sevenbridges-python documentation!¶

sevenbridges-python is a Python library that provides an interface for the Seven Bridges Platform and Cancer Genomics Cloud public APIs.

The Seven Bridges Platform is a cloud-based environment for conducting bioinformatic analyses. It is a central hub for teams to store, analyze, and jointly interpret their bioinformatic data. The Platform co-locates analysis pipelines alongside the largest genomic datasets to optimize processing, allocating storage and compute resources on demand.

The The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is also a cloud-based computation environment. It was built as one of three pilot systems funded by the National Cancer Institute to explore the paradigm of colocalizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them. The CGC makes more than a petabyte of multi-dimensional data available immediately to authorized researchers. You can add your own data to analyze alongside TCGA using predefined analytical workflows or your own tools.

Content¶

Installation¶

The easiest way to install sevenbridges-python is using pip.

$ pip install sevenbridges-python

Get the Code¶

sevenbridges-python is actively developed on GitHub, where the code is always available.

The easiest way to obtain the source is to clone the public repository:

$ git clone git://github.com/sbg/sevenbridges-python.git

Once you have a copy of the source, you can embed it in your Python package, or install it into your site-packages by invoking:

$ python setup.py install

If you are interested in reviewing this documentation locally, clone the repository and invoke:

::: $ make html

from the docs folder.

Quickstart¶

On this page, you’ll find a reference for the Seven Bridges API Python client.

We encourage you to consult our other API resources:

The Seven Bridges Github repository, okAPI, which includes Python example scripts such as recipes (which allow you to perform specific tasks) and tutorials (which will walk you through entire analyses) via the API. These recipes and tutorials make use of the sevenbridges-python bindings below.
The Seven Bridges API documentation on our Knowledge Center, which includes a reference collection of API requests to help you get started right away.

Authentication and Configuration¶

In order to authenticate with the API, you should pass the following items to sevenbridges-python:

Your authentication token

(b) The API endpoint you will be interacting with. This is either the endpoint for the Seven Bridges Platform or for the Seven Bridges Cancer Genomics Cloud (CGC) or for CAVATICA.

You can find your authentication token on the respective pages:

https://igor.sbgenomics.com/developer for the Seven Bridges Platform
https://cgc.sbgenomics.com/developer for the CGC
https://cavatica.sbgenomics.com/developer for Cavatica

The API endpoints for each environment are:

https://api.sbgenomics.com/v2 for the Seven Bridges Platform
https://cgc-api.sbgenomics.com/v2 for the CGC.
https://cavatica-api.sbgenomics.com/v2 for CAVATICA

Note

We will see below how to supply information about your auth token and endpoint to the library.

For more information about the API, including details of the available parameters for each API call, you should check the API documentation before using this library:

http://docs.sevenbridges.com/docs/the-api for the Seven Bridges Platform.
http://docs.cancergenomicscloud.org/docs/the-cgc-api for the CGC.
http://docs.cavatica.org/docs/the-api for CAVATICA

How to use the Quickstart¶

We recommend that you pay particular attention to the section ‘Managing Projects’ of this Quickstart, since it contains general information on working with any kind of Platform or CGC resource (projects, files, tasks, etc) via the Python methods available in this library.

Initializing the library¶

Once you have obtained your authentication token from one of the URLs listed above, you can initialize the Api object defined by this library by passing in your authentication token and endpoint. There are three methods to do this. Details of each method are given below:

Pass the parameters url and token and optional proxies explicitly when initializing the API object.
Set the API endpoint and token to the environment variables SB_API_ENDPOINT and SB_AUTH_TOKEN respectively.
Use a configuration file $HOME/.sevenbridges/credentials with the defined credentials parameters. If config is used proxy settings will be read from $HOME/.sevenbridges/sevenbridges-python/config .ini like file for section [proxies]

Note

Keep your authentication token safe! It encodes all your credentials on the Platform or CGC. Generally, we recommend storing the token in a configuration file, which will then be stored in your home folder rather than in the code itself. This prevents the authentication token from being committed to source code repositories.

Import the library¶

You should begin by importing the API library sevenbridges-python to your python script that will interact with the API:

import sevenbridges as sbg

Then, use one of the following three methods to initialize the library:

1. Initialize the library explicitly¶

The library can be also instantiated explicitly by passing the URL and authentication token as key-value arguments into the Api object.

api = sbg.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>')

Note - you can initialize several API clients with different credentials or environments.

2. Initialize the library using environment variables¶

import os

# Usually these variables would be set in the shell beforehand
os.environ['SB_API_ENDPOINT'] = '<https://api.sbgenomics.com/v2' # or 'https://cgc-api.sbgenomics.com/v2>' for cgc, or 'https://cavatica-api.sbgenomics.com/v2' for cavatica
os.environ['SB_AUTH_TOKEN'] = '<TOKEN_HERE>'

api = sbg.Api()

3. Initialize the library using a configuration file¶

The configuration file, $HOME/.sevenbridges/credentials, has a simple .ini file format, with the environment (the Seven Bridges Platform, or the CGC, or Cavatica) indicated in square brackets, as shown:

[default]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = <TOKEN_HERE>

[cgc]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token = <TOKEN_HERE>

[cavatica]
api_endpoint = https://cavatica-api.sbgenomics.com/v2
auth_token = <TOKEN_HERE>

The Api object is the central resource for querying, saving and performing other actions on your resources on the Seven Bridges Platform or CGC. Once you have instantiated the configuration class, pass it to the API class constructor.

c = sbg.Config(profile='cgc')
api = sbg.Api(config=c)

If not profile is set it will use the default profile.

Note

if user creates the api object api=sbg.Api() and does not pass any information the

library will first search whether the environment variables are set. If not it will check: if the configuration file is present and read the [default] profile. If that also fails it will raise an exception

Advance Access Features¶

Advance access features are subject to a change. To enable them just pass the advance_access=True flag when instantiating the library

api = sbg.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>', advance_access=True)

Note

Advance access features are subject to a change. No guarantee of any sort is given for AA API calls maintainability.

Proxy configuration¶

Proxy configuration can be supplied in three different ways.

explicit initialization

api = sb.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>',
       proxies={'https_proxy':'host:port', 'http_proxy': 'host:port'})

environment variables

os.environ['HTTP_PROXY'] = 'host:port'
os.environ['HTTPS_PROXY'] = 'host:port'

$HOME/.sevenbridges/sevenbridges-python/config configuration file

[proxies]
https_proxy=host:port
http_proxy=host:port

Explicit with config

config = sb.Config(profile='my-profile',
                   proxies={'https_proxy':'host:port', 'http_proxy': 'host:port'})
api = sb.Api(config=config)

Note

Once you set the proxy, all calls including upload and download will use the proxy settings.

Rate limit¶

For API requests that require authentication (i.e. all requests, except the call to list possible API paths), you can issue a maximum of 1000 requests per 300 seconds. Note that this limit is generally subject to change, depending on API usage and technical limits. Your current rate limit, the number of remaining requests available within the limit, and the time until your limit is reset can be obtained using your Api object, as follows.

api.limit
api.remaining
api.reset_time

Error Handlers¶

Error handler is a callable that accepts the api and response objects and returns the response object. They are most useful when additional logic needs to be implemented based on request result.

Example:

def error_handler(api, response):
    # Do something with the response object
    return response

sevenbridges-python library comes bundled with several useful error handlers. The most used ones are maintenance_sleeper and rate_limit_sleeper which pause your code execution until the SevenBridges/CGC public API is in maintenance mode or when the rate limit is breached.

Usage:

from sevenbridges.http.error_handlers import rate_limit_sleeper, maintenance_sleeper
api = sb.Api(url='https://api.sbgenomics.com/v2', token='<TOKEN_HERE>',
        error_handlers=[rate_limit_sleeper, maintenance_sleeper])

Note

Api object instantiated in this way with error handlers attached will be resilient to server maintenance and rate limiting.

Managing users¶

Currently any authenticated user can access his or her information by invoking the following method:

me = api.users.me()

Once you have initialized the library by authenticating yourself, the object me will contain your user information. This includes:

me.href
me.username
me.email
me.first_name
me.last_name
me.affiliation
me.phone
me.address
me.city
me.state
me.zip_code
me.country

For example, to obtain your email address invoke:

me.email

Managing projects¶

There are several methods on the Api object that can help you manage your projects.

Note

If you are not familiar with the project structure of the Seven Bridges Platform and CGC, take a look at their respective documentation: projects on the CGC and projects on the Seven Bridges Platform.

List Projects - introduction to pagination and iteration¶

In order to list your projects, invoke the api.projects.query method. This method follows server pagination and therefore allows pagination parameters to be passed to it. Passing a pagination parameter controls which resources you are shown. The offset parameter controls the start of the pagination while the limit parameter controls the number of items to be retrieved.

Note

See the Seven Bridges API overview or the CGC API overview for details of how to refer to a project, and for examples of the pagination parameters.

Below is an example of how to get all your projects, using the query method and the pagination parameters offset of 0 and limit of 10.

project_list = api.projects.query(offset=0, limit=10)

project_list has now been defined to be an object of the type collection which acts just like a regular python list, and so supports indexing, slicing, iterating and other list functions. All collections in the sevenbridges-python library have two methods: next_page and previous_page which allow you to load the next or previous pagination pages.

There are several things you can do with a collection of any kind of object:

The generic query, e.g. api.projects.query(), accepts the pagination parameters offset and limit as introduced above.
If you wish to iterate on a complete collection use the all() method, which returns an iterator
If you want to manually iterate on the collection (page by page), use next_page() and previous_page() methods on the collection.
You can easily cast the collection to the list, so you can re-use it later by issuing the standard Python project_list = list(api.projects.query().all()).

# Get details of my first 10 projects.
project_list = api.projects.query(limit=10)

# Iterate through all my projects and print their name and id
for project in api.projects.query().all():
    print (project.id,project.name)

# Get all my current projects and store them in a list
my_projects = list(api.projects.query().all())

Get details of a single project¶

You can get details of a single project by issuing the api.projects.get() method with the parameter id set to the id of the project in question. Note that this call, as well as other calls to the API server may raise an exception which you can catch and process if required.

Note - To process errors from the library, import SbgError from sevenbridges.errors, as shown below.

from sevenbridges.errors import SbgError
try:
    project_id = 'doesnotexist/forsure'
    project = api.projects.get(id=project_id)
except SbgError as e:
    print (e.message)

Errors in SbgError have the properties code and message which refer to the number and text of 4-digit API status codes that are specific to the Seven Bridges Platform and API. To see all the available codes, see the documentation:

http://docs.sevenbridges.com/docs/api-status-codes for the Seven Bridges Platform
http://docs.cancergenomicscloud.org/docs/api-status-codes for the CGC.

