changes to feature geometry

Author: Stephanie Reeder

src/Examples/Sample 1.1.py

@@ -78,12 +78,9 @@
     print "************************************************"
     print
 
-    ser = odm1service.get_series_by_id(1)
-    pp.pprint(ser)
-    ser = odm1service.get_series_by_id(173)
+    ser = odm1service.get_all_series()
+
     pp.pprint(ser)
-    if ser:
-        print ser.variable
 
 
     print
@@ -92,8 +89,9 @@
     print "************************************************"
     print
 
-    pp.pprint(odm1service.get_values_by_series(1))
-    pp.pprint(odm1service.get_values_by_series(173))
+    pp.pprint(odm1service.get_values_by_series(ser[0].id))
+
     print "The end"
 
 
+

src/Examples/Sample.py

@@ -8,10 +8,10 @@
 
 
 #this will be removed when we can installthe api
-this_file = os.path.realpath(__file__)
-directory = os.path.dirname(os.path.dirname(this_file))
-print directory
-sys.path.insert(0, directory)
+# this_file = os.path.realpath(__file__)
+# directory = os.path.dirname(os.path.dirname(this_file))
+# print directory
+# sys.path.insert(0, directory)
 
 from api.ODMconnection import dbconnection
 from api.ODM2.services.readService import *
@@ -23,6 +23,7 @@
 #createconnection (dbtype, servername, dbname, username, password)
 #session_factory = dbconnection.createConnection('mysql', 'localhost', 'odm2', 'ODM', 'odm')
 session_factory = dbconnection.createConnection('mysql', 'jws.uwrl.usu.edu', 'odm2', 'ODM', 'ODM123!!', 2)
+# session_factory= dbconnection.createConnection('mssql')
 
 
 
@@ -78,24 +79,25 @@
     print "Unable to demo getSamplingFeatureByCode: ", e
 
 #add sampling feature
+print "\n------------ Create Sampling Feature --------- \n",
 try:
     from api.ODM2.models import SamplingFeatures
     newsf = SamplingFeatures()
-    newsf = SamplingFeatures()
-    newsf.FeatureGeometry = sf.FeatureGeometry
+    session = session_factory.getSession()
+    newsf.FeatureGeometry = "POINT(-111.946 41.718)"
     newsf.Elevation_m=100
     newsf.ElevationDatumCV=sf.ElevationDatumCV
     newsf.SamplingFeatureCode= "TestSF"
     newsf.SamplingFeatureDescription = "this is a test to add Feature Geomotry"
-    newsf.SamplingFeatureGeotypeCV= sf.SamplingFeatureGeotypeCV
+    newsf.SamplingFeatureGeotypeCV= "Point"
     newsf.SamplingFeatureTypeCV=sf.SamplingFeatureTypeCV
-    newsf.SamplingFeatureUUID= sf.SamplingFeatureUUID+"1"
-    session_factory.getSession().add(newsf)
-    session_factory.getSession().commit()
-    print "new sampling deature added to database", newsf
+    newsf.SamplingFeatureUUID= sf.SamplingFeatureUUID+"2"
+    session.add(newsf)
+    session.commit()
+    print "new sampling feature added to database", newsf
 
 except Exception as e :
-    print "error adding a sampling feature" + e
+    print "error adding a sampling feature: " + str(e)
 
 
 # Drill down and get objects linked by foreign keys

src/api/ODM1_1_1/services/series_service.py

@@ -307,8 +307,7 @@ def get_series_from_filter(self):
         # Pass in probably a Series object, match it against the database
         pass
 
-
-    #Data Value Methods
+    # Data Value Methods
     def get_values_by_series(self, series_id):
         '''
 
@@ -492,7 +491,6 @@ def save_series(self, series, dvs):
             # there wasn't an existing file to overwrite
             raise Exception("Series does not exist, unable to save. Please select 'Save As'")
 
-
     def save_new_series(self, series, dvs):
         """ Create as a new catalog entry
         :param series:
@@ -514,7 +512,6 @@ def save_new_series(self, series, dvs):
                 self._session.rollback()
                 raise e
 
-
         #logger.debug("A new series was added to the database, series id: "+str(series.id))
         return True
 
