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Ingest client for the Boss

Project description

Boss Ingest Client

A Python command line application for performing distributed ingest of data into the Boss

theBoss.io Hex.pm Code Climate Coverage Status CircleCI

Overview

The ingest client application lets users move data from local storage into the Boss, quickly and reliably. It supports Python 3.6 and later. It uses a JSON configuration file to define ingest jobs, and a plugin system to support any local file organization.

Two types of ingest are supported:

  • Tile based
  • Volumetric

Tile Based Ingests

This ingest type uploads data in 2D image tiles. It supports many different formats, but it is not as efficient as volumetric ingests.

Volumetric Ingests

This type of ingest uploads data in the Boss' native storage format. 3D cuboids, that are 512, 512, 16, in x, y, z, respectively, are uploaded by the ingest client.

Installation

  • Use virtualenv to isolate the ingest client from your system Python installation

     virtualenv ingest-env
     . ingest-env/bin/activate
    
     mkvirtualenv ingest-env
    
  • Install the ingest client

     pip install boss-ingest
    

    If you get errors installing Pillow, it is most likely because you do not have all of Pillow's dependencies installed. Check out the "Installing Pillow Dependencies" section below for help.

Configuring Credentials

You must provide the ingest client with your Boss API token so it can make authenticated requests on your behalf.

Also remember that you must have write permissions to the resource (collection, experiment, and channel) where data is to be written, as specified in the ingest job configuration file. If you created the resources you will automatically have access.

There are three ways to provide your API token to the ingest client. The ingest client will try to use the first token it finds in the following order:

  1. Via command line arguments

    • You can directly pass your token to the ingest client when starting it from the command line. See the Usage section below.
  2. Via the intern environment variables

    • The ingest client can also reuse environment variables used to configure intern to set your API token
      export INTERN_TOKEN=<you_token_here>
    
  3. Via the intern configuration file

    • If you have already installed intern and added your API token to its configuration file, the ingest client will automatically load the token

Usage

The ingest client is installed as a system script and can be called from the command line directly as boss-ingest.

An ingest job is the act of uploading a dataset or sub-region of a dataset to the Boss. You do not need to upload an entire dataset at once if desired, and can specify in both space and time what data is to be written.

There are three primary operations you can perform with the ingest client: Create, Join, and Cancel an ingest job

  • Creating a NEW Ingest Job

    • Populate an ingest job configuration file to specify the correct plugins for your data, the Boss resource to use, the extent of the dataset to be ingested, and the tile size.

    • Refer to the Creating Configuration Files wiki page for more detail on how to do this. Also, a helper script to create the Boss resources necessary for an ingest is found here.

    • Assuming you have created a configuration file, simply call the ingest client

       boss-ingest <absolute_path_to_config_file>
      
    • After creating the new Ingest Job, the client will print the ingest job ID and it will be also logged.

      Remember this ID if you wish to restart the client or run the client on additional nodes for increased throughput

    • You have 14 days to complete uploading the data for this ingest job before the upload work queue automatically gets purged

  • Joining an EXISTING Ingest Job

    • You can join an existing ingest job and start uploading data any time after it has been created. This can be useful if the client has crashed, or if you want to run the client on additional nodes in parallel.

       boss-ingest <absolute_path_to_config_file> --job-id <ingest_job_id>
      

      or

       boss-ingest <absolute_path_to_config_file> -j <ingest_job_id>
      
  • Cancelling an Ingest Job

    • Sometimes you may want to stop an ingest job. You can do this by "cancelling" it. Currently this will delete all tiles that have been uploaded but not ingested into the Boss yet. Any data that made its way through the ingest pipeline will remain. Also temporary queues will be purged and deleted.

      boss-ingest --cancel --job-id <ingest_job_id>
      

      or

      boss-ingest -c -j <ingest_job_id>
      

      If you are working with the non-production Boss instance (api.theboss.io), then you can provide a configuration file specifying the desired host as the commands shown above will default to the production Boss environment.

      boss-ingest <absolute_path_to_config_file> -c -j <ingest_job_id>
      
  • Completing an Ingest Job

    • The ingest client now automatically "completes" an ingest job when the upload queue has been completely processed. This operation will ensure that all data has made it into the Boss, clean up temporary resources that have been provisioned by the Boss, and update the status of the ingest job. Note, it can take 5-60 seconds to finish completing a job.

