Complete Guide for Seven Bridges API R Client

Tengfei Yin <tengfei.yin@sevenbridges.com>
Nan Xiao <nan.xiao@sevenbridges.com>

2018-04-30

1 Introduction

sevenbridges is an R/Bioconductor package that provides an interface for Seven Bridges public API. The supported platforms includes the Seven Bridges Platform, Cancer Genomics Cloud (CGC), and Cavatica.

Learn more from our documentation on the Seven Bridges Platform and the Cancer Genomics Cloud (CGC).

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1.1 R Client for Seven Bridges API

The sevenbridges package only supports v2+ versions of the API, since versions prior to V2 are not compatible with the Common Workflow Language (CWL). This package provides a simple interface for accessing and trying out various methods.

There are two ways of constructing API calls. For instance, you can use low-level API calls which use arguments like path, query, and body. These are documented in the API reference libraries for the Seven Bridges Platform and the CGC. An example of a low-level request to “list all projects” is shown below. In this request, you can also pass query and body as a list.

(Advanced user option) The second way of constructing an API request is to directly use the httr package to make your API calls, as shown below.

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1.2 API General Information

Before we start, keep in mind the following:

offset and limit

Every API call accept arguments called offset and limit.

By default, offset is set to 0 and limit is set to 100. As such, your API request returns the first 100 items when you list items or search for items by name. To search and list all items, use complete = TRUE in your API request.

Search by ID

When searching by ID, your request will return your exact resource as it is unique. As such, you do not have to manually set offset and limit. It is a good practice to find your resources by their ID and pass this ID as an input to your task. You can find a resource’s ID in the final part of the URL on the visual interface or via the API requests to list resources or get a resource’s details.

Search by name

Search by name returns all partial matches unless you specify exact = TRUE.  

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1.3 Installation

The sevenbridges package is on both the Bioconductor released and devel branches, as shown below.

Since we are constantly improving our API and client libraries, please also visit our GitHub repository for most recent news and for latest version of the package.

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If you do not have devtools

This installation requires that you have the devtools package. If you do not have this package, you can install it from CRAN.

You may got an error and need system dependecies for curl and ssl. For example, in Ubuntu you probably need to do the following first in order to install devtools and in order to build vignettes since you need pandoc.

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If devtools is already installed

Install the latest version for sevenbridges from GitHub with the following:

If you have trouble with pandoc and do not want to install it, set build_vignettes = FALSE to avoid the vignettes build.

2 Quickstart

For more details about how to use the API client in R, please consult the Seven Bridges API Reference section below for a complete guide. This section is a Quickstart which walks through the basics of using the R cliet libary to help you get started.

2.1 Create Auth Object

Before you can access your account via the API, you have to provide your credentials. You can obtain your credentials in the form of an “authentication token” from the Developer Tab under Account Settings on the visual interface. Once you’ve obtained this, create an Auth object so it remembers your authentication token and the path for the API. All subsequent requests will draw upon these two pieces of information.

Let’s load the package first:

You have three different ways to provide your token. Choose from one method below:

  1. Direct authentication. This explicitly and temporarily sets up your token and platform type (or alternatively, API base url) in the function call arguments to Auth().
  2. Authentication via system environment variables. This will read the credential information from two system environment variables: SB_API_ENDPOINT and SB_AUTH_TOKEN.
  3. Authentication via user configuration file. This file, by default $HOME/.sevenbridges/credentials, provides an organized way to collect and manage all your API authentication information for Seven Bridges platforms.

Method 1: Direct authentication

This is the most common method to construct the Auth object. For example:

Using platform: cgc
== Auth ==
url : https://cgc-api.sbgenomics.com/v2/
token : <your_token>

Method 2: Environment variables

To set the two environment variables in your system, you could use the function sbg_set_env(). For example:

Note that this change might be just temporary, please feel free to use the standard method to set persistent environment variables according to your operation system.

