Merge pull request #27 from biosimulations/notebook-helpers

add notebook and reports
biosimulations · Feb 8, 2025 · 04824e9 · 04824e9
2 parents 84526df + 2e7075d
commit 04824e9
Show file tree

Hide file tree

Showing 102 changed files with 16,254 additions and 4,490 deletions.
diff --git a/.openapi-generator/FILES b/.openapi-generator/FILES
@@ -20,16 +20,14 @@ biosim_client/api/biosim/docs/HDF5File.md
 biosim_client/api/biosim/docs/HDF5Group.md
 biosim_client/api/biosim/docs/HTTPValidationError.md
 biosim_client/api/biosim/docs/Hdf5DataValues.md
-biosim_client/api/biosim/docs/OmexVerifyWorkflowOutput.md
-biosim_client/api/biosim/docs/OmexVerifyWorkflowStatus.md
 biosim_client/api/biosim/docs/RunData.md
-biosim_client/api/biosim/docs/RunsVerifyWorkflowOutput.md
-biosim_client/api/biosim/docs/RunsVerifyWorkflowStatus.md
 biosim_client/api/biosim/docs/SimulationRunInfo.md
 biosim_client/api/biosim/docs/ValidationError.md
 biosim_client/api/biosim/docs/ValidationErrorLocInner.md
 biosim_client/api/biosim/docs/Value.md
 biosim_client/api/biosim/docs/VerificationApi.md
+biosim_client/api/biosim/docs/VerifyWorkflowOutput.md
+biosim_client/api/biosim/docs/VerifyWorkflowStatus.md
 biosim_client/api/biosim/exceptions.py
 biosim_client/api/biosim/models/__init__.py
 biosim_client/api/biosim/models/biosim_simulation_run.py
@@ -44,15 +42,34 @@ biosim_client/api/biosim/models/hdf5_dataset.py
 biosim_client/api/biosim/models/hdf5_file.py
 biosim_client/api/biosim/models/hdf5_group.py
 biosim_client/api/biosim/models/http_validation_error.py
-biosim_client/api/biosim/models/omex_verify_workflow_output.py
-biosim_client/api/biosim/models/omex_verify_workflow_status.py
 biosim_client/api/biosim/models/run_data.py
-biosim_client/api/biosim/models/runs_verify_workflow_output.py
-biosim_client/api/biosim/models/runs_verify_workflow_status.py
 biosim_client/api/biosim/models/simulation_run_info.py
 biosim_client/api/biosim/models/validation_error.py
 biosim_client/api/biosim/models/validation_error_loc_inner.py
 biosim_client/api/biosim/models/value.py
+biosim_client/api/biosim/models/verify_workflow_output.py
+biosim_client/api/biosim/models/verify_workflow_status.py
 biosim_client/api/biosim/rest.py
 biosim_client/api/biosim/test/__init__.py
+biosim_client/api/biosim/test/test_biosim_simulation_run.py
+biosim_client/api/biosim/test/test_biosim_simulation_run_status.py
+biosim_client/api/biosim/test/test_biosimulator_version.py
+biosim_client/api/biosim/test/test_compare_settings.py
+biosim_client/api/biosim/test/test_comparison_statistics.py
+biosim_client/api/biosim/test/test_default_api.py
+biosim_client/api/biosim/test/test_generate_statistics_activity_output.py
+biosim_client/api/biosim/test/test_hdf5_attribute.py
+biosim_client/api/biosim/test/test_hdf5_data_values.py
+biosim_client/api/biosim/test/test_hdf5_dataset.py
+biosim_client/api/biosim/test/test_hdf5_file.py
+biosim_client/api/biosim/test/test_hdf5_group.py
+biosim_client/api/biosim/test/test_http_validation_error.py
+biosim_client/api/biosim/test/test_run_data.py
+biosim_client/api/biosim/test/test_simulation_run_info.py
+biosim_client/api/biosim/test/test_validation_error.py
+biosim_client/api/biosim/test/test_validation_error_loc_inner.py
+biosim_client/api/biosim/test/test_value.py
+biosim_client/api/biosim/test/test_verification_api.py
+biosim_client/api/biosim/test/test_verify_workflow_output.py
+biosim_client/api/biosim/test/test_verify_workflow_status.py
 biosim_client/api/biosim_README.md
diff --git a/biosim_client/api/api_specs/biosim.yaml b/biosim_client/api/api_specs/biosim.yaml
@@ -1,7 +1,7 @@
 openapi: 3.1.0
 info:
   title: biosim-server
-  version: 0.1.0
+  version: 0.2.0
 paths:
   /:
     get:
@@ -29,12 +29,12 @@ paths:
               schema:
                 type: string
                 title: Response Get Version Version Get
-  /verify_omex:
+  /verify/omex:
     post:
       tags:
         - Verification
-      summary: Request verification report for OMEX/COMBINE archive
-      operationId: start-verify-omex
+      summary: Request verification report for OMEX/COMBINE archive across simulators
+      operationId: verify-omex
       parameters:
         - name: workflow_id_prefix
           in: query
@@ -140,26 +140,26 @@ paths:
         content:
           multipart/form-data:
             schema:
-              $ref: "#/components/schemas/Body_start-verify-omex"
+              $ref: "#/components/schemas/Body_verify-omex"
       responses:
         "200":
           description: Successful Response
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/OmexVerifyWorkflowOutput"
+                $ref: "#/components/schemas/VerifyWorkflowOutput"
         "422":
           description: Validation Error
           content:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPValidationError"
-  /verify_omex/{workflow_id}:
+  /verify/{workflow_id}:
     get:
       tags:
         - Verification
       summary: Retrieve verification report for OMEX/COMBINE archive
-      operationId: get-verify-omex
+      operationId: get-verify-output
       parameters:
         - name: workflow_id
           in: path