@@ -526,7 +523,6 @@ def save_values(self, values):
         """
         values.to_sql(name="datavalues", if_exists='append', con=self._session_factory.engine, index=False)
 
-
     def create_new_series(self, data_values, site_id, variable_id, method_id, source_id, qcl_id):
         """
 
@@ -634,7 +630,6 @@ def create_qcl(self, code, definition, explanation):
         self._session.commit()
         return qcl
 
-
     def create_qualifier_by_qual(self, qualifier):
         self._session.add(qualifier)
         self._session.commit()
@@ -671,7 +666,6 @@ def delete_series(self, series):
         self._session.delete(delete_series)
         self._session.commit()
 
-
     def delete_values_by_series(self, series):
         """
 
@@ -738,6 +732,7 @@ def series_exists_quint(self, site_id, var_id, method_id, source_id, qcl_id):
             return True
         except:
             return False
+
     def qcl_exists(self, q):
         """
 
@@ -784,9 +779,6 @@ def variable_exists(self, v):
             return None
 
 
-
-
-
 ####CV_Service
 
     def get_vertical_datum_cvs(self):
@@ -796,6 +788,7 @@ def get_vertical_datum_cvs(self):
     def get_samples(self):
         result = self._session.query(ODM.Sample).order_by(ODM.Sample.lab_sample_code).all()
         return result
+
     def get_site_type_cvs(self):
         result = self._session.query(ODM.SiteTypeCV).order_by(ODM.SiteTypeCV.term).all()
         return result
@@ -857,7 +850,6 @@ def get_unit_by_id(self, unit_id):
         result = self._session.query(ODM.Unit).filter_by(id=unit_id).first()
         return result
 
-
     def copy_series(from_series):
         new = ODM.Series()
         new.site_id = from_series.site_id

src/api/ODM2/LikeODM1/models.py

@@ -28,7 +28,7 @@ class SpatialReference(Base):
     srs_id = Column('srsid', String)
     srs_name = Column('srsname', String)
     is_geographic = None
-    #is_geographic = Column('IsGeographic', Boolean)
+    # is_geographic = Column('IsGeographic', Boolean)
     notes = Column('description', String)
 
     def __repr__(self):
@@ -65,21 +65,18 @@ class Site(Base):
 
     local_x = None
     local_y = None
-    local_projection_id = None  #Column('LocalProjectionID', Integer, ForeignKey('SpatialReferences.SpatialReferenceID'))
+    local_projection_id = None  # Column('LocalProjectionID', Integer, ForeignKey('SpatialReferences.SpatialReferenceID'))
     pos_accuracy_m = None
     state = None
     county = None
     comments = None
 
-
-
     # relationships
     # TODO @sreeder, Please take a look at this line as it throws: sqlalchemy.exc.InvalidRequestError: Class <class 'ODM2.LikeODM1.model.Site2'> does not have a mapped column named 'lat_long_datum_id'
     # :)
-    #spatial_ref = relationship(SpatialReference, primaryjoin=("SpatialReference.id==Site2.lat_long_datum_id"))
-    #spatial_ref = relationship(SpatialReference)
-    #spatial_ref = relationship(SpatialReference, primaryjoin="Site.lat_long_datum_id == SpatialReference.id")
-
+    # spatial_ref = relationship(SpatialReference, primaryjoin=("SpatialReference.id==Site2.lat_long_datum_id"))
+    # spatial_ref = relationship(SpatialReference)
+    # spatial_ref = relationship(SpatialReference, primaryjoin="Site.lat_long_datum_id == SpatialReference.id")
 
     def __repr__(self):
         return "<Site('%s', '%s', '%s')>" % (self.code, self.name, self.elevation_m)
@@ -208,7 +205,6 @@ class Source(Base):
     email = source_join.c.odm2_affiliations_primaryemail  # Column('Email', String, nullable=False)
     address = source_join.c.odm2_affiliations_primaryaddress  # Column('Address', String, nullable=False)
 