      If you do not want the client to automatically compete the job for you, you can add a flag to disable this functionality, as shown below

      boss-ingest <absolute_path_to_config_file> --manual-complete
      

      or

      boss-ingest  <absolute_path_to_config_file> -m
      
  • Multiprocessing

    • You can choose to have multiple upload engines start in parallel processes by setting the -p argument as outlined in the example below. (Default number of upload processes = 1)

      boss-ingest <absolute_path_to_config_file> --processes_nb <number_of_processes>
      

      or

      boss-ingest <absolute_path_to_config_file> -p <number_of_processes>
      
    • If you are using multiple parallel client processes, you may choose to optionally pass a --ramp_seconds/-r flag with a number of seconds to delay in between creating processes. This is helpful when the source of ingest data needs time to scale (e.g. google cloud storage buckets, or a load-balanced web server).

  • Logging

    • You can choose where to write the log file by specifying and absolute file path suing the -l parameter. If omitted, data is logged in ~/.boss-ingest

      boss-ingest <absolute_path_to_config_file> --log-file <absolute_filename>
      

      or

      boss-ingest <absolute_path_to_config_file> -l <absolute_filename>
      
    • You can also control the logging level. By default it is set to WARNING, although some important information is forced to always log. The INFO level and lower result in very large log files and is not recommended for anything besides development and debug.

      boss-ingest <absolute_path_to_config_file> --log-level <critical|error|warning|info|debug>
      

      or

      boss-ingest <absolute_path_to_config_file> -v <critical|error|warning|info|debug>
      
      

Plugins

To handle the many different ways users can organize and store data, "plugins" are used to perform two operations. The first (Path Processor) is responsible for taking user specified parameters and tile indices provided from the upload task queue to generate an absolute file path to the correct data file associated with the image tile. The second (Tile Processor) is responsible for taking user specified parameters, tile indices, and generated file path to generate a file handle containing the image data. This handle is then used to upload the image tile.

The ingest client wiki on GitHub provides more detailed information on on how to create plugins and which plugins come pre-installed.

If you develop your own plugins, you simply need to make sure they are on your PYTHONPATH before calling boss-ingest

export PYTHONPATH=$PYTHONPATH:/<path_to_modules>

Installing Pillow Dependencies

The ingest client uses Pillow to handle image files. There are several dependencies you may need to install before you can run pip install Pillow. Pillow is installed automatically when you run pip install boss-ingest, so these external dependencies must already be installed for that command to successfully complete.

  • OSX

    Install jpeg and tiff libraries using Homebrew

     brew install libjpeg
     brew install libtiff
    

    Sometimes you may also need to install zlib development packages from XCode

     xcode-select --install
    
  • Linux (Ubuntu)

     sudo apt-get install libjpeg-dev libtiff5-dev zlib1g-dev libfreetype6-dev liblcms2-dev libopenjpeg-dev
    
  • Windows - Untested

Installation for Development

  • mkdir and cd to a directory of your choice

  • Clone the ingest client

     git clone https://github.com/jhuapl-boss/ingest-client.git
    
  • Use virtualenv to isolate the ingest client from your system Python installation

     virtualenv ingest-env
     . ingest-env/bin/activate
    
     mkvirtualenv ingest-env
    
  • Install Python dependencies

     cd ./ingest-client
     pip install -r requirements.txt
    
  • An additional token configuration method via the token.json file is available if you've cloned the ingest-client repository locally

    • Create a token.json file in the root directory of the repo

       vi ./token.json 
      
    • Get your API token. This can be done by visiting the Boss Management Console. After logging in, click on your username in the top right corner, then "API Token".

    • Copy your API token to the token.json file that looks like this:

       {
           "token": "<insert_token_here>",
           "host": "api.theboss.io"
       }
      

Testing

The nose2 library is used to run unit tests. From the ingest-client directory simply invoke nose2.

nose2

We use continuous integration to automatically run tests as well. Future work will expand on testing and add more complex integration testing.

Legal

Use or redistribution of the Boss system in source and/or binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code or binary forms must adhere to the terms and conditions of any applicable software licenses.
  2. End-user documentation or notices, whether included as part of a redistribution or disseminated as part of a legal or scientific disclosure (e.g. publication) or advertisement, must include the following acknowledgement: The Boss software system was designed and developed by the Johns Hopkins University Applied Physics Laboratory (JHU/APL).
  3. The names "The Boss", "JHU/APL", "Johns Hopkins University", "Applied Physics Laboratory", "MICrONS", or "IARPA" must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact BossAdmin@jhuapl.edu.
  4. This source code and library is distributed in the hope that it will be useful, but is provided without any warranty of any kind.

License

If not otherwise marked, all code in this repository falls under the license granted in LICENSE.md.

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