c48a03d66c553dc55215d35883c680fe0ab44c23aa4832800ccc855c74"},
-    {file = "google_cloud_storage-2.15.0-py2.py3-none-any.whl", hash = "sha256:5d9237f88b648e1d724a0f20b5cde65996a37fe51d75d17660b1404097327dd2"},
+    {file = "google-cloud-storage-2.16.0.tar.gz", hash = "sha256:dda485fa503710a828d01246bd16ce9db0823dc51bbca742ce96a6817d58669f"},
+    {file = "google_cloud_storage-2.16.0-py2.py3-none-any.whl", hash = "sha256:91a06b96fb79cf9cdfb4e759f178ce11ea885c79938f89590344d079305f5852"},
 ]
 
 [package.dependencies]
@@ -939,13 +941,13 @@ requests = ["requests (>=2.18.0,<3.0.0dev)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.62.0"
+version = "1.63.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "googleapis-common-protos-1.62.0.tar.gz", hash = "sha256:83f0ece9f94e5672cced82f592d2a5edf527a96ed1794f0bab36d5735c996277"},
-    {file = "googleapis_common_protos-1.62.0-py2.py3-none-any.whl", hash = "sha256:4750113612205514f9f6aa4cb00d523a94f3e8c06c5ad2fee466387dc4875f07"},
+    {file = "googleapis-common-protos-1.63.0.tar.gz", hash = "sha256:17ad01b11d5f1d0171c06d3ba5c04c54474e883b66b949722b4938ee2694ef4e"},
+    {file = "googleapis_common_protos-1.63.0-py2.py3-none-any.whl", hash = "sha256:ae45f75702f7c08b541f750854a678bd8f534a1a6bace6afe975f1d0a82d6632"},
 ]
 
 [package.dependencies]
@@ -956,19 +958,19 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"]
 
 [[package]]
 name = "graphviz"
-version = "0.20.1"
+version = "0.20.3"
 description = "Simple Python interface for Graphviz"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "graphviz-0.20.1-py3-none-any.whl", hash = "sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977"},
-    {file = "graphviz-0.20.1.zip", hash = "sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8"},
+    {file = "graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5"},
+    {file = "graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d"},
 ]
 
 [package.extras]
 dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
-docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
-test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=3)"]
+docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
+test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 
 [[package]]
 name = "greenlet"
@@ -1043,13 +1045,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "griffe"
-version = "0.41.3"
+version = "0.42.1"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "griffe-0.41.3-py3-none-any.whl", hash = "sha256:27b4610f1ba6e5d039e9f0a2c97232e13463df75e53cb1833e0679f3377b9de2"},
-    {file = "griffe-0.41.3.tar.gz", hash = "sha256:9edcfa9f57f4d9c5fcc6d5ce067c67a685b7101a21a7d11848ce0437368e474c"},
+    {file = "griffe-0.42.1-py3-none-any.whl", hash = "sha256:7e805e35617601355edcac0d3511cedc1ed0cb1f7645e2d336ae4b05bbae7b3b"},
+    {file = "griffe-0.42.1.tar.gz", hash = "sha256:57046131384043ed078692b85d86b76568a686266cc036b9b56b704466f803ce"},
 ]
 
