Update Export to Use Topic Instead

Author: Ezequiel-Valencia

python-restclient/README.md

@@ -97,7 +97,7 @@ Class | Method | HTTP request | Description
 *BioModelResourceApi* | [**get_bio_model_vcml**](docs/BioModelResourceApi.md#get_bio_model_vcml) | **GET** /api/v1/bioModel/{bioModelID}/vcml_download | Get the BioModel in VCML format.
 *BioModelResourceApi* | [**save_bio_model**](docs/BioModelResourceApi.md#save_bio_model) | **POST** /api/v1/bioModel | Save's the given BioModel. Optional parameters of name and simulations to update due to math changes. Returns saved BioModel as VCML.
 *ExportResourceApi* | [**export_n5**](docs/ExportResourceApi.md#export_n5) | **POST** /api/v1/export/N5 | 
-*ExportResourceApi* | [**export_status**](docs/ExportResourceApi.md#export_status) | **GET** /api/v1/export/status | 
+*ExportResourceApi* | [**export_status**](docs/ExportResourceApi.md#export_status) | **PATCH** /api/v1/export/status | 
 *FieldDataResourceApi* | [**advanced_create**](docs/FieldDataResourceApi.md#advanced_create) | **POST** /api/v1/fieldData/advancedCreate | Create Field Data with granular detail in one request.The following files are accepted: .tif and .zip.
 *FieldDataResourceApi* | [**analyze_file**](docs/FieldDataResourceApi.md#analyze_file) | **POST** /api/v1/fieldData/analyzeFile | Analyze uploaded image file (Tiff, Zip, and Non-GPL BioFormats) and return field data. Color mapped images not supported (the colors in those images will be interpreted as separate channels). Filenames must be lowercase alphanumeric, and can contain underscores.
 *FieldDataResourceApi* | [**copy_models_field_data**](docs/FieldDataResourceApi.md#copy_models_field_data) | **POST** /api/v1/fieldData/copyModelsFieldData | Copy all existing field data from a BioModel/MathModel that you have access to, but don't own.

python-restclient/docs/ExportEvent.md

@@ -12,8 +12,6 @@ Name | Type | Description | Notes
 **job_id** | **int** |  | [optional] 
 **data_key** | **str** |  | [optional] 
 **data_id_string** | **str** |  | [optional] 
-**time_specs** | [**TimeSpecs**](TimeSpecs.md) |  | [optional] 
-**variable_specs** | [**VariableSpecs**](VariableSpecs.md) |  | [optional] 
 **human_readable_data** | [**HumanReadableExportData**](HumanReadableExportData.md) |  | [optional] 
 
 ## Example

python-restclient/docs/ExportResourceApi.md

@@ -5,7 +5,7 @@ All URIs are relative to *https://vcell.cam.uchc.edu*
 Method | HTTP request | Description
 ------------- | ------------- | -------------
 [**export_n5**](ExportResourceApi.md#export_n5) | **POST** /api/v1/export/N5 | 
-[**export_status**](ExportResourceApi.md#export_status) | **GET** /api/v1/export/status | 
+[**export_status**](ExportResourceApi.md#export_status) | **PATCH** /api/v1/export/status | 
 
 
 # **export_n5**
@@ -84,11 +84,11 @@ Name | Type | Description  | Notes
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
 # **export_status**
-> List[ExportEvent] export_status()
+> List[ExportEvent] export_status(body=body)
 
 
 
-Get the status of your most recent export jobs.
+Get the status of your export jobs past the timestamp (UTC format).
 
 ### Example
 
@@ -115,9 +115,10 @@ configuration = vcell_client.Configuration(
 with vcell_client.ApiClient(configuration) as api_client:
     # Create an instance of the API class
     api_instance = vcell_client.ExportResourceApi(api_client)
+    body = '2013-10-20T19:20:30+01:00' # datetime |  (optional)
 
     try:
-        api_response = api_instance.export_status()
+        api_response = api_instance.export_status(body=body)
         print("The response of ExportResourceApi->export_status:\n")
         pprint(api_response)
     except Exception as e:
@@ -127,7 +128,10 @@ with vcell_client.ApiClient(configuration) as api_client:
 
 
 ### Parameters
-This endpoint does not need any parameter.
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **body** | **datetime**|  | [optional] 
 
 ### Return type
 
@@ -139,7 +143,7 @@ This endpoint does not need any parameter.
 
