Merge pull request #1568 from virtualcell/export-control

Export control

Author: Ezequiel-Valencia

docker/build/build.sh

@@ -102,13 +102,25 @@ build_api() {
 build_rest() {
 	echo "building $repo/vcell-rest:$tag"
 	echo "$SUDO_CMD docker buildx build --platform=linux/amd64 -f ../../vcell-rest/src/main/docker/Dockerfile.jvm --tag $repo/vcell-rest:$tag ../../vcell-rest"
+	mvn clean install -DskipTests -Dvcell.exporter=false -f ../../vcell-rest/pom.xml
 	$SUDO_CMD docker buildx build --platform=linux/amd64 -f ../../vcell-rest/src/main/docker/Dockerfile.jvm --tag $repo/vcell-rest:$tag ../../vcell-rest
 	if [[ $? -ne 0 ]]; then echo "docker buildx build --platform=linux/amd64 failed"; exit 1; fi
 	if [ "$skip_push" == "false" ]; then
 		$SUDO_CMD docker push $repo/vcell-rest:$tag
 	fi
 }
 
+build_exporter() {
+	echo "building $repo/vcell-rest:$tag"
+	echo "$SUDO_CMD docker buildx build --platform=linux/amd64 -f ../../vcell-rest/src/main/docker/Dockerfile.jvm --tag $repo/vcell-exporter:$tag ../../vcell-rest"
+	mvn clean install -DskipTests -Dvcell.exporter=true -f ../../vcell-rest/pom.xml
+	$SUDO_CMD docker buildx build --platform=linux/amd64 -f ../../vcell-rest/src/main/docker/Dockerfile.jvm --tag $repo/vcell-exporter:$tag ../../vcell-rest
+	if [[ $? -ne 0 ]]; then echo "docker buildx build --platform=linux/amd64 failed"; exit 1; fi
+	if [ "$skip_push" == "false" ]; then
+		$SUDO_CMD docker push $repo/vcell-exporter:$tag
+	fi
+}
+
 
 build_webapp_common() {
   config=$1
@@ -251,6 +263,7 @@ case $target in
 		;;
 	rest)
 		build_rest
+		build_exporter
 		exit $?
 		;;
 	webapp)

