Changed the naming conventions of input tensors and source code files

for UniSpec pytest

clients/python/test/UniSpec/arr-UniSpec_usprocess_charges.txt

@@ -0,0 +1,50 @@
+2
+2
+2
+3
+2
+2
+2
+3
+2
+2
+2
+2
+3
+3
+3
+3
+3
+3
+2
+2
+2
+2
+2
+2
+2
+3
+2
+2
+2
+2
+2
+2
+2
+3
+3
+4
+4
+2
+2
+2
+3
+2
+2
+2
+2
+2
+2
+3
+3
+3

clients/python/test/UniSpec/arr-UniSpec_usprocess_modseqs.txt

@@ -0,0 +1,50 @@
+YINGLDPEPLPLM[UNIMOD:35]DLC[UNIMOD:4]R
+YINGLDPEPLPLM[UNIMOD:35]DLC[UNIMOD:4]R
+YIRPEM[UNIMOD:35]PIADYR
+YIRPEM[UNIMOD:35]PIADYR
+YKPDTLAVAVENGTGTDR
+YKPDTLAVAVENGTGTDR
+YKPDTLAVAVENGTGTDR
+YKPDTLAVAVENGTGTDR
+YLQDLPTVSFGK
+YLSVVSPLSTLR
+YLSVVSPLSTLR
+YLSVVSPLSTLR
+YLSVVSPLSTLR
+YLSVVSPLSTLR
+YLSVVSPLSTLR
+YPEHGNPAILLM[UNIMOD:35]GSANGGPVVK
+YPEHGNPAILLM[UNIMOD:35]GSANGGPVVK
+YPEHGNPAILLM[UNIMOD:35]GSANGGPVVK
+YPPAANELTM[UNIMOD:35]R
+YPPAANELTM[UNIMOD:35]R
+YPPAANELTM[UNIMOD:35]R
+YSAEVHM[UNIMOD:35]SIPNVSLPLR
+YSAEVHM[UNIMOD:35]SIPNVSLPLR
+YSAEVHM[UNIMOD:35]SIPNVSLPLR
+YSGVNM[UNIMOD:35]TGFR
+YSHTAHVLNGK
+YSLLDHM[UNIMOD:35]QAM[UNIMOD:35]R
+YTC[UNIMOD:4]SPEFDFM[UNIMOD:35]EK
+YTC[UNIMOD:4]SPEFDFM[UNIMOD:35]EK
+YTC[UNIMOD:4]SPEFDFM[UNIMOD:35]EK
+YTIQLTTLSGLR
+YTIQLTTLSGLR
+YTM[UNIMOD:35]PSSLLAPAK
+YVPVRPRPPITLLR
+YVPVRPRPPITLLR
+YVPVRPRPPITLLR
+YVPVRPRPPITLLR
+YWVIVNPM[UNIMOD:35]GHSR
+YWVIVNPM[UNIMOD:35]GHSR
+YWVIVNPM[UNIMOD:35]GHSR
+YWVIVNPM[UNIMOD:35]GHSR
+YYHTLFTHSLPK
+YYHTLFTHSLPK
+YYHTLFTHSLPK
+YYLPHLFPSFTK
+YYLPHLFPSFTK
+YYLPHLFPSFTK
+YYLPHLFPSFTK
+YYLPHLFPSFTK
+YYLPHLFPSFTK

clients/python/test/UniSpec/arr-UniSpec_usprocess_nces.txt

@@ -0,0 +1,50 @@
+30.000000
+35.000000
+25.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+25.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+25.000000
+25.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+25.000000
+25.000000
+30.000000
+25.000000
+30.000000
+25.000000
+30.000000
+35.000000
+30.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000
+25.000000
+30.000000
+35.000000

clients/python/test/UniSpec/test_UniSpec_unispec23.py

@@ -0,0 +1,45 @@
+from test.server_config import SERVER_GRPC, SERVER_HTTP
+import tritonclient.grpc as grpcclient
+import numpy as np
+import requests
+from pathlib import Path
+
+
+# To ensure MODEL_NAME == test_<filename>.py
+MODEL_NAME = Path(__file__).stem.replace("test_", "")
+
+
+def test_available_http():
+    req = requests.get(f"{SERVER_HTTP}/v2/models/{MODEL_NAME}", timeout=1)
+    assert req.status_code == 200
+
+
+def test_available_grpc():
+    triton_client = grpcclient.InferenceServerClient(url=SERVER_GRPC)
+    assert triton_client.is_model_ready(MODEL_NAME)
+
+
+def test_inference():
+    INPUT = np.load("test/UniSpec/arr-UniSpec_unispec23_input_tensor.npy")
+    triton_client = grpcclient.InferenceServerClient(url=SERVER_GRPC)
+    in_INPUT = grpcclient.InferInput("input_tensor", INPUT.shape, "FP32")
+    in_INPUT.set_data_from_numpy(INPUT)
+    result = triton_client.infer(
+        MODEL_NAME,
+        inputs=[in_INPUT],
+        outputs=[
+            grpcclient.InferRequestedOutput("intensities"),
+        ],
+    )
+
+    intensities = result.as_numpy("intensities")
+
+    assert intensities.shape == (50, 7919)
+
+    # Assert intensities consistent
+    assert np.allclose(
+        intensities,
+        np.load("test/UniSpec/arr-UniSpec_unispec23_output_tensor.npy"),
+        rtol=0,
+        atol=1e-5,
+    )

