initial commit for sampling feature dataset query

Author: sreeder

Examples/Sample.py

@@ -17,15 +17,18 @@
 #connect to database
 # createconnection (dbtype, servername, dbname, username, password)
 # session_factory = dbconnection.createConnection('connection type: sqlite|mysql|mssql|postgresql', '/your/path/to/db/goes/here', 2.0)#sqlite
-session_factory = dbconnection.createConnection('postgresql', 'localhost', 'odm2', 'ODM', 'odm')
+# session_factory = dbconnection.createConnection('postgresql', 'localhost', 'odm2', 'ODM', 'odm')
 # session_factory = dbconnection.createConnection('mysql', 'localhost', 'odm2', 'ODM', 'odm')#mysql
 
 # session_factory= dbconnection.createConnection('mssql', "(local)", "ODM2", "ODM", "odm")#win MSSQL
 
+
 # session_factory= dbconnection.createConnection('mssql', "arroyoodm2", "", "ODM", "odm")#mac/linux MSSQL
 # session_factory = dbconnection.createConnection('sqlite', '/Users/stephanie/DEV/YODA-Tools/tests/test_files/XL_specimen.sqlite', 2.0)
 
 
+session_factory = dbconnection.createConnection('postgresql', 'odm2wofpy1.uwrl.usu.edu', 'odm2', 'dbadmin', 'pinkbananastastegross')
+
 
 
 
@@ -39,6 +42,9 @@
 create = CreateODM2(session_factory)
 
 
+ds= read.getSamplingFeatureDatasets(ids = [1])
+
+
 # Run some basic sample queries.
 # ------------------------------
 # Get all of the variables from the database and print their names to the console

odm2api/ODM2/models.py

@@ -316,6 +316,7 @@ class DataSets(Base):
     DataSetTitle = Column('datasettitle', String(255), nullable=False)
     DataSetAbstract = Column('datasetabstract', String(500), nullable=False)
 
+    # DatasetsResultsObj = relationship(DataSetsResults, primaryjoin='DatasetsResults.DatasetID == DataSets.ActionID')
 
 class ProcessingLevels(Base):
     """

odm2api/ODM2/services/readService.py

@@ -12,7 +12,7 @@
     CalibrationActions, CalibrationReferenceEquipment, CalibrationStandards,
     CategoricalResultValueAnnotations, CategoricalResultValues, CitationExtensionPropertyValues,
     CitationExternalIdentifiers, DataLoggerFileColumns, DataLoggerFiles, DataLoggerProgramFiles,
-    DataQuality, DataSetCitations, DataSets, DerivationEquations, Directives, Equipment,
+    DataQuality, DataSetCitations, DataSets, DataSetsResults, DerivationEquations, Directives, Equipment,
     EquipmentActions, EquipmentAnnotations, EquipmentModels, EquipmentUsed, ExtensionProperties,
     ExternalIdentifierSystems, FeatureActions, InstrumentOutputVariables, MaintenanceActions,
     MeasurementResultValueAnnotations, MeasurementResultValues, MethodAnnotations,
@@ -462,6 +462,8 @@ def getRelatedSamplingFeatures(self, sfid=None, rfid=None, relationshiptype=None
             print('Error running Query: {}'.format(e))
         return None
 
+
+
     # Action
     def getActions(self, ids=None, type=None, sfid=None):
         """
@@ -694,13 +696,70 @@ def getDataSets(self, codes=None, uuids=None):
         if codes:
             q = q.filter(DataSets.DataSetCode.in_(codes))
         if uuids:
-            q.q.filter(DataSets.DataSetUUID.in_(uuids))
+            q.filter(DataSets.DataSetUUID.in_(uuids))
         try:
             return q.all()
         except Exception as e:
             print('Error running Query {}'.format(e))
             return None
 
+    def getSamplingFeatureDatasets(self, ids=None, codes=None, uuids=None, type=None):
+        """Retrieve a list of Sampling Feature objects.
+        Retrieve a list of Datasets associated with the given sampling feature data.
+
+        Must specify either samplingFeatureID OR samplingFeatureUUID OR samplingFeatureCode)
+
+        Args:
+            ids (list, optional): List of SamplingFeatureIDs.
+            codes (list, optional): List of SamplingFeature Codes.
+            uuids (list, optional): List of UUIDs string.
+            type (str, optional): Type of Dataset from
+                `controlled vocabulary name <http://vocabulary.odm2.org/samplingfeaturetype/>`_.
+
+
+        Returns:
+            list: List of sampling feature objects along with their associated datasets
+
+        Examples:
+            >>> READ = ReadODM2(SESSION_FACTORY)
+            >>> READ.getSamplingFeatureDatasets(ids=[39, 40])
+            >>> READ.getSamplingFeatureDatasets(codes=['HOME', 'FIELD'])
+            >>> READ.getSamplingFeatureDatasets(uuids=['a6f114f1-5416-4606-ae10-23be32dbc202',
+            ...                                 '5396fdf3-ceb3-46b6-aaf9-454a37278bb4'])
+            >>> READ.getSamplingFeatureDatasets(type='singleTimeSeries')
+
+        """
+
+
+        # make sure one of the three arguments has been sent in
+        if all(v is None for v in [ids, codes, uuids]):
+            raise ValueError('Expected samplingFeatureID OR samplingFeatureUUID OR samplingFeatureCode argument')
+
+        sf_query = self._session.query(SamplingFeatures.SamplingFeatureID)
+
+        if ids:
+            sf_query = sf_query.filter(SamplingFeatures.SamplingFeatureID.in_(ids))
+        if codes:
+            sf_query = sf_query.filter(SamplingFeatures.SamplingFeatureCode.in_(codes))
+        if uuids:
+            sf_query = sf_query.filter(SamplingFeatures.SamplingFeatureUUID.in_(uuids))
+        sf_list = sf_query.all()
+
+        # , DataSetsResults)\
+        q = self._session.query(DataSetsResults)\
+            .join(Results)\
+            .join(FeatureActions)\
+            .filter(FeatureActions.SamplingFeatureID.in_(sf_list))
+
+        if type:
+            q = q.filter_by(DatasetTypeCV=type)
+
+        try:
+            return q.all()
+        except Exception as e:
+            print('Error running Query: {}'.format(e))
+            return None
+
     # Data Quality
     def getDataQuality(self):
         """