@@ -173,19 +173,19 @@ paths:
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/OmexVerifyWorkflowOutput"
+                $ref: "#/components/schemas/VerifyWorkflowOutput"
         "422":
           description: Validation Error
           content:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPValidationError"
-  /verify_runs:
+  /verify/runs:
     post:
       tags:
         - Verification
-      summary: Request verification report for biosimulation runs
-      operationId: start-verify-runs
+      summary: Request verification report for biosimulation runs by run IDs
+      operationId: verify-runs
       parameters:
         - name: workflow_id_prefix
           in: query
@@ -276,33 +276,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/RunsVerifyWorkflowOutput"
-        "422":
-          description: Validation Error
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/HTTPValidationError"
-  /verify_runs/{workflow_id}:
-    get:
-      tags:
-        - Verification
-      summary: Get verification report for biosimulation runs
-      operationId: get-verify-runs
-      parameters:
-        - name: workflow_id
-          in: path
-          required: true
-          schema:
-            type: string
-            title: Workflow Id
-      responses:
-        "200":
-          description: Successful Response
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/RunsVerifyWorkflowOutput"
+                $ref: "#/components/schemas/VerifyWorkflowOutput"
         "422":
           description: Validation Error
           content:
@@ -382,7 +356,7 @@ components:
         - created
         - updated
       title: BiosimulatorVersion
-    Body_start-verify-omex:
+    Body_verify-omex:
       properties:
         uploaded_file:
           type: string
@@ -392,7 +366,7 @@ components:
       type: object
       required:
         - uploaded_file
-      title: Body_start-verify-omex
+      title: Body_verify-omex
     CompareSettings:
       properties:
         user_description:
@@ -615,47 +589,6 @@ components:
         - shape
         - values
       title: Hdf5DataValues
-    OmexVerifyWorkflowOutput:
-      properties:
-        workflow_id:
-          type: string
-          title: Workflow Id
-        compare_settings:
-          $ref: "#/components/schemas/CompareSettings"
-        workflow_status:
-          $ref: "#/components/schemas/OmexVerifyWorkflowStatus"
-        timestamp:
-          type: string
-          title: Timestamp
-        workflow_run_id:
-          anyOf:
-            - type: string
-            - type: "null"
-          title: Workflow Run Id
-        workflow_error:
-          anyOf:
-            - type: string
-            - type: "null"
-          title: Workflow Error
-        workflow_results:
-          anyOf:
-            - $ref: "#/components/schemas/GenerateStatisticsActivityOutput"
-            - type: "null"
-      type: object
-      required:
-        - workflow_id
-        - compare_settings
-        - workflow_status
-        - timestamp
-      title: OmexVerifyWorkflowOutput
-    OmexVerifyWorkflowStatus:
-      type: string
-      enum:
-        - PENDING
-        - IN_PROGRESS
-        - COMPLETED
-        - FAILED
-      title: OmexVerifyWorkflowStatus
     RunData:
       properties:
         run_id:
@@ -678,15 +611,47 @@ components:
         - var_names
         - data
       title: RunData
-    RunsVerifyWorkflowOutput:
+    SimulationRunInfo:
+      properties:
+        biosim_sim_run:
+          $ref: "#/components/schemas/BiosimSimulationRun"
+        hdf5_file:
+          $ref: "#/components/schemas/HDF5File"
+      type: object
+      required:
+        - biosim_sim_run
+        - hdf5_file
+      title: SimulationRunInfo
+    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
+    VerifyWorkflowOutput:
       properties:
         workflow_id:
           type: string
           title: Workflow Id
         compare_settings:
           $ref: "#/components/schemas/CompareSettings"
         workflow_status:
-          $ref: "#/components/schemas/RunsVerifyWorkflowStatus"
+          $ref: "#/components/schemas/VerifyWorkflowStatus"
         timestamp:
           type: string
           title: Timestamp
@@ -710,45 +675,13 @@ components:
         - compare_settings
         - workflow_status
         - timestamp
-      title: RunsVerifyWorkflowOutput
-    RunsVerifyWorkflowStatus:
+      title: VerifyWorkflowOutput
+    VerifyWorkflowStatus:
       type: string
       enum:
         - PENDING
         - IN_PROGRESS
         - COMPLETED
         - FAILED
         - RUN_ID_NOT_FOUND
-      title: RunsVerifyWorkflowStatus
-    SimulationRunInfo:
-      properties:
-        biosim_sim_run:
-          $ref: "#/components/schemas/BiosimSimulationRun"
-        hdf5_file:
-          $ref: "#/components/schemas/HDF5File"
-      type: object
-      required:
-        - biosim_sim_run
-        - hdf5_file
-      title: SimulationRunInfo
-    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
+      title: VerifyWorkflowStatus
diff --git a/biosim_client/api/biosim/__init__.py b/biosim_client/api/biosim/__init__.py
@@ -7,7 +7,7 @@
 
