Merge Pull request #61 from ODM2/Dev1_0

resolve issues #60, #50, #36, #34, #33, #32, #29

Author: Stephanie Reeder

.gitignore

@@ -43,3 +43,4 @@ log
 .idea
 
 .DS_Store
+.ipynb_checkpoints

Examples/Sample.py

@@ -1,77 +1,75 @@
 __author__ = 'stephanie'
-import sys
-import os
+
 
 
 import matplotlib.pyplot as plt
 from matplotlib import dates
 
 
-#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)
 
 from odm2api.ODMconnection import dbconnection
 from odm2api.ODM2.services.readService import *
+from odm2api.ODM2.services import CreateODM2
 # Create a connection to the ODM2 database
 # ----------------------------------------
 
 
 #connect to database
-#createconnection (dbtype, servername, dbname, username, password)
-#session_factory = dbconnection.createConnection('mysql', 'localhost', 'odm2', 'ODM', 'odm')
-#session_factory = dbconnection.createConnection('connection type: sqlite|mysql|mssql|postgresql', '/your/path/to/db/goes/here', 2.0)
-session_factory = dbconnection.createConnection('sqlite', '/Users/denversmith/Downloads/ODM2.sqlite', 2.0)
-# session_factory= dbconnection.createConnection('mssql')
+# 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('mysql', 'localhost', 'odm2', 'ODM', 'odm')#mysql
+# session_factory= dbconnection.createConnection('mssql', "(local)", "LBRODM2", "ODM", "odm")#win MSSQL
+session_factory= dbconnection.createConnection('mssql', "arroyoodm2", "", "ODM", "odm")#mac/linux MSSQL
+# session_factory = dbconnection.createConnection('sqlite', '/Users/Stephanie/Desktop/TestODM2.db', 2.0)
 
 
 
 #_session = session_factory.getSession()
-
 read = ReadODM2(session_factory)
+create =CreateODM2(session_factory)
 
 
 
 # Run some basic sample queries.
 # ------------------------------
 # Get all of the variables from the database and print their names to the console
 allVars = read.getVariables()
-
+print ("\n-------- Information about Variables ---------")
 for x in allVars:
     print(x.VariableCode + ": " + x.VariableNameCV)
 
 
 
 # Get all of the people from the database
 allPeople = read.getPeople()
-
+print ("\n-------- Information about People ---------")
 for x in allPeople:
     print(x.PersonFirstName + " " + x.PersonLastName)
 
 try:
     print("\n-------- Information about an Affiliation ---------")
-    allaff = read.getAllAffiliations()
+    allaff = read.getAffiliations()
     for x in allaff:
         print(x.PersonObj.PersonFirstName + ": " + str(x.OrganizationID))
 except Exception as e:
     print("Unable to demo getAllAffiliations", e)
 
 # Get all of the SamplingFeatures from the database that are Sites
 try:
-    siteFeatures = read.getSamplingFeaturesByType('Site')
+    print ("\n-------- Information about Sites ---------")
+    siteFeatures = read.getSamplingFeatures()
+    # siteFeatures = read.getSamplingFeatures(type='Site')
     numSites = len(siteFeatures)
 
     for x in siteFeatures:
-        print(x.SamplingFeatureCode + ": " + x.SamplingFeatureName)
+        print(x.SamplingFeatureCode + ": " + x.SamplingFeatureTypeCV )
 except Exception as e:
     print("Unable to demo getSamplingFeaturesByType", e)
 
 
 # Now get the SamplingFeature object for a SamplingFeature code
 try:
-    sf = read.getSamplingFeatureByCode('USU-LBR-Mendon')
+    sf = read.getSamplingFeatures(code=['USU-LBR-Mendon'])[0]
     print(sf)
     print("\n-------- Information about an individual SamplingFeature ---------")
     print("The following are some of the attributes of a SamplingFeature retrieved using getSamplingFeatureByCode(): \n")
@@ -87,18 +85,14 @@
 #add sampling feature
 print("\n------------ Create Sampling Feature --------- \n")
 try:
-    from odm2api.ODM2.models import SamplingFeatures
-    newsf = SamplingFeatures()
+    # from odm2api.ODM2.models import SamplingFeatures
     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= "Point"
-    newsf.SamplingFeatureTypeCV=sf.SamplingFeatureTypeCV
-    newsf.SamplingFeatureUUID= sf.SamplingFeatureUUID+"2"
-    session.add(newsf)
+    newsf = Sites(FeatureGeometryWKT = "POINT(-111.946 41.718)", Elevation_m=100, ElevationDatumCV=sf.ElevationDatumCV,
+    SamplingFeatureCode= "TestSF",SamplingFeatureDescription = "this is a test to add Feature Geomotry",
+    SamplingFeatureGeotypeCV= "Point", SamplingFeatureTypeCV=sf.SamplingFeatureTypeCV,SamplingFeatureUUID= sf.SamplingFeatureUUID+"2",
+    SiteTypeCV="cave", Latitude= "100", Longitude= "-100", SpatialReferenceID= 0)
+
+    create.createSamplingFeature(newsf)
     #session.commit()
     print("new sampling feature added to database", newsf)
 