python-restclient/.openapi-generator/FILES

@@ -3,25 +3,39 @@
 README.md
 docs/AccesTokenRepresentationRecord.md
 docs/AdminResourceApi.md
+docs/AnalyticCurve.md
+docs/AnnotatedFunctionDTO.md
 docs/ApplicationInfo.md
 docs/BatchSystemType.md
 docs/BioModel.md
 docs/BioModelChildSummary.md
 docs/BioModelResourceApi.md
 docs/BioModelSummary.md
 docs/BiomodelRef.md
+docs/CompositeCurve.md
+docs/ControlPointCurve.md
+docs/Coordinate.md
+docs/Curve.md
+docs/CurveSelectionInfo.md
 docs/DataIdentifier.md
 docs/DetailedState.md
 docs/Domain.md
+docs/ExportEvent.md
+docs/ExportProgressType.md
+docs/ExportResourceApi.md
+docs/ExportableDataType.md
 docs/Extent.md
 docs/ExternalDataIdentifier.md
 docs/FieldData.md
 docs/FieldDataReference.md
 docs/FieldDataResourceApi.md
 docs/FieldDataSavedResults.md
 docs/FieldDataShape.md
+docs/FunctionCategory.md
 docs/GIFImage.md
+docs/GeometryMode.md
 docs/GeometryResourceApi.md
+docs/GeometrySpecDTO.md
 docs/GeometrySummary.md
 docs/GroupAccess.md
 docs/GroupAccessAll.md
@@ -30,6 +44,7 @@ docs/GroupAccessSome.md
 docs/HelloWorldApi.md
 docs/HelloWorldMessage.md
 docs/HtcJobID.md
+docs/HumanReadableExportData.md
 docs/ISize.md
 docs/Identity.md
 docs/MathModelChildSummary.md
@@ -38,11 +53,13 @@ docs/MathModelSummary.md
 docs/MathType.md
 docs/MathmodelRef.md
 docs/ModelType.md
+docs/N5ExportRequest.md
 docs/Origin.md
 docs/Publication.md
 docs/PublicationInfo.md
 docs/PublicationResourceApi.md
 docs/SPECIALCLAIM.md
+docs/SampledCurve.md
 docs/SchedulerStatus.md
 docs/SimulationExecutionStatusRecord.md
 docs/SimulationJobStatusRecord.md
@@ -53,8 +70,16 @@ docs/SimulationResourceApi.md
 docs/SimulationStatusPersistentRecord.md
 docs/SolverResourceApi.md
 docs/SourceModel.md
+docs/SpatialSelection.md
+docs/SpatialSelectionContour.md
+docs/SpatialSelectionMembrane.md
+docs/SpatialSelectionVolume.md
+docs/Spline.md
+docs/StandardExportInfo.md
 docs/Status.md
 docs/StatusMessage.md
+docs/TimeMode.md
+docs/TimeSpecs.md
 docs/User.md
 docs/UserIdentityJSONSafe.md
 docs/UserLoginInfoForMapping.md
@@ -68,6 +93,8 @@ docs/VCellHTTPError.md
 docs/VCellSite.md
 docs/VCellSoftwareVersion.md
 docs/VariableDomain.md
+docs/VariableMode.md
+docs/VariableSpecs.md
 docs/VariableType.md
 docs/Version.md
 docs/VersionFlag.md
@@ -77,6 +104,7 @@ vcell_client/__init__.py
 vcell_client/api/__init__.py
 vcell_client/api/admin_resource_api.py
 vcell_client/api/bio_model_resource_api.py
+vcell_client/api/export_resource_api.py
 vcell_client/api/field_data_resource_api.py
 vcell_client/api/geometry_resource_api.py
 vcell_client/api/hello_world_api.py
@@ -92,21 +120,34 @@ vcell_client/configuration.py
 vcell_client/exceptions.py
 vcell_client/models/__init__.py
 vcell_client/models/acces_token_representation_record.py
+vcell_client/models/analytic_curve.py
+vcell_client/models/annotated_function_dto.py
 vcell_client/models/application_info.py
 vcell_client/models/batch_system_type.py
 vcell_client/models/bio_model.py
 vcell_client/models/bio_model_child_summary.py
 vcell_client/models/bio_model_summary.py
 vcell_client/models/biomodel_ref.py
+vcell_client/models/composite_curve.py
+vcell_client/models/control_point_curve.py
+vcell_client/models/coordinate.py
+vcell_client/models/curve.py
+vcell_client/models/curve_selection_info.py
 vcell_client/models/data_identifier.py
 vcell_client/models/detailed_state.py
 vcell_client/models/domain.py
+vcell_client/models/export_event.py
+vcell_client/models/export_progress_type.py
+vcell_client/models/exportable_data_type.py
 vcell_client/models/extent.py
 vcell_client/models/external_data_identifier.py
 vcell_client/models/field_data.py
 vcell_client/models/field_data_reference.py
 vcell_client/models/field_data_saved_results.py
 vcell_client/models/field_data_shape.py
+vcell_client/models/function_category.py
+vcell_client/models/geometry_mode.py
+vcell_client/models/geometry_spec_dto.py
 vcell_client/models/geometry_summary.py
 vcell_client/models/gif_image.py
 vcell_client/models/group_access.py
@@ -115,16 +156,19 @@ vcell_client/models/group_access_none.py
 vcell_client/models/group_access_some.py
 vcell_client/models/hello_world_message.py
 vcell_client/models/htc_job_id.py
+vcell_client/models/human_readable_export_data.py
 vcell_client/models/i_size.py
 vcell_client/models/identity.py
 vcell_client/models/math_model_child_summary.py
 vcell_client/models/math_model_summary.py
 vcell_client/models/math_type.py
 vcell_client/models/mathmodel_ref.py
 vcell_client/models/model_type.py
+vcell_client/models/n5_export_request.py
 vcell_client/models/origin.py
 vcell_client/models/publication.py
 vcell_client/models/publication_info.py
+vcell_client/models/sampled_curve.py
 vcell_client/models/scheduler_status.py
 vcell_client/models/simulation_execution_status_record.py
 vcell_client/models/simulation_job_status_record.py
@@ -133,9 +177,17 @@ vcell_client/models/simulation_queue_entry_status_record.py
 vcell_client/models/simulation_queue_id.py
 vcell_client/models/simulation_status_persistent_record.py
 vcell_client/models/source_model.py
+vcell_client/models/spatial_selection.py
+vcell_client/models/spatial_selection_contour.py
+vcell_client/models/spatial_selection_membrane.py
+vcell_client/models/spatial_selection_volume.py
 vcell_client/models/specialclaim.py
+vcell_client/models/spline.py
+vcell_client/models/standard_export_info.py
 vcell_client/models/status.py
 vcell_client/models/status_message.py
+vcell_client/models/time_mode.py
+vcell_client/models/time_specs.py
 vcell_client/models/user.py
 vcell_client/models/user_identity_json_safe.py
 vcell_client/models/user_login_info_for_mapping.py
@@ -144,6 +196,8 @@ vcell_client/models/v_cell_http_error.py
 vcell_client/models/v_cell_site.py
 vcell_client/models/v_cell_software_version.py
 vcell_client/models/variable_domain.py
+vcell_client/models/variable_mode.py
+vcell_client/models/variable_specs.py
 vcell_client/models/variable_type.py
 vcell_client/models/vc_document_type.py
 vcell_client/models/vc_image_summary.py

