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A relaxed wrapper for FISS and dalmatian

Project description

Lapdog

PyPI

A relaxed wrapper for dalmatian and FISS

Prerequisites

  • Lapdog requires MacOS or Linux. Windows is not officially supported
  • Lapdog requires Python >= 3.3
  • Lapdog requires the Google Cloud SDK, which can be installed here.
    • Your gcloud --version should be at least 241.0.0. If it is not, please run gcloud components update
  • Lapdog uses your Gcloud application-default credentials
    • Use gcloud auth application-default login and gcloud config set account {account} before running Lapdog
  • Lapdog requires the Alpha and Beta suite for Gcloud
    • Alpha and Beta suite can be installed with gcloud components install alpha beta
  • (Optional) The Lapdog User Interface requires node and npm, which can be installed using your system's package manager
    • MacOS: brew install node npm
    • Linux: Install through system package manager or from source
    • Lapdog requires node --version >= 10.15.1
    • Lapdog requires npm --version >= 6.4.1

Installing

  1. Install lapdog via pip: pip install lapdog
    • If you already have lapdog installed, you can upgrade it with pip install --upgrade lapdog
    • If you encounter an error with PyYAML see the PyYaml Note below
  2. (Optional) Enable the Lapdog User Interface:
    • The UI runs locally by default. If you are installing Lapdog on a server, you'll need to set up an SSH tunnel for ports 4200 and 4201
    • Install node and npm if you don't already have them installed
      • If you're on Mac OS, run brew install node npm
    • Run lapdog ui --install. This may take a while

Usage

  1. lapdog may be imported within python as a drop-in replacement for dalmatian
    • lapdog presents a superset of features available in dalmatian
    • WorkspaceManagers in lapdog cache data when communicating with Firecloud. If Firecloud experiences an intermittent failure, the WorkspaceManager may be able to continue running in offline mode. Calling WorkspaceManager.sync() will reconnect to Firecloud, pushing out any data updates that were queued while in offline mode
    • WorkspaceManagers in lapdog present the execution api via WorkspaceManager.execute(). Executions differ from submissions in that they run directly on Google and results are uploaded back to Firecloud afterwards
  2. lapdog may be used as a command line tool.
    • The tool provides the necessary functions to create a workspace, fill it with data, import or upload methods and configurations, and submit jobs (or execute them directly)
    • Run lapdog --help to get the list of available commands
  3. lapdog may be used via an interactive user interface which serves to run and monitor lapdog executions
    • Run lapdog ui to launch the user interface

Job Execution

Lapdog executes jobs through dedicated Google Projects ("Engines") for each FireCloud Namespace. A Lapdog Engine can only be initialized for a given Namespace by a billing account admin. To initialize a new Engine, contact your Namespace admin and ask them to run lapdog initialize-project.

After an Engine is initialized, you will have to register with it:

  • The Lapdog User Interface will automatically register you when you load a workspace in a namespace that you're not registered to
  • The Lapdog python module supports manual registration
    • When you create a WorkspaceManager in an unregistered Namespace, you will get a warning
    • You can also check your registration status by checking the value of WorkspaceManager.gateway.registered
    • You can then register by using WorkspaceManager.gateway.register()
    • If registration fails due to any FireCloud errors, simply wait a few minutes then try calling register() again
  • The Lapdog CLI does not support registration. You can register through the UI or python module

Workspace Permissions

In the UI, at the bottom of every page, you will find a firecloud.org email. This is a proxy group email which contains you, and all your service accounts. To allow the Lapdog Engine to run jobs, that proxy group email must be granted WRITE access to FireCloud workspaces where jobs will run. You may grant the group READ access to workspaces where data will be read from, but jobs cannot execute in workspaces without WRITE permissions. The proxy group email can be found by calling lapdog.cloud.proxy_group_for_user(YOUR_EMAIL).

NOTE: Due to a bug in FireCloud, permissions will not be granted if the group was already granted access to a workspace before you registered to that namespace's Lapdog Engine. If your proxy email definitely was granted access to a workspace, but your jobs are still failing with permissions errors, try removing access and then re-granting it. You can see FireCloud's response to this bug report here


Roadmap

See the milestones page to read the development roadmap.

Pro/Con with Firecloud

Pros
  • Each submission has a dedicated Cromwell instance. Your jobs will never queue, unless you hit a Google usage quota
  • Lapdog supports Requester Pays buckets and GPUs
  • Workspace cache: Lapdog caches most data received from Firecloud.
    • In the event of a Firecloud error, Lapdog will attempt to keep running by using it's cached data. Any data updates will by pushed back to Firecloud when the workspace is synced
  • Data caches: The Lapdog API caches data sent to the UI and read from Google
    • These caches greatly improve UI performance by storing results whenever possible
  • Streamlined UI: The Lapdog UI was built with efficiency in mind
  • Quality of life features:
    • Save time updating methods. Set methodRepoMethod.methodVersion to "latest" and let Lapdog figure out what the snapshot ID is
    • Easy data uploads. Call prepare_entity_df on a DataFrame before uploading to Firecloud. Any local filepaths will be uploaded to the workspace's bucket in the background and a new DataFrame will be returned containing the new gs:// paths
    • Automatic reference uploads. When you call update_attributes, any values which refer to local filepaths will be uploaded in the background (just like prepare_entity_df). update_attributes now returns a dictionary containing the attributes exactly as uploaded
Cons
  • You pay an additional 5¢/hour fee for each submission to run the Cromwell server
  • There is no call cache in Lapdog yet. This is still in development
  • Submission results must be manually uploaded to Firecloud by clicking the Upload Results button in the UI.
  • There are small overhead costs billed to the Lapdog Engine for operation. These costs are for calls to the API and for storage of metadata, both of which should be very cheap

PyYAML Note

Often, when installing Lapdog, the installation fails when upgrading PyYAML because it is unable to uninstall the current PyYAML version.

This is because some older versions of PyYAML were distributed through distutils which prevents packages from being uninstalled. New versions of PyYAML are distributed through setuptools which can be successfully uninstalled.

To resolve this issue, navigate to your Python site-packages directory. The site-packages directory usually ends with .../lib/python{version}/site-packages/. The exact location depends on your platform, environment manager, and python configuration.

  • For anaconda, this path is within anaconda's installation folder: /{path to anaconda}/envs/{environment}/lib/python{version}/site-packages
  • For virtualenvs, this path is within the environment's installation folder: /{path to environment}/lib/python{version}/site-packages
  • For system python on Unix systems: /usr/local/lib/python{version}/site-packages

An easy way to locate this folder is to open python and then:

import yaml
yaml

This expression will evaluate and print the path to the yaml module, which will be within your site-packages directory.

After locating the site-packages directory, you must remove the following two directories:

  • .../site-packages/yaml/
  • .../site-packages/PyYAML*.egg-info

Once removed, you can try the installation command for lapdog again.

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