added unit test for vcell api get publications, fixed some python typing

virtualcell · Jan 23, 2025 · a8c099c · a8c099c
1 parent efd77e8
commit a8c099c
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Showing 7 changed files with 103 additions and 10 deletions.
diff --git a/examples/vcell_publications.ipynb b/examples/vcell_publications.ipynb
@@ -3,10 +3,9 @@
   {
    "cell_type": "code",
    "source": [
-    "from pyvcell.api.vcell_client.api_client import ApiClient, Configuration\n",
+    "from pyvcell.api.vcell_client import ApiClient, Configuration, PublicationResourceApi\n",
     "from pyvcell.api.vcell_client.auth.auth_utils import login_interactive\n",
-    "from pyvcell.api.vcell_client import Publication\n",
-    "from pyvcell.api.vcell_client.api.publication_resource_api import PublicationResourceApi"
+    "from pyvcell.api.vcell_client.models import Publication"
    ],
    "metadata": {
     "collapsed": false,

diff --git a/pyvcell/api/vcell_client/__init__.py b/pyvcell/api/vcell_client/__init__.py
@@ -75,3 +75,23 @@
 from pyvcell.api.vcell_client.models.vc_simulation_identifier import VCSimulationIdentifier
 from pyvcell.api.vcell_client.models.variable_domain import VariableDomain
 from pyvcell.api.vcell_client.models.variable_type import VariableType
+
+__all__ = [
+    "AdminResourceApi",
+    "BioModelResourceApi",
+    "FieldDataResourceApi",
+    "HelloWorldApi",
+    "PublicationResourceApi",
+    "SimulationResourceApi",
+    "UsersResourceApi",
+
+    "ApiResponse",
+    "ApiClient",
+    "Configuration",
+    "OpenApiException",
+    "ApiTypeError",
+    "ApiValueError",
+    "ApiKeyError",
+    "ApiAttributeError",
+    "ApiException",
+]
diff --git a/pyvcell/api/vcell_client/models/__init__.py b/pyvcell/api/vcell_client/models/__init__.py
@@ -52,3 +52,44 @@
 from pyvcell.api.vcell_client.models.vc_simulation_identifier import VCSimulationIdentifier
 from pyvcell.api.vcell_client.models.variable_domain import VariableDomain
 from pyvcell.api.vcell_client.models.variable_type import VariableType
+
+
+__all__ = [
+    "AccesTokenRepresentationRecord",
+    "AnalyzedResultsFromFieldData",
+    "BatchSystemType",
+    "BioModel",
+    "BiomodelRef",
+    "DataIdentifier",
+    "DetailedState",
+    "Domain",
+    "Extent",
+    "ExternalDataIdentifier",
+    "FieldDataReference",
+    "FieldDataSaveResults",
+    "FieldDataShape",
+    "HelloWorldMessage",
+    "HtcJobID",
+    "ISize",
+    "Identity",
+    "KeyValue",
+    "MathmodelRef",
+    "Origin",
+    "Publication",
+    "SchedulerStatus",
+    "SimulationExecutionStatusRecord",
+    "SimulationJobStatusRecord",
+    "SimulationMessage",
+    "SimulationQueueEntryStatusRecord",
+    "SimulationQueueID",
+    "SimulationStatusPersistentRecord",
+    "Status",
+    "StatusMessage",
+    "User",
+    "UserIdentityJSONSafe",
+    "UserLoginInfoForMapping",
+    "UserRegistrationInfo",
+    "VCSimulationIdentifier",
+    "VariableDomain",
+    "VariableType",
+]
diff --git a/tests/__init__.py b/tests/__init__.py
diff --git a/tests/expression_test.py b/tests/expression_test.py
@@ -1,4 +1,5 @@
 import numpy as np
+from numpy.typing import NDArray
 
 from pyvcell.simdata.simdata_models import NamedFunction, VariableType
 
@@ -11,7 +12,7 @@ def test_namedfunction_eval_add() -> None:
     bindings = {"v0": a, "v1": b, "v2": c}
 
     function = NamedFunction(name="func1", vcell_expression=vcell_expression, variable_type=VariableType.VOLUME)
-    d: np.ndarray = function.evaluate(variable_bindings=bindings)
+    d: NDArray[np.float64] = function.evaluate(variable_bindings=bindings)
 