 [package.dependencies]
@@ -1106,6 +1108,17 @@ files = [
     {file = "ijson-3.2.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:4a3a6a2fbbe7550ffe52d151cf76065e6b89cfb3e9d0463e49a7e322a25d0426"},
     {file = "ijson-3.2.3-cp311-cp311-win32.whl", hash = "sha256:6a4db2f7fb9acfb855c9ae1aae602e4648dd1f88804a0d5cfb78c3639bcf156c"},
     {file = "ijson-3.2.3-cp311-cp311-win_amd64.whl", hash = "sha256:ccd6be56335cbb845f3d3021b1766299c056c70c4c9165fb2fbe2d62258bae3f"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:055b71bbc37af5c3c5861afe789e15211d2d3d06ac51ee5a647adf4def19c0ea"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:c075a547de32f265a5dd139ab2035900fef6653951628862e5cdce0d101af557"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:457f8a5fc559478ac6b06b6d37ebacb4811f8c5156e997f0d87d708b0d8ab2ae"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9788f0c915351f41f0e69ec2618b81ebfcf9f13d9d67c6d404c7f5afda3e4afb"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:fa234ab7a6a33ed51494d9d2197fb96296f9217ecae57f5551a55589091e7853"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bdd0dc5da4f9dc6d12ab6e8e0c57d8b41d3c8f9ceed31a99dae7b2baf9ea769a"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:c6beb80df19713e39e68dc5c337b5c76d36ccf69c30b79034634e5e4c14d6904"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:a2973ce57afb142d96f35a14e9cfec08308ef178a2c76b8b5e1e98f3960438bf"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:105c314fd624e81ed20f925271ec506523b8dd236589ab6c0208b8707d652a0e"},
+    {file = "ijson-3.2.3-cp312-cp312-win32.whl", hash = "sha256:ac44781de5e901ce8339352bb5594fcb3b94ced315a34dbe840b4cff3450e23b"},
+    {file = "ijson-3.2.3-cp312-cp312-win_amd64.whl", hash = "sha256:0567e8c833825b119e74e10a7c29761dc65fcd155f5d4cb10f9d3b8916ef9912"},
     {file = "ijson-3.2.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:eeb286639649fb6bed37997a5e30eefcacddac79476d24128348ec890b2a0ccb"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:396338a655fb9af4ac59dd09c189885b51fa0eefc84d35408662031023c110d1"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0e0243d166d11a2a47c17c7e885debf3b19ed136be2af1f5d1c34212850236ac"},
@@ -1177,13 +1190,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.0.2"
+version = "7.1.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.0.2-py3-none-any.whl", hash = "sha256:f4bc4c0c070c490abf4ce96d715f68e95923320370efb66143df00199bb6c100"},
-    {file = "importlib_metadata-7.0.2.tar.gz", hash = "sha256:198f568f3230878cb1b44fbd7975f87906c22336dba2e4a7f05278c281fbd792"},
+    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
+    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
 ]
 
 [package.dependencies]
@@ -1192,22 +1205,22 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.3"
+version = "6.4.0"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.3-py3-none-any.whl", hash = "sha256:4c0269e3580fe2634d364b39b38b961540a7738c02cb984e98add8b4221d793d"},
-    {file = "importlib_resources-6.1.3.tar.gz", hash = "sha256:56fb4525197b78544a3354ea27793952ab93f935bb4bf746b846bb1015020f2b"},
+    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
+    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.collections", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "inflection"
@@ -1343,13 +1356,13 @@ hbreader = "*"
 
 [[package]]
 name = "jsonlines"
-version = "3.1.0"
+version = "4.0.0"
 description = "Library with helpers for the jsonlines file format"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "jsonlines-3.1.0-py3-none-any.whl", hash = "sha256:632f5e38f93dfcb1ac8c4e09780b92af3a55f38f26e7c47ae85109d420b6ad39"},
-    {file = "jsonlines-3.1.0.tar.gz", hash = "sha256:2579cb488d96f815b0eb81629e3e6b0332da0962a18fa3532958f7ba14a5c37f"},
+    {file = "jsonlines-4.0.0-py3-none-any.whl", hash = "sha256:185b334ff2ca5a91362993f42e83588a360cf95ce4b71a73548502bda52a7c55"},
+    {file = "jsonlines-4.0.0.tar.gz", hash = "sha256:0c6d2c09117550c089995247f605ae4cf77dd1533041d366351f6f298822ea74"},
 ]
 
 [package.dependencies]
@@ -1457,13 +1470,13 @@ test = ["tox"]
 
 [[package]]
 name = "kghub-downloader"
-version = "0.3.5"
+version = "0.3.7"
 description = "Downloads and caches files for knowledge graph ETL"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = "<4.0,>=3.8"
 files = [
-    {file = "kghub_downloader-0.3.5-py3-none-any.whl", hash = "sha256:f1712117f1d88cf54fd6cb18dd4cf3c5f90e6d92fad27e9fa2e2e0f717254a35"},
-    {file = "kghub_downloader-0.3.5.tar.gz", hash = "sha256:0fa0bad8446dc22b907eb19b4fe5fabd381d1528c74971f8c830449af36be152"},
+    {file = "kghub_downloader-0.3.7-py3-none-any.whl", hash = "sha256:c06320e79812a48e9ee88a0fba738d974fb628ee9999eaf0554245caeec85e09"},
+    {file = "kghub_downloader-0.3.7.tar.gz", hash = "sha256:36125e06bd96ebbffc3109c92c23568da55ecd9ec93f440c62ff1ed9739cd046"},
 ]
 