Create an Auth object:

Method 3: User configuration file

Assume we have already created the configuration file named credentials under the directory $HOME/.sevenbridges/:

[aws-us-tengfei]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user

# This is a comment:
# another user on the same platform
[aws-us-yintengfei]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user

[default]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token = token_for_this_user

[gcp]
api_endpoint = https://gcp-api.sbgenomics.com/v2
auth_token = token_for_this_user

To load the user profile aws-us-tengfei from this configuration file, simply use:

If profile_name is not specified, we will try to load the profile named [default]:

Note: API paths (base URLs) differ for each Seven Bridges environment. Be sure to provide the correct path for the environment you are using. API paths for some of the environments are as follows:

Platform API Base URL Platform Name
Cancer Genomics Cloud (CGC) https://cgc-api.sbgenomics.com/v2 "cgc"
Seven Bridges Platform on Amazon Web Services (US) https://api.sbgenomics.com/v2 "aws-us"
Seven Bridges Platform on Amazon Web Services (EU) https://eu-api.sbgenomics.com/v2 "aws-eu"
Seven Bridges Platform on Google Cloud Platform (GCP) https://gcp-api.sbgenomics.com/v2 "gcp"
Cavatica https://cavatica-api.sbgenomics.com/v2 "cavatica"

Please refer to the API reference section for more usage and technical details about the three authentication methods.

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2.2 Get User Information

Get your own information

This call returns information about your account.

== User ==
href : https://cgc-api.sbgenomics.com/v2/users/tengfei
username : tengfei
email : tengfei.yin@sevenbridges.com
first_name : Tengfei
last_name : Yin
affiliation : Seven Bridges Genomics
country : United States
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Get information about a user

This call returns information about the specified user. Note that currently you can view only your own user information, so this call is equivalent to the call to get information about your account.

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2.3 Rate Limit

This call returns information about your current rate limit. This is the number of API calls you can make in one hour.

== Rate Limit ==
limit : 1000
remaining : 993
reset : 1457980957
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2.4 Show Billing Information

Each project must have a Billing Group associated with it. This Billing Group pays for the storage and computation in the project.

For example, your first project(s) were created with the free funds from the Pilot Funds Billing Group assigned to each user at sign-up. To get information about billing:

For more information, use breakdown = TRUE.

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2.5 Create Project

Projects are the core building blocks of the platform. Each project corresponds to a distinct scientific investigation, serving as a container for its data, analysis tools, results, and team of collaborators.

Create a new project called “api testing” with the billing group id obtained above.

== Project ==
id : tengfei/api-testing
name : api testing
description : Just a test
billing_group_id : <fake_bid>
type : v2
-- Permission --
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2.6 Get Details about Existing Project

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2.7 Copy Public Apps into Your Project

Seven Bridges maintains workflows and tools available to all of its users in the Public Apps repository.

To find out more about public apps, you can do the following:

Now, from your Auth object, you copy an App id into your project id with a new name, following this logic.

The short name is changed to newcopyofstar.

== App ==
id : tengfei/api-testing/newcopyofstar/0
name : RNA-seq Alignment - STAR
project : tengfei/api-testing-2
revision : 0

Alternatively, you can copy it from the app object.

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2.8 Import CWL App and Run a Task

You can also upload your own Common Workflow Language JSON file which describes your app to your project.

Note: Alternatively, you can directly describe your CWL tool in R with this package. Please read the vignette on “Describe CWL Tools/Workflows in R and Execution”.