     assert np.array_equal(d, a + b + c)
     assert np.array_equal(d, np.array([12, 15, 18]))
@@ -26,7 +27,7 @@ def test_namedfunction_eval_power() -> None:
     bindings = {"v0": a, "v1": b, "v2": c}
 
     function = NamedFunction(name="func1", vcell_expression=vcell_expression, variable_type=VariableType.VOLUME)
-    d: np.ndarray = function.evaluate(variable_bindings=bindings)
+    d: NDArray[np.float64] = function.evaluate(variable_bindings=bindings)
 
     assert np.array_equal(d, a + b**c)
     assert np.array_equal(d, np.array([a[0] + b[0] ** c[0], a[1] + b[1] ** c[1], a[2] + b[2] ** c[2]]))

diff --git a/tests/vcell_client/test_publication_api.py b/tests/vcell_client/test_publication_api.py
@@ -0,0 +1,31 @@
+from datetime import date
+
+from pyvcell.api.vcell_client import Configuration, ApiClient, PublicationResourceApi
+from pyvcell.api.vcell_client.models import Publication, BiomodelRef
+
+
+def test_get_publications() -> None:
+    api_url: str = "https://vcell-dev.cam.uchc.edu"  # vcell base url
+
+    public_client = ApiClient(configuration=Configuration(host=api_url))
+
+    public_publication_api = PublicationResourceApi(public_client)
+    pubs: list[Publication] = public_publication_api.get_publications()
+    example_pub = Publication(pub_key=279906235,  # type: ignore
+                              title='A continuum model of mechanosensation based on contractility kit assembly',
+                              authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'],
+                              year=2024,
+                              citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2',
+                              pubmedid='39521955',
+                              doi='https://doi.org/10.1016/j.bpj.2024.10.020',
+                              endnoteid=0,
+                              url='url',
+                              wittid=0,
+                              biomodel_refs=[BiomodelRef(bm_key=279851639,  # type: ignore
+                                                         name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly',
+                                                         owner_name='Dolgitzer',
+                                                         owner_key=259537152,
+                                                         version_flag=3)],
+                              mathmodel_refs=[],
+                              var_date=date(year=2024, month=11, day=26))
+    assert pubs[0] == example_pub
diff --git a/tests/vcell_parsing_test.py b/tests/vcell_parsing_test.py
@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import numpy as np
+from numpy.typing import NDArray
 
 from pyvcell.simdata.mesh import CartesianMesh
 from pyvcell.simdata.postprocessing import ImageMetadata, PostProcessing, StatisticType, VariableInfo
@@ -53,7 +54,7 @@ def test_parse_vcelldata() -> None:
     for t in pde_dataset.times():
         for v in pde_dataset.variables_block_headers():
             data = pde_dataset.get_data(v.var_info, t)
-            if data.size > 0 and v == "cytosol::RanC_cyt":
+            if data.size > 0 and v.var_info.var_name == "cytosol::RanC_cyt":
                 print(f"v={v}, t={t}, shape={data.shape}, min={np.min(data)}, max={np.max(data)}")
     teardown_files()
 
@@ -158,11 +159,11 @@ def test_function_eval() -> None:
     max_values = []
     for t in pde_dataset.times():
         # for "RanC_cyt - (1000.0 * C_cyt * Ran_cyt)"
-        RanC_cyt: np.ndarray = pde_dataset.get_data("cytosol::RanC_cyt", t)
-        C_cyt: np.ndarray = pde_dataset.get_data("cytosol::C_cyt", t)
-        Ran_cyt: np.ndarray = pde_dataset.get_data("cytosol::Ran_cyt", t)
+        RanC_cyt: NDArray[np.float64] = pde_dataset.get_data("cytosol::RanC_cyt", t)
+        C_cyt: NDArray[np.float64] = pde_dataset.get_data("cytosol::C_cyt", t)
+        Ran_cyt: NDArray[np.float64] = pde_dataset.get_data("cytosol::Ran_cyt", t)
         bindings = {"RanC_cyt": RanC_cyt, "C_cyt": C_cyt, "Ran_cyt": Ran_cyt}
-        J_r0: np.ndarray = function_J_r0.evaluate(bindings)
+        J_r0: NDArray[np.float64] = function_J_r0.evaluate(bindings)
 
         assert J_r0.shape == (126025,)
         assert np.allclose(J_r0, RanC_cyt - (1000.0 * C_cyt * Ran_cyt))