Project properties¶

Once you have obtained the id of a Project instance, you can see its properties. All projects have the following properties:

href - Project href on the API

id - Id of the project

name - name of the project

description - description of the project

billing_group - billing group attached to the project

type - type of the project (v1 or v2)

tags - list of project tags

The property href href is a URL on the server that uniquely identifies the resource in question. All resources have this attribute. Each project also has a name, identifier, description indicating its use, a type, some tags and also a billing_group identifier representing the billing group that is attached to the project.

Project methods – an introduction to methods in the sevenbridges-python library¶

There are two types of methods in the sevenbridges-python library: static and dynamic. Static methods are invoked on the Api object instance. Dynamic methods are invoked from the instance of the object representing the resource (e.g. the project).

Static methods include:

Create a new resource: for example, api.projects.create(name="My new project", billing_group='296a98a9-424c-43f3-aec5-306e0e41c799') creates a new resource. The parameters used will depend on the resource in question.
Get a resource: the method api.projects.get(id='user/project') returns details of a specific resource, denoted by its id.
Query resources - the method api.projects.query() method returns a pageable list of type collection of projects. The same goes for other resources, so api.tasks.query(status='COMPLETED') returns a collection of completed tasks with default paging.

Dynamic methods can be generic (for all resources) or specific to a single resource. They are called on a concrete object, such as a Project object.

So, suppose that project is an instance of Project object. Then, we can:

Delete the resource: project.delete() deletes the object (if deletion of this resource is supported on the API).
Reload the resource from server: project.reload() reloads the state of the object from the server.
Save changes to the server: project.save() saves all properties

The following example shows some of the methods used to manipulate projects.

# Get a collection of projects
projects = api.projects.query()

# Grab the first billing group
bg = api.billing_groups.query(limit=1)[0]

# Create a project using the billing group grabbed above
new_project = api.projects.create(name="My new project", billing_group=bg.id)

# Add a new member to the project
new_project.add_member(user='newuser', permissions= {'write':True, 'execute':True})

Other project methods include:

Get members of the project and their permissions - project.get_members() - returns a Collection of members and their permissions
Add a member to the project - project.add_member()
Add a team member to the project - project.add_member_team()
Add a division member to the project - project.add_member_division()
Remove a member from the project - project.remove_member()
List files from the project - project.get_files()
Add files to the project - project.add_files() - you can add a single File or a Collection of files
List apps from the project - project.get_apps()
List tasks from the project - project.get_tasks()

Manage billing¶

There are several methods on the Api object to can help you manage your billing information. The billing resources that you can interact with are billing groups and invoices.

Manage billing groups¶

Querying billing groups will return a standard collection object.

# Query billing groups
bgroup_list = api.billing_groups.query(offset=0, limit=10)

# Fetch a billing group's information
bg = api.billing_groups.get(id='f1969c90-da54-4118-8e96-c3f0b49a163d')

Billing group properties¶

The following properties are attached to each billing group:

href - Billing group href on the API server.

id - Billing group identifier.

owner - Username of the user that owns the billing group.

name - Billing group name.

type - Billing group type (free or regular)

pending - True if billing group is not yet approved, False if the billing group has been approved.

disabled - True if billing group is disabled, False if its enabled.

balance - Billing group balance.

Billing group methods¶

There is one billing group method:

breakdown() fetches a cost breakdown by project and analysis for the selected billing group.

Manage invoices¶

Querying invoices will return an Invoices collection object.

invoices = api.invoices.query()

Once you have obtained the invoice identifier you can also fetch specific invoice information.

invoices = api.invoices.get(id='6351830069')

Invoice properties¶

The following properties are attached to each invoice.

href - Invoice href on the API server.

id - Invoice identifier.

pending - Set to True if invoice has not yet been approved by Seven Bridges, False otherwise.

analysis_costs - Costs of your analysis.

storage_costs - Storage costs.

total - Total costs.

invoice_period - Invoicing period (from-to)

Managing files¶

Files are an integral part of each analysis. As for as all other resources, the sevenbridges-python library enables you to effectively query files, in order to retrieve each file’s details and metadata. The request to get a file’s information can be made in the same manner as for projects and billing, presented above.

The available methods for fetching specific files are query and get:

# Query all files in a project
file_list = api.files.query(project='user/my-project')

# Get a single file's information
file = api.files.get(id='5710141760b2b14e3cc146af')

File properties¶

Each file has the following properties:

href - File href on the API server.

id - File identifier.

name - File name.

size - File size in bytes.

project - Identifier of the project that file is located in.

created_on - Date of the file creation.

modified_on - Last modification of the file.

origin - File origin information, indicating the task that created the file.

tags - File tags.

metadata - File metadata.

File methods¶

Files have the following methods:

Refresh the file with data from the server: reload()
Copy the file from one project to another: copy()
Download the file: download()
Save modifications to the file to the server save()
Delete the resource: delete()

See the examples below for information on the arguments these methods take:

Examples¶

# Filter files by name to find only file names containing the specified string:
files = api.files.query(project='user/my-project')
my_file = [file for file in files if 'fasta' in file.name]

# Or simply query files by name if you know their exact file name(s)
files = api.files.query(project='user/myproject', names=['SRR062634.filt.fastq.gz','SRR062635.filt.fastq.gz'])
my_files = api.files.query(project='user/myproject', metadata = {'sample_id': 'SRR062634'} )


# Edit a file's metadata
my_file = my_files[0]
my_file.metadata['sample_id'] = 'my-sample'
my_file.metadata['library'] = 'my-library'


# Add metadata (if you are starting with a file without metadata)
my_file = my_files[0]
my_file.metadata = {'sample_id' : 'my-sample',
                    'library' : 'my-library'
                  }

# Also set a tag on that file
my_file.tags = ['example']

# Save modifications
my_file.save()

# Copy a file between projects
new_file = my_file.copy(project='user/my-other-project', name='my-new-file')

# Download a file to the current working directory
# Optionally, path can contain a full path on local filesystem
new_file.download(path='my_new_file_on_disk')

Managing file upload and download¶

sevenbridges-python library provides both synchronous and asynchronous way of uploading or downloading files.

File Download¶

Synchronous file download:

file = api.files.get('file-identifier')
file.download('/home/bar/foo/file.bam')

Asynchronous file download:

file = api.files.get('file-identifier')
download = file.download('/home/bar/foo.bam', wait=False)

download.path # Gets the target file path of the download.
download.status # Gets the status of the download.
download.progress # Gets the progress of the download as percentage.
download.start_time # Gets the start time of the download.
download.duration # Gets the download elapsed time.

download.start() # Starts the download.
download.pause() # Pauses the download.
download.resume() # Resumes the download.
download.stop() # Stops the download.
download.wait() # Block the main loop until download completes.

You can register the callback or error callback function to the download handle: download.add_callback(callback=my_callback, errorback=my_error_back)

Registered callback method will be invoked on completion of the download. The errorback method will be invoked if error happens during download.

File Upload¶

Synchronous file upload:

# Get the project where we want to upload files.
project = api.projects.get('project-identifier')
api.files.upload('/home/bar/foo/file.fastq', project)
# Optionally we can set file name of the uploaded file.
api.files.upload('/home/bar/foo/file.fastq', project, file_name='new.fastq')

Asynchronous file upload:

upload = api.files.upload('/home/bar/foo/file.fastq', 'project-identifier', wait=False)

upload.file_name # Gets the file name of the upload.
upload.status # Gets the status of the upload.
upload.progress # Gets the progress of the upload as percentage.
upload.start_time # Gets the start time of the upload.
upload.duration # Gets the upload elapsed time.

upload.start() # Starts the upload.
upload.pause() # Pauses the upload.
upload.resume() # Resumes the upload.
upload.stop() # Stops the upload.
upload.wait() # Block the main loop until upload completes.

You can register the callback or error callback in the same manner as it was described for asynchronous file download.

Managing volumes: connecting cloud storage to the Platform¶

Volumes authorize the Platform to access and query objects on a specified cloud storage (Amazon Web Services or Google Cloud Storage) on your behalf. As for as all other resources, the sevenbridges-python library enables you to effectively query volumes, import files from a volume to a project or export files from a project to the volume.

The available methods for listing volumes, imports and exports are query and get, as for other objects:

# Query all volumes
volume_list = api.volumes.query()
# Query all imports
all_imports = api.imports.query()
# Query failed exports
failed_exports = api.exports.query(state='FAILED')

# Get a single volume's information
volume = api.volumes.get(id='user/volume')
# Get a single import's information
i = api.imports.get(id='08M4ywDZkQuJOb3L5M8mMSvzoeGezTdh')
# Get a single export's information
e = api.exports.get(id='0C7T8sBDP6aiNbwvXv12QZFPW55wJ3GJ')

Volume properties¶

Each volume has the following properties:

href - Volume href on the API server.

id - Volume identifier in format owner/name.

name - Volume name. Learn more about this in our Knowledge Center.

access_mode - Whether the volume was created as read-only (RO) or read-write (RW). Learn more about this in our Knowledge Center.

active - Whether or not this volume is active.

created_on - Time when the volume was created.

modified_on - Time when the volume was last modified.

description - An optional description of this volume.

service - This object contains the information about the cloud service that this volume represents.

Volume methods¶

Volumes have the following methods:

Refresh the volume with data from the server: reload()
Get imports for a particular volume get_imports()
Get exports for a particular volume get_exports()
Create a new volume based on the AWS S3 service - create_s3_volume()
Create a new volume based on Google Cloud Storage service - create_google_volume()
Save modifications to the volume to the server save()
Unlink the volume delete()
Get volume members get_members()
Add a member to the project - add_member()
Add a team member to the project - add_member_team()
Add a division member to the project - add_member_division()

See the examples below for information on the arguments these methods take:

Examples¶

# Create a new volume based on AWS S3 for importing files
volume_import = api.volumes.create_s3_volume(name='my_input_volume', bucket='my_bucket',access_key_id='AKIAIOSFODNN7EXAMPLE',secret_access_key = 'wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY',access_mode='RO')

# Create a new volume based on AWS S3 for exporting files
volume_export = api.volumes.create_s3_volume(name='my_output_volume', bucket='my_bucket', access_key_id='AKIAIOSFODNN7EXAMPLE',secret_access_key = 'wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY',access_mode='RW')
# List all volumes available
volumes = api.volumes.query()

Import properties¶

When you import a file from a volume into a project on the Platform, you are importing a file from your cloud storage provider (Amazon Web Services or Google Cloud Storage) via the volume onto the Platform.

If successful, an alias will be created on the Platform. Aliases appear as files on the Platform and can be copied, executed, and modified as such. They refer back to the respective file on the given volume.

Each import has the following properties:

href - Import href on the API server.

id - Import identifier.

source - Source of the import, object of type VolumeFile, contains info on volume and file location on the volume

destination - Destination of the import, object of type ImportDestination, containing info on project where the file was imported to and name of the file in the project

state - State of the import. Can be PENDING, RUNNING, COMPLETED and FAILED.

result - If the import was completed, contains the result of the import - a File object.

error - Contains the Error object if the import failed.

overwrite - Whether the import was set to overwrite file at destination or not.

started_on - Contains the date and time when the import was started.

finished_on - Contains the date and time when the import was finished.