 [package.dependencies]
@@ -1497,7 +1510,7 @@ docker = "^6.0.0"
 docutils = "^0.18.1"
 ijson = "^3.1.3"
 inflection = "^0.5.1"
-jsonlines = "^3.1.0"
+jsonlines = "^4.0.0"
 jsonstreams = "^0.6.0"
 linkml = "^1.5.0"
 linkml-runtime = "^1.5.0"
@@ -1525,7 +1538,7 @@ validators = "^0.20.0"
 type = "git"
 url = "https://github.com/biolink/kgx"
 reference = "master"
-resolved_reference = "47efd9fc0ae74a5865e5a2e64cb62090ede13c7a"
+resolved_reference = "8e5981697b4549b0be36ff37bf8b9f0eea06a7fc"
 
 [[package]]
 name = "koza"
@@ -1668,13 +1681,13 @@ dev = ["Sphinx (==7.2.5)", "colorama (==0.4.5)", "colorama (==0.4.6)", "exceptio
 
 [[package]]
 name = "markdown"
-version = "3.5.2"
+version = "3.6"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Markdown-3.5.2-py3-none-any.whl", hash = "sha256:d43323865d89fc0cb9b20c75fc8ad313af307cc087e84b657d9eec768eddeadd"},
-    {file = "Markdown-3.5.2.tar.gz", hash = "sha256:e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8"},
+    {file = "Markdown-3.6-py3-none-any.whl", hash = "sha256:48f276f4d8cfb8ce6527c8f79e2ee29708508bf4d40aa410fbc3b4ee832c850f"},
+    {file = "Markdown-3.6.tar.gz", hash = "sha256:ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224"},
 ]
 
 [package.extras]
@@ -1919,38 +1932,38 @@ test = ["codacy-coverage", "coveralls", "parameterized", "pytest", "pytest-cov",
 
 [[package]]
 name = "mypy"
-version = "1.8.0"
+version = "1.9.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mypy-1.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:485a8942f671120f76afffff70f259e1cd0f0cfe08f81c05d8816d958d4577d3"},
-    {file = "mypy-1.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:df9824ac11deaf007443e7ed2a4a26bebff98d2bc43c6da21b2b64185da011c4"},
-    {file = "mypy-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2afecd6354bbfb6e0160f4e4ad9ba6e4e003b767dd80d85516e71f2e955ab50d"},
-    {file = "mypy-1.8.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:8963b83d53ee733a6e4196954502b33567ad07dfd74851f32be18eb932fb1cb9"},
-    {file = "mypy-1.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:e46f44b54ebddbeedbd3d5b289a893219065ef805d95094d16a0af6630f5d410"},
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+
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-version = "0.33.0"
+version = "0.34.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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@@ -3087,39 +3127,39 @@ files = [
 
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 name = "ruff"
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+version = "0.3.4"
 description = "An extremely fast Python linter and code formatter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "ruff-0.3.4-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:986f2377f7cf12efac1f515fc1a5b753c000ed1e0a6de96747cdf2da20a1b369"},
+    {file = "ruff-0.3.4-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:c4fd98e85869603e65f554fdc5cddf0712e352fe6e61d29d5a6fe087ec82b76c"},
+    {file = "ruff-0.3.4-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:64abeed785dad51801b423fa51840b1764b35d6c461ea8caef9cf9e5e5ab34d9"},
+    {file = "ruff-0.3.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:df52972138318bc7546d92348a1ee58449bc3f9eaf0db278906eb511889c4b50"},
+    {file = "ruff-0.3.4-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:98e98300056445ba2cc27d0b325fd044dc17fcc38e4e4d2c7711585bd0a958ed"},
+    {file = "ruff-0.3.4-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:519cf6a0ebed244dce1dc8aecd3dc99add7a2ee15bb68cf19588bb5bf58e0488"},
+    {file = "ruff-0.3.4-py3-none-musllinux_1_2_i686.whl", hash = "sha256:bb0acfb921030d00070539c038cd24bb1df73a2981e9f55942514af8b17be94e"},
+    {file = "ruff-0.3.4-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:cf187a7e7098233d0d0c71175375c5162f880126c4c716fa28a8ac418dcf3378"},
+    {file = "ruff-0.3.4-py3-none-win32.whl", hash = "sha256:af27ac187c0a331e8ef91d84bf1c3c6a5dea97e912a7560ac0cef25c526a4102"},
+    {file = "ruff-0.3.4-py3-none-win_amd64.whl", hash = "sha256:de0d5069b165e5a32b3c6ffbb81c350b1e3d3483347196ffdf86dc0ef9e37dd6"},
+    {file = "ruff-0.3.4-py3-none-win_arm64.whl", hash = "sha256:6810563cc08ad0096b57c717bd78aeac888a1bfd38654d9113cb3dc4d3f74232"},
+    {file = "ruff-0.3.4.tar.gz", hash = "sha256:f0f4484c6541a99862b693e13a151435a279b271cff20e37101116a21e2a1ad1"},
 ]
 
