Hari Sekhon PyTools

Hadoop, Spark / PySpark, HBase, Pig, Ambari, IPython and Linux Tools

A few of the Big Data, NoSQL & Linux tools I've written over the years. All programs have --help to list the available options.

For many more tools see the Tools and Advanced Nagios Plugins Collection repos which contains many Hadoop, NoSQL, Web and infrastructure tools and Nagios plugins.

Hari Sekhon

Big Data Contractor, United Kingdom

https://www.linkedin.com/in/harisekhon

Make sure you run `make update` if updating and not just `git pull` as you will often need the latest library submodule and possibly new upstream libraries.

Quick Start

Ready to run Docker image

All programs and their pre-compiled dependencies can be found ready to run on DockerHub.

List all programs:

docker run harisekhon/pytools

Run any given program:

docker run harisekhon/pytools <program> <args>

Automated Build from source

git clone https://github.com/harisekhon/pytools
cd pytools
make

Make sure to read Detailed Build Instructions further down for more information.

Some Hadoop tools with require Jython, see Jython for Hadoop Utils for details.

Usage

All programs come with a --help switch which includes a program description and the list of command line options.

Environment variables are supported for convenience and also to hide credentials from being exposed in the process list eg. $PASSWORD, $TRAVIS_TOKEN. These are indicated in the --help descriptions in brackets next to each option and often have more specific overrides with higher precedence eg. $AMBARI_HOST, $HBASE_HOST take priority over $HOST.

