Full working example of connecting Netezza from Java and python

Before start connecting you must make sure you can access the Netezza database and table from the machine where you are trying to run Java and or Python samples.

Connecting Netezza server from Python Sample

Check out my Ipython Jupyter Notebook with Python Sample

Step 1: Importing python jaydebeapi library

import jaydebeapi

Step 2: Setting Database connection settings

dsn_database = "avkash"            
dsn_hostname = "172.16.181.131" 
dsn_port = "5480"                
dsn_uid = "admin"        
dsn_pwd = "password"      
jdbc_driver_name = "org.netezza.Driver"
jdbc_driver_loc = "/Users/avkashchauhan/learn/customers/netezza/nzjdbc3.jar"
###jdbc:netezza://" + server + "/" + dbName ;
connection_string='jdbc:netezza://'+dsn_hostname+':'+dsn_port+'/'+dsn_database
url = '{0}:user={1};password={2}'.format(connection_string, dsn_uid, dsn_pwd)
print("URL: " + url)
print("Connection String: " + connection_string)

Step 3:Creating Database Connection

conn = jaydebeapi.connect("org.netezza.Driver", connection_string, {'user': dsn_uid, 'password': dsn_pwd},
                         jars = "/Users/avkashchauhan/learn/customers/netezza/nzjdbc3.jar")
curs = conn.cursor()

Step 4:Processing SQL Query

curs.execute("select * from allusers")
result = curs.fetchall()
print("Total records: " + str(len(result)))
print(result[0])

Step 5: Printing all records

for i in range(len(result)):
    print(result[i])

Step 6: Closing all connections

curs.close()
conn.close()

Connecting Netezza server from Java Code Sample

Step 1: Have the Netezza driver as nzjdbc3.jar in a folder.

Step 2: Create netezzaJdbcMain.java as below in the same folder where nzjdbc3.jar is placed.

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
public class netezzaJdbcMain {
    public static void main(String[] args) {
        String server = "x.x.x.x";
        String port = "5480";
        String dbName = "_db_name_";
        String url = "jdbc:netezza://" + server + "/" + dbName ;
        String user = "admin";
        String pwd = "password";
        String schema = "db_schema";
        Connection conn = null;
        Statement st = null;
        ResultSet rs = null;
        try {
            Class.forName("org.netezza.Driver");
            System.out.println(" Connecting ... ");
            conn = DriverManager.getConnection(url, user, pwd);
            System.out.println(" Connected "+conn);
            
            String sql = "select * from allusers";
            st = conn.createStatement();
            rs = st.executeQuery(sql);

            System.out.println("Printing result...");
            int i = 0;
            while (rs.next()) {
                String userName = rs.getString("name");
                int year = rs.getInt("age");
                System.out.println("User: " + userName +
                        ", age is: " + year);
                i++;
            }
            if (i==0){
                System.out.println(" No data found");
            }
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            try {
                if( rs != null) 
                    rs.close();
                if( st!= null)
                    st.close();
                if( conn != null)
                    conn.close();
            } catch (SQLException e1) {
                    e1.printStackTrace();
                }
        }
    }
}

Step 3: Compile code as below:

$ javac -cp nzjdbc3.jar -J-Xmx2g -J-XX:MaxPermSize=128m netezzaJdbcMin.java                                                                                                                                
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=128m; support was removed in 8.0

Note: You should see your main class is compiled without any problem.

Step 4: Run compiled class as below:

$ java -cp .:nzjdbc3.jar netezzaJdbcMain

 Connecting ...
 Connected org.netezza.sql.NzConnection@3feba861
Printing result...
User: John                , age is: 30
User: Jason               , age is: 26
User: Jim                 , age is: 20
User: Kyle                , age is: 21
User: Kim                 , age is: 27

Note: You will see results something as above.

Thats it, enjoy!!

Advertisements

Python example of building GLM, GBM and Random Forest Binomial Model with H2O

Here is an example of using H2O machine learning library and then building GLM, GBM and Distributed Random Forest models for categorical response variable.

Lets import h2o library and initialize the H2O machine learning cluster:

import h2o
h2o.init()

Importing dataset and getting familiar with it:

df = h2o.import_file("https://raw.githubusercontent.com/h2oai/sparkling-water/master/examples/smalldata/prostate.csv")
df.summary()
df.col_names

Lets configure our predictors and response variables from the ingested dataset:

y = 'CAPSULE'
x = df.col_names
x.remove(y)
print("Response = " + y)
print("Pridictors = " + str(x))

Now we need to set the response column as categorical or factor:

df['CAPSULE'] = df['CAPSULE'].asfactor()

Now we will the levels in our response variable:

 

df['CAPSULE'].levels()
[['0', '1']]

Note: Because there are only 2 levels or values, the model will be called Binomial model.

Now we will split our dataset into training, validation and testing datasets:

train, valid, test = df.split_frame(ratios=[.8, .1])
print(df.shape)
print(train.shape)
print(valid.shape)
print(test.shape)

Lets build Generalized Linear Regression (Logistic – response variable is categorical) model first:

from h2o.estimators.glm import H2OGeneralizedLinearEstimator
glm_logistic = H2OGeneralizedLinearEstimator(family = "binomial")
glm_logistic.train(x=x, y= y, training_frame=train, validation_frame=valid, 
 model_id="glm_logistic")

Now we will take a look at few model metrics:

glm_logistic.varimp()
Warning: This model doesn't have variable importances

Lets have a look at model coefficients:

glm_logistic.coef()

Lets perform the prediction using the testing dataset:

glm_logistic.predict(test_data=test)

Now we are checking the model performance metrics “rmse” based on testing and other datasets:

print(glm_logistic.model_performance(test_data=test).rmse())
print(glm_logistic.model_performance(test_data=valid).rmse())
print(glm_logistic.model_performance(test_data=train).rmse())

Now we are checking the model performance metrics “r2” based on testing and other datasets:

print(glm.model_performance(test_data=test).r2())
print(glm.model_performance(test_data=valid).r2())
print(glm.model_performance(test_data=train).r2())

Lets build Gradient Boosting Model now:

from h2o.estimators.gbm import H2OGradientBoostingEstimator
gbm = H2OGradientBoostingEstimator()
gbm.train(x=x, y =y, training_frame=train, validation_frame=valid)

Now get to know our model metrics, starting with confusion metrics first:

gbm.confusion_matrix()

Now have a look at variable importance plots:

gbm.varimp_plot()

Now have a look at the variable importance table:

gbm.varimp()

Lets build Distributed Random Forest model:

from h2o.estimators.random_forest import H2ORandomForestEstimator
drf = H2ORandomForestEstimator()
drf.train(x=x, y = y, training_frame=train, validation_frame=valid)

lets understand random forest model metrics starting confusion metrics:

drf.confusion_matrix()

We can have a look at gains and lift table also:

drf.gains_lift()

Note:

  • We can get all model metrics as other model type as applied.
  • We can also get model perform based on training, validation and testing data for all models.

Thats it, enjoy!!

 

Visualizing H2O GBM and Random Forest MOJO Models Trees in python

In this example we will build a tree based model first using H2O machine learning library and the save that model as MOJO. Using GraphViz/Dot library we will extract individual trees/cross validated model trees from the MOJO and visualize them. If you are new to H2O MOJO model, learn here.

You can also get full working Ipython Notebook for this example from here.

Lets build the model first using H2O GBM algorithm. You can also use Distributed Random Forest Model as well for tree visualization.