 [[package]]
 name = "s3transfer"
-version = "0.10.0"
+version = "0.10.1"
 description = "An Amazon S3 Transfer Manager"
 optional = false
 python-versions = ">= 3.8"
 files = [
-    {file = "s3transfer-0.10.0-py3-none-any.whl", hash = "sha256:3cdb40f5cfa6966e812209d0994f2a4709b561c88e90cf00c2696d2df4e56b2e"},
-    {file = "s3transfer-0.10.0.tar.gz", hash = "sha256:d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b"},
+    {file = "s3transfer-0.10.1-py3-none-any.whl", hash = "sha256:ceb252b11bcf87080fb7850a224fb6e05c8a776bab8f2b64b7f25b969464839d"},
+    {file = "s3transfer-0.10.1.tar.gz", hash = "sha256:5683916b4c724f799e600f41dd9e10a9ff19871bf87623cc8f491cb4f5fa0a19"},
 ]
 
 [package.dependencies]
@@ -3172,18 +3212,18 @@ test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov",
 
 [[package]]
 name = "setuptools"
-version = "69.1.1"
+version = "69.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-69.1.1-py3-none-any.whl", hash = "sha256:02fa291a0471b3a18b2b2481ed902af520c69e8ae0919c13da936542754b4c56"},
-    {file = "setuptools-69.1.1.tar.gz", hash = "sha256:5c0806c7d9af348e6dd3777b4f4dbb42c7ad85b190104837488eab9a7c945cf8"},
+    {file = "setuptools-69.2.0-py3-none-any.whl", hash = "sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c"},
+    {file = "setuptools-69.2.0.tar.gz", hash = "sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -3510,13 +3550,13 @@ sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "sssom"
-version = "0.4.4"
+version = "0.4.5"
 description = "Operations on SSSOM mapping tables"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = "<4.0,>=3.8"
 files = [
-    {file = "sssom-0.4.4-py3-none-any.whl", hash = "sha256:bc2a01865ea2cf1805420d82a1cbd7d0e180fc86af77f4e3eedd4fed5a569fc7"},
-    {file = "sssom-0.4.4.tar.gz", hash = "sha256:9395c5614f2d1ff321450100d5448388642dccca6060dd8c03a5664d227da7b0"},
+    {file = "sssom-0.4.5-py3-none-any.whl", hash = "sha256:8fd582082b9b5e748f05d1831362f1af9f700837a01f1d5fca09361519657d54"},
+    {file = "sssom-0.4.5.tar.gz", hash = "sha256:753b3481083a6a62d39f11d6dc18e6038fc0edaa27929e0881e1c7fee8f8bcbe"},
 ]
 
 [package.dependencies]
@@ -3584,13 +3624,13 @@ files = [
 
 [[package]]
 name = "tox"
-version = "4.14.1"
+version = "4.14.2"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.14.1-py3-none-any.whl", hash = "sha256:b03754b6ee6dadc70f2611da82b4ed8f625fcafd247e15d1d0cb056f90a06d3b"},
-    {file = "tox-4.14.1.tar.gz", hash = "sha256:f0ad758c3bbf7e237059c929d3595479363c3cdd5a06ac3e49d1dd020ffbee45"},
+    {file = "tox-4.14.2-py3-none-any.whl", hash = "sha256:2900c4eb7b716af4a928a7fdc2ed248ad6575294ed7cfae2ea41203937422847"},
+    {file = "tox-4.14.2.tar.gz", hash = "sha256:0defb44f6dafd911b61788325741cc6b2e12ea71f987ac025ad4d649f1f1a104"},
 ]
 
