Merge pull request #47 from biosimulations/improve-package-representation-in-db

Improve Package Representation in DB

Author: Ezequiel-Valencia

compose_api/api/client/api/simulators/__init__.py

@@ -0,0 +1 @@
+"""Contains endpoint functions for accessing the API"""

compose_api/api/client/api/simulations/get_simulator_build_status.py renamed to compose_api/api/client/api/simulators/get_simulator_build_status.py

@@ -1,30 +1,38 @@
 """Contains all the data models used in inputs/outputs"""
 
+from .bi_graph_compute_type import BiGraphComputeType
+from .bi_graph_process import BiGraphProcess
+from .bi_graph_step import BiGraphStep
 from .body_analyze_simulation_omex import BodyAnalyzeSimulationOmex
 from .body_run_simulation import BodyRunSimulation
 from .check_health_health_get_response_check_health_health_get import CheckHealthHealthGetResponseCheckHealthHealthGet
 from .containerization_file_repr import ContainerizationFileRepr
-from .experiment_primary_dependencies import ExperimentPrimaryDependencies
 from .hpc_run import HpcRun
 from .http_validation_error import HTTPValidationError
 from .job_status import JobStatus
 from .job_type import JobType
+from .package_type import PackageType
+from .registered_package import RegisteredPackage
 from .registered_simulators import RegisteredSimulators
 from .simulation_experiment import SimulationExperiment
 from .simulation_experiment_metadata import SimulationExperimentMetadata
 from .simulator_version import SimulatorVersion
 from .validation_error import ValidationError
 
 __all__ = (
+    "BiGraphComputeType",
+    "BiGraphProcess",
+    "BiGraphStep",
     "BodyAnalyzeSimulationOmex",
     "BodyRunSimulation",
     "CheckHealthHealthGetResponseCheckHealthHealthGet",
     "ContainerizationFileRepr",
-    "ExperimentPrimaryDependencies",
     "HpcRun",
     "HTTPValidationError",
     "JobStatus",
     "JobType",
+    "PackageType",
+    "RegisteredPackage",
     "RegisteredSimulators",
     "SimulationExperiment",
     "SimulationExperimentMetadata",

compose_api/api/client/api/simulations/get_simulator_list.py renamed to compose_api/api/client/api/simulators/get_simulator_list.py

@@ -0,0 +1,9 @@
+from enum import Enum
+
+
+class BiGraphComputeType(str, Enum):
+    PROCESS = "process"
+    STEP = "step"
+
+    def __str__(self) -> str:
+        return str(self.value)

compose_api/api/client/models/__init__.py

@@ -0,0 +1,102 @@
+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
+
+from ..types import UNSET, Unset
+
+from ..models.bi_graph_compute_type import BiGraphComputeType
+
+
+T = TypeVar("T", bound="BiGraphProcess")
+
+
+@_attrs_define
+class BiGraphProcess:
+    """
+    Attributes:
+        database_id (int):
+        module (str):
+        name (str):
+        compute_type (BiGraphComputeType):
+        inputs (str):
+        outputs (str):
+    """
+
+    database_id: int
+    module: str
+    name: str
+    compute_type: BiGraphComputeType
+    inputs: str
+    outputs: str
+    additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
+
+    def to_dict(self) -> dict[str, Any]:
+        database_id = self.database_id
+
+        module = self.module
+
+        name = self.name
+
+        compute_type = self.compute_type.value
+
+        inputs = self.inputs
+
+        outputs = self.outputs
+
+        field_dict: dict[str, Any] = {}
+        field_dict.update(self.additional_properties)
+        field_dict.update({
+            "database_id": database_id,
+            "module": module,
+            "name": name,
+            "compute_type": compute_type,
+            "inputs": inputs,
+            "outputs": outputs,
+        })
+
+        return field_dict
+
+    @classmethod
+    def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
+        d = dict(src_dict)
+        database_id = d.pop("database_id")
+
+        module = d.pop("module")
+
+        name = d.pop("name")
+
+        compute_type = BiGraphComputeType(d.pop("compute_type"))
+
+        inputs = d.pop("inputs")
+
+        outputs = d.pop("outputs")
+
+        bi_graph_process = cls(
+            database_id=database_id,
+            module=module,
+            name=name,
+            compute_type=compute_type,
+            inputs=inputs,
+            outputs=outputs,
+        )
+
+        bi_graph_process.additional_properties = d
+        return bi_graph_process
+
+    @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/bi_graph_compute_type.py

@@ -0,0 +1,102 @@
+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
+
+from ..types import UNSET, Unset
+
+from ..models.bi_graph_compute_type import BiGraphComputeType
+
+
+T = TypeVar("T", bound="BiGraphStep")
+
+
+@_attrs_define
+class BiGraphStep:
+    """
+    Attributes:
+        database_id (int):
+        module (str):
+        name (str):
+        compute_type (BiGraphComputeType):
+        inputs (str):
+        outputs (str):
+    """
+
+    database_id: int
+    module: str
+    name: str
+    compute_type: BiGraphComputeType
+    inputs: str
+    outputs: str
+    additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
+
+    def to_dict(self) -> dict[str, Any]:
+        database_id = self.database_id
+
+        module = self.module
+
+        name = self.name
+
+        compute_type = self.compute_type.value
+
+        inputs = self.inputs
+
+        outputs = self.outputs
+
+        field_dict: dict[str, Any] = {}
+        field_dict.update(self.additional_properties)
+        field_dict.update({
+            "database_id": database_id,
+            "module": module,
+            "name": name,
+            "compute_type": compute_type,
+            "inputs": inputs,
+            "outputs": outputs,
+        })
+
+        return field_dict
+
+    @classmethod
+    def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
+        d = dict(src_dict)
+        database_id = d.pop("database_id")
+
+        module = d.pop("module")
+
+        name = d.pop("name")
+
+        compute_type = BiGraphComputeType(d.pop("compute_type"))
+
+        inputs = d.pop("inputs")
+
+        outputs = d.pop("outputs")
+
+        bi_graph_step = cls(
+            database_id=database_id,
+            module=module,
+            name=name,
+            compute_type=compute_type,
+            inputs=inputs,
+            outputs=outputs,
+        )
+
+        bi_graph_step.additional_properties = d
+        return bi_graph_step
+
+    @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/bi_graph_process.py

@@ -0,0 +1,9 @@
+from enum import Enum
+
+
+class PackageType(str, Enum):
+    CONDA = "conda"
+    PYPI = "pypi"
+
+    def __str__(self) -> str:
+        return str(self.value)