Let’s first import key python models:

import h2o
import subprocess
from IPython.display import Image

Now we will be building GBM Model using a public PROSTATE dataset:

h2o.init()
df = h2o.import_file('https://raw.githubusercontent.com/h2oai/sparkling-water/master/examples/smalldata/prostate.csv')
y = 'CAPSULE'
x = df.col_names
x.remove(y)
df[y] = df[y].asfactor()
train, valid, test = df.split_frame(ratios=[.8,.1])
from h2o.estimators.gbm import H2OGradientBoostingEstimator
gbm_cv3 = H2OGradientBoostingEstimator(nfolds=3)
gbm_cv3.train(x=x, y=y, training_frame=train)

## Getting all cross validated models 
all_models = gbm_cv3.cross_validation_models()
print("Total cross validation models: " + str(len(all_models)))

Now lets set all the default parameters to create the graph tree first and then tree images (in PNG format) in the local disk. Make sure you have a writable path where you can create and save these intermediate files. You also need to provide the path for latest H2O (h2o.jar) which is used to generate MOJO Model.

mojo_file_name = "/Users/avkashchauhan/Downloads/my_gbm_mojo.zip"
h2o_jar_path= '/Users/avkashchauhan/tools/h2o-3/h2o-3.14.0.3/h2o.jar'
mojo_full_path = mojo_file_name
gv_file_path = "/Users/avkashchauhan/Downloads/my_gbm_graph.gv"

Now lets definie Image file name which we will generate from the Tree ID.  Based on Tree ID the image file will have my_gbm_tree_ID.png file name

image_file_name = "/Users/avkashchauhan/Downloads/my_gbm_tree"
Now we will be downloading GBM MOJO Model by saving to disk:
 gbm_cv3.download_mojo(mojo_file_name)

Now lets define the function to generate graphViz tree from the saved MOJO model:

def generateTree(h2o_jar_path, mojo_full_path, gv_file_path, image_file_path, tree_id = 0):
    image_file_path = image_file_path + "_" + str(tree_id) + ".png"
    result = subprocess.call(["java", "-cp", h2o_jar_path, "hex.genmodel.tools.PrintMojo", "--tree", str(tree_id), "-i", mojo_full_path , "-o", gv_file_path ], shell=False)
    result = subprocess.call(["ls",gv_file_path], shell = False)
    if result is 0:
        print("Success: Graphviz file " + gv_file_path + " is generated.")
    else: 
        print("Error: Graphviz file " + gv_file_path + " could not be generated.")

Now lets defined the method to generate Tree image as PNG from the saved GraphViz tree:

def generateTreeImage(gv_file_path, image_file_path, tree_id):
    image_file_path = image_file_path + "_" + str(tree_id) + ".png"
    result = subprocess.call(["dot", "-Tpng", gv_file_path, "-o", image_file_path], shell=False)
    result = subprocess.call(["ls",image_file_path], shell = False)
    if result is 0:
        print("Success: Image File " + image_file_path + " is generated.")
        print("Now you can execute the follow line as-it-is to see the tree graph:") 
        print("Image(filename='" + image_file_path + "\')")
    else:
        print("Error: Image file " + image_file_path + " could not be generated.")

Note: I had to write 2 steps process above because If I put all in 1 step the process hung after graphviz is created.

Now lets generate tree by passing all parameters defined above and proper TREE ID as the last parameter.

#Just change the tree id in the function below to get which particular tree you want
generateTree(h2o_jar_path, mojo_full_path, gv_file_path, image_file_name, 3)

Now we will be generating PNG Tree Image from the saved GraphViz content.

generateTreeImage(gv_file_path, image_file_name, 3)
# Note: If this step hangs, you can look at "dot" active process in osx and try killing it

Lets visualize the main model tree:

# Just pass the Tree Image file name depending on your tree
Image(filename='/Users/avkashchauhan/Downloads/my_gbm_tree_0.png')

tree-0

Lets Visualize the first Cross Validation tree (Cross Validation ID- 1)

# Just pass the Tree Image file name depending on your tree
Image(filename='/Users/avkashchauhan/Downloads/my_gbm_tree_1.png')

tree-1

Lets Visualize the first Cross Validation tree (Cross Validation ID- 2)

# Just pass the Tree Image file name depending on your tree
Image(filename='/Users/avkashchauhan/Downloads/my_gbm_tree_2.png')

tree-2

Lets Visualize the first Cross Validation tree (Cross Validation ID- 3)

Just pass the Tree Image file name depending on your tree

Image(filename=’/Users/avkashchauhan/Downloads/my_gbm_tree_3.png’)

tree-3

After looking at these tree, you can visualize how the decision are made.

