Merge pull request #188 from the-virtual-brain/TVB-2731

TVB-2731: REST API - provide extra information for various TS analysis results

framework_tvb/tvb/adapters/datatypes/db/fcd.py

@@ -43,6 +43,12 @@ class FcdIndex(DataTypeMatrix):
 
     labels_ordering = Column(String)
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
     def fill_from_has_traits(self, datatype):
         # type: (Fcd)  -> None
         super(FcdIndex, self).fill_from_has_traits(datatype)

framework_tvb/tvb/adapters/datatypes/db/graph.py

@@ -65,6 +65,12 @@ class CorrelationCoefficientsIndex(DataTypeMatrix):
 
     labels_ordering = Column(String)
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
     def fill_from_has_traits(self, datatype):
         # type: (CorrelationCoefficients)  -> None
         super(CorrelationCoefficientsIndex, self).fill_from_has_traits(datatype)

framework_tvb/tvb/adapters/datatypes/db/mode_decompositions.py

@@ -49,6 +49,12 @@ def fill_from_has_traits(self, datatype):
         super(PrincipalComponentsIndex, self).fill_from_has_traits(datatype)
         self.fk_source_gid = datatype.source.gid
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
 
 class IndependentComponentsIndex(DataType):
     id = Column(Integer, ForeignKey(DataType.id), primary_key=True)
@@ -70,6 +76,12 @@ def fill_from_has_traits(self, datatype):
         self.ndim = len(datatype.unmixing_matrix.shape)
         self.array_has_complex = numpy.iscomplex(datatype.unmixing_matrix).any().item()
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
     @property
     def parsed_shape(self):
         try:

framework_tvb/tvb/adapters/datatypes/db/spectral.py

@@ -55,6 +55,12 @@ def fill_from_has_traits(self, datatype):
         self.max_frequency = datatype.max_frequency
         self.fk_source_gid = datatype.source.gid.hex
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
 
 class WaveletCoefficientsIndex(DataTypeMatrix):
     id = Column(Integer, ForeignKey(DataTypeMatrix.id), primary_key=True)
@@ -83,6 +89,12 @@ def fill_from_has_traits(self, datatype):
         self.frequencies_min, self.frequencies_max, _ = from_ndarray(datatype.frequencies)
         self.fk_source_gid = datatype.source.gid.hex
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
 
 class CoherenceSpectrumIndex(DataTypeMatrix):
     id = Column(Integer, ForeignKey(DataTypeMatrix.id), primary_key=True)
@@ -101,6 +113,12 @@ def fill_from_has_traits(self, datatype):
         self.frequencies_min, self.frequencies_max, _ = from_ndarray(datatype.frequency)
         self.fk_source_gid = datatype.source.gid.hex
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
 
 class ComplexCoherenceSpectrumIndex(DataTypeMatrix):
     id = Column(Integer, ForeignKey(DataTypeMatrix.id), primary_key=True)
@@ -124,3 +142,9 @@ def fill_from_has_traits(self, datatype):
         self.frequency_step = datatype.freq_step
         self.max_frequency = datatype.max_freq
         self.fk_source_gid = datatype.source.gid.hex
+
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict

framework_tvb/tvb/adapters/datatypes/db/temporal_correlations.py

@@ -44,6 +44,12 @@ class CrossCorrelationIndex(DataTypeMatrix):
 
     labels_ordering = Column(String, nullable=False)
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.source.labels_ordering
+        labels_dict["labels_dimensions"] = self.source.labels_dimensions
+        return labels_dict
+
     def fill_from_has_traits(self, datatype):
         # type: (CrossCorrelation)  -> None
         super(CrossCorrelationIndex, self).fill_from_has_traits(datatype)

framework_tvb/tvb/adapters/datatypes/db/time_series.py

@@ -59,6 +59,12 @@ class TimeSeriesIndex(DataType):
     has_volume_mapping = Column(Boolean, nullable=False, default=False)
     has_surface_mapping = Column(Boolean, nullable=False, default=False)
 
+    def get_extra_info(self):
+        labels_dict = {}
+        labels_dict["labels_ordering"] = self.labels_ordering
+        labels_dict["labels_dimensions"] = self.labels_dimensions
+        return labels_dict
+
     def fill_from_has_traits(self, datatype):
         # type: (TimeSeries)  -> None
         super(TimeSeriesIndex, self).fill_from_has_traits(datatype)

framework_tvb/tvb/core/entities/model/model_datatype.py

@@ -120,6 +120,9 @@ class DataType(HasTraitsIndex):
     # Transient info
     fixed_generic_attributes = False
 