Import methods¶

Imports have the following methods:

Refresh the import with data from the server: reload()
Start an import by specifying the source and the destination of the import - submit_import()
Delete the import - delete()

See the examples below for information on the arguments these methods take:

Examples¶

# Import a  file to a project
my_project = api.projects.get(id='my_project')
bucket_location = 'fastq/my_file.fastq'
imp = api.imports.submit_import(volume=volume_import, project=my_project, location=bucket_location)
# Wait until the import finishes
while True:
      import_status = imp.reload().state
      if import_status in (ImportExportState.COMPLETED, ImportExportState.FAILED):
           break
      time.sleep(10)
# Continue with the import
if imp.state == ImportExportState.COMPLETED:
      imported_file = imp.result

Export properties¶

When you export a file from a project on the Platform into a volume, you are essentially writing to your cloud storage bucket on Amazon Web Services or Google Cloud Storage via the volume.

Note that the file selected for export must not be a public file or an alias. Aliases are objects stored in your cloud storage bucket which have been made available on the Platform.

The volume you are exporting to must be configured for read-write access. To do this, set the access_mode parameter to RW when creating or modifying a volume. Learn more about this from our Knowledge Center.

Each export has the following properties:

href - Export href on the API server.

id - Export identifier.

source - Source of the export, object of type File

destination - Destination of the export, object of type VolumeFile, containing info on project where the file was imported to and name of the file in the project

state - State of the export. Can be PENDING, RUNNING, COMPLETED and FAILED.

result - If the export was completed, this contains the result of the import - a File object.

error - Contains the Error object if the export failed.

overwrite - Whether or not the export was set to overwrite the file at the destination.

started_on - Contains the date and time when the export was started.

finished_on - Contains the date and time when the export was finished.

Export methods¶

Exports have the following methods:

Refresh the export with data from the server: reload()
Submit export, by specifying source and destination of the import: submit_import()
Delete the export: delete()

See the examples below for information on the arguments these methods take:

Examples¶

# Export a set of files to a volume
# Get files from a project
files_to_export = api.files.query(project=my_project).all()
# And export all the files to the output bucket
exports = []
for f in files_to_export:
      export = api.exports.submit_export(file=f, volume = volume_export, location=f.name)
      exports.append(export)
# Wait for exports to finish:
num_exports = len(exports)
done = False

while not done:
      done_len = 0
      for e in exports:
             if e.reload().state in (ImportExportState.COMPLETED, ImportExportState.FAILED):
                    done_len += 1
             time.sleep(10)
      if done_len == num_exports:
             done = True

Managing apps¶

Managing apps (tools and workflows) with the sevenbridges-python library is simple. Apps on the Seven Bridges Platform and CGC are implemented using the Common Workflow Language (CWL) specification https://github.com/common-workflow-language/common-workflow-language. The sevenbridges-python currently supports only Draft 2 format of the CWL. Each app has a CWL description, expressed in JSON.

Querying all apps or getting the details of a single app can be done in the same way as for other resources, using the query() and get methods. You can also invoke the following class-specific methods:

get_revision() - Returns a specific app revision.
install_app() - Installs your app on the server, using its CWL description.
create_revision() - Creates a new revision of the specified app.

Note

Listing public apps can be achieved by invoking api.apps.query(visibility='public')

App properties¶

Each app has the following available properties:

href - The URL of the app on the API server.

id - App identifier.

name - App name.

project - Identifier of the project that app is located in.

revision - App revision.

raw - Raw CWL description of the app.

App methods¶

App only has class methods that were mentioned above.

Managing tasks¶

Tasks (pipeline executions) are easy to handle using the sevenbridges-python library. As with all resources you can query() your tasks, and get() a single task instance. You can also do much more. We will outline task properties and methods and show in the examples how easy is to run your first analysis using Python.

Task properties¶

href - Task URL on the API server.

id - Task identifier.

name - Task name.

status - Task status.

project - Identifier of the project that the task is located in.

app - The identifier of the app that was used for the task.

type - Task type.

created_by - Username of the task creator.

executed_by- Username of the task executor.

batch - Boolean flag: True for batch tasks, False for regular & child tasks.

batch_by - Batching criteria.

batch_group - Batch group assigned to the child task calculated from the batch_by criteria.

batch_input - Input identifier on to which to apply batching.

parent - Parent task for a batch child.

end_time - Task end time.

execution_status - Task execution status.

price - Task cost.

inputs - Inputs that were submitted to the task.

outputs - Generated outputs from the task.

Note

Check the documentation on the Seven Bridges API and the CGC API for more details on batching criteria.

Task methods¶

The following class and instance methods are available for tasks:

Create a task on the server and, optionally, run it: create().
Query tasks: query().
Get single task’s information: get().
Abort a running task: abort().
Run a draft task: run()
Delete a draft task from the server: delete().
Refresh the task object information with the date from the server: refresh().
Save task modifications to the sever: save().
Get task execution details: get_execution_details().
Get batch children if the task is a batch task: get_batch_children().

Task creation hints¶

Both input files and parameters are passed the same way together in a single dictionary to inputs.
api.files.query always return an array of files. For single file inputs, use api.files.query(project='my-project', names=["one_file.fa"])[0].

Task Examples¶

Single task¶

# Task name
name = 'my-first-task'

# Project in which I want to run a task.
project = 'my-username/my-project'

# App I want to use to run a task
app = 'my-username/my-project/my-app'

# Inputs
inputs = {}
inputs['FastQC-Reads'] = api.files.query(project='my-project', metadata={'sample': 'some-sample'})

try:
    task = api.tasks.create(name=name, project=project, app=app, inputs=inputs, run=True)
except SbError:
    print('I was unable to run the task.')

# Task can also be ran by invoking .run() method on the draft task.
task.run()

Batch task¶

# Task name
name = 'my-first-task'

# Project in which to run the task.
project = 'my-username/my-project'

# App to use to run the task
app = 'my-username/my-project/my-app'

# Inputs
inputs = {}
inputs['FastQC-Reads'] = api.files.query(project=project, metadata={'sample': 'some-sample'})

# Specify that one task should be created per file (i.e. batch tasks by file).
batch_by = {'type': 'item'}


# Specify that the batch input is FastQC-Reads
batch_input = 'FastQC-Reads'

try:
    task = api.tasks.create(name=name, project=project, app=app,
                            inputs=inputs, batch_input=batch_input, batch_by=batch_by, run=True)
except SbError:
    print('I was unable to run a batch task.')

sevenbridges package¶

sevenbridges-python¶

copyright:	2016 Seven Bridges Genomics Inc.
license:	Apache 2.0

class sevenbridges.Api(url=None, token=None, oauth_token=None, config=None, timeout=None, download_max_workers=16, upload_max_workers=16, proxies=None, error_handlers=None, advance_access=False)¶

Bases: sevenbridges.http.client.HttpClient

Api aggregates all resource classes into single place

actions¶: alias of Actions

apps¶: alias of App

billing_groups¶: alias of BillingGroup

divisions¶: alias of Division

endpoints¶: alias of Endpoints

exports¶: alias of Export

files¶: alias of File

imports¶: alias of Import

invoices¶: alias of Invoice

markers¶: alias of Marker

projects¶: alias of Project

rate_limit¶: alias of RateLimit

tasks¶: alias of Task

teams¶: alias of Team

users¶: alias of User

volumes¶: alias of Volume

class sevenbridges.Config(profile=None, proxies=None, advance_access=None)¶

Bases: object

Utility configuration class.

class sevenbridges.Invoice(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing invoices.

analysis_costs¶

deepcopy()¶

equals(other)¶

href = None¶

id = None¶

invoice_period¶

pending = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) invoices. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

storage_costs¶

total¶

class sevenbridges.BillingGroup(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing billing groups.

balance¶

breakdown()¶: Get Billing group breakdown for the current billing group.

deepcopy()¶

disabled = None¶

equals(other)¶

href = None¶

id = None¶

name = None¶

owner = None¶

pending = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) billing group. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object. :param api: Api instance.

type = None¶

class sevenbridges.BillingGroupBreakdown(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing billing group breakdowns.

deepcopy()¶

equals(other)¶

href = None¶

project_breakdown¶

total_spending¶

class sevenbridges.User(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing tasks.

address = None¶

affiliation = None¶

city = None¶

country = None¶

deepcopy()¶

email = None¶

equals(other)¶

first_name = None¶

classmethod get(user, api=None)¶

href = None¶

last_name = None¶

classmethod me(api=None)¶: Retrieves current user information. :param api: Api instance. :return: User object.

phone = None¶

state = None¶

username = None¶

zip_code = None¶

class sevenbridges.Endpoints(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing Endpoints.

action_url = None¶

apps_url = None¶

billing_url = None¶

deepcopy()¶

equals(other)¶

files_url = None¶

classmethod get(api=None, **kwargs)¶: Get api links. :param api: Api instance. :return: Endpoints object.

projects_url = None¶

rate_limit_url = None¶

tasks_url = None¶

upload_url = None¶

user_url = None¶

users_url = None¶

class sevenbridges.Project(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing projects.

add_files(files)¶: Adds files to this project. :param files: List of files or a Collection object.

add_member(user, permissions)¶: Add a member to the project. :param user: Member username :param permissions: Permissions dictionary. :return: Member object.

add_member_division(division, permissions)¶: Add a member (team) to a project. :param division: Division object or division identifier. :param permissions: Permissions dictionary. :return: Member object.

add_member_email(email, permissions=None)¶: Add a member to the project using member email. :param email: Member email. :param permissions: Permissions dictionary. :return: Member object.

add_member_team(team, permissions)¶: Add a member (team) to a project. :param team: Team object or team identifier. :param permissions: Permissions dictionary. :return: Member object.

billing_group = None¶

classmethod create(name, billing_group=None, description=None, tags=None, settings=None, api=None)¶: Create a project. :param name: Project name. :param billing_group: Project billing group. :param description: Project description. :param tags: Project tags. :param settings: Project settings. :param api: Api instance. :return:

create_task(name, app, revision=None, batch_input=None, batch_by=None, inputs=None, description=None, run=False, disable_batch=False, interruptible=True)¶

Creates a task for this project.

Parameters:

name – Task name.
app – CWL app identifier.
revision – CWL app revision.
batch_input – Batch input.
batch_by – Batch criteria.
inputs – Input map.
description – Task description.
run – True if you want to run a task upon creation.
disable_batch – True if you want to disable batching.
interruptible – True if you want to use interruptible instances.

