updates

biosimulator_processes/processes/copasi_process.py

@@ -37,7 +37,7 @@ class CopasiProcess(SedProcess):
                 specification requires the presence of reactions which inherently define species types and optionally
                 addition parameters. See Basico for more details. There are two types of objects that are accepted
                 for this specification:
-                    - A high-level api object from `biosimulator_processes.data_model`,
+                    - A high-level server object from `biosimulator_processes.data_model`,
                         ie: `TimeCourseModel` or `SedModel`. (Recommended for first-time users). The parameters with
                         which these dataclasses are instantiated correspond to the `config_schema` for a given
                         process implementation. In the config schema, the outermost keys could be considered
@@ -271,7 +271,7 @@ class workingcopasiprocess(SedProcess):
                 specification requires the presence of reactions which inherently define species types and optionally
                 addition parameters. See Basico for more details. There are two types of objects that are accepted
                 for this specification:
-                    - A high-level api object from `biosimulator_processes.data_model`,
+                    - A high-level server object from `biosimulator_processes.data_model`,
                         ie: `TimeCourseModel` or `SedModel`. (Recommended for first-time users). The parameters with
                         which these dataclasses are instantiated correspond to the `config_schema` for a given
                         process implementation. In the config schema, the outermost keys could be considered

biosimulator_processes/server/main.py

@@ -0,0 +1,36 @@
+import tempfile
+
+from fastapi import FastAPI, UploadFile, File
+from fastapi.middleware.cors import CORSMiddleware
+import uvicorn
+
+from biosimulator_processes.server.src.io import save_omex_archive
+
+
+app = FastAPI(title='biosimulator-processes-server')
+
+
+origins = [
+    "http://localhost:4200",
+]
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+@app.post("/upload-omex")
+async def upload_omex(file: UploadFile = File(...)):
+    contents = await file.read()
+
+    save_dir = tempfile.mkdtemp()
+    archive_response = save_omex_archive(contents, save_dir)
+    print(archive_response['archive'].contents)
+    return {"filename": archive_response['source']}
+
+
+if __name__ == "__main__":
+    uvicorn.run(app, host="0.0.0.0", port=8000)

biosimulator_processes/server/spec/openapi_3_1_0_generated.yaml

@@ -0,0 +1,69 @@
+openapi: 3.1.0
+info:
+  title: biosimulator-processes-server
+  version: 0.1.0
+paths:
+  /upload-omex:
+    post:
+      summary: Upload Omex
+      operationId: upload_omex_upload_omex_post
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_upload_omex_upload_omex_post'
+        required: true
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+components:
+  schemas:
+    Body_upload_omex_upload_omex_post:
+      properties:
+        file:
+          type: string
+          format: binary
+          title: File
+      type: object
+      required:
+      - file
+      title: Body_upload_omex_upload_omex_post
+    HTTPValidationError:
+      properties:
+        detail:
+          items:
+            $ref: '#/components/schemas/ValidationError'
+          type: array
+          title: Detail
+      type: object
+      title: HTTPValidationError
+    ValidationError:
+      properties:
+        loc:
+          items:
+            anyOf:
+            - type: string
+            - type: integer
+          type: array
+          title: Location
+        msg:
+          type: string
+          title: Message
+        type:
+          type: string
+          title: Error Type
+      type: object
+      required:
+      - loc
+      - msg
+      - type
+      title: ValidationError

biosimulator_processes/server/src/io.py

@@ -0,0 +1,16 @@
+import tempfile
+
+from biosimulators_utils.combine.io import CombineArchiveReader
+
+
+def unpack_omex(archive_fp: str, save_dir: str):
+    return CombineArchiveReader().run(archive_fp, save_dir)
+
+
+def save_omex_archive(contents: bytes, save_dir: str):
+    with tempfile.NamedTemporaryFile(delete=False, suffix='.omex') as temp_file:
+        temp_file.write(contents)
+        archive_path = temp_file.name
+
+    return {'source': archive_path, 'archive': unpack_omex(archive_path, save_dir), 'save_dir': save_dir}
+

biosimulator_processes/server/src/openapi_spec.py

@@ -0,0 +1,36 @@
+import json
+import os
+
+import yaml
+from fastapi.openapi.utils import get_openapi
+
+from biosimulator_processes.server.main import app
+
+
+def main():
+    openapi_spec = get_openapi(
+        title=app.title,
+        version=app.version,
+        openapi_version=app.openapi_version,
+        description=app.description,
+        routes=app.routes,
+    )
+
+    # Convert the JSON OpenAPI spec to YAML
+    openapi_spec_yaml = yaml.dump(json.loads(json.dumps(openapi_spec)), sort_keys=False)
+
+    current_directory = os.path.dirname(os.path.realpath(__file__))
+
+    # Write the YAML OpenAPI spec to a file in subdirectory spec
+    openapi_version = app.openapi_version.replace('.', '_')
+    spec_fp = f"{current_directory}/../spec/openapi_{openapi_version}_generated.yaml"
+    if os.path.exists(spec_fp):
+        print('Spec exists, overwriting')
+        os.remove(spec_fp)
+
+    with open(spec_fp, "w") as f:
+        f.write(openapi_spec_yaml)
+
+
+if __name__ == "__main__":
+    main()

biosimulator_processes/services/rest_service.py

@@ -39,7 +39,7 @@ async def _search_source(cls, query: str) -> ProjectsQuery:
             print(f'Failed to fetch OMEX archive:\n{e}')
 
     @classmethod
-    async def _get_files(cls, run_id: str, project_name: str) -> ArchiveFiles:
+    def get_project_files(cls, run_id: str, project_name: str = None) -> ArchiveFiles:
         get_files_url = f'https://api.biosimulations.dev/files/{run_id}'
         # get_files_url = f'https://api.biosimulations.dev/results/{run_id}/download'
         headers = {'accept': 'application/json'}
@@ -60,7 +60,7 @@ async def fetch_files(cls, query: str) -> ArchiveFiles:
 
         selected_project_id = options_menu[user_selection]
         simulation_run_id = archive_query.project_data[selected_project_id]['simulationRun']
-        simulation_run_files = await cls._get_files(simulation_run_id, selected_project_id)
+        simulation_run_files = cls.get_project_files(simulation_run_id, selected_project_id)
         return simulation_run_files
 
     @classmethod

biosimulator_processes/verify/core.py

@@ -56,7 +56,7 @@ def verify_ode_process_outputs(process_name: str, target_report_fp: str, biomode
 # TODO: make this more general
 def verify_ode_process_output_names(process_name: str, source_report_fp: str, biomodel_id: str = None, sbml_model_file: str = None) -> OutputAspectVerification:
     # Get the class from the module
-    # TODO: Automatically generate this from the biosimulations rest api
+    # TODO: Automatically generate this from the biosimulations rest server
     process = create_ode_process_instance(process_name, biomodel_id, sbml_model_file)
     process_keys = list(process.inputs()['floating_species_concentrations'].keys())