 No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
 
-The version of the OpenAPI document: 0.1.0
+The version of the OpenAPI document: 0.2.0
 Generated by OpenAPI Generator (https://openapi-generator.tech)
 
 Do not edit the class manually.
@@ -43,12 +43,10 @@
 from biosim_client.api.biosim.models.hdf5_group import HDF5Group
 from biosim_client.api.biosim.models.http_validation_error import HTTPValidationError
 from biosim_client.api.biosim.models.hdf5_data_values import Hdf5DataValues
-from biosim_client.api.biosim.models.omex_verify_workflow_output import OmexVerifyWorkflowOutput
-from biosim_client.api.biosim.models.omex_verify_workflow_status import OmexVerifyWorkflowStatus
 from biosim_client.api.biosim.models.run_data import RunData
-from biosim_client.api.biosim.models.runs_verify_workflow_output import RunsVerifyWorkflowOutput
-from biosim_client.api.biosim.models.runs_verify_workflow_status import RunsVerifyWorkflowStatus
 from biosim_client.api.biosim.models.simulation_run_info import SimulationRunInfo
 from biosim_client.api.biosim.models.validation_error import ValidationError
 from biosim_client.api.biosim.models.validation_error_loc_inner import ValidationErrorLocInner
 from biosim_client.api.biosim.models.value import Value
+from biosim_client.api.biosim.models.verify_workflow_output import VerifyWorkflowOutput
+from biosim_client.api.biosim.models.verify_workflow_status import VerifyWorkflowStatus
diff --git a/biosim_client/api/biosim/api/default_api.py b/biosim_client/api/biosim/api/default_api.py
@@ -3,7 +3,7 @@
 
 No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
 
-The version of the OpenAPI document: 0.1.0
+The version of the OpenAPI document: 0.2.0
 Generated by OpenAPI Generator (https://openapi-generator.tech)
 
 Do not edit the class manually.