Readdy addition

compose_api/api/client/models/registered_package.py

@@ -10,8 +10,8 @@
 from typing import cast
 
 if TYPE_CHECKING:
-    from ..models.bi_graph_process import BiGraphProcess
     from ..models.bi_graph_step import BiGraphStep
+    from ..models.bi_graph_process import BiGraphProcess
 
 
 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_process import BiGraphProcess
         from ..models.bi_graph_step import BiGraphStep
+        from ..models.bi_graph_process import BiGraphProcess
 
         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_process import BiGraphProcess
         from ..models.bi_graph_step import BiGraphStep
+        from ..models.bi_graph_process import BiGraphProcess
 
         d = dict(src_dict)
         database_id = d.pop("database_id")

compose_api/api/introspect_package.py

@@ -12,9 +12,9 @@
 def introspect_package(dependencies: ExperimentPrimaryDependencies) -> list[PackageOutline]:
     package_outlines = []
     for dep in dependencies.get_pypi_dependencies():
-        package_outlines.append(PackageOutline(package_type=PackageType.PYPI, name=dep, compute=[]))
+        package_outlines.append(PackageOutline(package_type=PackageType.PYPI, name=dep.get_name(), compute=[]))
     for dep in dependencies.get_conda_dependencies():
-        package_outlines.append(PackageOutline(package_type=PackageType.CONDA, name=dep, compute=[]))
+        package_outlines.append(PackageOutline(package_type=PackageType.CONDA, name=dep.get_name(), compute=[]))
     return package_outlines
 
 
@@ -38,13 +38,3 @@ def _get_package_github_origin(pypi_package: str) -> ParseResult:
 
 # def _live_pypi_introspection(pypi_package: str) -> BiGraphPackage:
 #     return BiGraphPackage()
-
-
-if __name__ == "__main__":
-    packages = introspect_package(
-        ExperimentPrimaryDependencies(
-            pypi_dependencies=["git+https://github.com/biosimulators/bspil-basico.git@initial_work"],
-            conda_dependencies=[],
-        )
-    )
-    print(packages)

compose_api/api/routers/curated.py

@@ -1,7 +1,7 @@
 import logging
 import os
 
-from fastapi import APIRouter, BackgroundTasks, Depends, UploadFile
+from fastapi import APIRouter, BackgroundTasks, Depends, HTTPException, UploadFile
 from jinja2 import Template
 
 from compose_api.common.gateway.models import RouterConfig, ServerMode
@@ -10,10 +10,11 @@
     get_database_service,
 )
 from compose_api.simulation.handlers import (
-    run_pbif,
+    run_curated_pbif,
 )
 from compose_api.simulation.models import (
     SimulationExperiment,
+    SimulationFileType,
 )
 
 logger = logging.getLogger(__name__)
@@ -42,11 +43,13 @@ async def run_copasi(
     with open(os.path.dirname(__file__) + "/templates/copasi.jinja") as f:
         template = Template(f.read())
         render = template.render(start_time=start_time, duration=duration, num_data_points=num_data_points)
-    loaded_sbml = await get_file_from_uploaded_file(sbml)
-    return await run_pbif(
+    request = await get_file_from_uploaded_file(sbml)
+    if request.simulation_file_type is not SimulationFileType.SBML:
+        raise HTTPException(status_code=400, detail="Expected a SBML file.")
+    return await run_curated_pbif(
         templated_pbif=render,
         simulator_name="Copasi",
-        loaded_sbml=loaded_sbml,
+        loaded_sbml=request.request_file_path,
         background_tasks=background_tasks,
         use_interesting=True,
     )
@@ -66,7 +69,12 @@ async def run_tellurium(
     with open(os.path.dirname(__file__) + "/templates/tellurium.jinja") as f:
         template = Template(f.read())
         render = template.render(start_time=start_time, end_time=end_time, num_data_points=num_data_points)
-    loaded_sbml = await get_file_from_uploaded_file(sbml)
-    return await run_pbif(
-        templated_pbif=render, simulator_name="Tellurium", loaded_sbml=loaded_sbml, background_tasks=background_tasks
+    request = await get_file_from_uploaded_file(sbml)
+    if request.simulation_file_type is not SimulationFileType.SBML:
+        raise HTTPException(status_code=400, detail="Expected a SBML file.")
+    return await run_curated_pbif(
+        templated_pbif=render,
+        simulator_name="Tellurium",
+        loaded_sbml=request.request_file_path,
+        background_tasks=background_tasks,
     )

compose_api/api/routers/simulation.py

@@ -15,7 +15,6 @@
 from compose_api.simulation.models import (
     PBAllowList,
     SimulationExperiment,
-    SimulationRequest,
 )
 
 logger = logging.getLogger(__name__)
@@ -54,8 +53,7 @@ async def submit_simulation(background_tasks: BackgroundTasks, uploaded_file: Up
     logger.warning("NO VALIDATION YET")
     # Tmp file for future implementation
 
-    up_file = await get_file_from_uploaded_file(uploaded_file=uploaded_file)
-    simulation_request = SimulationRequest(omex_archive=up_file)
+    simulation_request = await get_file_from_uploaded_file(uploaded_file=uploaded_file)
 
     try:
         return await run_simulation(

compose_api/api/spec/openapi_3_1_0_generated.yaml

@@ -1,7 +1,7 @@
 openapi: 3.1.0
 info:
   title: compose-api
-  version: 0.2.4
+  version: 0.3.2
 paths:
   /curated/copasi:
     post:

compose_api/common/gateway/utils.py

@@ -5,7 +5,7 @@
 from fastapi import HTTPException, UploadFile
 
 from compose_api.db.database_service import DatabaseService
-from compose_api.simulation.models import HpcRun, JobType
+from compose_api.simulation.models import HpcRun, JobType, SimulationFileType, SimulationRequest
 
 logger = logging.getLogger(__name__)
 