-
     @property
     def city(self):
         return "Unknown"
@@ -233,7 +229,7 @@ def citation(self):
     #iso_metadata_id = Column('MetadataID', Integer, ForeignKey('ODM2.ISOMetadata.Metadataid'), nullable=False)
     '''
     # relationships
-    #iso_metadata = relationship(ISOMetadata)
+    # iso_metadata = relationship(ISOMetadata)
 
     def __repr__(self):
         return "<Source('%s', '%s', '%s', '%s', '%s', '%s', '%s')>" % \
@@ -530,29 +526,24 @@ class DataValue(Base):
     utc_offset = joined_table.c.odm2_timeseriesresultvalues_valuedatetimeutcoffset
     site_id = joined_table.c.odm2_featureactions_SFID  #joined_table.c.odm2_featureactions_FeAID
     variable_id = joined_table.c.odm2_results_variableid
-    offset_value = None  #column_property(-1)  ## Question for jeff
-    offset_type_id = None  #column_property(-1)#None  ## Question for Jeff
+    offset_value = None  # column_property(-1)  ## Question for jeff
+    offset_type_id = None  # column_property(-1)#None  ## Question for Jeff
     censor_code = joined_table.c.odm2_timeseriesresultvalues_censorcodecv
 
     method_id = joined_table.c.odm2_actions_methodid
     source_id = joined_table.c.odm2_actionby_affiliationid
-    sample_id = column_property(site_id)  ## Question for jeff
-    derived_from_id = None  #column_property(-1)
+    sample_id = column_property(site_id)  # Question for jeff
+    derived_from_id = None  # column_property(-1)
     quality_control_level_id = joined_table.c.odm2_timeseriesresultvalues_qualitycodecv
 
-    qualifier_id = None  ## Join with annotations..
-    # date_time_utc = column_property(local_date_time+utc_offset)  ## column propertly datetimeutcoffset
+    qualifier_id = None  # Join with annotations..
+    # date_time_utc = column_property(local_date_time+utc_offset)  ## column property datetimeutcoffset
     # @declared_attr
+
     @property
     def date_time_utc(cls):
         return cls.local_date_time - timedelta(hours=cls.utc_offset)
 
-    # @classmethod
-    # def date_time_utc(cls):
-    #     return select([])
-
-
-
     # relationships
     # site = relationship(Site, primaryjoin = site_id==Site.id)
     variable = relationship(Variable, primaryjoin=variable_id == Variable.id)
@@ -587,22 +578,27 @@ def __repr__(self):
 method_table = select([
     method_table.c.methodid,
     method_table.c.methoddescription,
-    #method_table.c.organizationid.label('methodorgid'),
+    # method_table.c.organizationid.label('methodorgid'),
 
 ]).alias("odm2_methods")
 
 processing_levels_table = ProcessingLevels().__table__
-
+'''
 joined_table_2 = feature_action_table.join(result_aliased_table, feature_action_table.c.FeAID ==
                                            result_aliased_table.c.FAID)
+# Obtain TSResults
+joined_table_2 = joined_table_2.join(ts_table, joined_table_2.c.odm2_results_RID ==
+                                     ts_table.c.resultid)
+'''
+joined_table_2 = result_aliased_table.join(ts_table, result_aliased_table.c.RID== ts_table.c.resultid)
+joined_table_2= joined_table_2.join(feature_action_table, joined_table_2.c.odm2_results_FAID== feature_action_table.c.FeAID)
+
 joined_table_2 = joined_table_2.join(site_join, joined_table_2.c.odm2_featureactions_SFID ==
                                      site_join.c.odm2_sites_samplingfeatureid)
 joined_table_2 = joined_table_2.join(variables_table, joined_table_2.c.odm2_results_variableid ==
                                      variables_table.c.variableid)
 
-# Obtain TSResults
-joined_table_2 = joined_table_2.join(ts_table, joined_table_2.c.odm2_results_RID ==
-                                     ts_table.c.resultid)
+
 # Obtaining Action
 joined_table_2 = joined_table_2.join(action_aliased_table, joined_table_2.c.odm2_featureactions_actid ==
                                      action_aliased_table.c.AID)
@@ -666,7 +662,7 @@ class Series(Base):
 
     # begin_date_time_utc = None  # Column('BeginDateTimeUTC', DateTime)
     # end_date_time_utc = None  # Column('EndDateTimeUTC', DateTime)
-    utc_offset = -7  #joined_table_2.c.odm2_timeseriesresultvalues_valuedatetimeutcoffset
+    utc_offset = -7  # joined_table_2.c.odm2_timeseriesresultvalues_valuedatetimeutcoffset
 