You will get an app id, like the one below:

"tengfei/api-testing/starlocal/0"

It’s composed of the following elements:

  1. project id : tengfei/api
  2. app short name : runif
  3. revision : 0

Alternatively, you can describe tools in R directly, as shown below:

library("sevenbridges")

in.lst <- list(
    input(id = "number",
          description = "number of observations",
          type = "integer",
          label = "number",
          prefix = "--n",
          default = 1,
          required = TRUE,
          cmdInclude = TRUE),
    input(id = "min",
          description = "lower limits of the distribution",
          type = "float",
          label = "min",
          prefix = "--min",
          default = 0),
    input(id = "max",
          description = "upper limits of the distribution",
          type = "float",
          label = "max",
          prefix = "--max",
          default = 1),
    input(id = "seed",
          description = "seed with set.seed",
          type = "float",
          label = "seed",
          prefix = "--seed",
          default = 1))

# the same method for outputs
out.lst <- list(
    output(id = "random",
           type = "file",
           label = "output",
           description = "random number file",
           glob = "*.txt"),
    output(id = "report",
           type = "file",
           label = "report",
           glob = "*.html"))

rbx <- Tool(
    id = "runif",
    label = "Random number generator",
    hints = requirements(docker(pull = "tengfei/runif"), cpu(1), mem(2000)),
    baseCommand = "runif.R",
    inputs = in.lst,  # or ins.df
    outputs = out.lst)

fl <- "inst/docker/sevenbridges/rabix/runif.json"
write(rbx$toJSON(pretty = TRUE), fl)

Then, you can add it like this:

Please consult another tutorial vignette("apps", "sevenbridges") about how to describe tools and flows in R.

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2.9 Execute a New Task

2.9.1 Find your app inputs

Once you have copied the public app admin/sbg-public-data/rna-seq-alignment-star/5 into your project, username/api-testing, the app id in your current project is username/api-testing/newcopyofstar. Conversely, you can use another app you already have in your project for this Quickstart.

To draft a new task, you need to specify the following:

  • The name of the task
  • An optional description
  • The app id of the workflow you are executing
  • The inputs for your workflow. In this case, the CWL app accepts four parameters: number, min, max, and seed.

You can always check the App details on the visual interface for task input requirements. To find the required inputs with R, you need to get an App object first.

Conversely, you can load the app from a CWL JSON and convert it into an R object first, as shown below.

##                                id                    label    type
## 1                    #sjdbGTFfile              sjdbGTFfile File...
## 2                          #fastq                    fastq File...
## 3               #genomeFastaFiles         genomeFastaFiles    File
## 4 #sjdbGTFtagExonParentTranscript      Exons' parents name  string
## 5       #sjdbGTFtagExonParentGene                Gene name  string
## 6          #winAnchorMultimapNmax         Max loci anchors     int
## 7             #winAnchorDistNbins Max bins between anchors     int
##   required fileTypes
## 1    FALSE      null
## 2     TRUE      null
## 3     TRUE      null
## 4    FALSE      null
## 5    FALSE      null
## 6    FALSE      null
## 7    FALSE      null
##                                id                    label    type
## 1                    #sjdbGTFfile              sjdbGTFfile File...
## 2                          #fastq                    fastq File...
## 3               #genomeFastaFiles         genomeFastaFiles    File
## 4 #sjdbGTFtagExonParentTranscript      Exons' parents name  string
## 5       #sjdbGTFtagExonParentGene                Gene name  string
## 6          #winAnchorMultimapNmax         Max loci anchors     int
## 7             #winAnchorDistNbins Max bins between anchors     int
##                  id            label    type
## 2            #fastq            fastq File...
## 3 #genomeFastaFiles genomeFastaFiles    File

Note input_matrix and output_matrix are useful accessor for Tool, Flow, App object as shown below in App example, you can directly call these two function on a JSON file as well.

In the response body, locate the names of the required inputs. Note that task inputs need to match the expected data type and name. In the above example, we see two required fields:

  • fastq: This input takes a file array as indicated by “File…”
  • genomeFastaFiles: This is a single file as indicated by “File”.

We also want to provide a gene feature file:

  • sjdbGTFfile: A single file as indicated by “File”.

