Merge pull request #98 from wilhelm-lab/ll_unispec

Add unispec to Koina
wilhelm-lab · Jul 31, 2024 · b537c2e · b537c2e
2 parents 3a863ae + 00f4c37
commit b537c2e
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diff --git a/clients/python/test/UniSpec/arr-unispec23-input_tensor.npy b/clients/python/test/UniSpec/arr-unispec23-input_tensor.npy
diff --git a/clients/python/test/UniSpec/arr-unispec23-intensities.npy b/clients/python/test/UniSpec/arr-unispec23-intensities.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-annotation.npy b/clients/python/test/UniSpec/arr-usprocess-annotation.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-collision_energies.npy b/clients/python/test/UniSpec/arr-usprocess-collision_energies.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-instrument_types.npy b/clients/python/test/UniSpec/arr-usprocess-instrument_types.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-intensities.npy b/clients/python/test/UniSpec/arr-usprocess-intensities.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-mz.npy b/clients/python/test/UniSpec/arr-usprocess-mz.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-peptide_sequences.npy b/clients/python/test/UniSpec/arr-usprocess-peptide_sequences.npy
diff --git a/clients/python/test/UniSpec/arr-usprocess-precursor_charges.npy b/clients/python/test/UniSpec/arr-usprocess-precursor_charges.npy
diff --git a/clients/python/test/UniSpec/test_unispec23.py b/clients/python/test/UniSpec/test_unispec23.py
@@ -0,0 +1,23 @@
+from test.server_config import SERVER_GRPC, SERVER_HTTP
+from pathlib import Path
+from test.lib import (
+    lib_test_available_grpc,
+    lib_test_available_http,
+    lib_test_inference,
+)
+
+
+# To ensure MODEL_NAME == test_<filename>.py
+MODEL_NAME = Path(__file__).stem.replace("test_", "")
+
+
+def test_available_http():
+    lib_test_available_http(MODEL_NAME, SERVER_HTTP)
+
+
+def test_available_grpc():
+    lib_test_available_grpc(MODEL_NAME, SERVER_GRPC)
+
+
+def test_inference():
+    lib_test_inference(MODEL_NAME, SERVER_GRPC)
diff --git a/clients/python/test/UniSpec/test_usprocess.py b/clients/python/test/UniSpec/test_usprocess.py
@@ -0,0 +1,23 @@
+from test.server_config import SERVER_GRPC, SERVER_HTTP
+from pathlib import Path
+from test.lib import (
+    lib_test_available_grpc,
+    lib_test_available_http,
+    lib_test_inference,
+)
+
+
+# To ensure MODEL_NAME == test_<filename>.py
+MODEL_NAME = Path(__file__).stem.replace("test_", "")
+
+
+def test_available_http():
+    lib_test_available_http(MODEL_NAME, SERVER_HTTP)
+
+
+def test_available_grpc():
+    lib_test_available_grpc(MODEL_NAME, SERVER_GRPC)
+
+
+def test_inference():
+    lib_test_inference(MODEL_NAME, SERVER_GRPC)
diff --git a/models/UniSpec/unispec23/1/.zenodo b/models/UniSpec/unispec23/1/.zenodo
@@ -0,0 +1,2 @@
+https://zenodo.org/records/10391561/files/model.zip?download=1
+md5:c8b1fcc14e43bb5ebbb91421fda8227a
diff --git a/models/UniSpec/unispec23/config.pbtxt b/models/UniSpec/unispec23/config.pbtxt
@@ -0,0 +1,17 @@
+name: "unispec23"
+backend: "pytorch"
+max_batch_size: 1000
+input [
+  {
+   name: 'input_tensor',
+   data_type: TYPE_FP32,
+   dims: [38, 40]
+  }
+]
+output [
+  {
+   name: 'intensities',
+   data_type: TYPE_FP32,
+   dims: [ 7918 ]
+  }
+]