     @property
     def begin_date_time_utc(cls):

src/api/ODM2/apiCustomType.py

@@ -41,30 +41,38 @@ def saves_as_bound(cls):
 
     @compiles(cls)
     def compile_function(element, compiler, **kw):
-        return element.__str__()
+        return element
 
     @compiles(cls, 'postgresql')
     def compile_function(element, compiler, **kw):
         #print "postgresql Save : %s" % element.__str__()
-        return element.__str__()
+        return "%s(%s)"%(element.name, "'POINT(30 10)'")
 
     @compiles(cls, 'mysql')
     def compile_function(element, compiler, **kw):
-        print "mysql Save Table %s Alter column %s" % (element.name, element.__str__())
-        #return "%s(%s)"%(element.name, "'POINT (30 10)'")
-        return element.__str__()
+        name= element.name.split('_')[-1]
+
+        # GeomFromText("POINT(30 10)")
+        # GeomFromText(:featuregeometry)
+
+        val = "%s(%s)"%(name, element.clauses.clauses[0])
+        return val
 
     @compiles(cls, 'sqlite')
     def compile_function(element, compiler, **kw):
-        element.name= element.name.split('_')[-1]
-        # print element.name
+        name= element.name.split('_')[-1]
         #return "%s(%s)" % (element.name.replace('_', ''), "'POINT (30 10)'")
-        return element.__str__()
+
+        return "%s(%s)"%(name, "'POINT(30 10)'")
 
     @compiles(cls, 'mssql')
     def compile_function(element, compiler, **kw):
         #return "Geometry::%s(%s, 0)"%(element.name.replace('_', ''), "'POINT (30 10)'")
-        element.name = "Geometry::%s" % element.name.replace('_', '')
+        name = "Geometry::%s" % element.name.replace('_', '')
+        return "%s(%s,0)"%(name, "'POINT(30 10)'")
+
+
+
     return cls
 
 
@@ -81,7 +89,7 @@ class ST_AsText(FunctionElement):
 class ST_AsBinary(FunctionElement):
     name = 'ST_AsBinary'
 
-
+from sqlalchemy import String, type_coerce
 class Geometry(GeometryBase):
 
     def column_expression(self, col):
@@ -91,12 +99,15 @@ def column_expression(self, col):
         return value
 
     def bind_expression(self, bindvalue):
-        val = None
-        try:
-            val = GeometryBase.bind_expression(self, bindvalue)
-        except:
-            pass
-        val = ST_GeomFromText(bindvalue, type_=self)
+
+        #mysql, sqlite
+        val = func.GeomFromText(bindvalue, type_=self)
+
+        #postgresql
+        #val = func.ST_GeomFromText(bindvalue, type_=self)
+        #mssql
+        if val is None:
+            val = ST_GeomFromText(bindvalue, type_=self)
         return val
 
 

src/api/ODM2/models.py

@@ -545,9 +545,9 @@ class SamplingFeatures(Base):
     FeatureGeometry = Column('featuregeometry', Geometry)
 
     def __repr__(self):
-        return "<SamplingFeatures('%s', '%s', '%s', '%s')>" % (
+        return "<SamplingFeatures('%s', '%s', '%s', '%s', '%s')>" % (
             self.SamplingFeatureCode, self.SamplingFeatureName, self.SamplingFeatureDescription,
-            self.Elevation_m)  # self.FeatureGeometry)
+            self.Elevation_m, self.FeatureGeometry)
 
 
 class FeatureActions(Base):
@@ -1401,7 +1401,8 @@ class SamplingFeatureExternalIdentifiers(Base):
                                         ForeignKey(ExternalIdentifierSystems.ExternalIdentifierSystemID),
                                         nullable=False)
     SamplingFeatureExternalIdentifier = Column('samplingfeatureexternalidentifier', String(255), nullable=False)
-    SamplingFeatureExternalIdentifierURI = Column('samplingfeatureexternalidentifieruri', String(255))
+    SamplingFeatureExternalIdentifierURI = Column('samplingfeatureexternalidentiferuri', String(255))
+
 
     ExternalIdentifierSystemObj = relationship(ExternalIdentifierSystems)
     SamplingFeatureObj = relationship(SamplingFeatures)