Merge branch 'master' into fixRelated

Conflicts:
	odm2api/ODM2/services/readService.py

Author: valentinedwv

.travis.yml

@@ -46,13 +46,13 @@ before_install:
 # python -m pip makes the install go into the virtualenv
   - python -m pip install pandas
   - export PYMSSQL_BUILD_WITH_BUNDLED_FREETDS=1;python -m  pip install pymssql
-  - python -m  pip install mysql-python
+#  - python -m  pip install mysql-python
 install: # now just our code
   - pip install git+https://github.com/ODM2/geoalchemy.git@odm2#egg=geoalchemy-0.7.3
   - pip install   .
   - pip install  -r requirements_tests.txt  --allow-external pyodbc --allow-unverified pyodbc
     # pysqlite
-  - pip install pysqlite
+#  - pip install pysqlite
   - pip list
 
 # don't forget to open up the azure mssql server to these addreses

Examples/Sample.py

@@ -40,52 +40,52 @@
 allVars = read.getVariables()
 
 for x in allVars:
-    print x.VariableCode + ": " + x.VariableNameCV
+    print(x.VariableCode + ": " + x.VariableNameCV)
 
 
 
 # Get all of the people from the database
 allPeople = read.getPeople()
 
 for x in allPeople:
-    print x.PersonFirstName + " " + x.PersonLastName
+    print(x.PersonFirstName + " " + x.PersonLastName)
 
 try:
-    print "\n-------- Information about an Affiliation ---------"
+    print("\n-------- Information about an Affiliation ---------")
     allaff = read.getAllAffiliations()
     for x in allaff:
-        print x.PersonObj.PersonFirstName + ": " + str(x.OrganizationID)
+        print(x.PersonObj.PersonFirstName + ": " + str(x.OrganizationID))
 except Exception as e:
-    print "Unable to demo getAllAffiliations", e
+    print("Unable to demo getAllAffiliations", e)
 
 # Get all of the SamplingFeatures from the database that are Sites
 try:
     siteFeatures = read.getSamplingFeaturesByType('Site')
     numSites = len(siteFeatures)
 
     for x in siteFeatures:
-        print x.SamplingFeatureCode + ": " + x.SamplingFeatureName
+        print(x.SamplingFeatureCode + ": " + x.SamplingFeatureName)
 except Exception as e:
-    print "Unable to demo getSamplingFeaturesByType", e
+    print("Unable to demo getSamplingFeaturesByType", e)
 
 
 # Now get the SamplingFeature object for a SamplingFeature code
 try:
     sf = read.getSamplingFeatureByCode('USU-LBR-Mendon')
-    print sf
-    print "\n-------- Information about an individual SamplingFeature ---------"
-    print "The following are some of the attributes of a SamplingFeature retrieved using getSamplingFeatureByCode(): \n"
-    print "SamplingFeatureCode: " + sf.SamplingFeatureCode
-    print "SamplingFeatureName: " + sf.SamplingFeatureName
-    print "SamplingFeatureDescription: %s" % sf.SamplingFeatureDescription
-    print "SamplingFeatureGeotypeCV: %s" % sf.SamplingFeatureGeotypeCV
-    print "SamplingFeatureGeometry: %s" % sf.FeatureGeometry
-    print "Elevation_m: %s" % str(sf.Elevation_m)
+    print(sf)
+    print("\n-------- Information about an individual SamplingFeature ---------")
+    print("The following are some of the attributes of a SamplingFeature retrieved using getSamplingFeatureByCode(): \n")
+    print("SamplingFeatureCode: " + sf.SamplingFeatureCode)
+    print("SamplingFeatureName: " + sf.SamplingFeatureName)
+    print("SamplingFeatureDescription: %s" % sf.SamplingFeatureDescription)
+    print("SamplingFeatureGeotypeCV: %s" % sf.SamplingFeatureGeotypeCV)
+    print("SamplingFeatureGeometry: %s" % sf.FeatureGeometry)
+    print("Elevation_m: %s" % str(sf.Elevation_m))
 except Exception as e:
-    print "Unable to demo getSamplingFeatureByCode: ", e
+    print("Unable to demo getSamplingFeatureByCode: ", e)
 