@@ -48,15 +48,17 @@ async def get_hpc_run_status(db_service: DatabaseService, ref_id: int, job_type:
     return simulation_hpcrun
 
 
-async def get_file_from_uploaded_file(uploaded_file: UploadFile) -> Path:
+async def get_file_from_uploaded_file(uploaded_file: UploadFile) -> SimulationRequest:
     if uploaded_file is None or uploaded_file.filename is None or uploaded_file.size == 0:
         raise HTTPException(status_code=400, detail="Empty uploaded file")
 
-    # TODO Make the suffix dynamic
-    with tempfile.NamedTemporaryFile(delete=False, suffix="." + uploaded_file.filename.rsplit(".", 1)[1]) as tmp_file:
+    suffix = Path(uploaded_file.filename).suffix
+    with tempfile.NamedTemporaryFile(delete=False, suffix=suffix) as tmp_file:
         contents = await uploaded_file.read()
         tmp_file.write(contents)
-    return Path(tmp_file.name)
+    return SimulationRequest(
+        request_file_path=Path(tmp_file.name), simulation_file_type=SimulationFileType.get_file_type(suffix)
+    )
 
 
 allow_list = [

compose_api/db/services/packages_db.py

@@ -60,11 +60,11 @@ async def delete_bigraph_package(self, package_id: RegisteredPackage) -> None:
     async def delete_bigraph_compute(self, compute: BiGraphCompute) -> None:
         pass
 
-    @abstractmethod
-    async def dependencies_not_in_database(
-        self, dependencies: ExperimentPrimaryDependencies
-    ) -> ExperimentPrimaryDependencies:
-        pass
+    # @abstractmethod
+    # async def dependencies_not_in_database(
+    #     self, dependencies: ExperimentPrimaryDependencies
+    # ) -> ExperimentPrimaryDependencies:
+    #     pass
 
     @abstractmethod
     async def list_packages_from_dependencies(
@@ -221,33 +221,33 @@ async def delete_bigraph_compute(self, compute: BiGraphCompute) -> None:
                 raise ValueError(f"Compute id: {compute.database_id} not found in database")
             await session.delete(db_rep)
 
-    async def dependencies_not_in_database(
-        self, dependencies: ExperimentPrimaryDependencies
-    ) -> ExperimentPrimaryDependencies:
-        async with self.async_session_maker() as session:
-            stmt = select(ORMPackage).where(ORMPackage.name.in_(dependencies.pypi_dependencies))
-            result: Result[tuple[ORMPackage]] = await session.execute(stmt)
-            orm_packages = result.scalars().all()
-            names: tuple[str, ...] = tuple(package.name for package in orm_packages)
-            pypi_not_in_database: list[str] = []
-            for pypi in dependencies.pypi_dependencies:
-                if pypi not in names:
-                    pypi_not_in_database.append(pypi)
-            conda_not_in_database: list[str] = []
-            for conda in dependencies.conda_dependencies:
-                if conda not in names:
-                    conda_not_in_database.append(conda)
-            return ExperimentPrimaryDependencies(
-                pypi_dependencies=pypi_not_in_database, conda_dependencies=conda_not_in_database
-            )
+    # async def dependencies_not_in_database(
+    #     self, dependencies: ExperimentPrimaryDependencies
+    # ) -> ExperimentPrimaryDependencies:
+    #     async with self.async_session_maker() as session:
+    #         stmt = select(ORMPackage).where(ORMPackage.name.in_(dependencies.pypi_dependencies))
+    #         result: Result[tuple[ORMPackage]] = await session.execute(stmt)
+    #         orm_packages = result.scalars().all()
+    #         names: tuple[str, ...] = tuple(package.name for package in orm_packages)
+    #         pypi_not_in_database: list[str] = []
+    #         for pypi in dependencies.pypi_dependencies:
+    #             if pypi not in names:
+    #                 pypi_not_in_database.append(pypi)
+    #         conda_not_in_database: list[str] = []
+    #         for conda in dependencies.conda_dependencies:
+    #             if conda not in names:
+    #                 conda_not_in_database.append(conda)
+    #         return ExperimentPrimaryDependencies(
+    #             pypi_dependencies=pypi_not_in_database, conda_dependencies=conda_not_in_database
+    #         )
 
     async def list_packages_from_dependencies(
         self, dependencies: ExperimentPrimaryDependencies
     ) -> list[RegisteredPackage]:
         async with self.async_session_maker() as session:
             packages: list[RegisteredPackage] = []
-            for dep_type in (dependencies.pypi_dependencies, dependencies.conda_dependencies):
-                stmt = select(ORMPackage).where(ORMPackage.name.in_(dep_type))
+            for package in dependencies.get_pypi_dependencies() + dependencies.get_conda_dependencies():
+                stmt = select(ORMPackage).where(ORMPackage.name.in_(package.get_name()))
                 result: Result[tuple[ORMPackage]] = await session.execute(stmt)
                 orm_packages = result.scalars().all()
                 for row in orm_packages: