Merge branch 'master' of https://github.com/ODM2/ODM2PythonAPI

Conflicts:
	odm2api/ODM2/models_sqlite.py
	odm2api/ODM2/services/readService.py
	tests/test_odm2/test_createservice.py
	tests/test_odm2/test_readservice.py

Author: valentinedwv

.gitignore

@@ -1,6 +1,6 @@
 *.py[cod]
 *~
-.ipynb_checkpoints
+
 
 #  C extensions
 *.so
@@ -40,6 +40,9 @@ nosetests.xml
 
 log
 *.log
-.idea
+
 
 .DS_Store
+.ipynb_checkpoints
+.cache
+.idea

.travis.yml

@@ -1,4 +1,4 @@
-language: python
+git blanguage: python
 sudo: required
 # if the https://travis-ci.org/ODM2/ODM2PythonAPI/requests ever says: missing config
 # validate at: http://lint.travis-ci.org/
@@ -38,17 +38,19 @@ addons:
       - libspatialite-dev
 #  mariadb: '10.1'
 before_script:
-  - ./scripts/mysql_setup.sh
-  - ./scripts/postgres_setup.sh
-  - ./scripts/freetds.sh
+  - ./ci-helpers/mysql_setup.sh
+  - ./ci-helpers/postgres_setup.sh
+  - ./ci-helpers/travis/freetds.sh
+
 
 before_install:
 # python -m pip makes the install go into the virtualenv
-  - python -m pip install pandas
+  - sudo pip install --upgrade pip
+  - sudo python -m pip install pandas
   - export PYMSSQL_BUILD_WITH_BUNDLED_FREETDS=1;python -m  pip install pymssql
 #  - 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 -e git+https://github.com/ODM2/geoalchemy.git@v0.7.4#egg=geoalchemy-0.7.4
   - pip install   .
   - pip install  -r requirements_tests.txt  --allow-external pyodbc --allow-unverified pyodbc
     # pysqlite

Examples/Sample.py

@@ -1,77 +1,76 @@
 __author__ = 'stephanie'
-import sys
-import os
 
 
-import matplotlib.pyplot as plt
-from matplotlib import dates
+
+# import matplotlib.pyplot as plt
+
 
 
-#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/DEV/ODM2/usecases/WOF_to_ODM2/ODM2.sqlite', 2.0)
 
 
 
-#_session = session_factory.getSession()
 
+#_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)
-
+    print ("Successful query")
     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(codes=['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")
@@ -87,20 +86,16 @@
 #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 in sample.py",
+    SamplingFeatureGeotypeCV= "Point", SamplingFeatureTypeCV=sf.SamplingFeatureTypeCV,SamplingFeatureUUID= sf.SamplingFeatureUUID+"2",
+    SiteTypeCV="cave", Latitude= "100", Longitude= "-100", SpatialReferenceID= 0)
+
+    c=create.createSamplingFeature(newsf)
     #session.commit()
-    print("new sampling feature added to database", newsf)
+    print("new sampling feature added to database", c)
 
 except Exception as e :
     print("error adding a sampling feature: " + str(e))
@@ -125,29 +120,29 @@
 
 
 # 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 +154,9 @@
 # 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)

Forms/clsDBConfig.py

@@ -115,6 +115,9 @@ def __init__( self, parent ):
 		self.btnTest.Bind( wx.EVT_BUTTON, self.OnBtnTest )
 		self.btnSave.Bind( wx.EVT_BUTTON, self.OnBtnSave )
 		self.btnCancel.Bind( wx.EVT_BUTTON, self.OnBtnCancel )
+
+		self.btnTest.SetFocus()
+
 
 	def __del__( self ):
 		pass

Forms/frmDBConfig.py

@@ -78,6 +78,7 @@ def validateInput(self, conn_dict):
             if self.service_manager.test_connection(conn_dict):
                 message = "This connection is valid"
                 wx.MessageBox(message, 'Test Connection', wx.OK)
+                self.btn
             else:
                 #TODO add error message if user cannont connect to the database ( not using VPN) but the db is still 1.1.1)
                 if not (self.service_manager.get_db_version(conn_dict)):

README.md

@@ -1,33 +1,52 @@
 ODM2 Python API
 ====
 
-A Python-based application programmer's interface for the Observations Data Model 2 (ODM2) 
+A Python-based application programmer's interface for the [Observations Data Model 2 (ODM2)](http://odm2.org).
 