+    def get_extra_info(self):
+        return {}
+
     def __init__(self, gid=None, **kwargs):
 
         self.gid = gid

framework_tvb/tvb/core/entities/storage/datatype_dao.py

@@ -375,7 +375,11 @@ def get_datatype_details(self, datatype_gid):
         return result_dt
 
 
-    def get_datatype_by_gid(self, gid, load_lazy=True):
+    def get_datatype_extra_info(self, datatype_gid):
+        datatype = self.get_datatype_by_gid(datatype_gid, False, True)
+        return datatype.get_extra_info()
+
+    def get_datatype_by_gid(self, gid, load_lazy=True, load_lazy_extra_info=False):
         """
         Retrieve a DataType DB reference by a global identifier.
         """
@@ -393,6 +397,8 @@ def get_datatype_by_gid(self, gid, load_lazy=True):
                 result_dt.parent_operation.algorithm.algorithm_category
                 result_dt.parent_operation.operation_group
                 result_dt._parent_burst
+            if load_lazy_extra_info:
+                result_dt.get_extra_info()
 
             return result_dt
         except NoResultFound as excep:

framework_tvb/tvb/interfaces/rest/client/datatype/datatype_api.py

@@ -67,6 +67,14 @@ def get_operations_for_datatype(self, datatype_gid):
             })))
         return response, AlgorithmDto
 
+    @handle_response
+    def get_extra_info(self, datatype_gid):
+        response = self.secured_request().get(
+            self.build_request_url(RestLink.DATATYPE_EXTRA_INFO.compute_url(True, {
+                LinkPlaceholder.DATATYPE_GID.value: datatype_gid
+            })))
+        return response, dict
+
     def load_datatype_from_file(self, datatype_path):
         datatype, _ = h5.load_with_links(datatype_path)
         return datatype

framework_tvb/tvb/interfaces/rest/client/examples/fire_simulation.py

@@ -103,6 +103,17 @@ def fire_simulation_example(tvb_client_instance):
         operation_gid = tvb_client_instance.launch_operation(project_gid, FourierAdapter, fourier_model)
         logger.info("Fourier Analyzer operation has launched with gid {}".format(operation_gid))
 
+        data_in_project = tvb_client_instance.get_data_in_project(project_gid)
+        logger.info("We have {} datatypes".format(len(data_in_project)))
+        ggid = None
+        for datatype in data_in_project:
+            if datatype.type == 'FourierSpectrum':
+                ggid = datatype.gid
+                break
+
+        extra_info = tvb_client_instance.get_extra_info(ggid)
+        logger.info("The extra information for Fourier {}".format(extra_info))
+
         logger.info("Download the connectivity file...")
         connectivity_path = tvb_client_instance.retrieve_datatype(connectivity_gid, tvb_client_instance.temp_folder)
         logger.info("The connectivity file location is: {}".format(connectivity_path))

framework_tvb/tvb/interfaces/rest/client/tvb_client.py

@@ -237,3 +237,9 @@ def get_operation_results(self, operation_gid):
         operation if it has finished and an empty list, if the operation is still running, has failed or simply has no results.
         """
         return self.operation_api.get_operations_results(operation_gid)
+
+    def get_extra_info(self, datatype_gid):
+        """
+        Given an datatype gid, this function returns a dict containing the extra information of the datatype.
+        """
+        return self.datatype_api.get_extra_info(datatype_gid)

framework_tvb/tvb/interfaces/rest/commons/strings.py

@@ -86,6 +86,7 @@ class RestLink(Enum):
     # DATATYPES
     GET_DATATYPE = "/{" + LinkPlaceholder.DATATYPE_GID.value + "}"
     DATATYPE_OPERATIONS = "/{" + LinkPlaceholder.DATATYPE_GID.value + "}/operations"
+    DATATYPE_EXTRA_INFO = "/{" + LinkPlaceholder.DATATYPE_GID.value + "}/extra_info"
 