 #add sampling feature
-print "\n------------ Create Sampling Feature --------- \n",
+print("\n------------ Create Sampling Feature --------- \n")
 try:
     from odm2api.ODM2.models import SamplingFeatures
     newsf = SamplingFeatures()
@@ -100,19 +100,19 @@
     newsf.SamplingFeatureUUID= sf.SamplingFeatureUUID+"2"
     session.add(newsf)
     #session.commit()
-    print "new sampling feature added to database", newsf
+    print("new sampling feature added to database", newsf)
 
 except Exception as e :
-    print "error adding a sampling feature: " + str(e)
+    print("error adding a sampling feature: " + str(e))
 
 
 # Drill down and get objects linked by foreign keys
-print "\n------------ Foreign Key Example --------- \n",
+print("\n------------ Foreign Key Example --------- \n",)
 try:
     # Call getResults, but return only the first result
     firstResult = read.getResults()[0]
-    print "The FeatureAction object for the Result is: ", firstResult.FeatureActionObj
-    print "The Action object for the Result is: ", firstResult.FeatureActionObj.ActionObj
+    print("The FeatureAction object for the Result is: ", firstResult.FeatureActionObj)
+    print("The Action object for the Result is: ", firstResult.FeatureActionObj.ActionObj)
     print ("\nThe following are some of the attributes for the Action that created the Result: \n" +
            "ActionTypeCV: " + firstResult.FeatureActionObj.ActionObj.ActionTypeCV + "\n" +
            "ActionDescription: " + firstResult.FeatureActionObj.ActionObj.ActionDescription + "\n" +
@@ -121,11 +121,11 @@
            "MethodName: " + firstResult.FeatureActionObj.ActionObj.MethodObj.MethodName + "\n" +
            "MethodDescription: " + firstResult.FeatureActionObj.ActionObj.MethodObj.MethodDescription)
 except Exception as e:
-    print "Unable to demo Foreign Key Example: ", e
+    print("Unable to demo Foreign Key Example: ", e)
 
 
 # Now get a particular Result using a ResultID
-print "\n------- Example of Retrieving Attributes of a Time Series Result -------"
+print("\n------- Example of Retrieving Attributes of a Time Series Result -------")
 try:
     tsResult = read.getTimeSeriesResultByResultId(1)
     print (
@@ -142,19 +142,19 @@
         "SamplingFeature: " + tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj.SamplingFeatureCode + " - " +
         tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj.SamplingFeatureName)
 except Exception as e:
-    print "Unable to demo Example of retrieving Attributes of a time Series Result: ", e
+    print("Unable to demo Example of retrieving Attributes of a time Series Result: ", e)
 
 # Get the values for a particular TimeSeriesResult
-print "\n-------- Example of Retrieving Time Series Result Values ---------"
+print("\n-------- Example of Retrieving Time Series Result Values ---------")
 
 tsValues = read.getTimeSeriesResultValuesByResultId(1)  # Return type is a pandas dataframe
 
 # Print a few Time Series Values to the console
 # tsValues.set_index('ValueDateTime', inplace=True)
 try:
-    print tsValues.head()
+    print(tsValues.head())
 except Exception as e:
-    print e
+    print(e)
 
 # Plot the time series
 
@@ -173,4 +173,4 @@
     ax.grid(True)
     plt.show()
 except Exception as e:
-    print "Unable to demo plotting of tsValues: ", e
+    print("Unable to demo plotting of tsValues: ", e)

odm2api/ODM1_1_1/services/edit_service.py

@@ -457,7 +457,7 @@ def updateSeries(self, var=None, method=None, qcl=None, is_new_series=False):
                 print("Save existing series ID: %s" % str(series.id))
                 series = tseries
             else:
-                print "Series doesn't exist (if you are not, you should be running SaveAs)"
+                print("Series doesn't exist (if you are not, you should be running SaveAs)")
 
         if is_new_series:
 

odm2api/ODM1_1_1/services/export_service.py

@@ -19,7 +19,7 @@ def export_series_data(self, series_id, filename, utc=False, site=False, var=Fal
             return False
 