You can find a list of possible input types below:

  • number, character or integer: you can directly pass these to the input parameter as it is.
  • enum type: Pass this value to the input parameter.
  • file: This input is a file. However, while some inputs accept only single file (File), other inputs takes more than one file (File arrays, FilesList, or ‘File...’ ). This input require you to pass a Files object (for a single file input) or FilesList object (for inputs which accept more than one file) or simply a list in a “Files” object. You can search for your file by id or by name with an exact match (exact = TRUE), as shown in the example below.
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2.9.4 Draft a batch task

Now let’s do a batch with 8 files in 4 groups, which is batched by metadata sample_id and library_id. We will assume each file has these two metadata fields entered. Since these files can be evenly grouped into 4, we will have a single parent batch task with 4 child tasks.

Now you have a draft batch task, please check it out in the visual interface. Your response body should inform you of any errors or warnings.

Note: you can also directly pass file id or file names as characters to inputs list, the package will first guess if the passed strings are file id (24 bit hexdecimal) or names, then convert it to Files or FilesList object. However, as a good practice, we recommend you construct your files object(e.g. p$file(id = , name = )) first, check the value, then pass it to task_add inputs, this is a more safe approach.

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2.10 Run a Task

Now, we are ready to run our task.

Before you run your task, you can adjust your draft task if you have any final modifications. Or, you can delete the draft task if you no longer wish to run it.

After you run a task, you can abort it

If you want to update your task and then re-run it, follow the example below.

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2.11 Task Monitoring

To monitor your task as it runs, you can always request a task update to ask your task to report its status. Or, you can monitor a running task with a hook function, which triggers the function when that status is “completed”. Please check the details in section below.

By default, your task alerts you by email when it has been completed.

Use the following to download all files from a completed task.

Instead of the default task monitor action, you can use setTaskHook to connect a function call to the status of a task. When you run tsk$monitor(time = 30) it will check your task every 30 seconds to see if the current task status matches one of the following statuses: “queued”, “draft”, “running”, “completed”, “aborted”, and “failed”. When it finds a match for the task status, getTaskHook returns the function call for the specific status.

## function (...) 
## {
##     cat("\r", "completed")
##     return(TRUE)
## }
## <environment: 0x6d466e8>

If you want to customize the monitor function, you can adjust the following requirement. Your function must return TRUE or FALSE in the end. When it is TRUE (or non-logical value) it means the monitoring will be terminated after it finds a status matched and the function executes, such as when the task is completed. When it is FALSE it means the monitoring will continue for the next iteration of checking, e.g. when it is “running”, you want to keep tracking.

Follow the example below to set a new function to monitor the status “completed”. Then, when the task is completed, it will download all task output files to local folder.

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3 Seven Bridges API Reference

The sevenbridges package provides a user-friendly interface so you do not have to combine several api() calls and constantly reference the API documentation to issue API requests.

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3.1 Authentication

Before you can interact with the API, you need to construct an Auth object which stores the following information:

The general authentication logic for Auth() is as follows:

  1. The package will use the direct authentication method if from is not specified explicitly or specified as from = "direct".
  2. The package will load the authentication information from environment variables when from = "env", or user configuration file when from = "file".

3.1.1 Direct authentication

To use direct authentication, users need to specify one of platform or url, with the corresponding token. Examples of direct authentication:

The above will use the Seven Bridges Platform on AWS (US).

The above will use the specified url as base URL for the API calls. In this example, the url points to the Seven Bridges Platform on Google Cloud Platform (GCP).

The above will use the Cancer Genomics Cloud environment, since no platform nor url were explicitly specified (not recommended).

Note: platform and url should not be specified in the same time.

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3.1.2 Authentication via system environment variables

The R API client supports reading authentication information stored in system environment variables.

To set the two environment variables in your system, you could use the function sbg_set_env(). For example:

See if the environment variables are correctly set:

To create an Auth object:

To unset the two environment variables:

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3.1.3 Authentication via user configuration file

You can create an ini-like file named credentials under the folder $HOME/.sevenbridges/ and maintain your credentials for multiple accounts across various Seven Bridges environments. An example:

[aws-us-tengfei]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user

# This is a comment:
# another user on the same platform
[aws-us-yintengfei]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user

[default]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token = token_for_this_user

[gcp]
api_endpoint = https://gcp-api.sbgenomics.com/v2
auth_token = token_for_this_user

Please make sure to have two fields exactly named as api_endpoint and auth_token under each profile.