Returns:

Task object.

deepcopy()¶

description = None¶

equals(other)¶

get_apps(offset=None, limit=None)¶: Retrieves apps in this project. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_exports(volume=None, state=None, offset=None, limit=None)¶: Fetches exports for this volume. :param volume: Optional volume identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_files(offset=None, limit=None)¶: Retrieves files in this project. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_imports(volume=None, state=None, offset=None, limit=None)¶: Fetches imports for this project. :param volume: Optional volume identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_members(offset=None, limit=None)¶: Retrieves project members. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_tasks(status=None, offset=None, limit=None)¶: Retrieves tasks in this project. :param status: Optional task status. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

href = None¶

id = None¶

name = None¶

classmethod query(owner=None, offset=None, limit=None, api=None)¶: Query (List) projects :param owner: Owner username. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

remove_member(user)¶: Remove member from the project. :param user: User to be removed.

save(obj, *args, **kwargs)¶

settings¶

tags = None¶

type = None¶

class sevenbridges.Task(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing tasks.

abort(obj, *args, **kwargs)¶

app = None¶

batch = None¶

batch_by¶

batch_group¶

batch_input = None¶

classmethod create(name, project, app, revision=None, batch_input=None, batch_by=None, inputs=None, description=None, run=False, disable_batch=False, interruptible=True, api=None)¶: Creates a task on server. :param name: Task name. :param project: Project identifier. :param app: CWL app identifier. :param revision: CWL app revision. :param batch_input: Batch input. :param batch_by: Batch criteria. :param inputs: Input map. :param description: Task description. :param run: True if you want to run a task upon creation. :param disable_batch: If True disables batching of a batch task. :param interruptible: If True interruptible instance will be used. :param api: Api instance. :return: Task object. :raises: TaskValidationError if validation Fails. :raises: SbgError if any exception occurs during request.

created_by = None¶

created_time = None¶

deepcopy()¶

description = None¶

end_time = None¶

equals(other)¶

errors = None¶

executed_by = None¶

execution_status¶

get_batch_children()¶: Retrieves batch child tasks for this task if its a batch task. :return: Collection instance. :raises SbError if task is not a batch task.

get_execution_details()¶: Retrieves execution details for a task. :return: Execution details instance.

href = None¶

id = None¶

inputs¶

name = None¶

outputs¶

parent = None¶

price¶

project = None¶

classmethod query(project=None, status=None, batch=None, parent=None, created_from=None, created_to=None, started_from=None, started_to=None, ended_from=None, ended_to=None, offset=None, limit=None, api=None)¶: Query (List) tasks. Date parameters may be both strings and python date objects. :param project: Target project. optional. :param status: Task status. :param batch: Only batch tasks. :param parent: Parent batch task identifier. :param ended_to: All tasks that ended until this date. :param ended_from: All tasks that ended from this date. :param started_to: All tasks that were started until this date. :param started_from: All tasks that were started from this date. :param created_to: All tasks that were created until this date. :param created_from: All tasks that were created from this date. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

run(obj, *args, **kwargs)¶

save(obj, *args, **kwargs)¶

start_time = None¶

status = None¶

type = None¶

use_interruptible_instances = None¶

warnings = None¶

class sevenbridges.App(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing apps.

copy(project, name=None)¶: Copies the current app. :param project: Destination project. :param name: Destination app name. :return: Copied App object.

classmethod create_revision(id, revision, raw, api=None)¶: Create a new app revision. :param id: App identifier. :param revision: App revision. :param raw: Raw cwl object. :param api: Api instance. :return: App object.

deepcopy()¶

equals(other)¶

classmethod get_revision(id, revision, api=None)¶: Get app revision. :param id: App identifier. :param revision: App revision :param api: Api instance. :return: App object.

href = None¶

id¶

classmethod install_app(id, raw, api=None)¶: Installs and app. :param id: App identifier. :param raw: Raw cwl data. :param api: Api instance. :return: App object.

name = None¶

project = None¶

classmethod query(project=None, visibility=None, q=None, id=None, offset=None, limit=None, api=None)¶: Query (List) apps. :param project: Source project. :param visibility: private|public for private or public apps. :param q: List containing search terms. :param id: List contains app ids. Fetch apps with specific ids. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: collection object

raw = None¶

revision = None¶

sync()¶: Syncs the parent app changes with the current app instance. :return: Synced App object.

class sevenbridges.Member(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing members. This resource is reused on both projects and volumes.

deepcopy()¶

email = None¶

equals(other)¶

href = None¶

id = None¶

permissions¶

save(obj, *args, **kwargs)¶

type = None¶

username = None¶

class sevenbridges.Permissions(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Members permissions resource.

class sevenbridges.File(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing files.

content(path=None, overwrite=True)¶

Downloads file to the specified path or as temporary file and reads the file content in memory.

Should not be used on very large files.

Parameters:	path – Path for file download If omitted tmp file will be used. overwrite – Overwrite file if exists locally
Returns:	File content.

copy(project, name=None)¶: Copies the current file. :param project: Destination project. :param name: Destination file name. :return: Copied File object.

created_on = None¶

deepcopy()¶

download(path, retry=5, timeout=10, chunk_size=5242880, wait=True, overwrite=False)¶: Downloads the file and returns a download handle. Download will not start until .start() method is invoked. :param path: Full path to the new file. :param retry: Number of retries if error occurs during download. :param timeout: Timeout for http requests. :param chunk_size: Chunk size in bytes. :param wait: If true will wait for download to complete. :param overwrite: If True will silently overwrite existing file. :return: Download handle.

download_info()¶: Fetches download information containing file url that can be used to download file. :return: Download info object.

equals(other)¶

href = None¶

id = None¶

metadata¶

modified_on = None¶

name = None¶

origin¶

project = None¶

classmethod query(project, names=None, metadata=None, origin=None, tags=None, offset=None, limit=None, api=None)¶: Query ( List ) projects :param project: Project id :param names: Name list :param metadata: Metadata query dict :param origin: Origin query dict :param tags: List of tags to filter on :param offset: Pagination offset :param limit: Pagination limit :param api: Api instance. :return: Collection object.

reload()¶: Refreshes the file with the data from the server.

save(obj, *args, **kwargs)¶

size = None¶

storage¶

stream(part_size=32768)¶: Creates an iterator which can be used to stream the file content. :param part_size: Size of the part in bytes. Default 32KB :return Iterator

tags = None¶

classmethod upload(path, project, file_name=None, overwrite=False, retry=5, timeout=10, part_size=5242880, wait=True, api=None)¶

Uploads a file using multipart upload and returns an upload handle if the wait parameter is set to False. If wait is set to True it will block until the upload is completed.

Parameters:

path – File path on local disc.
project – Project identifier
file_name – Optional file name.
overwrite – If true will overwrite the file on the server.
retry – Number of retries if error occurs during upload.
timeout – Timeout for http requests.
part_size – Part size in bytes.
wait – If true will wait for upload to complete.
api – Api instance.

class sevenbridges.Export(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing exports.

deepcopy()¶

destination¶

equals(other)¶

error¶

finished_on = None¶

href = None¶

id = None¶

overwrite = None¶

properties¶

classmethod query(volume=None, state=None, offset=None, limit=None, api=None)¶: Query (List) exports. :param volume: Optional volume identifier. :param state: Optional import sate. :param api: Api instance. :return: Collection object.

result¶

source¶

started_on = None¶

state = None¶

classmethod submit_export(file, volume, location, properties=None, overwrite=False, copy_only=False, api=None)¶: Submit new export job. :param file: File to be exported. :param volume: Volume identifier. :param location: Volume location. :param properties: Properties dictionary. :param overwrite: If true it will overwrite file if exists :param copy_only: If true files are kept on SevenBridges bucket. :param api: Api Instance. :return: Export object.

class sevenbridges.Import(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing imports.

deepcopy()¶

destination¶

equals(other)¶

error¶

finished_on = None¶

href = None¶

id = None¶

overwrite = None¶

classmethod query(project=None, volume=None, state=None, offset=None, limit=None, api=None)¶: Query (List) imports. :param project: Optional project identifier. :param volume: Optional volume identifier. :param state: Optional import sate. :param api: Api instance. :return: Collection object.

result¶

source¶

started_on = None¶

state = None¶

classmethod submit_import(volume, location, project, name=None, overwrite=False, properties=None, api=None)¶: Submits new import job. :param volume: Volume identifier. :param location: Volume location. :param project: Project identifier. :param name: Optional file name. :param overwrite: If true it will overwrite file if exists. :param properties: Properties dictionary. :param api: Api instance. :return: Import object.

class sevenbridges.Volume(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing volumes.

access_mode = None¶

active = None¶

add_member(user, permissions)¶: Add a member to the volume. :param user: Member username :param permissions: Permissions dictionary. :return: Member object.

add_member_division(division, permissions)¶: Add a member (team) to a volume. :param division: Division object or division identifier. :param permissions: Permissions dictionary. :return: Member object.

add_member_team(team, permissions)¶: Add a member (team) to a volume. :param team: Team object or team identifier. :param permissions: Permissions dictionary. :return: Member object.

classmethod create_google_volume(name, bucket, client_email, private_key, access_mode, description=None, prefix=None, properties=None, api=None)¶: Create s3 volume. :param name: Volume name. :param bucket: Referenced bucket. :param client_email: Google client email. :param private_key: Google client private key. :param access_mode: Access Mode. :param description: Volume description. :param prefix: Volume prefix. :param properties: Volume properties. :param api: Api instance. :return: Volume object.

classmethod create_s3_volume(name, bucket, access_key_id, secret_access_key, access_mode, description=None, prefix=None, properties=None, api=None)¶: Create s3 volume. :param name: Volume name. :param bucket: Referenced bucket. :param access_key_id: Amazon access key identifier. :param secret_access_key: Amazon secret access key. :param access_mode: Access Mode. :param description: Volume description. :param prefix: Volume prefix. :param properties: Volume properties. :param api: Api instance. :return: Volume object.

created_on = None¶

deepcopy()¶

description = None¶

equals(other)¶

get_exports(state=None, offset=None, limit=None)¶: Fetches exports for this volume. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_imports(project=None, state=None, offset=None, limit=None)¶: Fetches imports for this volume. :param project: Optional project identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_members(offset=None, limit=None)¶: Retrieves volume members. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_volume_object_info(location)¶: Fetches information about single volume object - usually file :param location: object location :return:

href = None¶

id = None¶

list(prefix=None, limit=50)¶

modified_on = None¶

name = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) volumes. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

remove_member(user)¶: Remove member from the volume. :param user: User to be removed.

save(obj, *args, **kwargs)¶

service¶

class sevenbridges.Marker(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

chromosome = None¶

classmethod create(file, name, position, chromosome, private=True, api=None)¶: Create a marker on a file. :param file: File object or identifier. :param name: Marker name. :param position: Marker position object. :param chromosome: Chromosome number. :param private: Whether the marker is private or public. :param api: Api instance. :return: Marker object.

created_by = None¶

created_time = None¶

deepcopy()¶

delete()¶

equals(other)¶

file = None¶

href = None¶

id = None¶

name = None¶

position¶

classmethod query(file, offset=None, limit=None, api=None)¶: Queries genome markers on a file. :param file: Genome file - Usually bam file. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

reload()¶

save(obj, *args, **kwargs)¶

class sevenbridges.Division(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing divisions.

deepcopy()¶

equals(other)¶

classmethod get(id, api=None)¶

get_teams(offset=None, limit=None)¶

href = None¶

id = None¶

name = None¶

classmethod query(offset=None, limit=None, api=None)¶

Query (List) divisions.

Parameters:	offset – Pagination offset. limit – Pagination limit. api – Api instance.
Returns:	Collection object.

reload()¶

class sevenbridges.TransferState¶

Bases: object

ABORTED = 'ABORTED'¶

COMPLETED = 'COMPLETED'¶

FAILED = 'FAILED'¶

PAUSED = 'PAUSED'¶

PREPARING = 'PREPARING'¶

RUNNING = 'RUNNING'¶

STOPPED = 'STOPPED'¶

class sevenbridges.VolumeType¶

Bases: object

GOOGLE = 'GCS'¶

S3 = 'S3'¶

class sevenbridges.VolumeAccessMode¶

Bases: object

READ_ONLY = 'RO'¶

READ_WRITE = 'RW'¶

class sevenbridges.FileStorageType¶

Bases: object

PLATFORM = 'PLATFORM'¶

VOLUME = 'VOLUME'¶

class sevenbridges.ImportExportState¶

Bases: object

COMPLETED = 'COMPLETED'¶

FAILED = 'FAILED'¶

PENDING = 'PENDING'¶

RUNNING = 'RUNNING'¶

class sevenbridges.TaskStatus¶

Bases: object

ABORTED = 'ABORTED'¶

COMPLETED = 'COMPLETED'¶

CREATING = 'CREATING'¶

DRAFT = 'DRAFT'¶

FAILED = 'FAILED'¶

QUEUED = 'QUEUED'¶

RUNNING = 'RUNNING'¶

exception sevenbridges.SbgError(message=None, code=None, status=None, more_info=None)¶

Bases: Exception

Base class for SBG errors.

Provides a base exception for all errors that are thrown by sevenbridges-python library.

exception sevenbridges.ResourceNotModified¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.ReadOnlyPropertyError(message)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.ValidationError(message)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.TaskValidationError(message, task=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.PaginationError(message)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.BadRequest(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.Unauthorized(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.Forbidden(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.NotFound(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.Conflict(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.TooManyRequests(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.ServerError(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.ServiceUnavailable(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.MethodNotAllowed(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.RequestTimeout(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.LocalFileAlreadyExists(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.ExecutionDetailsInvalidTaskType(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

Subpackages¶

sevenbridges.http package¶

Submodules¶

sevenbridges.http.client module¶

class sevenbridges.http.client.AAHeader¶

Bases: object

key = 'X-Sbg-Advance-Access'¶

value = 'Advance'¶

class sevenbridges.http.client.HttpClient(url=None, token=None, oauth_token=None, config=None, timeout=None, proxies=None, error_handlers=None, advance_access=None)¶

Bases: object

Implementation of all low-level API stuff, creating and sending requests, returning raw responses, authorization, etc.

add_error_handler(handler)¶

delete(url, headers=None, params=None, append_base=True)¶

get(url, headers=None, params=None, data=None, append_base=True, stream=False)¶

limit¶

patch(url, headers=None, params=None, data=None, append_base=True)¶

post(url, headers=None, params=None, data=None, append_base=True)¶

put(url, headers=None, params=None, data=None, append_base=True)¶

remaining¶

remove_error_handler(handler)¶

request_id¶

reset_time¶

session¶

sevenbridges.http.client.config_vars(profiles)¶: Utility method to fetch config vars using ini section profile :param profiles: profile name. :return:

sevenbridges.http.client.generate_session(proxies=None)¶: Utility method to generate request sessions. :param proxies: Proxies dictionary. :return: requests.Session object.

sevenbridges.http.error_handlers module¶

sevenbridges.http.error_handlers.general_error_sleeper(api, response, sleep=300)¶: Pauses the execution if response status code is > 500. :param api: Api instance. :param response: requests.Response object :param sleep: Time to sleep in between the requests.

sevenbridges.http.error_handlers.maintenance_sleeper(api, response, sleep=300)¶: Pauses the execution if sevenbridges api is under maintenance. :param api: Api instance. :param response: requests.Response object. :param sleep: Time to sleep in between the requests.

sevenbridges.http.error_handlers.rate_limit_sleeper(api, response)¶: Pauses the execution if rate limit is breached. :param api: Api instance. :param response: requests.Response object

sevenbridges.meta package¶

Submodules¶

sevenbridges.meta.collection module¶

class sevenbridges.meta.collection.Collection(resource, href, total, items, links, api)¶

Bases: list

Wrapper for SevenBridges pageable resources. Among the actual collection items it contains information regarding the total number of entries available in on the server and resource href.

all()¶: Fetches all available items. :return: Collection object.

next_page()¶: Fetches next result set. :return: Collection object.

previous_page()¶: Fetches previous result set. :return: Collection object.

resource = None¶

total¶

class sevenbridges.meta.collection.VolumeCollection(href, items, links, prefixes, api)¶

Bases: sevenbridges.meta.collection.Collection

previous_page()¶

total¶

sevenbridges.meta.comp_mutable_dict module¶

class sevenbridges.meta.comp_mutable_dict.CompoundMutableDict(**kwargs)¶

Bases: dict

Resource used for mutable compound dictionaries.

equals(other)¶

items()¶

update(E=None, **F)¶

sevenbridges.meta.data module¶

class sevenbridges.meta.data.DataContainer(urls, api)¶

Bases: object

Utility for fetching data from the API server using, resource identifier or href.

fetch()¶

sevenbridges.meta.fields module¶

class sevenbridges.meta.fields.BasicListField(name=None, read_only=False, max_length=None)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

class sevenbridges.meta.fields.BooleanField(name=None, read_only=False)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

class sevenbridges.meta.fields.CompoundField(cls, name=None, read_only=False, validator=None)¶: Bases: sevenbridges.meta.fields.Field

class sevenbridges.meta.fields.CompoundListField(cls, name=None, read_only=True)¶: Bases: sevenbridges.meta.fields.Field

class sevenbridges.meta.fields.DateTimeField(name=None, read_only=True)¶: Bases: sevenbridges.meta.fields.Field

class sevenbridges.meta.fields.DictField(name=None, read_only=False)¶: Bases: sevenbridges.meta.fields.Field, dict

class sevenbridges.meta.fields.Field(name=None, read_only=True, validator=None)¶

Bases: object

validate(value)¶

class sevenbridges.meta.fields.FloatField(name=None, read_only=False)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

class sevenbridges.meta.fields.HrefField(name=None)¶: Bases: sevenbridges.meta.fields.Field

class sevenbridges.meta.fields.IntegerField(name=None, read_only=False)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

class sevenbridges.meta.fields.ObjectIdField(name=None, read_only=True)¶: Bases: sevenbridges.meta.fields.Field

class sevenbridges.meta.fields.StringField(name=None, read_only=False, max_length=None)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

class sevenbridges.meta.fields.UuidField(name=None, read_only=True)¶

Bases: sevenbridges.meta.fields.Field

validate(value)¶

sevenbridges.meta.resource module¶

class sevenbridges.meta.resource.Resource(api)¶

Bases: object

Resource is base class for all resources, hiding implementation details of magic of injecting instance of API and common operations (like generic query).

delete()¶: Deletes the resource on the server.

classmethod get(id, api=None)¶: Fetches the resource from the server. :param id: Resource identifier :param api: sevenbridges Api instance. :return: Resource object.

reload()¶: Refreshes the resource with the data from the server.

class sevenbridges.meta.resource.ResourceMeta¶

Bases: type

Metaclass for all resources, knows how to inject instance of API from class that contains classes with this meta. Class that contains this class has to have ‘api’ property which will be injected into class level API property of Resource class.

Creates constructors for all resources and manages instantiation of resource fields.

sevenbridges.meta.transformer module¶

class sevenbridges.meta.transformer.Transform¶

Bases: object

static to_app(app)¶

static to_billing_group(billing_group)¶

static to_datestring(d)¶

static to_division(division)¶

static to_file(file_)¶

static to_marker(marker)¶

static to_project(project)¶

static to_task(task)¶

static to_team(team)¶

static to_user(user)¶

static to_volume(volume)¶

sevenbridges.models package¶

Subpackages¶

sevenbridges.models.compound package¶

Subpackages¶

sevenbridges.models.compound.billing package¶

Submodules¶

sevenbridges.models.compound.billing.invoice_period module¶

class sevenbridges.models.compound.billing.invoice_period.InvoicePeriod(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Invoice period resource contains datetime information about the invoice. It has from and to fields which represent the interval period for this invoice.

deepcopy()¶

equals(other)¶

from_ = None¶

to = None¶

sevenbridges.models.compound.billing.project_breakdown module¶

class sevenbridges.models.compound.billing.project_breakdown.ProjectBreakdown(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Project breakdown resource contains information regarding billing group project breakdown costs.

analysis_spending¶

deepcopy()¶

equals(other)¶

href = None¶

task_breakdown¶

sevenbridges.models.compound.billing.task_breakdown module¶

class sevenbridges.models.compound.billing.task_breakdown.TaskBreakdown(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Task breakdown resource contains information regarding billing group analysis breakdown costs.

deepcopy()¶

equals(other)¶

href = None¶

runner_username = None¶

task_cost¶

time_finished = None¶

time_started = None¶

sevenbridges.models.compound.files package¶

Submodules¶

sevenbridges.models.compound.files.download_info module¶

class sevenbridges.models.compound.files.download_info.DownloadInfo(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Download info resource contains download url for the file.

deepcopy()¶

equals(other)¶

url = None¶

sevenbridges.models.compound.files.file_origin module¶

class sevenbridges.models.compound.files.file_origin.FileOrigin(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

File origin resource contains information about origin of a file. Among others it contains information about the task if the file was produced during executions of a analysis.

deepcopy()¶

equals(other)¶

task = None¶

sevenbridges.models.compound.files.file_storage module¶

class sevenbridges.models.compound.files.file_storage.FileStorage(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

File storage resource contains information about the storage location of the file if the file is imported on or exported to an external volume.

deepcopy()¶

equals(other)¶

location = None¶

type = None¶

volume = None¶

sevenbridges.models.compound.files.metadata module¶

class sevenbridges.models.compound.files.metadata.Metadata(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

File metadata resource.

sevenbridges.models.compound.jobs package¶

Submodules¶

sevenbridges.models.compound.jobs.job module¶

class sevenbridges.models.compound.jobs.job.Job(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Job resource contains information for a single executed node in the analysis.