         writer = csv.writer(open(filename, 'wb'))
-        print "filename: ", filename
+        print("filename: ", filename)
         self.write_data_header(writer, utc, site, var, offset, qual, src, qcl)
         for dv in series.data_values:
             self.write_data_row(writer, series, dv, utc, site, var, offset, qual, src, qcl)

odm2api/ODM1_1_1/services/series_service.py

@@ -286,7 +286,7 @@ def get_series_by_id(self, series_id):
         try:
             return self._session.query(ODM.Series).filter_by(id=series_id).first()
         except Exception as e:
-            print e
+            print(e)
             return None
 
     def get_series_by_id_quint(self, site_id, var_id, method_id, source_id, qcl_id):

odm2api/ODM2/services/createService.py

@@ -262,7 +262,7 @@ def createAffiliation(self, personid, organizationid, email, phone=None, address
         #self._session.flush()
         # self._session.refresh(a)
 
-        print a.OrganizationID
+        print(a.OrganizationID)
 
         return a
 
@@ -523,8 +523,8 @@ def createTimeSeriesResultValues(self, datavalues):
 
 
             return datavalues
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
             return None
 
 

odm2api/ODM2/services/readService.py

@@ -331,8 +331,8 @@ def getProcessingLevelByCode(self, processingCode):
         """
         try:
             return self._session.query(ProcessingLevels).filter_by(ProcessingLevelCode=str(processingCode)).first()
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
             return None
 
     """
@@ -387,7 +387,7 @@ def getSamplingFeaturesByType(self, samplingFeatureTypeCV):
         try:
             return self._session.query(SamplingFeatures).filter_by(SamplingFeatureTypeCV=samplingFeatureTypeCV).all()
         except Exception as e:
-            print e
+            print(e)
             return None
 
     def getSamplingFeatureByGeometry(self, wkt_geometry):
@@ -396,17 +396,17 @@ def getSamplingFeatureByGeometry(self, wkt_geometry):
             # ST_Equals(geometry, geometry)
             return self._session.query(SamplingFeatures).filter(
                 func.ST_AsText(SamplingFeatures.FeatureGeometry) == func.ST_AsText(wkt_geometry)).first()
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
             return None
 
     def getGeometryTest(self, TestGeom):
         Geom = self._session.query(SamplingFeatures).first()
-        print "Queried Geometry: ", self._session.query(Geom.FeatureGeometry.ST_AsText()).first()
+        print("Queried Geometry: ", self._session.query(Geom.FeatureGeometry.ST_AsText()).first())
         GeomText = self._session.query(
             func.ST_Union(Geom.FeatureGeometry, func.ST_GeomFromText(TestGeom)).ST_AsText()).first()
 
-        print GeomText
+        print(GeomText)
 
     """
     Action
@@ -773,13 +773,13 @@ def getTimeSeriesResultValuesByResultId(self, resultId):
         """
         try:
             q = self._session.query(TimeSeriesResultValues).filter_by(ResultID=resultId).all()
-            print type(q[0]), q[0]
+            print(type(q[0]), q[0])
             df = pd.DataFrame([dv.list_repr() for dv in q])
             df.columns = q[0].get_columns()
             return df
             # return self._session.query(Timeseriesresultvalue).filter_by(ResultID=resultId).all()
         except Exception as e:
-            print e
+            print(e)
             return None
 
     def getTimeSeriesResultValuesByCode(self, timeSeriesCode):
@@ -944,10 +944,8 @@ def getRelatedModelsByID(self, modelid):
         :return: all models related to the specified id
         """
         try:
-            # note this was RelatedModelID = modelid  which would return all Parent models of  RelatedModelID
-            return self._session.query(RelatedModels).filter_by(ModelID=modelid).all()
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
         return None
 
     def getRelatedModelsByCode(self, modelcode):
@@ -957,11 +955,9 @@ def getRelatedModelsByCode(self, modelcode):
         :return: all models related to the provided model code
         """
         try:
-            # note this was RelatedModels.RelatedModelID == Models.ModelID which would return all Parent models of  RelatedModelID
-            return self._session.query(RelatedModels).join(Models, RelatedModels.ModelID == Models.ModelID) \
                 .filter(Models.ModelCode == modelcode).all()
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
         return None
 
     def getResultsBySimulationID(self, simulationID):
@@ -971,8 +967,8 @@ def getResultsBySimulationID(self, simulationID):
                     .join(Actions) \
                     .join(Simulations) \
                     .filter(Simulations.SimulationID == simulationID).all()
-        except Exception, e:
-            print e
+        except Exception as e:
+            print(e)
         return None
 