To load the default profile (named [default]) from the default user configuration file ($HOME/.sevenbridges/credentials), please use:

To load the user profile aws-us-tengfei from this configuration file, change the profile_name:

To use a user configuration file from other locations (not recommended), please specify the file path using the argument config_file. For example:

Note: If you edited the credentials file, please use Auth() to re-authenticate.

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3.2 List All API Calls

If you did not pass any parameters to api() from Auth, it will list all API calls. Any parameters you provide will be passed to the api() function, but you do not have to pass your input token and path once more ince the Auth object already has this information. The following call fromt he Auth object will check the response as well.

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3.3 Offset, Limit, Search, and Advance Access Features

3.3.1 offset and limit

Every API call accepts two arguments named offset and limit.

  • offset defines where the retrieved items started.
  • limit defines the quantity of items you want to get.

By default, offset is set to 0 and limit is set to 50. As such, your API request returns the first 100 items when you list items or search for items by name. To search and list all items, use complete = TRUE in your API request.

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3.3.2 Search by ID

When searching by ID, your request will return your exact resource as it is unique. As such, you do not have to manually set offset and limit. It is a good practice to find your resources by their ID and pass this ID as an input to your task. You can find a resource’s ID in the final part of the URL on the visual interface or via the API requests to list resources or get a resource’s details.

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3.3.3 Search by name

Search by name returns all partial matches unless you specify exact = TRUE. This type of search will only search across current pulled content, so use complete = TRUE if you want to search across everything.

For example, to list all public apps, use visibility argument, but make sure you pass complete = TRUE to it, to show every single things. This arguments generally works for items like “App”, “Project”, “Task”, “File”, etc.

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3.3.4 Experiment with Advance Access features

Similar to offset and limit, every API call accepts an argument named advance_access. This argument was first introduced in August 2017 and controls if a special field in the HTTP request header will be sent, which can enable the access to the “Advance Access” features in the Seven Bridges API. Note that the Advance Access features in the API are not officially released yet, therefore the API usages are subject to change, so please use with discretion.

In addition to modifying each API call that uses Advance Access features, the option can be also set globally at the beginning of your API script. This offers a one-button switch for users who wants to experiment with the Advance Access features. The option is disabled by default:

## [1] FALSE

For example, the “folders” API is in Advance Access as of August, 2017. If we try to use the folders API to create a folder with the advance_access option disabled, it will return an error message:

## [1] "Advance access feature needs X-SBG-Advance-Access: advance header."

To enable the Advance Access features, one can use

at the beginning of their scripts. Let’s check if the option has been enabled:

## [1] TRUE

Send the API call again:

The information of the newly created folder will be returned:

## $href
## [1] "https://api.sbgenomics.com/v2/files/{folder_id}"
##
## $id
## [1] "folder_id"
##
## $name
## [1] "new-folder"
##
## $project
## [1] "owner/project"
##
## $parent
## [1] "parent_folder_id"
##
## $type
## [1] "folder"
##
## $created_on
## [1] "2017-08-22T12:49:21Z"
##
## $modified_on
## [1] "2017-08-22T12:49:21Z"
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3.4 Query Parameter 'fields'

Please read the documentation detail.

All API calls take the optional query parameter fields. This parameter enables you to specify the fields you want to be returned when listing resources (e.g. all your projects) or getting details of a specific resource (e.g. a given project).

The fields parameter can be used in the following ways:

  1. No fields parameter specified: calls return default fields. For calls that return complete details of a single resource, this is all their properties; for calls that list resources of a certain type, this is some default properties.