Helpful documentation:

Thats it, enjoy!!

Reading nested parquet file in Scala and exporting to CSV

Recently we were working on a problem where the parquet compressed file had lots of nested tables and some of the tables had columns with array type and our objective was to read it and save it to CSV.

We wrote a script in Scala which does the following

  • Handles nested parquet compressed content
  • Look for columns as “Array” and then remove those columns

Here is a the script

def flattenSchema(schema: StructType, prefix: String = null) : Array[Column] = {
  schema.fields.flatMap(f => {
    val colPath = if (prefix == null) s"`${f.name}`" else s"${prefix}.`${f.name}`"

    f.dataType match {
      case st: StructType => flattenSchema(st, colPath)
      // Skip user defined types like array or vectors
      case x if x.isInstanceOf[ArrayType] => Array.empty[Column]
      case _ => Array(col(colPath).alias(colPath.replaceAll("[.`]", "_")))
    }
  })
}

Here are the all the steps you would need to take while reading the parquet compressed content and then exporting it to disk as CSV.

val spark = new org.apache.spark.sql.SQLContext(sc)
import org.apache.spark.sql.types._
import org.apache.spark.sql.Column
import org.apache.spark.sql.types._
import org.apache.spark.sql.functions._

scala> :paste
// Entering paste mode (ctrl-D to finish)

def flattenSchema(schema: StructType, prefix: String = null) : Array[Column] = {
  schema.fields.flatMap(f => {
    val colPath = if (prefix == null) s"`${f.name}`" else s"${prefix}.`${f.name}`"

    f.dataType match {
      case st: StructType => flattenSchema(st, colPath)
      // Skip user defined types like array or vectors
      case x if x.isInstanceOf[ArrayType] => Array.empty[Column]
      case _ => Array(col(colPath).alias(colPath.replaceAll("[.`]", "_")))
    }
  })
}

// Exiting paste mode, now interpreting.

flattenSchema: (schema: org.apache.spark.sql.types.StructType, prefix: String)Array[org.apache.spark.sql.Column]

scala >

val df = spark.read.parquet("/user/avkash/test.parquet")

df.select(flattenSchema(df.schema):_*).write.format("com.databricks.spark.csv").save("/Users/avkashchauhan/Downloads/saveit/result.csv")

If you want to see the full working scripts with output you can visit any of the following link based on your Spark Version:

  • Here is the full working demo in Spark 2.1.0
  • Here is the full working demo in Spark 1.6.x.

We got some help from the StackOverflow discussion here. Michal K and Michal M helped me to write above solution.

Thats it, enjoy!!

Stacked Ensemble Model in Scala using H2O GBM and Deep Learning Models

In this full Scala sample we will be using H2O Stacked Ensembles algorithm. Stacked ensemble is a process of building models of various types first with cross-validation and keep fold columns for each model. In the next step building the stacked ensemble model using all the CV folds. You can learn more about Stacked Ensembles here.

In this Stacked Ensemble we will be using GBM and Deep Learning Algorithms and then finally building the Stacked Ensemble model using the GBM and Deep Learning models.