@@ -125,29 +119,29 @@
 
 
 # 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 Result -------")
 try:
-    tsResult = read.getTimeSeriesResultByResultId(1)
+    tsResult = read.getResults(ids = [1])[0]
     print (
-        "The following are some of the attributes for the TimeSeriesResult retrieved using getTimeSeriesResultByResultID(): \n" +
-        "ResultTypeCV: " + tsResult.ResultObj.ResultTypeCV + "\n" +
+        "The following are some of the attributes for the TimeSeriesResult retrieved using getResults(ids=[1]): \n" +
+        "ResultTypeCV: " + tsResult.ResultTypeCV + "\n" +
         # Get the ProcessingLevel from the TimeSeriesResult's ProcessingLevel object
-        "ProcessingLevel: " + tsResult.ResultObj.ProcessingLevelObj.Definition + "\n" +
-        "SampledMedium: " + tsResult.ResultObj.SampledMediumCV + "\n" +
+        "ProcessingLevel: " + tsResult.ProcessingLevelObj.Definition + "\n" +
+        "SampledMedium: " + tsResult.SampledMediumCV + "\n" +
         # Get the variable information from the TimeSeriesResult's Variable object
-        "Variable: " + tsResult.ResultObj.VariableObj.VariableCode + ": " + tsResult.ResultObj.VariableObj.VariableNameCV + "\n"
-                                                                                                        "AggregationStatistic: " + tsResult.AggregationStatisticCV + "\n" +
-        "Elevation_m: " + str(sf.Elevation_m) + "\n" +
+        "Variable: " + tsResult.VariableObj.VariableCode + ": " + tsResult.VariableObj.VariableNameCV + "\n"
+                               #"AggregationStatistic: " + tsResult.AggregationStatisticCV + "\n" +
+
         # Get the site information by drilling down
-        "SamplingFeature: " + tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj.SamplingFeatureCode + " - " +
-        tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj.SamplingFeatureName)
+        "SamplingFeature: " + tsResult.FeatureActionObj.SamplingFeatureObj.SamplingFeatureCode + " - " +
+        tsResult.FeatureActionObj.SamplingFeatureObj.SamplingFeatureName)
 except Exception as 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 ---------")
 
-tsValues = read.getTimeSeriesResultValuesByResultId(1)  # Return type is a pandas dataframe
+tsValues = read.getResultValues(resultid = 1)  # Return type is a pandas datafram
 
 # Print a few Time Series Values to the console
 # tsValues.set_index('ValueDateTime', inplace=True)
@@ -159,18 +153,9 @@
 # Plot the time series
 
 try:
-    fig = plt.figure()
-    ax = fig.add_subplot(111)
-    tsValues.plot(x='ValueDateTime', y='DataValue', kind='line',
-                  title=tsResult.ResultObj.VariableObj.VariableNameCV + " at " + tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj.SamplingFeatureName,
-                  ax=ax)
-    ax.set_ylabel(tsResult.ResultObj.VariableObj.VariableNameCV + " (" + tsResult.ResultObj.UnitsObj.UnitsAbbreviation + ")")
-    ax.set_xlabel("Date/Time")
-    ax.xaxis.set_minor_locator(dates.MonthLocator())
-    ax.xaxis.set_minor_formatter(dates.DateFormatter('%b'))
-    ax.xaxis.set_major_locator(dates.YearLocator())
-    ax.xaxis.set_major_formatter(dates.DateFormatter('\n%Y'))
-    ax.grid(True)
+    plt.figure()
+    ax=tsValues.plot(x='ValueDateTime', y='DataValue')
+
     plt.show()
 except Exception as e:
     print("Unable to demo plotting of tsValues: ", e)