 ### HTTP request headers
 
- - **Content-Type**: Not defined
+ - **Content-Type**: application/json
  - **Accept**: application/json
 
 ### HTTP response details

python-restclient/vcell_client/api/export_resource_api.py

@@ -24,6 +24,8 @@
 except ImportError:
     from typing_extensions import Annotated
 
+from datetime import datetime
+
 from typing import List, Optional
 
 from vcell_client.models.export_event import ExportEvent
@@ -340,6 +342,7 @@ def _export_n5_serialize(
     @validate_call
     def export_status(
         self,
+        body: Optional[datetime] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -355,8 +358,10 @@ def export_status(
     ) -> List[ExportEvent]:
         """export_status
 
-        Get the status of your most recent export jobs.
+        Get the status of your export jobs past the timestamp (UTC format).
 
+        :param body:
+        :type body: datetime
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -380,6 +385,7 @@ def export_status(
         """ # noqa: E501
 
         _param = self._export_status_serialize(
+            body=body,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -407,6 +413,7 @@ def export_status(
     @validate_call
     def export_status_with_http_info(
         self,
+        body: Optional[datetime] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -422,8 +429,10 @@ def export_status_with_http_info(
     ) -> ApiResponse[List[ExportEvent]]:
         """export_status
 
-        Get the status of your most recent export jobs.
+        Get the status of your export jobs past the timestamp (UTC format).
 
+        :param body:
+        :type body: datetime
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -447,6 +456,7 @@ def export_status_with_http_info(
         """ # noqa: E501
 
         _param = self._export_status_serialize(
+            body=body,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -474,6 +484,7 @@ def export_status_with_http_info(
     @validate_call
     def export_status_without_preload_content(
         self,
+        body: Optional[datetime] = None,
         _request_timeout: Union[
             None,
             Annotated[StrictFloat, Field(gt=0)],
@@ -489,8 +500,10 @@ def export_status_without_preload_content(
     ) -> RESTResponseType:
         """export_status
 
-        Get the status of your most recent export jobs.
+        Get the status of your export jobs past the timestamp (UTC format).
 
+        :param body:
+        :type body: datetime
         :param _request_timeout: timeout setting for this request. If one
                                  number provided, it will be total request
                                  timeout. It can also be a pair (tuple) of
@@ -514,6 +527,7 @@ def export_status_without_preload_content(
         """ # noqa: E501
 
         _param = self._export_status_serialize(
+            body=body,
             _request_auth=_request_auth,
             _content_type=_content_type,
             _headers=_headers,
@@ -536,6 +550,7 @@ def export_status_without_preload_content(
 
     def _export_status_serialize(
         self,
+        body,
         _request_auth,
         _content_type,
         _headers,
@@ -560,6 +575,8 @@ def _export_status_serialize(
         # process the header parameters
         # process the form parameters
         # process the body parameter
+        if body is not None:
+            _body_params = body
 
 
         # set the HTTP header `Accept`
@@ -569,14 +586,27 @@ def _export_status_serialize(
             ]
         )
 
+        # set the HTTP header `Content-Type`
+        if _content_type:
+            _header_params['Content-Type'] = _content_type
+        else:
+            _default_content_type = (
+                self.api_client.select_header_content_type(
+                    [
+                        'application/json'
+                    ]
+                )
+            )
+            if _default_content_type is not None:
+                _header_params['Content-Type'] = _default_content_type
 
         # authentication setting
         _auth_settings: List[str] = [
             'openId'
         ]
 
         return self.api_client.param_serialize(
-            method='GET',
+            method='PATCH',
             resource_path='/api/v1/export/status',
             path_params=_path_params,
             query_params=_query_params,

python-restclient/vcell_client/models/export_event.py

@@ -24,9 +24,7 @@
 from pydantic import Field
 from vcell_client.models.export_progress_type import ExportProgressType
 from vcell_client.models.human_readable_export_data import HumanReadableExportData
-from vcell_client.models.time_specs import TimeSpecs
 from vcell_client.models.user import User
-from vcell_client.models.variable_specs import VariableSpecs
 try:
     from typing import Self
 except ImportError:
@@ -44,10 +42,8 @@ class ExportEvent(BaseModel):
     job_id: Optional[StrictInt] = Field(default=None, alias="jobID")
     data_key: Optional[StrictStr] = Field(default=None, alias="dataKey")
     data_id_string: Optional[StrictStr] = Field(default=None, alias="dataIdString")
-    time_specs: Optional[TimeSpecs] = Field(default=None, alias="timeSpecs")
-    variable_specs: Optional[VariableSpecs] = Field(default=None, alias="variableSpecs")
     human_readable_data: Optional[HumanReadableExportData] = Field(default=None, alias="humanReadableData")
-    __properties: ClassVar[List[str]] = ["eventType", "progress", "format", "location", "user", "jobID", "dataKey", "dataIdString", "timeSpecs", "variableSpecs", "humanReadableData"]
+    __properties: ClassVar[List[str]] = ["eventType", "progress", "format", "location", "user", "jobID", "dataKey", "dataIdString", "humanReadableData"]
 