First lets import key classes specific to H2O:

import org.apache.spark.h2o._
import water.Key
import java.io.File

Now we will create H2O context so we can call key H2O function specific to data ingest and Deep Learning algorithms:

val h2oContext = H2OContext.getOrCreate(sc)
import h2oContext._
import h2oContext.implicits._

Lets import data from local file system as H2O Data Frame:

val prostateData = new H2OFrame(new File("/Users/avkashchauhan/src/github.com/h2oai/sparkling-water/examples/smalldata/prostate.csv"))

In this Stacked Ensemble we will be using GBM and Deep Learning Algorithms so lets first build the deep learning model:

import _root_.hex.deeplearning.DeepLearning
import _root_.hex.deeplearning.DeepLearningModel.DeepLearningParameters

val dlParams = new DeepLearningParameters()
dlParams._epochs = 100
dlParams._train = prostateData
dlParams._response_column = 'CAPSULE
dlParams._variable_importances = true
dlParams._nfolds = 5
dlParams._seed = 1111
dlParams._keep_cross_validation_predictions = true;
val dl = new DeepLearning(dlParams, Key.make("dlProstateModel.hex"))
val dlModel = dl.trainModel.get

Now lets build the GBM model:

import _root_.hex.tree.gbm.GBM
import _root_.hex.tree.gbm.GBMModel.GBMParameters

val gbmParams = new GBMParameters()
gbmParams._train = prostateData
gbmParams._response_column = 'CAPSULE
gbmParams._nfolds = 5
gbmParams._seed = 1111
gbmParams._keep_cross_validation_predictions = true;
val gbm = new GBM(gbmParams,Key.make("gbmRegModel.hex"))
val gbmModel = gbm.trainModel().get()

Now build the Stacked Ensemble Models so first we need classes required for Stacked Ensembles as below:

import _root_.hex.Model
import _root_.hex.StackedEnsembleModel
import _root_.hex.ensemble.StackedEnsemble

Now we will define Stacked Ensembles parameters as below:

val stackedEnsembleParameters = new StackedEnsembleModel.StackedEnsembleParameters()
stackedEnsembleParameters._train = prostateData._key
stackedEnsembleParameters._response_column = 'CAPSULE

Now we need to pass all the different algorithms we would want to use in the Stacked Ensemble by passing their keys as below:

type T_MODEL_KEY = Key[Model[_, _ <: Model.Parameters, _ <:Model.Output]]

// Option 1
stackedEnsembleParameters._base_models = Array(gbmRegModel._key.asInstanceOf[T_MODEL_KEY], dlModel._key.asInstanceOf[T_MODEL_KEY])
// Option 2 
stackedEnsembleParameters._base_models = Array(gbmRegModel, dlModel).map(model => model._key.asInstanceOf[T_MODEL_KEY])

// Note: You can choose any of the above option to pass the model keys

Finally defining the stacked ensemble job as below:

val stackedEnsembleJob = new StackedEnsemble(stackedEnsembleParameters)

And as the last steps let build the stacked ensemble model:

val stackedEnsembleModel = stackedEnsembleJob.trainModel().get();

Now we can take a look at our Stacked Ensemble model as below:

stackedEnsembleModel

Thats it, enjoy!!

Helpful content: https://github.com/h2oai/h2o-3/blob/a554bffabda6770386a31d47e05f00543d7b9ac3/h2o-algos/src/test/java/hex/ensemble/StackedEnsembleTest.java

 

Logistic Regression with H2O Deep Learning in Scala

Here is the sample code which show using Feed Forward Network based Deep Learning algorithms from H2O to perform a logistic regression .

First lets import key classes specific to H2O

import org.apache.spark.h2o._
import water.Key
import java.io.File

Now we will create H2O context so we can call key H2O function specific to data ingest and Deep Learning algorithms:

val h2oContext = H2OContext.getOrCreate(sc)
import h2oContext._
import h2oContext.implicits._

Lets import data from local file system as H2O Data Frame:

val prostateData = new H2OFrame(new File("/Users/avkashchauhan/src/github.com/h2oai/sparkling-water/examples/smalldata/prostate.csv"))