 [List of current and planned functions included in the API](https://github.com/ODM2/ODM2PythonAPI/blob/master/doc/APIFunctionList.md)
 
-### Installation
+## Installation
 
-Currently the easiest and most reliable way to install the ODM2 Python API (`odm2api`) is using the [Conda package management system](http://conda.pydata.org/docs/) via either [Anaconda](https://www.continuum.io/downloads) or [Miniconda](http://conda.pydata.org/miniconda.html). To create a new `odm2api` environment, first download the conda environment file [condaenvironment_1.yml](https://raw.githubusercontent.com/ODM2/ODM2PythonAPI/master/condaenvironment_1.yml). Then, on a terminal shell:
+The easiest and most reliable way to install the ODM2 Python API (`odm2api`) is using the [Conda package management system](http://conda.pydata.org/docs/) via either [Anaconda](https://www.continuum.io/downloads) or [Miniconda](http://conda.pydata.org/miniconda.html). To start using conda (if it's not your system default), add conda to the PATH; on MacOSX and Linux, it's something like `export PATH=$HOME/miniconda/bin:$PATH`, but the exact path may vary.
 
-1. Add conda to the PATH; on MacOSX and Linux, it's something like `export PATH=$HOME/miniconda/bin:$PATH`, but the exact path may vary.
-2. Go to the directory where `condaenvironment_1.yml` was downloaded.
-3. Create a new conda environment. This command will create an environment called 'odm2api_env1':    
+To activate a conda environment, say, "myenv":
+```bash
+activate myenv  # On Windows
+source activate myenv  # On MacOSX or Linux
+```
 
-  ```bash
-  conda env create -f condaenvironment_1.yml
-  ```
-4. Activate the new environment:    
+**Note:** `odm2api` currently is only tested on Python 2.7. Some changes have been made to support Python 3.x, but they haven't been tested thoroughly.
 
-  ```bash
-  activate odm2api_env1  # On Windows
-  source activate odm2api_env1  # On MacOSX or Linux
-  ```
-5. Install the `odm2api` package into the environment:  
 
-  ```bash
-  pip install --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git
-  ```
-  
-### Credits
+### Latest release, from ODM2 anaconda.org channel
+
+The [latest `odm2api` release](https://github.com/ODM2/ODM2PythonAPI/releases) is available on the [ODM2 anaconda.org channel](https://anaconda.org/odm2/odm2api) for all major OS paltforms (linux, OSX, win32/win64). To install it on an existing conda environment:
+```
+conda install -c odm2 odm2api
+```
+All dependencies are installed, including Pandas and its dependencies (numpy, etc).
+
+To create a new environment "myenv" with the `odm2api` package:
+```
+conda create -n myenv -c odm2 python=2.7 odm2api
+```
+
+### Installing the development version from the `master` branch on github
+
+**Note from 4/26/2016:** These instructions may be slightly outdated. Follow these directions for installing the bleeding edge github master branch, mainly for development and testing purposes.
+
+To create a new environment "myenv" with `odm2api`, first download the conda environment file [condaenvironment_1.yml](https://raw.githubusercontent.com/ODM2/ODM2PythonAPI/master/condaenvironment_1.yml). Go to the directory where `condaenvironment_1.yml` was downloaded. Then, on a terminal shell:
+```bash
+conda env create -n myenv --file py2_conda_environment.yml
+```
+Activate the new environment, then install `odm2api` into the environment:
+```bash
+activate myenv  # On Windows
+source activate myenv  # On MacOSX or Linux
+
+pip install --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git
+```
+
+## Credits
 
 This work was supported by National Science Foundation Grants [EAR-1224638](http://www.nsf.gov/awardsearch/showAward?AWD_ID=1224638) and [ACI-1339834](http://www.nsf.gov/awardsearch/showAward?AWD_ID=1339834). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.