  2. The fields parameter can be set to a list of fields: for example, to return the fields id, name and size for files in a project, you may issue the call p$file(fields = "id,name,size")

  3. The fields parameter can be used to exclude a specific file: if you wish to omit certain field from the response, do so using the fields parameter with the prefix !. For example, to get the details of a file without listing its metadata, issue a call p$file(fields = '!metadata') The entire metadata field will be removed from the response.

  4. The fields parameter can be used to include or omit certain nested fields, in the same way as listed in 2 and 3 above: for example, you can use metadata.sample_id or origin.task for files.

  5. To see all fields for a resource, specify fields="_all". This returns all fields for each resource returned. Note that if you are getting the details of a specific resource, the use of fields="_all" won’t return any more properties than would have been shown without this parameter — the use case is instead for when you are listing details of many resources. Please use with care if your resource has particularly large fields; for example, the raw field for an app resource contains the complete CWL specification of the app which can result in bulky response if listing many apps.

  6. Negations and nesting can be combined freely, so, for example, you can issue p$file(fields="id,name,status,!metadata.library,!origin") or p$task(fields="!inputs,!outputs").

Please try following examples

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3.5 Rate Limits

This call returns information about your current rate limit. This is the number of API calls you can make in one hour.

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3.6 Users

This call returns a list of the resources, such as projects, billing groups, and organizations, that are accessible to you. Currently, this call will only return a successful response if {username} is replaced with your own username. Be sure to capitalize your username in the same way as when you registered for an account.

If you did not provide a username, your user information will be shown.

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3.7 Billing Group and Invoices

3.7.1 For billing

If no billing group id is provided, this call returns a list of paths used to access billing information via the API. If a username is provided, this call lists all your billing groups, including groups that are pending or which have been disabled. If you specify breakdown = TRUE, the call below returns a breakdown of the spending per-project for the billing group specified by billing_group. Information is also displayed for each of the projects a particular billing group is associated with, including task executions, their initiating user, start and end time, and their cost.

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3.7.2 For invoices

If no Billing Group id provided, This call returns a list of invoices, with information about each, including whether or not the invoice is pending and the billing period it covers. This call returns information about all your available invoices, unless you use the query parameter bg_id to specify the ID of a particular Billing Group, in which case it will return the invoice incurred by that Billing Group only. If an invoice id is provided, this call retrieves information about the specified invoice, including the costs for analysis and storage and the invoice period.

Note: Currently, invoice is not an object. Instead, it just returns a list.

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3.8 Project

Projects are the basic units to organize different entities: files, tasks, apps, etc. As such, many actions stem from the Project object.

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3.8.1 List all projects

The following call returns a list of all projects of which you are a member. Each project’s project_id and path will be returned.

If you want to list the projects owned by and accessible to a particular user, specify the owner argument as follows. Each project’s ID and path will be returned.

To get details about project(s), use detail = TRUE, as shown below.

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3.8.2 Partial match project name

For a more friendly interface and convenient search, the sevenbridges package supports partial name matching. The first argument for the following request is name.

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3.8.3 Create a new project

To create a new project, users need to specify the following:

  • name (required)
  • billing_group_id (required)
  • description (optional)
  • tags (optional): This has to be a list(). If you are using the API on the CGC environment, you can create a TCGA Controlled Data project by specifying TCGA in tags.
  • type (optional): By default, we create a V2, CWL compatible project.
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3.8.4 Create a new project with TCGA controlled data on CGC

Follow the directions above, but pass tcga as a value for tags.

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3.8.5 Delete a project

You can delete a single project by making the request to $delete(). Note that the returned object from a$project() sometimes returns list if you use partial matching by name. The $delete() request cannot operate on a list. If you want to operate on a list of object, read more about batch functions in the relevant section below.

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3.8.6 Update/edit a project

You can update the following information about an existing project:

  • name
  • description
  • billing_group_id

3.8.7 Project member

3.8.7.1 List members

This call returns a list of the members of the specified project. For each member, the response lists:

  • The member’s username
  • The member’s permissions in the specified project
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3.8.7.2 Add a member

This call adds a new user to the specified project. It can only be made by a user who has admin permissions in the project.