command_line = None¶

deepcopy()¶

docker¶

end_time = None¶

equals(other)¶

instance¶

logs¶

name = None¶

retried = None¶

start_time = None¶

status = None¶

sevenbridges.models.compound.jobs.job_docker module¶

class sevenbridges.models.compound.jobs.job_docker.JobDocker(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

JobDocker resource contains information for a docker image that was used for execution of a single job.

checksum = None¶

deepcopy()¶

equals(other)¶

sevenbridges.models.compound.jobs.job_instance module¶

class sevenbridges.models.compound.jobs.job_instance.Instance(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Instance resource contains information regarding the instance on which the job was executed.

deepcopy()¶

disk¶

equals(other)¶

id = None¶

provider = None¶

type = None¶

sevenbridges.models.compound.jobs.job_instance_disk module¶

class sevenbridges.models.compound.jobs.job_instance_disk.Disk(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Disk resource contains information about EBS disk size.

deepcopy()¶

equals(other)¶

size = None¶

type = None¶

unit = None¶

sevenbridges.models.compound.jobs.job_log module¶

class sevenbridges.models.compound.jobs.job_log.Logs(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Task output resource.

sevenbridges.models.compound.limits package¶

Submodules¶

sevenbridges.models.compound.limits.rate module¶

class sevenbridges.models.compound.limits.rate.Rate(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Rate resource.

deepcopy()¶

equals(other)¶

limit = None¶

remaining = None¶

reset = None¶

sevenbridges.models.compound.markers package¶

Submodules¶

sevenbridges.models.compound.markers.position module¶

class sevenbridges.models.compound.markers.position.MarkerPosition(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Marker position resource

sevenbridges.models.compound.projects package¶

Submodules¶

sevenbridges.models.compound.projects.permissions module¶

class sevenbridges.models.compound.projects.permissions.Permissions(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Members permissions resource.

sevenbridges.models.compound.projects.settings module¶

class sevenbridges.models.compound.projects.settings.Settings(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Project settings resource.

sevenbridges.models.compound.tasks package¶

sevenbridges.models.compound.tasks.map_input_output(item, api)¶: Maps item to appropriate sevebridges object. :param item: Input/Output value. :param api: Api instance. :return: Mapped object.

Submodules¶

sevenbridges.models.compound.tasks.batch_by module¶

class sevenbridges.models.compound.tasks.batch_by.BatchBy(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource, dict

Task batch by resource.

equals(other)¶

update(E=None, **F)¶

sevenbridges.models.compound.tasks.batch_group module¶

class sevenbridges.models.compound.tasks.batch_group.BatchGroup(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Batch group for a batch task. Represents the group that is assigned to the child task from the batching criteria that was used when the task was started.

deepcopy()¶

equals(other)¶

fields = None¶

value = None¶

sevenbridges.models.compound.tasks.execution_status module¶

class sevenbridges.models.compound.tasks.execution_status.ExecutionStatus(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Task execution status resource.

Contains information about the number of completed task steps, total number of task steps, current execution message and information regarding computation limits.

In case of a batch task it also contains the number of queued, running, completed, failed and aborted tasks.

aborted = None¶

account_limit = None¶

completed = None¶

deepcopy()¶

duration = None¶

equals(other)¶

execution_duration = None¶

failed = None¶

instance_init = None¶

message = None¶

message_code = None¶

queued = None¶

queued_duration = None¶

running = None¶

running_duration = None¶

steps_completed = None¶

steps_total = None¶

system_limit = None¶

sevenbridges.models.compound.tasks.input module¶

class sevenbridges.models.compound.tasks.input.Input(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Task input resource.

sevenbridges.models.compound.tasks.output module¶

class sevenbridges.models.compound.tasks.output.Output(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Task output resource.

sevenbridges.models.compound.volumes package¶

Submodules¶

sevenbridges.models.compound.volumes.credentials module¶

sevenbridges.models.compound.volumes.import_destination module¶

class sevenbridges.models.compound.volumes.import_destination.ImportDestination(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

ImportDestination resource describes the location of the file imported on to SevenBridges platform or related product.

deepcopy()¶

equals(other)¶

name = None¶

project = None¶

sevenbridges.models.compound.volumes.properties module¶

class sevenbridges.models.compound.volumes.properties.VolumeProperties(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Volume permissions resource.

sevenbridges.models.compound.volumes.service module¶

class sevenbridges.models.compound.volumes.service.VolumeService(**kwargs)¶

Bases: sevenbridges.meta.comp_mutable_dict.CompoundMutableDict, sevenbridges.meta.resource.Resource

Volume Service resource. Contains information about external storage provider.

sevenbridges.models.compound.volumes.volume_file module¶

class sevenbridges.models.compound.volumes.volume_file.VolumeFile(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

VolumeFile resource describes the location of the file on the external volume.

deepcopy()¶

equals(other)¶

location = None¶

volume = None¶

sevenbridges.models.compound.volumes.volume_object module¶

class sevenbridges.models.compound.volumes.volume_object.VolumeObject(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Volume object resource contains information about single file (object) entry in a specific volume.

deepcopy()¶

equals(other)¶

href = None¶

location = None¶

metadata = None¶

type = None¶

volume = None¶

sevenbridges.models.compound.volumes.volume_prefix module¶

class sevenbridges.models.compound.volumes.volume_prefix.VolumePrefix(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Volume prefix resource contains information about volume prefixes

deepcopy()¶

equals(other)¶

href = None¶

prefix = None¶

volume = None¶

Submodules¶

sevenbridges.models.compound.error module¶

class sevenbridges.models.compound.error.Error(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Error resource describes the error that happened and provides http status, custom codes and messages as well as the link to online resources.

code = None¶

deepcopy()¶

equals(other)¶

message = None¶

more_info = None¶

status = None¶

sevenbridges.models.compound.price module¶

class sevenbridges.models.compound.price.Price(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Price resource contains an information regarding the currency and the monet value of a certain resource.

amount = None¶

breakdown¶

currency = None¶

deepcopy()¶

equals(other)¶

sevenbridges.models.compound.price_breakdown module¶

class sevenbridges.models.compound.price_breakdown.Breakdown(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Breakdown resource contains price breakdown by storage and computation.

computation = None¶

deepcopy()¶

equals(other)¶

storage = None¶

Submodules¶

sevenbridges.models.actions module¶

class sevenbridges.models.actions.Actions(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

classmethod bulk_copy_files(files, destination_project, api=None)¶: Bulk copy of files. :param files: List containing files to be copied. :param destination_project: Destination project. :param api: Api instance. :return: MultiStatus copy result.

deepcopy()¶

equals(other)¶

classmethod send_feedback(type='IDEA', text=None, api=None)¶: Sends feedback to sevenbridges. :param type: FeedbackType wither IDEA, PROBLEM or THOUGHT. :param text: Feedback text. :param api: Api instance.

sevenbridges.models.app module¶

class sevenbridges.models.app.App(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing apps.

copy(project, name=None)¶: Copies the current app. :param project: Destination project. :param name: Destination app name. :return: Copied App object.

classmethod create_revision(id, revision, raw, api=None)¶: Create a new app revision. :param id: App identifier. :param revision: App revision. :param raw: Raw cwl object. :param api: Api instance. :return: App object.

deepcopy()¶

equals(other)¶

classmethod get_revision(id, revision, api=None)¶: Get app revision. :param id: App identifier. :param revision: App revision :param api: Api instance. :return: App object.

href = None¶

id¶

classmethod install_app(id, raw, api=None)¶: Installs and app. :param id: App identifier. :param raw: Raw cwl data. :param api: Api instance. :return: App object.

name = None¶

project = None¶

classmethod query(project=None, visibility=None, q=None, id=None, offset=None, limit=None, api=None)¶: Query (List) apps. :param project: Source project. :param visibility: private|public for private or public apps. :param q: List containing search terms. :param id: List contains app ids. Fetch apps with specific ids. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: collection object

raw = None¶

revision = None¶

sync()¶: Syncs the parent app changes with the current app instance. :return: Synced App object.

sevenbridges.models.billing_breakdown module¶

class sevenbridges.models.billing_breakdown.BillingGroupBreakdown(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing billing group breakdowns.

deepcopy()¶

equals(other)¶

href = None¶

project_breakdown¶

total_spending¶

sevenbridges.models.billing_group module¶

class sevenbridges.models.billing_group.BillingGroup(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing billing groups.

balance¶

breakdown()¶: Get Billing group breakdown for the current billing group.

deepcopy()¶

disabled = None¶

equals(other)¶

href = None¶

id = None¶

name = None¶

owner = None¶

pending = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) billing group. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object. :param api: Api instance.

type = None¶

sevenbridges.models.division module¶

class sevenbridges.models.division.Division(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing divisions.

deepcopy()¶

equals(other)¶

classmethod get(id, api=None)¶

get_teams(offset=None, limit=None)¶

href = None¶

id = None¶

name = None¶

classmethod query(offset=None, limit=None, api=None)¶

Query (List) divisions.

Parameters:	offset – Pagination offset. limit – Pagination limit. api – Api instance.
Returns:	Collection object.

reload()¶

sevenbridges.models.endpoints module¶

class sevenbridges.models.endpoints.Endpoints(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing Endpoints.

action_url = None¶

apps_url = None¶

billing_url = None¶

deepcopy()¶

equals(other)¶

files_url = None¶

classmethod get(api=None, **kwargs)¶: Get api links. :param api: Api instance. :return: Endpoints object.

projects_url = None¶

rate_limit_url = None¶

tasks_url = None¶

upload_url = None¶

user_url = None¶

users_url = None¶

sevenbridges.models.enums module¶

class sevenbridges.models.enums.FeedbackType¶

Bases: object

IDEA = 'IDEA'¶

PROBLEM = 'PROBLEM'¶

THOUGHT = 'THOUGHT'¶

class sevenbridges.models.enums.FileStorageType¶

Bases: object

PLATFORM = 'PLATFORM'¶

VOLUME = 'VOLUME'¶

class sevenbridges.models.enums.ImportExportState¶

Bases: object

COMPLETED = 'COMPLETED'¶

FAILED = 'FAILED'¶

PENDING = 'PENDING'¶

RUNNING = 'RUNNING'¶

class sevenbridges.models.enums.PartSize¶

Bases: object

DOWNLOAD_MINIMUM_PART_SIZE = 5242880¶

GB = 1073741824¶

KB = 1024¶

MAXIMUM_OBJECT_SIZE = 5497558138880¶

MAXIMUM_TOTAL_PARTS = 10000¶

MAXIMUM_UPLOAD_SIZE = 5368709120¶

MB = 1048576¶

TB = 1099511627776¶

UPLOAD_MINIMUM_PART_SIZE = 5242880¶

class sevenbridges.models.enums.TaskStatus¶

Bases: object

ABORTED = 'ABORTED'¶

COMPLETED = 'COMPLETED'¶

CREATING = 'CREATING'¶

DRAFT = 'DRAFT'¶

FAILED = 'FAILED'¶

QUEUED = 'QUEUED'¶

RUNNING = 'RUNNING'¶

class sevenbridges.models.enums.TransferState¶

Bases: object

ABORTED = 'ABORTED'¶

COMPLETED = 'COMPLETED'¶

FAILED = 'FAILED'¶

PAUSED = 'PAUSED'¶

PREPARING = 'PREPARING'¶

RUNNING = 'RUNNING'¶

STOPPED = 'STOPPED'¶

class sevenbridges.models.enums.VolumeAccessMode¶

Bases: object

READ_ONLY = 'RO'¶

READ_WRITE = 'RW'¶

class sevenbridges.models.enums.VolumeType¶

Bases: object

GOOGLE = 'GCS'¶

S3 = 'S3'¶

sevenbridges.models.execution_details module¶

class sevenbridges.models.execution_details.ExecutionDetails(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Task execution details.

deepcopy()¶

end_time = None¶

equals(other)¶

href = None¶

jobs¶

message = None¶

start_time = None¶

status = None¶

sevenbridges.models.file module¶

class sevenbridges.models.file.File(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing files.

content(path=None, overwrite=True)¶

Downloads file to the specified path or as temporary file and reads the file content in memory.