Now lets import Deep Learning classes:

import root.hex.deeplearning.DeepLearning
import root.hex.deeplearning.DeepLearningModel.DeepLearningParameters

Now we will define all key parameters specific to H2O Deep Learning Algorithm

val dlParams = new DeepLearningParameters()
dlParams._epochs = 100
dlParams._train = prostateData
dlParams._response_column = 'CAPSULE
dlParams._variable_importances = true
dlParams._nfolds = 5
dlParams._seed = 1111
dlParams._keep_cross_validation_predictions = true;

Now we will create the Deep Learning Algorithm key first and then start the deep learning algorithm in blocking mode:

val dl = new DeepLearning(dlParams, Key.make("dlProstateModel.hex"))
val dlModel = dl.trainModel.get()

Lets learn more about our model:

dlModel

Now we can perform the prediction by passing an H2O Dataframe (Here I am simply passing the original data frame however you can load your test  data frame and pass it as H2O frame to perform prediction.):

val predictionH2OFrame = dlModel.score(prostateData)('predict)
val predictionsFromModel = asRDD[DoubleHolder](predictionH2OFrame).collect.map(_.result.getOrElse(Double.NaN))

Thats it, enjoy!!

 

 

H2O AutoML examples in python and Scala

AutoML is included into H2O version 3.14.0.1 and above. You can learn more about AutoML in the H2O blog here.

H2O’s AutoML can be used for automating a large part of the machine learning workflow, which includes automatic training and tuning of many models within a user-specified time-limit. The user can also use a performance metric-based stopping criterion for the AutoML process rather than a specific time constraint. Stacked Ensembles will be automatically trained on the collection individual models to produce a highly predictive ensemble model which, in most cases, will be the top performing model in the AutoML Leaderboard.

Here is the full working python code taken from here:

import h2o
from h2o.automl import H2OAutoML

h2o.init()
df = h2o.import_file("https://raw.githubusercontent.com/h2oai/sparkling-water/master/examples/smalldata/prostate.csv")
train, test = df.split_frame(ratios=[.9])
# Identify predictors and response
x = train.columns
y = "CAPSULE"
x.remove(y)

# For binary classification, response should be a factor
train[y] = train[y].asfactor()
test[y] = test[y].asfactor()

# Run AutoML for 60 seconds
aml = H2OAutoML(max_runtime_secs = 60)
aml.train(x = x, y = y, training_frame = train, leaderboard_frame = test)

# View the AutoML Leaderboard
aml.leaderboard
aml.leader

# To generate predictions on a test set, use `"H2OAutoML"` object, or on the leader model object directly as below:
preds = aml.predict(test)
# or
preds = aml.leader.predict(test)

Here is the full working Scala code:

import ai.h2o.automl.AutoML;
import ai.h2o.automl.AutoMLBuildSpec
import org.apache.spark.h2o._
val h2oContext = H2OContext.getOrCreate(sc)
import h2oContext._
import java.io.File
import h2oContext.implicits._
import water.Key
val prostateData = new H2OFrame(new File("/Users/avkashchauhan/src/github.com/h2oai/sparkling-water/examples/smalldata/prostate.csv"))
val autoMLBuildSpec = new AutoMLBuildSpec()
autoMLBuildSpec.input_spec.training_frame = prostateData
autoMLBuildSpec.input_spec.response_column = "CAPSULE";
autoMLBuildSpec.build_control.loss = "AUTO"
autoMLBuildSpec.build_control.stopping_criteria.set_max_runtime_secs(5)
import java.util.Date;
val aml = AutoML.makeAutoML(Key.make(), new Date(), autoMLBuildSpec)
AutoML.startAutoML(aml)
// Note: In some cases the above call is non-blocking
// So using the following alternative function will block the next commmand, untill the exection of action command
AutoML.startAutoML(autoMLBuildSpec).get()  ## This is forced blocking call
aml.leader
aml.leaderboard

IF you want to see the full code execution visit here.

Thats it, enjoy!!