Largely from https://github.com/ODM2/ODM2PythonAPI/blob/master/Examples/Sample.py
sfgeometry_em_1 branch, with my overhauls. Using odm2api_dev env.odm2api_jan31test). The code also fails the same way with the odm2api env, but it does still run fine with the odm2api_jan21 env! I'm investigating the differences between those two envs.Emilio Mayorga
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%matplotlib inline
import sys
import os
import matplotlib.pyplot as plt
from matplotlib import dates
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from odm2api.ODMconnection import dbconnection
from odm2api.ODM2.services.readService import *
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# Create a connection to the ODM2 database
# ----------------------------------------
odm2db_fpth = '/home/mayorga/Desktop/TylerYeats/ODM2-LittleBear1.sqlite'
session_factory = dbconnection.createConnection('sqlite', odm2db_fpth, 2.0)
read = ReadODM2(session_factory)
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# Run some basic sample queries.
# ------------------------------
# Get all of the variables from the database and print their names to the console
allVars = read.getVariables()
for x in allVars:
print x.VariableCode + ": " + x.VariableNameCV
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# Get all of the people from the database
allPeople = read.getPeople()
for x in allPeople:
print x.PersonFirstName + " " + x.PersonLastName
try:
print "\n-------- Information about an Affiliation ---------"
allaff = read.getAllAffiliations()
for x in allaff:
print x.PersonObj.PersonFirstName + ": " + str(x.OrganizationID)
except Exception as e:
print "Unable to demo getAllAffiliations", e
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allaff = read.getAllAffiliations()
type(allaff)
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from odm2api.ODM2.models import SamplingFeatures
read._session.query(SamplingFeatures).filter_by(SamplingFeatureTypeCV='Site').all()
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read.getSamplingFeaturesByType('Site')
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# 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
except Exception as e:
print "Unable to demo getSamplingFeaturesByType", e
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read.getSamplingFeatures()
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read.getSamplingFeatureByCode('USU-LBR-Mendon')
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# Now get the SamplingFeature object for a SamplingFeature code
sf = read.getSamplingFeatureByCode('USU-LBR-Mendon')
# vars(sf)
# 1/31/2016: Leads to error with latest from odm2api master:
# "TypeError: vars() argument must have __dict__ attribute"
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print sf, "\n"
print type(sf)
print type(sf.FeatureGeometry)
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vars(sf.FeatureGeometry)
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sf.FeatureGeometry.__doc__
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sf.FeatureGeometry.geom_wkb, sf.FeatureGeometry.geom_wkt
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type(sf.shape()), sf.shape().wkt
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# Drill down and get objects linked by foreign keys
print "\n------------ Foreign Key Example --------- \n",
try:
# Call getResults, but return only the first result
firstResult = read.getResults()[0]
action_firstResult = firstResult.FeatureActionObj.ActionObj
print "The FeatureAction object for the Result is: ", firstResult.FeatureActionObj
print "The Action object for the Result is: ", action_firstResult
print ("\nThe following are some of the attributes for the Action that created the Result: \n" +
"ActionTypeCV: " + action_firstResult.ActionTypeCV + "\n" +
"ActionDescription: " + action_firstResult.ActionDescription + "\n" +
"BeginDateTime: " + str(action_firstResult.BeginDateTime) + "\n" +
"EndDateTime: " + str(action_firstResult.EndDateTime) + "\n" +
"MethodName: " + action_firstResult.MethodObj.MethodName + "\n" +
"MethodDescription: " + action_firstResult.MethodObj.MethodDescription)
except Exception as e:
print "Unable to demo Foreign Key Example: ", e
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# Now get a particular Result using a ResultID
print "\n------- Example of Retrieving Attributes of a Time Series Result -------"
try:
tsResult = read.getTimeSeriesResultByResultId(1)
# Get the site information by drilling down
sf_tsResult = tsResult.ResultObj.FeatureActionObj.SamplingFeatureObj
print(
"Some of the attributes for the TimeSeriesResult retrieved using getTimeSeriesResultByResultID(): \n" +
"ResultTypeCV: " + tsResult.ResultObj.ResultTypeCV + "\n" +
# Get the ProcessingLevel from the TimeSeriesResult's ProcessingLevel object
"ProcessingLevel: " + tsResult.ResultObj.ProcessingLevelObj.Definition + "\n" +
"SampledMedium: " + tsResult.ResultObj.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" +
# Get the site information by drilling down
"Elevation_m: " + str(sf_tsResult.Elevation_m) + "\n" +
"SamplingFeature: " + sf_tsResult.SamplingFeatureCode + " - " +
sf_tsResult.SamplingFeatureName)
except Exception as e:
print "Unable to demo Example of retrieving Attributes of a time Series Result: ", e
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tsResult = read.getTimeSeriesResultByResultId(1)
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type(tsResult), vars(tsResult)
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vars(tsResult.ResultObj)
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# 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
# Print a few Time Series Values to the console
# tsValues.set_index('ValueDateTime', inplace=True)
tsValues.head()
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# 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)
except Exception as e:
print "Unable to demo plotting of tsValues: ", e
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