Should not be used on very large files.

Parameters:	path – Path for file download If omitted tmp file will be used. overwrite – Overwrite file if exists locally
Returns:	File content.

copy(project, name=None)¶: Copies the current file. :param project: Destination project. :param name: Destination file name. :return: Copied File object.

created_on = None¶

deepcopy()¶

download(path, retry=5, timeout=10, chunk_size=5242880, wait=True, overwrite=False)¶: Downloads the file and returns a download handle. Download will not start until .start() method is invoked. :param path: Full path to the new file. :param retry: Number of retries if error occurs during download. :param timeout: Timeout for http requests. :param chunk_size: Chunk size in bytes. :param wait: If true will wait for download to complete. :param overwrite: If True will silently overwrite existing file. :return: Download handle.

download_info()¶: Fetches download information containing file url that can be used to download file. :return: Download info object.

equals(other)¶

href = None¶

id = None¶

metadata¶

modified_on = None¶

name = None¶

origin¶

project = None¶

classmethod query(project, names=None, metadata=None, origin=None, tags=None, offset=None, limit=None, api=None)¶: Query ( List ) projects :param project: Project id :param names: Name list :param metadata: Metadata query dict :param origin: Origin query dict :param tags: List of tags to filter on :param offset: Pagination offset :param limit: Pagination limit :param api: Api instance. :return: Collection object.

reload()¶: Refreshes the file with the data from the server.

save(obj, *args, **kwargs)¶

size = None¶

storage¶

stream(part_size=32768)¶: Creates an iterator which can be used to stream the file content. :param part_size: Size of the part in bytes. Default 32KB :return Iterator

tags = None¶

classmethod upload(path, project, file_name=None, overwrite=False, retry=5, timeout=10, part_size=5242880, wait=True, api=None)¶

Uploads a file using multipart upload and returns an upload handle if the wait parameter is set to False. If wait is set to True it will block until the upload is completed.

Parameters:

path – File path on local disc.
project – Project identifier
file_name – Optional file name.
overwrite – If true will overwrite the file on the server.
retry – Number of retries if error occurs during upload.
timeout – Timeout for http requests.
part_size – Part size in bytes.
wait – If true will wait for upload to complete.
api – Api instance.

sevenbridges.models.invoice module¶

class sevenbridges.models.invoice.Invoice(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing invoices.

analysis_costs¶

deepcopy()¶

equals(other)¶

href = None¶

id = None¶

invoice_period¶

pending = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) invoices. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

storage_costs¶

total¶

sevenbridges.models.link module¶

class sevenbridges.models.link.Link(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Pagination links.

deepcopy()¶

equals(other)¶

href = None¶

method = None¶

rel = None¶

sevenbridges.models.marker module¶

class sevenbridges.models.marker.Marker(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

chromosome = None¶

classmethod create(file, name, position, chromosome, private=True, api=None)¶: Create a marker on a file. :param file: File object or identifier. :param name: Marker name. :param position: Marker position object. :param chromosome: Chromosome number. :param private: Whether the marker is private or public. :param api: Api instance. :return: Marker object.

created_by = None¶

created_time = None¶

deepcopy()¶

delete()¶

equals(other)¶

file = None¶

href = None¶

id = None¶

name = None¶

position¶

classmethod query(file, offset=None, limit=None, api=None)¶: Queries genome markers on a file. :param file: Genome file - Usually bam file. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

reload()¶

save(obj, *args, **kwargs)¶

sevenbridges.models.member module¶

class sevenbridges.models.member.Member(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing members. This resource is reused on both projects and volumes.

deepcopy()¶

email = None¶

equals(other)¶

href = None¶

id = None¶

permissions¶

save(obj, *args, **kwargs)¶

type = None¶

username = None¶

sevenbridges.models.project module¶

class sevenbridges.models.project.Project(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing projects.

add_files(files)¶: Adds files to this project. :param files: List of files or a Collection object.

add_member(user, permissions)¶: Add a member to the project. :param user: Member username :param permissions: Permissions dictionary. :return: Member object.

add_member_division(division, permissions)¶: Add a member (team) to a project. :param division: Division object or division identifier. :param permissions: Permissions dictionary. :return: Member object.

add_member_email(email, permissions=None)¶: Add a member to the project using member email. :param email: Member email. :param permissions: Permissions dictionary. :return: Member object.

add_member_team(team, permissions)¶: Add a member (team) to a project. :param team: Team object or team identifier. :param permissions: Permissions dictionary. :return: Member object.

billing_group = None¶

classmethod create(name, billing_group=None, description=None, tags=None, settings=None, api=None)¶: Create a project. :param name: Project name. :param billing_group: Project billing group. :param description: Project description. :param tags: Project tags. :param settings: Project settings. :param api: Api instance. :return:

create_task(name, app, revision=None, batch_input=None, batch_by=None, inputs=None, description=None, run=False, disable_batch=False, interruptible=True)¶

Creates a task for this project.

Parameters:

name – Task name.
app – CWL app identifier.
revision – CWL app revision.
batch_input – Batch input.
batch_by – Batch criteria.
inputs – Input map.
description – Task description.
run – True if you want to run a task upon creation.
disable_batch – True if you want to disable batching.
interruptible – True if you want to use interruptible instances.

Returns:

Task object.

deepcopy()¶

description = None¶

equals(other)¶

get_apps(offset=None, limit=None)¶: Retrieves apps in this project. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_exports(volume=None, state=None, offset=None, limit=None)¶: Fetches exports for this volume. :param volume: Optional volume identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_files(offset=None, limit=None)¶: Retrieves files in this project. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_imports(volume=None, state=None, offset=None, limit=None)¶: Fetches imports for this project. :param volume: Optional volume identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_members(offset=None, limit=None)¶: Retrieves project members. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_tasks(status=None, offset=None, limit=None)¶: Retrieves tasks in this project. :param status: Optional task status. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

href = None¶

id = None¶

name = None¶

classmethod query(owner=None, offset=None, limit=None, api=None)¶: Query (List) projects :param owner: Owner username. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

remove_member(user)¶: Remove member from the project. :param user: User to be removed.

save(obj, *args, **kwargs)¶

settings¶

tags = None¶

type = None¶

sevenbridges.models.rate_limit module¶

class sevenbridges.models.rate_limit.RateLimit(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Rate limit resource contains info regarding request and computation rate limits.

deepcopy()¶

equals(other)¶

classmethod get(id=None, api=None)¶

instance_limit¶

rate¶

sevenbridges.models.storage_export module¶

class sevenbridges.models.storage_export.Export(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing exports.

deepcopy()¶

destination¶

equals(other)¶

error¶

finished_on = None¶

href = None¶

id = None¶

overwrite = None¶

properties¶

classmethod query(volume=None, state=None, offset=None, limit=None, api=None)¶: Query (List) exports. :param volume: Optional volume identifier. :param state: Optional import sate. :param api: Api instance. :return: Collection object.

result¶

source¶

started_on = None¶

state = None¶

classmethod submit_export(file, volume, location, properties=None, overwrite=False, copy_only=False, api=None)¶: Submit new export job. :param file: File to be exported. :param volume: Volume identifier. :param location: Volume location. :param properties: Properties dictionary. :param overwrite: If true it will overwrite file if exists :param copy_only: If true files are kept on SevenBridges bucket. :param api: Api Instance. :return: Export object.

sevenbridges.models.storage_import module¶

class sevenbridges.models.storage_import.Import(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing imports.

deepcopy()¶

destination¶

equals(other)¶

error¶

finished_on = None¶

href = None¶

id = None¶

overwrite = None¶

classmethod query(project=None, volume=None, state=None, offset=None, limit=None, api=None)¶: Query (List) imports. :param project: Optional project identifier. :param volume: Optional volume identifier. :param state: Optional import sate. :param api: Api instance. :return: Collection object.

result¶

source¶

started_on = None¶

state = None¶

classmethod submit_import(volume, location, project, name=None, overwrite=False, properties=None, api=None)¶: Submits new import job. :param volume: Volume identifier. :param location: Volume location. :param project: Project identifier. :param name: Optional file name. :param overwrite: If true it will overwrite file if exists. :param properties: Properties dictionary. :param api: Api instance. :return: Import object.

sevenbridges.models.task module¶

class sevenbridges.models.task.Task(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing tasks.

abort(obj, *args, **kwargs)¶

app = None¶

batch = None¶

batch_by¶

batch_group¶

batch_input = None¶

classmethod create(name, project, app, revision=None, batch_input=None, batch_by=None, inputs=None, description=None, run=False, disable_batch=False, interruptible=True, api=None)¶: Creates a task on server. :param name: Task name. :param project: Project identifier. :param app: CWL app identifier. :param revision: CWL app revision. :param batch_input: Batch input. :param batch_by: Batch criteria. :param inputs: Input map. :param description: Task description. :param run: True if you want to run a task upon creation. :param disable_batch: If True disables batching of a batch task. :param interruptible: If True interruptible instance will be used. :param api: Api instance. :return: Task object. :raises: TaskValidationError if validation Fails. :raises: SbgError if any exception occurs during request.

created_by = None¶

created_time = None¶

deepcopy()¶

description = None¶

end_time = None¶

equals(other)¶

errors = None¶

executed_by = None¶

execution_status¶

get_batch_children()¶: Retrieves batch child tasks for this task if its a batch task. :return: Collection instance. :raises SbError if task is not a batch task.

get_execution_details()¶: Retrieves execution details for a task. :return: Execution details instance.