     # OPERATIONS
     LAUNCH_OPERATION = "/{" + LinkPlaceholder.PROJECT_GID.value + "}/algorithm/{" + LinkPlaceholder.ALG_MODULE.value + "}/{" + LinkPlaceholder.ALG_CLASSNAME.value + "}"
@@ -111,7 +112,7 @@ def compute_url(self, include_namespace=False, values=None):
 _namespace_url_dict = {
     RestNamespace.USERS: [RestLink.LOGIN, RestLink.PROJECTS, RestLink.USEFUL_URLS],
     RestNamespace.PROJECTS: [RestLink.DATA_IN_PROJECT, RestLink.OPERATIONS_IN_PROJECT, RestLink.PROJECT_MEMBERS],
-    RestNamespace.DATATYPES: [RestLink.GET_DATATYPE, RestLink.DATATYPE_OPERATIONS],
+    RestNamespace.DATATYPES: [RestLink.GET_DATATYPE, RestLink.DATATYPE_OPERATIONS, RestLink.DATATYPE_EXTRA_INFO],
     RestNamespace.OPERATIONS: [RestLink.LAUNCH_OPERATION, RestLink.OPERATION_STATUS, RestLink.OPERATION_RESULTS],
     RestNamespace.SIMULATION: [RestLink.FIRE_SIMULATION]
 }

framework_tvb/tvb/interfaces/rest/server/facades/datatype_facade.py

@@ -32,7 +32,7 @@
 from tvb.core.entities.storage import dao
 from tvb.core.neocom.h5 import h5_file_for_index
 from tvb.core.services.algorithm_service import AlgorithmService
-from tvb.interfaces.rest.commons.dtos import AlgorithmDto
+from tvb.interfaces.rest.commons.dtos import AlgorithmDto, DataTypeDto
 
 
 class DatatypeFacade:
@@ -49,3 +49,11 @@ def get_datatype_operations(self, datatype_gid):
         datatype = dao.get_datatype_by_gid(datatype_gid)
         _, filtered_adapters, _ = self.algorithm_service.get_launchable_algorithms_for_datatype(datatype, categories)
         return [AlgorithmDto(algorithm) for algorithm in filtered_adapters]
+
+    @staticmethod
+    def get_extra_info(datatype_gid):
+        extra_info = dao.get_datatype_extra_info(datatype_gid)
+        if extra_info is None:
+            return None
+
+        return extra_info

framework_tvb/tvb/interfaces/rest/server/resources/datatype/datatype_resource.py

@@ -47,6 +47,18 @@ def get(self, datatype_gid):
         file_name = os.path.basename(h5_file_path)
         return flask.send_file(h5_file_path, as_attachment=True, attachment_filename=file_name)
 
+class GetExtraInfoForDatatypeResource(RestResource):
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.datatypes_facade = DatatypeFacade()
+
+    @check_permission(DataTypeAccessPermission, 'datatype_gid')
+    def get(self, datatype_gid):
+        """
+        :return the results of DataType.
+        """
+        return self.datatypes_facade.get_extra_info(datatype_gid)
 
 class GetOperationsForDatatypeResource(RestResource):
 

framework_tvb/tvb/interfaces/rest/server/run.py

@@ -41,7 +41,7 @@
 from tvb.interfaces.rest.commons.strings import RestNamespace, RestLink, LinkPlaceholder, Strings
 from tvb.interfaces.rest.server.decorators.encoders import CustomFlaskEncoder
 from tvb.interfaces.rest.server.resources.datatype.datatype_resource import RetrieveDatatypeResource, \
-    GetOperationsForDatatypeResource
+    GetOperationsForDatatypeResource, GetExtraInfoForDatatypeResource
 from tvb.interfaces.rest.server.resources.operation.operation_resource import GetOperationStatusResource, \
     GetOperationResultsResource, LaunchOperationResource
 from tvb.interfaces.rest.server.resources.project.project_resource import GetOperationsInProjectResource, \
@@ -110,6 +110,8 @@ def initialize_flask():
         values={LinkPlaceholder.DATATYPE_GID.value: '<string:datatype_gid>'}))
     name_space_datatypes.add_resource(GetOperationsForDatatypeResource, RestLink.DATATYPE_OPERATIONS.compute_url(
         values={LinkPlaceholder.DATATYPE_GID.value: '<string:datatype_gid>'}))
+    name_space_datatypes.add_resource(GetExtraInfoForDatatypeResource, RestLink.DATATYPE_EXTRA_INFO.compute_url(
+        values={LinkPlaceholder.DATATYPE_GID.value: '<string:datatype_gid>'}))
 
     # Operations namespace
     name_space_operations = api.namespace(build_path(RestNamespace.OPERATIONS),