Merge pull request #55 from biosimulations/simple-sedml-endpoint

Simple sedml endpoint

Author: Ezequiel-Valencia

.python-version

@@ -1 +1 @@
-3.12
+3.13

Dockerfile-api

@@ -6,7 +6,7 @@ ARG APP_UID=16997
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-    openssh-client && \
+    openssh-client libexpat1 && \
     rm -rf /var/lib/apt/lists/*
 
 # Set environment variables

Makefile

@@ -4,6 +4,11 @@ install: ## Install the virtual environment and install the pre-commit hooks
 	@uv sync
 	@uv run pre-commit install
 
+.PHONY: run
+run: ##
+	@echo "🚀 Run local server."
+	@uvicorn compose_api.api.main:app --host 0.0.0.0 --port 8000 --reload
+
 .PHONY: check
 check: ## Run code quality tools.
 	@echo "🚀 Checking lock file consistency with 'pyproject.toml'"

compose_api/api/client/api/simulations/execute_sedml.py

@@ -0,0 +1,186 @@
+from http import HTTPStatus
+from typing import Any, Optional, Union, cast
+
+import httpx
+
+from ...client import AuthenticatedClient, Client
+from ...types import Response, UNSET
+from ... import errors
+
+from ...models.body_execute_sedml import BodyExecuteSedml
+from ...models.http_validation_error import HTTPValidationError
+from ...models.simulation_experiment import SimulationExperiment
+from ...models.tool_suites import ToolSuites
+from typing import cast
+
+
+def _get_kwargs(
+    *,
+    body: BodyExecuteSedml,
+    tool_suite: ToolSuites,
+) -> dict[str, Any]:
+    headers: dict[str, Any] = {}
+
+    params: dict[str, Any] = {}
+
+    json_tool_suite = tool_suite.value
+    params["tool_suite"] = json_tool_suite
+
+    params = {k: v for k, v in params.items() if v is not UNSET and v is not None}
+
+    _kwargs: dict[str, Any] = {
+        "method": "post",
+        "url": "/core/simulation/execute/sedml",
+        "params": params,
+    }
+
+    _kwargs["files"] = body.to_multipart()
+
+    _kwargs["headers"] = headers
+    return _kwargs
+
+
+def _parse_response(
+    *, client: Union[AuthenticatedClient, Client], response: httpx.Response
+) -> Optional[Union[HTTPValidationError, SimulationExperiment]]:
+    if response.status_code == 200:
+        response_200 = SimulationExperiment.from_dict(response.json())
+
+        return response_200
+    if response.status_code == 422:
+        response_422 = HTTPValidationError.from_dict(response.json())
+
+        return response_422
+    if client.raise_on_unexpected_status:
+        raise errors.UnexpectedStatus(response.status_code, response.content)
+    else:
+        return None
+
+
+def _build_response(
+    *, client: Union[AuthenticatedClient, Client], response: httpx.Response
+) -> Response[Union[HTTPValidationError, SimulationExperiment]]:
+    return Response(
+        status_code=HTTPStatus(response.status_code),
+        content=response.content,
+        headers=response.headers,
+        parsed=_parse_response(client=client, response=response),
+    )
+
+
+def sync_detailed(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyExecuteSedml,
+    tool_suite: ToolSuites,
+) -> Response[Union[HTTPValidationError, SimulationExperiment]]:
+    """Execute sedml
+
+    Args:
+        tool_suite (ToolSuites):
+        body (BodyExecuteSedml):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[Union[HTTPValidationError, SimulationExperiment]]
+    """
+
+    kwargs = _get_kwargs(
+        body=body,
+        tool_suite=tool_suite,
+    )
+
+    response = client.get_httpx_client().request(
+        **kwargs,
+    )
+
+    return _build_response(client=client, response=response)
+
+
+def sync(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyExecuteSedml,
+    tool_suite: ToolSuites,
+) -> Optional[Union[HTTPValidationError, SimulationExperiment]]:
+    """Execute sedml
+
+    Args:
+        tool_suite (ToolSuites):
+        body (BodyExecuteSedml):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Union[HTTPValidationError, SimulationExperiment]
+    """
+
+    return sync_detailed(
+        client=client,
+        body=body,
+        tool_suite=tool_suite,
+    ).parsed
+
+
+async def asyncio_detailed(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyExecuteSedml,
+    tool_suite: ToolSuites,
+) -> Response[Union[HTTPValidationError, SimulationExperiment]]:
+    """Execute sedml
+
+    Args:
+        tool_suite (ToolSuites):
+        body (BodyExecuteSedml):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[Union[HTTPValidationError, SimulationExperiment]]
+    """
+
+    kwargs = _get_kwargs(
+        body=body,
+        tool_suite=tool_suite,
+    )
+
+    response = await client.get_async_httpx_client().request(**kwargs)
+
+    return _build_response(client=client, response=response)
+
+
+async def asyncio(
+    *,
+    client: Union[AuthenticatedClient, Client],
+    body: BodyExecuteSedml,
+    tool_suite: ToolSuites,
+) -> Optional[Union[HTTPValidationError, SimulationExperiment]]:
+    """Execute sedml
+
+    Args:
+        tool_suite (ToolSuites):
+        body (BodyExecuteSedml):
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Union[HTTPValidationError, SimulationExperiment]
+    """
+
+    return (
+        await asyncio_detailed(
+            client=client,
+            body=body,
+            tool_suite=tool_suite,
+        )
+    ).parsed

compose_api/api/client/models/__init__.py

@@ -4,6 +4,7 @@
 from .bi_graph_process import BiGraphProcess
 from .bi_graph_step import BiGraphStep
 from .body_analyze_simulation_omex import BodyAnalyzeSimulationOmex
+from .body_execute_sedml import BodyExecuteSedml
 from .body_run_copasi import BodyRunCopasi
 from .body_run_simulation import BodyRunSimulation
 from .body_run_tellurium import BodyRunTellurium
@@ -19,13 +20,15 @@
 from .simulation_experiment import SimulationExperiment
 from .simulation_experiment_metadata import SimulationExperimentMetadata
 from .simulator_version import SimulatorVersion
+from .tool_suites import ToolSuites
 from .validation_error import ValidationError
 