 [package.dependencies]
@@ -3667,13 +3707,13 @@ typer = ">=0.4.0,<=0.7.0"
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.8.19.20240106"
+version = "2.9.0.20240316"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"},
-    {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"},
+    {file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"},
+    {file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"},
 ]
 
 [[package]]
@@ -3714,18 +3754,18 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.0.7"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
-    {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
@@ -3950,20 +3990,20 @@ dev = ["doc8", "flake8", "flake8-import-order", "rstcheck[sphinx]", "sphinx"]
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+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", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.12"
-content-hash = "78603fc5ad175e67cd88471191136ffd4a6f28e0fef8b9dd3d59d5c6b74d76e5"
+content-hash = "5fcf5202d13b5ed2ae6f419745d1f97f0b9f1e9936588ba7061651b1a1ffc1fc"
diff --git a/pyproject.toml b/pyproject.toml
index abe1e9b1..266adf57 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,9 +16,9 @@ packages = [
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.12"
-# biolink-model = "^4.1.7"
-# When 4.1.7 (or any release after 4.1.6) is released, we can remove the git dependency
-biolink-model = { git = "https://github.com/biolink/biolink-model", rev = "dc87efc" }
+# biolink-model = "^4.2.0"
+# When 4.2.0 (or any release after 4.1.6) is released, we can remove the git dependency
+biolink-model = { git = "https://github.com/biolink/biolink-model", tag = "v4.2.0-rc.2" }
 bmt = "^1.0.15"
 cat-merge = ">=0.2.0"
 closurizer = "0.5.1"
@@ -46,7 +46,7 @@ optional = true
 pytest = "^7.1.1"
 mkdocs = "^1.3.0"
 mkdocs-material = "^8.2.9"
-black = "^23.10.0"
+black = "^24.3"
 ruff = "*"
 
 [tool.poetry.scripts]

From cbabe69d556662e1f44d56975f26ba3236194098 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 27 Mar 2024 14:32:35 -0600
Subject: [PATCH 4/4] add test

---
 tests/unit/pombase/test_pombase_gene.py | 27 +++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/tests/unit/pombase/test_pombase_gene.py b/tests/unit/pombase/test_pombase_gene.py
index b16306df..e5fa3750 100644
--- a/tests/unit/pombase/test_pombase_gene.py
+++ b/tests/unit/pombase/test_pombase_gene.py
@@ -22,6 +22,27 @@ def gene_information_entities(mock_koza, taxon_label_map_cache, global_table):
         global_table=global_table,
     )
 
+@pytest.fixture
+def gene_entity_no_name(mock_koza, taxon_label_map_cache, global_table):
+    row = {
+        'gene_systematic_id': 'SPAC1002.06c',
+        'gene_systematic_id_with_prefix': 'POMBASE:SPAC1002.06c',
+        'gene_name': '',
+        'chromosome_id': 'chromosome_1',
+        'gene_product': 'bouquet formation protein Bqt2',
+        'uniprot_id': 'Q9US52',
+        'gene type': 'protein coding gene',
+        'synonyms': 'mug18,rec23',
+    }
+
+    return mock_koza(
+        "pombase_gene",
+        iter([row]),
+        "./src/monarch_ingest/ingests/pombase/gene.py",
+        map_cache=taxon_label_map_cache,
+        global_table=global_table,
+    )
+
 
 def test_gene_information_gene(gene_information_entities):
     assert len(gene_information_entities) == 1
@@ -43,3 +64,9 @@ def test_gene_information_id(gene_information_entities):
 def test_gene_xref(gene_information_entities):
     gene = gene_information_entities[0]
     assert "UniProtKB:Q9US52" in gene.xref
+
+def test_gene_systematic_id_as_name(gene_entity_no_name):
+    gene = gene_entity_no_name[0]
+    assert gene.name == "SPAC1002.06c"
+    assert gene.full_name == "SPAC1002.06c"
+    assert gene.symbol == "SPAC1002.06c"
\ No newline at end of file