href = None¶

id = None¶

inputs¶

name = None¶

outputs¶

parent = None¶

price¶

project = None¶

classmethod query(project=None, status=None, batch=None, parent=None, created_from=None, created_to=None, started_from=None, started_to=None, ended_from=None, ended_to=None, offset=None, limit=None, api=None)¶: Query (List) tasks. Date parameters may be both strings and python date objects. :param project: Target project. optional. :param status: Task status. :param batch: Only batch tasks. :param parent: Parent batch task identifier. :param ended_to: All tasks that ended until this date. :param ended_from: All tasks that ended from this date. :param started_to: All tasks that were started until this date. :param started_from: All tasks that were started from this date. :param created_to: All tasks that were created until this date. :param created_from: All tasks that were created from this date. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

run(obj, *args, **kwargs)¶

save(obj, *args, **kwargs)¶

start_time = None¶

status = None¶

type = None¶

use_interruptible_instances = None¶

warnings = None¶

sevenbridges.models.team module¶

class sevenbridges.models.team.Team(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing teams.

add_member(user)¶: Add member to team :param user: User object or user’s username :return: Added user.

classmethod create(name, division, api=None)¶: Create team within a division :param name: Team name. :param division: Parent division. :param api: Api instance. :return: Team object.

deepcopy()¶

delete()¶

equals(other)¶

classmethod get(id, api=None)¶

get_members(offset=None, limit=None)¶: Fetch team members for current team. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

href = None¶

id = None¶

name = None¶

classmethod query(division, offset=None, limit=None, api=None)¶

reload()¶

remove_member(user)¶: Remove member from the team. :param user: User to be removed.

save(obj, *args, **kwargs)¶

sevenbridges.models.team_member module¶

class sevenbridges.models.team_member.TeamMember(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing team members.

deepcopy()¶

equals(other)¶

href = None¶

id = None¶

role = None¶

username = None¶

sevenbridges.models.user module¶

class sevenbridges.models.user.User(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing tasks.

address = None¶

affiliation = None¶

city = None¶

country = None¶

deepcopy()¶

email = None¶

equals(other)¶

first_name = None¶

classmethod get(user, api=None)¶

href = None¶

last_name = None¶

classmethod me(api=None)¶: Retrieves current user information. :param api: Api instance. :return: User object.

phone = None¶

state = None¶

username = None¶

zip_code = None¶

sevenbridges.models.volume module¶

class sevenbridges.models.volume.Volume(**kwargs)¶

Bases: sevenbridges.meta.resource.Resource

Central resource for managing volumes.

access_mode = None¶

active = None¶

add_member(user, permissions)¶: Add a member to the volume. :param user: Member username :param permissions: Permissions dictionary. :return: Member object.

add_member_division(division, permissions)¶: Add a member (team) to a volume. :param division: Division object or division identifier. :param permissions: Permissions dictionary. :return: Member object.

add_member_team(team, permissions)¶: Add a member (team) to a volume. :param team: Team object or team identifier. :param permissions: Permissions dictionary. :return: Member object.

classmethod create_google_volume(name, bucket, client_email, private_key, access_mode, description=None, prefix=None, properties=None, api=None)¶: Create s3 volume. :param name: Volume name. :param bucket: Referenced bucket. :param client_email: Google client email. :param private_key: Google client private key. :param access_mode: Access Mode. :param description: Volume description. :param prefix: Volume prefix. :param properties: Volume properties. :param api: Api instance. :return: Volume object.

classmethod create_s3_volume(name, bucket, access_key_id, secret_access_key, access_mode, description=None, prefix=None, properties=None, api=None)¶: Create s3 volume. :param name: Volume name. :param bucket: Referenced bucket. :param access_key_id: Amazon access key identifier. :param secret_access_key: Amazon secret access key. :param access_mode: Access Mode. :param description: Volume description. :param prefix: Volume prefix. :param properties: Volume properties. :param api: Api instance. :return: Volume object.

created_on = None¶

deepcopy()¶

description = None¶

equals(other)¶

get_exports(state=None, offset=None, limit=None)¶: Fetches exports for this volume. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_imports(project=None, state=None, offset=None, limit=None)¶: Fetches imports for this volume. :param project: Optional project identifier. :param state: Optional state. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_members(offset=None, limit=None)¶: Retrieves volume members. :param offset: Pagination offset. :param limit: Pagination limit. :return: Collection object.

get_volume_object_info(location)¶: Fetches information about single volume object - usually file :param location: object location :return:

href = None¶

id = None¶

list(prefix=None, limit=50)¶

modified_on = None¶

name = None¶

classmethod query(offset=None, limit=None, api=None)¶: Query (List) volumes. :param offset: Pagination offset. :param limit: Pagination limit. :param api: Api instance. :return: Collection object.

remove_member(user)¶: Remove member from the volume. :param user: User to be removed.

save(obj, *args, **kwargs)¶

service¶

sevenbridges.transfer package¶

Submodules¶

sevenbridges.transfer.download module¶

class sevenbridges.transfer.download.DPartedFile(file_path, session, url, file_size, part_size, retry, timeout, pool)¶

Bases: object

done()¶

get_parts()¶: Partitions the file and saves the part information in memory.

submit()¶: Partitions the file into chunks and submits them into group of 4 for download on the api download pool.

class sevenbridges.transfer.download.Download(url, file_path, part_size=5242880, retry_count=5, timeout=60, api=None)¶

Bases: threading.Thread

add_callback(callback=None, errorback=None)¶: Adds a callback that will be called when the download finishes successfully or when error is raised.

add_progress_callback(callback=None)¶

Adds a progress callback that will be called each time a get_parts is successfully downloaded. The first argument of the progress callback will be a progress object described in sevenbridges.transfer.utils

Parameters:	callback – Callback function

duration¶

path¶

pause()¶: Pauses the download. :raises SbgError: If upload is not in RUNNING state.

progress¶

resume()¶: Resumes the download. :raises SbgError: If download is not in RUNNING state.

run()¶: Runs the thread! Should not be used use start() method instead.

start()¶: Starts the download. :raises SbgError: If download is not in PREPARING state.

start_time¶

status¶

stop()¶: Stops the download. :raises SbgError: If download is not in PAUSED or RUNNING state.

wait()¶: Blocks until download is completed.

sevenbridges.transfer.upload module¶

class sevenbridges.transfer.upload.UPartedFile(fp, file_size, part_size, upload, retry_count, timeout, storage_session, api)¶

Bases: object

done()¶

get_parts()¶: Partitions the file and saves the parts to be uploaded in memory.

submit()¶: Partitions the file into chunks and submits them into group of 4 for upload on the api upload pool. :return: Futures

class sevenbridges.transfer.upload.Upload(file_path, project, file_name=None, overwrite=False, part_size=5242880, retry_count=5, timeout=60, api=None)¶

Bases: threading.Thread

add_callback(callback=None, errorback=None)¶: Adds a callback that will be called when the upload finishes successfully or when error is raised.

add_progress_callback(callback=None)¶

Adds a progress callback that will be called each time a get_parts is successfully uploaded. The first argument of the progress callback will be a progress object described in sevenbridges.transfer.utils

Parameters:	callback – Callback function

duration¶

file_name¶

pause()¶: Pauses the upload. :raises SbgError: If upload is not in RUNNING state.

progress¶

result()¶

resume()¶: Resumes the upload that was paused. :raises SbgError: If upload is not in PAUSED state.

run()¶: Runs the thread! Should not be used use start() method instead.

start()¶: Starts the upload. :raises SbgError: If upload is not in PREPARING state.

start_time¶

status¶

stop()¶: Stops the upload. :raises SbgError: If upload is not in PAUSED or RUNNING state.

wait()¶: Blocks until upload is completed.

sevenbridges.transfer.utils module¶

class sevenbridges.transfer.utils.Part(start=None, size=None)¶

Bases: object

size¶

start¶

class sevenbridges.transfer.utils.Progress(num_of_parts, parts_done, bytes_done, file_size, duration)¶

Bases: object

bandwidth¶

bytes_done¶

duration¶

file_size¶

num_of_parts¶

parts_done¶

progress¶

sevenbridges.transfer.utils.simple_progress_bar(progress)¶

sevenbridges.transfer.utils.total_parts(file_size, part_size)¶

Submodules¶

sevenbridges.api module¶

class sevenbridges.api.Api(url=None, token=None, oauth_token=None, config=None, timeout=None, download_max_workers=16, upload_max_workers=16, proxies=None, error_handlers=None, advance_access=False)¶

Bases: sevenbridges.http.client.HttpClient

Api aggregates all resource classes into single place

actions¶: alias of Actions

apps¶: alias of App

billing_groups¶: alias of BillingGroup

divisions¶: alias of Division

endpoints¶: alias of Endpoints

exports¶: alias of Export

files¶: alias of File

imports¶: alias of Import

invoices¶: alias of Invoice

markers¶: alias of Marker

projects¶: alias of Project

rate_limit¶: alias of RateLimit

tasks¶: alias of Task

teams¶: alias of Team

users¶: alias of User

volumes¶: alias of Volume

sevenbridges.config module¶

class sevenbridges.config.Config(profile=None, proxies=None, advance_access=None)¶

Bases: object

Utility configuration class.

class sevenbridges.config.Profile(profile)¶

Bases: object

CONFIG = '/home/docs/.sevenbridges/sevenbridges-python/config'¶

CREDENTIALS = '/home/docs/.sevenbridges/credentials'¶

advance_access¶

api_endpoint¶

auth_token¶

proxies¶

sevenbridges.config.format_proxies(proxies)¶: Helper method for request proxy key compatibility. :param proxies: Proxies dictionary :return: Dict compatible with request proxy format.

sevenbridges.decorators module¶

sevenbridges.decorators.check_for_error(func)¶: Executes the wrapped function and inspects the response object for specific errors.

sevenbridges.decorators.inplace_reload(method)¶: Executes the wrapped function and reloads the object with data returned from the server.

sevenbridges.decorators.retry(retry_count)¶: Retry decorator used during file upload and download.

sevenbridges.decorators.retry_on_excs(excs, retry_count=3, delay=5)¶

Retry decorator used to retry callables on for specific exceptions.

Parameters:	excs – Exceptions tuple. retry_count – Retry count. delay – Delay in seconds between retries.
Returns:	Wrapped function object.

sevenbridges.errors module¶

exception sevenbridges.errors.AdvanceAccessError(message=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.BadRequest(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.Conflict(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.ExecutionDetailsInvalidTaskType(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.Forbidden(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.LocalFileAlreadyExists(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.MethodNotAllowed(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.NotFound(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.PaginationError(message)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.ReadOnlyPropertyError(message)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.RequestTimeout(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.ResourceNotModified¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.SbgError(message=None, code=None, status=None, more_info=None)¶

Bases: Exception

Base class for SBG errors.

Provides a base exception for all errors that are thrown by sevenbridges-python library.

exception sevenbridges.errors.ServerError(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.ServiceUnavailable(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.TaskValidationError(message, task=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.TooManyRequests(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.Unauthorized(code=None, message=None, more_info=None)¶: Bases: sevenbridges.errors.SbgError

exception sevenbridges.errors.ValidationError(message)¶: Bases: sevenbridges.errors.SbgError