 __all__ = (
     "BiGraphComputeType",
     "BiGraphProcess",
     "BiGraphStep",
     "BodyAnalyzeSimulationOmex",
+    "BodyExecuteSedml",
     "BodyRunCopasi",
     "BodyRunSimulation",
     "BodyRunTellurium",
@@ -41,5 +44,6 @@
     "SimulationExperiment",
     "SimulationExperimentMetadata",
     "SimulatorVersion",
+    "ToolSuites",
     "ValidationError",
 )

compose_api/api/client/models/body_execute_sedml.py

@@ -0,0 +1,75 @@
+from collections.abc import Mapping
+from typing import Any, TypeVar, Optional, BinaryIO, TextIO, TYPE_CHECKING, Generator
+
+from attrs import define as _attrs_define
+from attrs import field as _attrs_field
+import json
+from .. import types
+
+from ..types import UNSET, Unset
+
+from ..types import File, FileTypes
+from io import BytesIO
+
+
+T = TypeVar("T", bound="BodyExecuteSedml")
+
+
+@_attrs_define
+class BodyExecuteSedml:
+    """
+    Attributes:
+        uploaded_file (File):
+    """
+
+    uploaded_file: File
+    additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
+
+    def to_dict(self) -> dict[str, Any]:
+        uploaded_file = self.uploaded_file.to_tuple()
+
+        field_dict: dict[str, Any] = {}
+        field_dict.update(self.additional_properties)
+        field_dict.update({
+            "uploaded_file": uploaded_file,
+        })
+
+        return field_dict
+
+    def to_multipart(self) -> types.RequestFiles:
+        files: types.RequestFiles = []
+
+        files.append(("uploaded_file", self.uploaded_file.to_tuple()))
+
+        for prop_name, prop in self.additional_properties.items():
+            files.append((prop_name, (None, str(prop).encode(), "text/plain")))
+
+        return files
+
+    @classmethod
+    def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
+        d = dict(src_dict)
+        uploaded_file = File(payload=BytesIO(d.pop("uploaded_file")))
+
+        body_execute_sedml = cls(
+            uploaded_file=uploaded_file,
+        )
+
+        body_execute_sedml.additional_properties = d
+        return body_execute_sedml
+
+    @property
+    def additional_keys(self) -> list[str]:
+        return list(self.additional_properties.keys())
+
+    def __getitem__(self, key: str) -> Any:
+        return self.additional_properties[key]
+
+    def __setitem__(self, key: str, value: Any) -> None:
+        self.additional_properties[key] = value
+
+    def __delitem__(self, key: str) -> None:
+        del self.additional_properties[key]
+
+    def __contains__(self, key: str) -> bool:
+        return key in self.additional_properties

compose_api/api/client/models/registered_package.py

@@ -10,8 +10,8 @@
 from typing import cast
 
 if TYPE_CHECKING:
-    from ..models.bi_graph_step import BiGraphStep
     from ..models.bi_graph_process import BiGraphProcess
+    from ..models.bi_graph_step import BiGraphStep
 
 
 T = TypeVar("T", bound="RegisteredPackage")
@@ -36,8 +36,8 @@ class RegisteredPackage:
     additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
 
     def to_dict(self) -> dict[str, Any]:
-        from ..models.bi_graph_step import BiGraphStep
         from ..models.bi_graph_process import BiGraphProcess
+        from ..models.bi_graph_step import BiGraphStep
 
         database_id = self.database_id
 
@@ -69,8 +69,8 @@ def to_dict(self) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
-        from ..models.bi_graph_step import BiGraphStep
         from ..models.bi_graph_process import BiGraphProcess
+        from ..models.bi_graph_step import BiGraphStep
 
         d = dict(src_dict)
         database_id = d.pop("database_id")

compose_api/api/client/models/simulator_version.py

@@ -14,8 +14,8 @@
 import datetime
 
 if TYPE_CHECKING:
-    from ..models.containerization_file_repr import ContainerizationFileRepr
     from ..models.registered_package import RegisteredPackage
+    from ..models.containerization_file_repr import ContainerizationFileRepr
 
 
 T = TypeVar("T", bound="SimulatorVersion")
@@ -40,8 +40,8 @@ class SimulatorVersion:
     additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
 
     def to_dict(self) -> dict[str, Any]:
-        from ..models.containerization_file_repr import ContainerizationFileRepr
         from ..models.registered_package import RegisteredPackage
+        from ..models.containerization_file_repr import ContainerizationFileRepr
 
         singularity_def = self.singularity_def.to_dict()
 
@@ -82,8 +82,8 @@ def to_dict(self) -> dict[str, Any]:
 
     @classmethod
     def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
-        from ..models.containerization_file_repr import ContainerizationFileRepr
         from ..models.registered_package import RegisteredPackage
+        from ..models.containerization_file_repr import ContainerizationFileRepr
 
         d = dict(src_dict)
         singularity_def = ContainerizationFileRepr.from_dict(d.pop("singularity_def"))

compose_api/api/client/models/tool_suites.py

@@ -0,0 +1,9 @@
+from enum import Enum
+
+
+class ToolSuites(str, Enum):
+    BASICO = "basico"
+    TELLURIUM = "tellurium"
+
+    def __str__(self) -> str:
+        return str(self.value)