     model_config = {
         "populate_by_name": True,
@@ -88,12 +84,6 @@ def to_dict(self) -> Dict[str, Any]:
         # override the default output from pydantic by calling `to_dict()` of user
         if self.user:
             _dict['user'] = self.user.to_dict()
-        # override the default output from pydantic by calling `to_dict()` of time_specs
-        if self.time_specs:
-            _dict['timeSpecs'] = self.time_specs.to_dict()
-        # override the default output from pydantic by calling `to_dict()` of variable_specs
-        if self.variable_specs:
-            _dict['variableSpecs'] = self.variable_specs.to_dict()
         # override the default output from pydantic by calling `to_dict()` of human_readable_data
         if self.human_readable_data:
             _dict['humanReadableData'] = self.human_readable_data.to_dict()
@@ -122,8 +112,6 @@ def from_dict(cls, obj: Dict) -> Self:
             "jobID": obj.get("jobID"),
             "dataKey": obj.get("dataKey"),
             "dataIdString": obj.get("dataIdString"),
-            "timeSpecs": TimeSpecs.from_dict(obj.get("timeSpecs")) if obj.get("timeSpecs") is not None else None,
-            "variableSpecs": VariableSpecs.from_dict(obj.get("variableSpecs")) if obj.get("variableSpecs") is not None else None,
             "humanReadableData": HumanReadableExportData.from_dict(obj.get("humanReadableData")) if obj.get("humanReadableData") is not None else None
         })
         return _obj

tools/openapi.yaml

@@ -462,18 +462,22 @@ paths:
       - openId:
         - user
   /api/v1/export/status:
-    get:
+    patch:
       tags:
       - Export Resource
-      description: Get the status of your most recent export jobs.
+      description: Get the status of your export jobs past the timestamp (UTC format).
       operationId: exportStatus
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/Instant'
       responses:
         "200":
           description: OK
           content:
             application/json:
               schema:
-                uniqueItems: true
                 type: array
                 items:
                   $ref: '#/components/schemas/ExportEvent'
@@ -2511,10 +2515,6 @@ components:
           $ref: '#/components/schemas/KeyValue'
         dataIdString:
           type: string
-        timeSpecs:
-          $ref: '#/components/schemas/TimeSpecs'
-        variableSpecs:
-          $ref: '#/components/schemas/VariableSpecs'
         humanReadableData:
           $ref: '#/components/schemas/HumanReadableExportData'
     ExportProgressType:

vcell-api-types/src/main/java/org/vcell/api/types/utils/DTOModelTransformerV0.java

@@ -55,36 +55,21 @@ public static DataJobEvent dataJobEventFromJsonRep(Object eventSource, DataJobEv
 
     public static ExportEvent exportEventFromJsonRep(Object eventSource, ExportEventRepresentation rep) {
         User user = new User(rep.username, new KeyValue(rep.userkey));
-        TimeSpecs timeSpecs = null;
-        if (rep.exportTimeSpecs!=null) {
-            timeSpecs = timeSpecsFromJsonRep(rep.exportTimeSpecs);
-        }
-        VariableSpecs variableSpecs = null;
-        if (rep.exportVariableSpecs!=null) {
-            variableSpecs = variableSpecsFromJsonRep(rep.exportVariableSpecs);
-        }
         HumanReadableExportData humanReadableExportData1 = null;
         if (rep.exportHumanReadableDataSpec!=null){
             humanReadableExportData1 = humanReadableExportDataFromJsonRep(rep.exportHumanReadableDataSpec);
         }
         ExportEvent event = new ExportEvent(
                 eventSource, rep.jobid, user,
                 rep.dataIdString, new KeyValue(rep.dataKey), ExportEnums.ExportProgressType.getExportProgressType(rep.eventType),
-                rep.format, rep.location, rep.progress,
-                timeSpecs, variableSpecs);
+                rep.format, rep.location, rep.progress);
         event.setHumanReadableExportData(humanReadableExportData1);
         return event;
     }
 