 # ################################################################################

odm2api/ODMconnection.py

@@ -119,7 +119,7 @@ def testEngine(self, connection_string, echo = False ):
             s.test_Session().query(Variable2.VariableCode).limit(1).first()
 
         except Exception as e:
-            print "Connection was unsuccessful ", e.message
+            print("Connection was unsuccessful ", e.message)
             return False
         return True
 
@@ -131,7 +131,7 @@ def testEngine1_1(self, connection_string, echo = False ):
             s.test_Session().query(ODM.Variable.code).limit(1).first()
 
         except Exception as e:
-            print "Connection was unsuccessful ", e.message
+            print("Connection was unsuccessful ", e.message)
             return False
         return True
 

requirements.txt

@@ -1,7 +1,7 @@
 pyodbc
 six
 sqlalchemy
--e git+https://github.com/ODM2/geoalchemy.git@odm2#egg=geoalchemy-0.7.3
+-e git+https://github.com/ODM2/geoalchemy.git@v0.7.4#egg=geoalchemy-0.7.4
 shapely
 pandas
 #psycopg2  # Commented out because I could not pip install it.

requirements_tests.txt

@@ -4,10 +4,11 @@ pytest-cov
 mock
 #db support
 pymysql
-pysqlite
+#pysqlite
+#sqlite
 pymssql
 psycopg2
 #pyspatialite
-mysql-python
+#mysql-python
 
 

setup.py

@@ -98,7 +98,7 @@
     # ],
     # dependency_links- geoalchemy from the ODM repository
     dependency_links=[
-        "git+https://github.com/ODM2/[email protected].3#egg=geoalchemy-0.7.3"
+        "git+https://github.com/ODM2/[email protected].4#egg=geoalchemy-0.7.4"
     ],
 
     # List additional groups of dependencies here (e.g. development

tests/test_SessionFactory.py

@@ -12,7 +12,7 @@
     ['mysql"root@Localhost/', 'mysql', 'mysql+pymysql://root@localhost/'],
     ['mysql:ODM@Localhost/odm2', 'mysql', 'mysql+pymysql://ODM:odm@localhost/odm2'],
     ['mysql"root@Localhost/odm2', 'mysql', 'mysql+pymysql://root@localhost/odm2'],
-   [' mysql + mysqldb:', 'mysql', 'mysql+mysqldb://root@localhost/odm2'],
+  # [' mysql + mysqldb:', 'mysql', 'mysql+mysqldb://root@localhost/odm2'],
                      #'mysql+pymysql://ODM:[email protected]/odm2'
      ['postgresql_marchantariats_none', 'postgresql', 'postgresql+psycopg2://postgres:None@localhost/marchantariats', 'marchantariats', 'postgres',  None],
     ['postgresql_marchantariats_empty', 'postgresql', 'postgresql+psycopg2://postgres@localhost/marchantariats', 'marchantariats', 'postgres',  None],

tests/test_odm1/test_odmdata/test_memory_db_1_1.py

@@ -31,7 +31,7 @@ def test_get_data_values(self):
     def test_update_points(self):
         self.memory_db.update([{"value":15,"id":1}])
         dvs = self.memory_db.getDataValuesDF()
-        print dvs["DataValue"]
+        print ( dvs["DataValue"] )
         assert dvs["DataValue"][1-1] == 9
 
     def test_update_value(self):

tests/test_odm2/test_createservice.py

@@ -32,7 +32,7 @@ def build_db(self):
         for line in ddl.split(');')[:-1]:
             try:
                 db.engine.execute(line + ');')
-            except Exception, e:
+            except Exception as e:
                 print e
 
         self.write = CreateODM2(db)

tests/test_odm2/test_readservice.py

@@ -58,7 +58,7 @@ def build_db(self):
         for line in ddl.split(');')[:-1]:
             try:
                 db.engine.execute(line + ');')
-            except Exception, e:
+            except Exception as e:
                 print e
 
         self.reader = ReadODM2(db)