python-restclient/README.md

@@ -96,6 +96,8 @@ Class | Method | HTTP request | Description
 *BioModelResourceApi* | [**get_bio_model_summary**](docs/BioModelResourceApi.md#get_bio_model_summary) | **GET** /api/v1/bioModel/{bioModelID}/summary | All of the text based information about a BioModel (summary, version, publication status, etc...), but not the actual BioModel itself.
 *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 | 
 *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.
@@ -146,40 +148,56 @@ Class | Method | HTTP request | Description
 ## Documentation For Models
 
  - [AccesTokenRepresentationRecord](docs/AccesTokenRepresentationRecord.md)
+ - [AnalyticCurve](docs/AnalyticCurve.md)
+ - [AnnotatedFunctionDTO](docs/AnnotatedFunctionDTO.md)
  - [ApplicationInfo](docs/ApplicationInfo.md)
  - [BatchSystemType](docs/BatchSystemType.md)
  - [BioModel](docs/BioModel.md)
  - [BioModelChildSummary](docs/BioModelChildSummary.md)
  - [BioModelSummary](docs/BioModelSummary.md)
  - [BiomodelRef](docs/BiomodelRef.md)
+ - [CompositeCurve](docs/CompositeCurve.md)
+ - [ControlPointCurve](docs/ControlPointCurve.md)
+ - [Coordinate](docs/Coordinate.md)
+ - [Curve](docs/Curve.md)
+ - [CurveSelectionInfo](docs/CurveSelectionInfo.md)
  - [DataIdentifier](docs/DataIdentifier.md)
  - [DetailedState](docs/DetailedState.md)
  - [Domain](docs/Domain.md)
+ - [ExportEvent](docs/ExportEvent.md)
+ - [ExportProgressType](docs/ExportProgressType.md)
+ - [ExportableDataType](docs/ExportableDataType.md)
  - [Extent](docs/Extent.md)
  - [ExternalDataIdentifier](docs/ExternalDataIdentifier.md)
  - [FieldData](docs/FieldData.md)
  - [FieldDataReference](docs/FieldDataReference.md)
  - [FieldDataSavedResults](docs/FieldDataSavedResults.md)
  - [FieldDataShape](docs/FieldDataShape.md)
+ - [FunctionCategory](docs/FunctionCategory.md)
  - [GIFImage](docs/GIFImage.md)
+ - [GeometryMode](docs/GeometryMode.md)
+ - [GeometrySpecDTO](docs/GeometrySpecDTO.md)
  - [GeometrySummary](docs/GeometrySummary.md)
  - [GroupAccess](docs/GroupAccess.md)
  - [GroupAccessAll](docs/GroupAccessAll.md)
  - [GroupAccessNone](docs/GroupAccessNone.md)
  - [GroupAccessSome](docs/GroupAccessSome.md)
  - [HelloWorldMessage](docs/HelloWorldMessage.md)
  - [HtcJobID](docs/HtcJobID.md)
+ - [HumanReadableExportData](docs/HumanReadableExportData.md)
  - [ISize](docs/ISize.md)
  - [Identity](docs/Identity.md)
  - [MathModelChildSummary](docs/MathModelChildSummary.md)
  - [MathModelSummary](docs/MathModelSummary.md)
  - [MathType](docs/MathType.md)
  - [MathmodelRef](docs/MathmodelRef.md)
  - [ModelType](docs/ModelType.md)
+ - [N5ExportRequest](docs/N5ExportRequest.md)
  - [Origin](docs/Origin.md)
  - [Publication](docs/Publication.md)
  - [PublicationInfo](docs/PublicationInfo.md)
  - [SPECIALCLAIM](docs/SPECIALCLAIM.md)
+ - [SampledCurve](docs/SampledCurve.md)
  - [SchedulerStatus](docs/SchedulerStatus.md)
  - [SimulationExecutionStatusRecord](docs/SimulationExecutionStatusRecord.md)
  - [SimulationJobStatusRecord](docs/SimulationJobStatusRecord.md)
@@ -188,8 +206,16 @@ Class | Method | HTTP request | Description
  - [SimulationQueueID](docs/SimulationQueueID.md)
  - [SimulationStatusPersistentRecord](docs/SimulationStatusPersistentRecord.md)
  - [SourceModel](docs/SourceModel.md)
+ - [SpatialSelection](docs/SpatialSelection.md)
+ - [SpatialSelectionContour](docs/SpatialSelectionContour.md)
+ - [SpatialSelectionMembrane](docs/SpatialSelectionMembrane.md)
+ - [SpatialSelectionVolume](docs/SpatialSelectionVolume.md)
+ - [Spline](docs/Spline.md)
+ - [StandardExportInfo](docs/StandardExportInfo.md)
  - [Status](docs/Status.md)
  - [StatusMessage](docs/StatusMessage.md)
+ - [TimeMode](docs/TimeMode.md)
+ - [TimeSpecs](docs/TimeSpecs.md)
  - [User](docs/User.md)
  - [UserIdentityJSONSafe](docs/UserIdentityJSONSafe.md)
  - [UserLoginInfoForMapping](docs/UserLoginInfoForMapping.md)
@@ -201,6 +227,8 @@ Class | Method | HTTP request | Description
  - [VCellSite](docs/VCellSite.md)
  - [VCellSoftwareVersion](docs/VCellSoftwareVersion.md)
  - [VariableDomain](docs/VariableDomain.md)
+ - [VariableMode](docs/VariableMode.md)
+ - [VariableSpecs](docs/VariableSpecs.md)
  - [VariableType](docs/VariableType.md)
  - [Version](docs/Version.md)
  - [VersionFlag](docs/VersionFlag.md)