     public static ExportEventRepresentation exportEventToJsonRep(ExportEvent event) {
         ExportTimeSpecs exportTimeSpecs = null;
-        if (event.getTimeSpecs()!=null) {
-            exportTimeSpecs = exportTimeSpecsToJsonRep(event.getTimeSpecs());
-        }
         ExportVariableSpecs exportVariableSpecs = null;
-        if (event.getVariableSpecs()!=null) {
-            exportVariableSpecs = variableSpecsToJsonRep(event.getVariableSpecs());
-        }
         ExportHumanReadableDataSpec exportHumanReadableDataSpec = null;
         if (event.getHumanReadableData() != null){
             exportHumanReadableDataSpec = humanReadableExportDataToJsonRep(event.getHumanReadableData());

vcell-apiclient/src/main/java/org/vcell/api/messaging/LocalDataSetControllerMessaging.java

@@ -308,7 +308,7 @@ public ExportEvent makeRemoteFile(OutputContext outputContext,ExportSpecs export
 		// N5 export is handled by the N5ExportService
 		try {
 			long jobID = vCellApiClient.getExportApi().exportN5(DtoModelTransforms.n5ExportRequestFromExportSpecs(exportSpecs));
-            return new ExportEvent(this, jobID, null, exportSpecs.getVCDataIdentifier(), ExportEnums.ExportProgressType.EXPORT_START, exportSpecs.getFormat().name(), "", 0.0, exportSpecs.getTimeSpecs(), exportSpecs.getVariableSpecs());
+            return new ExportEvent(this, jobID, null, exportSpecs.getVCDataIdentifier(), ExportEnums.ExportProgressType.EXPORT_START, exportSpecs.getFormat().name(), "", 0.0);
 		}  catch (ApiException e) {
 			ExceptionHandler.onlyDataAccessOrPermissionException(e);
 			throw new RuntimeException("Error should not reach here: " + e.getMessage(), e);

vcell-apiclient/src/main/java/org/vcell/api/server/AsynchMessageManager.java

@@ -9,6 +9,8 @@
  */
 
 package org.vcell.api.server;
+import java.time.Instant;
+import java.time.OffsetDateTime;
 import java.util.List;
 import java.util.Set;
 import java.util.concurrent.ScheduledExecutorService;
@@ -70,6 +72,7 @@ public class AsynchMessageManager implements AsyncMessageManagerInterface {
     private long pollTime = BASE_POLL_SECONDS;
 	private AtomicBoolean bPoll = new AtomicBoolean(false);
 	private ScheduledFuture<?> pollingHandle = null;
+	private OffsetDateTime lastPoll = OffsetDateTime.now();
 	/**
 	 * for {@link #schedule(long)} method
 	 */
@@ -140,9 +143,10 @@ private void poll( )  {
 		    pollTime = BASE_POLL_SECONDS;
 	    	queuedEvents = clientServerManager.getMessageEvents();
 			try{
-				Set<org.vcell.restclient.model.ExportEvent> setOfExports = clientServerManager.getVCellApiClient().getExportApi().exportStatus();
+				List<org.vcell.restclient.model.ExportEvent> setOfExports = clientServerManager.getVCellApiClient().getExportApi().exportStatus(lastPoll);
 				List<ExportEvent> exportEvents = setOfExports.stream().map(DtoModelTransforms::dtoToExportEvent).toList();
 				queuedEvents = Stream.concat(exportEvents.stream(), Stream.of(queuedEvents)).toArray(MessageEvent[]::new);
+				lastPoll = OffsetDateTime.now();
 			} catch (ApiException ex){
 				throw ExceptionHandler.getProperException(ex);
 			}

vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java

@@ -2674,7 +2674,6 @@ private static void updateExportMetaData(final ExportEvent exportEvent){
 
 				HumanReadableExportData humanReadableExportData = exportEvent.getHumanReadableData();
 				DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
-				double[] exportTimes = exportEvent.getTimeSpecs().getAllTimes();
 
 
 				if (jsonFile.exists()){
@@ -2699,8 +2698,8 @@ private static void updateExportMetaData(final ExportEvent exportEvent){
 							humanReadableExportData.simulationName,
 							humanReadableExportData.applicationName,
 							humanReadableExportData.biomodelName,
-                            Arrays.toString(exportEvent.getVariableSpecs().getVariableNames()),
-							exportTimes[exportEvent.getTimeSpecs().getBeginTimeIndex()] + "/" + exportTimes[exportEvent.getTimeSpecs().getEndTimeIndex()],
+                            null,
+							null,
 							humanReadableExportData.differentParameterValues,
 							humanReadableExportData.serverSavedFileName,
 							humanReadableExportData.applicationType,