clients/python/test/UniSpec/test_UniSpec_usprocess.py

@@ -0,0 +1,137 @@
+from test.server_config import SERVER_GRPC, SERVER_HTTP
+import tritonclient.grpc as grpcclient
+import numpy as np
+import requests
+from pathlib import Path
+import re
+
+# To ensure MODEL_NAME == test_<filename>.py
+MODEL_NAME = Path(__file__).stem.replace("test_", "")
+
+mdicum = {
+    1: "Acetyl",
+    4: "Carbamidomethyl",
+    28: "Gln->pyro-Glu",
+    27: "Glu->pyro-Glu",
+    35: "Oxidation",
+    21: "Phospho",
+    26: "Pyro-carbamidomethyl",
+    # 4: 'CAM'
+}
+rev_mdicum = {n: m for m, n in mdicum.items()}
+
+
+def str2dat(label):
+    seq, other = label.split("/")
+    [charge, mods, ev, nce] = other.split("_")
+    return (seq, mods, int(charge), float(ev[:-2]), float(nce[3:]))
+
+
+def label2modseq(labels):
+    modseqs = []
+    charges = []
+    nces = []
+    for label in labels:
+
+        seq, mod, charge, ev, nce = str2dat(label)
+        charges.append(int(charge))
+        nces.append(float(nce))
+
+        mseq = seq
+        Mstart = mod.find("(") if mod != "0" else 1
+        modamt = int(mod[0:Mstart])
+        if modamt > 0:
+            hold = [re.sub("[()]", "", n) for n in mod[Mstart:].split(")(")]
+            hold.reverse()
+            for n in hold:
+                [pos, aa, modtyp] = n.split(",")
+                pos = int(pos)
+                assert seq[pos] == aa
+                assert "Carbamidomethyl" in rev_mdicum.keys(), print(rev_mdicum.keys())
+                mseq = (
+                    list(mseq)[: pos + 1]
+                    + list("[UNIMOD:%d]" % rev_mdicum[modtyp])
+                    + list(mseq)[pos + 1 :]
+                )
+                mseq = "".join(mseq)
+        modseqs.append(mseq)
+    Modseqs = np.array(modseqs)[:, None].astype(np.object_)
+    Charges = np.array(charges)[:, None].astype(np.int32)
+    Nces = np.array(nces)[:, None].astype(np.float32)
+
+    return Modseqs, Charges, Nces
+
+
+def test_available_http():
+    req = requests.get(f"{SERVER_HTTP}/v2/models/{MODEL_NAME}", timeout=1)
+    assert req.status_code == 200
+
+
+def test_available_grpc():
+    triton_client = grpcclient.InferenceServerClient(url=SERVER_GRPC)
+    assert triton_client.is_model_ready(MODEL_NAME)
+
+
+def test_inference():
+
+    # labels = open("test/UniSpec/labels_input2.txt").read().split("\n")
+    # SEQUENCES, charge, ces = label2modseq(labels)
+    SEQUENCES = np.array(
+        open("test/UniSpec/arr-UniSpec_usprocess_modseqs.txt").read().split("\n"), dtype=np.object_
+    )[:, None]
+    charge = np.loadtxt("test/UniSpec/arr-UniSpec_usprocess_charges.txt")[:, None].astype(np.int32)
+    ces = np.loadtxt("test/UniSpec/arr-UniSpec_usprocess_nces.txt")[:, None].astype(np.float32)
+    instr = np.array(50 * ["Lumos"])[:, None].astype(np.object_)
+
+    triton_client = grpcclient.InferenceServerClient(url=SERVER_GRPC)
+
+    in_pep_seq = grpcclient.InferInput("peptide_sequences", SEQUENCES.shape, "BYTES")
+    in_pep_seq.set_data_from_numpy(SEQUENCES)
+
+    in_charge = grpcclient.InferInput("precursor_charges", charge.shape, "INT32")
+    in_charge.set_data_from_numpy(charge)
+
+    in_ces = grpcclient.InferInput("collision_energies", ces.shape, "FP32")
+    in_ces.set_data_from_numpy(ces)
+
+    in_instr = grpcclient.InferInput("instrument_types", instr.shape, "BYTES")
+    in_instr.set_data_from_numpy(instr)
+
+    result = triton_client.infer(
+        MODEL_NAME,
+        inputs=[in_pep_seq, in_charge, in_ces, in_instr],
+        outputs=[
+            grpcclient.InferRequestedOutput("intensities"),
+            grpcclient.InferRequestedOutput("mz"),
+            grpcclient.InferRequestedOutput("annotation"),
+        ],
+    )
+
+    intensities = result.as_numpy("intensities")
+    mz = result.as_numpy("mz")
+    ann = result.as_numpy("annotation")
+
+    # Assert expected ions are in each prediction
+    ions = np.load("test/UniSpec/arr-UniSpec_usprocess_top200_convertedions.npy")
+    for i in range(50):
+        for j in ions[i]:
+            assert str.encode(j) in ann[i]
+
+    # Assert intensities consistent
+    # Because of residuals in mz, the argsort comes out a little different between koina
+    # and my github repo implementation. Thus intensities and anns would return false in
+    # np.allclose
+    # assert np.allclose(
+    #    intensities,
+    #    np.load("test/UniSpec/arr-UniSpec_usprocess_top200_intensities.npy"),
+    #    rtol=0,
+    #    atol=1e-4,
+    # )
+
+    # Assert masses are consistent
+    assert np.allclose(
+        mz,
+        np.load("test/UniSpec/arr-UniSpec_usprocess_top200_mz.npy"),
+        rtol=0,
+        atol=1e-8,
+    )