python-restclient/docs/AnalyticCurve.md

@@ -0,0 +1,36 @@
+# AnalyticCurve
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**type** | **str** |  | [default to 'AnalyticCurve']
+**exp_x** | **str** |  | [optional] 
+**exp_y** | **str** |  | [optional] 
+**exp_z** | **str** |  | [optional] 
+**offset** | [**Coordinate**](Coordinate.md) |  | [optional] 
+**analytic_offset** | [**Coordinate**](Coordinate.md) |  | [optional] 
+**default_num_samples** | **int** |  | [optional] 
+**segment_count** | **int** |  | [optional] 
+**valid** | **bool** |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.analytic_curve import AnalyticCurve
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AnalyticCurve from a JSON string
+analytic_curve_instance = AnalyticCurve.from_json(json)
+# print the JSON string representation of the object
+print AnalyticCurve.to_json()
+
+# convert the object into a dict
+analytic_curve_dict = analytic_curve_instance.to_dict()
+# create an instance of AnalyticCurve from a dict
+analytic_curve_form_dict = analytic_curve.from_dict(analytic_curve_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+

python-restclient/docs/AnnotatedFunctionDTO.md

@@ -0,0 +1,33 @@
+# AnnotatedFunctionDTO
+
+
+## Properties
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**function_name** | **str** |  | [optional] 
+**function_expression** | **str** |  | [optional] 
+**error** | **str** |  | [optional] 
+**domain** | [**Domain**](Domain.md) |  | [optional] 
+**function_type** | [**VariableType**](VariableType.md) |  | [optional] 
+**category** | [**FunctionCategory**](FunctionCategory.md) |  | [optional] 
+
+## Example
+
+```python
+from vcell_client.models.annotated_function_dto import AnnotatedFunctionDTO
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AnnotatedFunctionDTO from a JSON string
+annotated_function_dto_instance = AnnotatedFunctionDTO.from_json(json)
+# print the JSON string representation of the object
+print AnnotatedFunctionDTO.to_json()
+
+# convert the object into a dict
+annotated_function_dto_dict = annotated_function_dto_instance.to_dict()
+# create an instance of AnnotatedFunctionDTO from a dict
+annotated_function_dto_form_dict = annotated_function_dto.from_dict(annotated_function_dto_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+