PyTools

Ambari:
- ambari_blueprints.py - Blueprint cluster templating and deployment tool using Ambari API to find and fetch all blueprints or a specific blueprint to local json files, blueprint an existing cluster, or create a new cluster using a blueprint. Sorts and prettifies the resulting JSON template, and optionally strips out the excessive and overly specific configs to create generic more reusable templates. See the ambari_blueprints directory for a variety of Ambari blueprint templates generated by and deployable using this tool
- ambari_ams_*.sh - query the Ambari Metrics Collector API for a given metrics, list all metrics or hosts
- ambari_cancel_all_requests.sh - cancel all ongoing operations using the Ambari API
- ambari_trigger_service_checks.py - trigger service checks using the Ambari API
Hadoop HDFS:
- hadoop_hdfs_time_block_reads.jy - HDFS per-block read timing debugger with datanode and rack locations for a given file or directory tree. Reports the slowest Hadoop datanodes in descending order at the end. Helps find cluster data layer bottlenecks such as slow datanodes, faulty hardware or misconfigured top-of-rack switch ports.
- hadoop_hdfs_files_native_checksums.jy - fetches native HDFS checksums for quicker file comparisons (about 100x faster than doing hdfs dfs -cat | md5sum)
- hadoop_hdfs_files_stats.jy - fetches HDFS file stats. Useful to generate a list of all files in a directory tree showing block size, replication factor, underfilled blocks and small files
HBase:
- hbase_generate_data.py - inserts random generated data in to a given HBase table, with optional skew support with configurable skew percentage. Useful for testing region splitting, balancing, CI tests etc. Outputs stats for number of rows written, time taken, rows per sec and volume per sec written.
- hbase_show_table_region_ranges.py - dumps HBase table region ranges information, useful when pre-splitting tables
- hbase_table_region_row_distribution.py - calculates the distribution of rows across regions in an HBase table, giving per region row counts and % of total rows for the table as well as median and quartile row counts per regions
- hbase_table_row_key_distribution.py - calculates the distribution of row keys by configurable prefix length in an HBase table, giving per prefix row counts and % of total rows for the table as well as median and quartile row counts per prefix
- hbase_compact_tables.py - compacts HBase tables (for off-peak compactions). Defaults to finding and iterating on all tables or takes an optional regex and compacts only matching tables.
- hbase_flush_tables.py - flushes HBase tables. Defaults to finding and iterating on all tables or takes an optional regex and flushes only matching tables.
- hbase_regions_by_*size.py - queries given RegionServers JMX to lists topN regions by storeFileSize or memStoreSize, ascending or descending
- hbase_region_requests.py - calculates requests per second per region across all given RegionServers or average since RegionServer startup, configurable intervals and count, can filter to any combination of reads / writes / total requests per second. Useful for watching more granular region stats to detect region hotspotting
- hbase_regionserver_requests.py - calculates requests per regionserver second across all given regionservers or average since regionserver(s) startup(s), configurable interval and count, can filter to any combination of read, write, total, rpcScan, rpcMutate, rpcMulti, rpcGet, blocked per second. Useful for watching more granular RegionServer stats to detect RegionServer hotspotting
- hbase_regions_least_used.py - finds topN biggest/smallest regions across given RegionServers than have received the least requests (requests below a given threshold)
OpenTSDB:
- opentsdb_import_metric_distribution.py - calculates metric distribution in bulk import file(s) to find data skew and help avoid HBase region hotspotting
- opentsdb_list_metrics.sh - lists OpenTSDB metric names, tagk or tagv from HBase and optionally their created date, sorted ascending
Pig
- pig-text-to-elasticsearch.pig / pig-text-to-solr.pig - bulk index unstructured files in Hadoop to Elasticsearch or Solr / SolrCloud clusters
- pig_udfs.jy - Pig Jython UDFs for Hadoop
ipython-notebook-pyspark.py - per-user authenticated IPython Notebook + PySpark integration to allow each user to auto-create their own password protected IPython Notebook running Spark
Data Format Converters:
- json_to_xml.py - JSON to XML converter
- xml_to_json.py - XML to JSON converter
- json_docs_to_bulk_multiline.py - converts json files to bulk multi-record one-line-per-json-document format for pre-processing and loading to big data systems like Hadoop and MongoDB, can recurse directory trees, and mix json-doc-per-file / bulk-multiline-json / directories / standard input, combines all json documents and outputs bulk-one-json-document-per-line to standard output for convenient command line chaining and redirection, optionally continues on error, collects broken records to standard error for logging and later reprocessing for bulk batch jobs, even supports single quoted json while not technically valid json is used by MongoDB and even handles embedded double quotes in 'single quoted json'
Spark:
- spark_avro_to_parquet.py - PySpark Avro => Parquet converter
- spark_parquet_to_avro.py - PySpark Parquet => Avro converter
- spark_csv_to_avro.py - PySpark CSV => Avro converter, supports both inferred and explicit schemas
- spark_csv_to_parquet.py - PySpark CSV => Parquet converter, supports both inferred and explicit schemas
- spark_json_to_avro.py - PySpark JSON => Avro converter
- spark_json_to_parquet.py - PySpark JSON => Parquet converter
Docker:
- docker_registry_show_tags.py / dockerhub_show_tags.py / quay_show_tags.py - shows tags for docker repos in a docker registry or on DockerHub or Quay.io - Docker CLI doesn't support this yet but it's a very useful thing to be able to see live on the command line or use in shell scripts (use -q/--quiet to return only the tags for easy shell scripting). You can use this to pre-download all tags of a docker image before running tests across versions in a simple bash for loop, eg. docker_pull_all_tags.sh
- dockerhub_search.py - search DockerHub with a configurable number of returned results (official docker search is limited to only 25 results), using --verbose will also show you how many results were returned to the termainal and how many DockerHub has in total (use -q / --quiet to return only the image names for easy shell scripting). This can be used to download all of my DockerHub images in a simple bash for loop eg. docker_pull_all_images.sh and can be chained with dockerhub_show_tags.py to download all tagged versions for all docker images eg. docker_pull_all_images_all_tags.sh
- dockerfiles_check_git*.py - check Git tags & branches align with the containing Dockerfile's ARG *_VERSION
welcome.py - cool spinning welcome message greeting your username and showing last login time and user (there is also a perl version in my Tools repo)
find_duplicate_files.py - finds duplicate files in one or more directory trees via multiple methods including file basename, size, MD5 comparison of same sized files, or bespoke regex capture of partial file basename
find_active_server.py - generic solution to return the first available healthy server or active master in high availability deployments, useful for chaining with single argument tools. Configurable tests include socket, http, https, ping, url and/or regex content match, multi-threaded for speed. Designed to extend tools that only accept a single --host option but for which the technology has later added multi-master support or active-standby masters (eg. Hadoop, HBase) or where you want to query cluster wide information available from any online peer (eg. Elasticsearch)
- The following are simplified specialisations of the above program, just pass host arguments, all the details have been baked in, no switches required
  - find_active_hadoop_namenode.py - finds the active Hadoop Namenode in HDFS HA
  - find_active_hadoop_resource_manager.py - finds the active Hadoop Resource Manager in Yarn HA
  - find_active_hbase_master.py - finds the active HBase Master in HBase HA
  - find_active_hbase_thrift.py - finds the first available HBase Thrift Server (run multiple of these for load balancing)
  - find_active_hbase_stargate.py - finds the first available HBase Stargate rest server (run multiple of these for load balancing)
  - find_active_apache_drill.py - finds the first available Apache Drill node
  - find_active_impala*.py - finds the first available Impala node of either Impalad, Catalog or Statestore
  - find_active_presto_coordinator.py - finds the first available Presto Coordinator
  - find_active_oozie.py - finds the first active Oozie server
  - find_active_solrcloud.py - finds the first available Solr / SolrCloud node
  - find_active_elasticsearch.py - finds the first available Elasticsearch node
  - see also: Advanced HAProxy configurations which are part of the Advanced Nagios Plugins Collection
travis_debug_session.py - launches a Travis CI interactive debug build session via Travis API, tracks session creation and drops user straight in to the SSH shell on the remote Travis build, very convenient one shot debug launcher for Travis CI
validate_*.py - validate files, directory trees and/or standard input streams
- supports the following file formats:
  - Avro
  - CSV
  - INI / Java Properties (also detects duplicate sections and duplicate keys within sections)
  - JSON (both normal and json-doc-per-line bulk / big data format as found in MongoDB and Hadoop json data files)
  - LDAP LDIF
  - Parquet
  - XML
  - YAML
- directories are recursed, testing any files with relevant matching extensions (.avro, .csv, json, parquet, .ini/.properties, .ldif, .xml, .yml/.yaml)
- used for Continuous Integration tests of various adjacent Spark data converters as well as configuration files for things like Presto, Ambari, Apache Drill etc found in my DockerHub images Dockerfiles master repo which contains docker builds and configurations for many open source Big Data & Linux technologies

Detailed Build Instructions

Manual Setup

Enter the pytools directory and run git submodule init and git submodule update to fetch my library repo:

git clone https://github.com/harisekhon/pytools
cd pytools
git submodule init
git submodule update
pip install -r requirements.txt

Mac OS X

The automated build also works on Mac OS X but you'll need to download and install Apple XCode. I also recommend you get HomeBrew to install other useful tools and libraries you may need like OpenSSL for development headers and tools such as wget (these are installed automatically if Homebrew is detected on Mac OS X):

brew install openssl wget

CPAN's Crypt::SSLeay may not find the OpenSSL header and error like so:

fatal error: 'openssl/opensslv.h' file not found
#include <openssl/opensslv.h>

In this case, give it the path to the OpenSSL lib to build:

sudo OPENSSL_INCLUDE=/usr/local/opt/openssl/include OPENSSL_LIB=/usr/local/opt/openssl/lib cpan Crypt::SSLeay

then continue with the rest of the build:

make

You may get errors trying to install to Python library paths even as root on newer versions of Mac, sometimes this is caused by pip 10 vs pip 9 and downgrading will work around it:

pip install --upgrade pip==9.0.1
make
pip install --upgrade pip
make

Jython for Hadoop Utils

The 3 Hadoop utility programs listed below require Jython (as well as Hadoop to be installed and correctly configured)

hadoop_hdfs_time_block_reads.jy
hadoop_hdfs_files_native_checksums.jy
hadoop_hdfs_files_stats.jy

Run like so:

jython -J-cp `hadoop classpath` hadoop_hdfs_time_block_reads.jy --help

The -J-cp `hadoop classpath` bit does the right thing in finding the Hadoop java classes required to use the Hadoop APIs.

See below for procedure to install Jython if you don't already have it.

Automated Jython Install

make jython-install

Manual Jython Install

Jython is a simple download and unpack and can be fetched from http://www.jython.org/downloads.html

Then add the Jython untarred directory to the $PATH or specify the /path/to/jythondir/bin/jython explicitly when calling jython.

Configuration for Strict Domain / FQDN validation

Strict validations include host/domain/FQDNs using TLDs which are populated from the official IANA list is done via my PyLib library submodule - see there for details on configuring this to permit custom TLDs like .local or .intranet (both supported by default).

Python SSL certificate verification problems

If you end up with an error like:

./dockerhub_show_tags.py centos ubuntu
[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:765)

It can be caused by an issue with the underlying Python + libraries due to changes in OpenSSL and certificates. One quick fix is to do the following:

pip uninstall -y certifi && pip install certifi==2015.04.28

Updating

Run make update. This will git pull and then git submodule update which is necessary to pick up corresponding library updates.

If you update often and want to just quickly git pull + submodule update but skip rebuilding all those dependencies each time then run make update-no-recompile (will miss new library dependencies - do full make update if you encounter issues).

Testing

Continuous Integration is run on this repo with tests for success and failure scenarios:

unit tests for the custom supporting python library
integration tests of the top level programs using the libraries for things like option parsing
functional tests for the top level programs using local test data and Docker containers

To trigger all tests run:

make test

which will start with the underlying libraries, then move on to top level integration tests and functional tests using docker containers if docker is available.

Contributions

Patches, improvements and even general feedback are welcome in the form of GitHub pull requests and issue tickets.

0xqq / pytools Goto Github PK

pytools's Introduction