Requests to add a project member must include the key permissions. However, if you do not include a value, the member’s permissions will be set to false by default.

Set permission by passing the following values: copy, write, execute, admin, or read.

Note: read is implicit and set by default. You can not be a project member without having read permissions.

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3.8.7.3 Update a member

This call edits a user’s permissions in the specified project. It can only be made by a user who has admin permissions in the project.

== Member ==
username : yintengfei
-- Permission --
read : TRUE
write : FALSE
copy_permission : TRUE
execute : FALSE
admin : FALSE
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3.8.7.4 Delete a member

To delete an existing member, just call the delete() action on the Member object.

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3.8.8 List all files

To list all files belonging to a project, use the following request:

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3.9 Files, Metadata, and Tags

3.9.1 List all files

A better way to list files in a project uses the following:

Alternatively you can get files from the Auth object.

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3.9.2 Search and filter file(s)

3.9.2.1 Rule of thumb

You can easily search by partial name, exact name, or id for many items like project, apps, files. Fortunately, we have more powerful filters for files. User could serach by metadata, tags, and original task id.

  1. First rule: understand the scope: We know we have default limit = 100 and offset = 0 for first 100 items, unless you are using arguments complete = TRUE. Things are different when it comes to files. When you search with exact name (search by name with exact = TRUE on), metadata, or tags, it searches through ALL files. You do not have to specify complete = TRUE. Simply provide the project id or make the call from a project object as shown below.

  2. Second rule: understand the operation: When filtering on any resource, including the same field several times with different filtering criteria results in an implicit OR operation for that field and the different criteria.When filtering by different specified fields, an implicit AND is performed between those criteria." so which are different fields, metadata, origin.task, tags, those are different fields. Note different metadata fields are treated as different fields as well, so it will be AND operation for different metadata field.

So for a quick example, this examples gives me all files in project “tengfei/demo” that with metadata sample_id “Sample1” OR “Sample2”, AND the library id has to be “EXAMPLE”, AND tags has either “hello” OR “world”.

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3.9.2.2 Search by name and id

There are two ways to return the exact file you want. One is by id, the other one is by exact name.

For advanced users: When searching by name with exact = TRUE, it directly uses our public API call to match exact name and return the object with a single query. When you turn off exact, it will grep all files or files defined with limit and offset first, then match by name, which could be slow.

To get the file id, you can check the url on the visual interface from the file details page.

To get more than one object, the arguments id and name both accept vectors, so you can pass more than one id or name to it.

If you did not use exact = TRUE, the API will assume it is pattern grep and use partial matching.

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3.9.2.3 Search by metadata

When you specify different metadata fields, the values use an AND operation, and when you specify the same metadata fields, the values use an OR operation.

To list all files in project “tengfei/demo”, that have a sample_id of “Sample1” OR “Sample2” AND another metadata field library_id set to “EXAMPLE”, make the following request

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3.9.2.4 Search by tags

Tags are more flexible than metadata. You can search with multiple tags using an OR operation.

This examples shows how to return all files with the tag “s1” OR “s2”.

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3.9.2.5 Search by original task id

You can also get all files from a task. There are two ways to do it:

  1. Started from the Task object;
  2. Use the filter criteria.
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3.9.3 Copy a file or group of files

This call copies the specified file to a new project. Files retain their metadata when copied, but may be assigned new names in their target project.

Note that Controlled Data files may not be copied to Open Data projects. To make this request, you should have copy permission within the project you are copying from.

Let’s try to copy a file from the Public File repository. The file’s id is “561e1b33e4b0aa6ec48167d7”.

You must provide

  • id: file id or list/vector of files ids
  • project: project id.
  • name (optional):if omitted, use the same name as the original file name

NOTE: To copy a group of files, you need the Auth$copyFile() interface. The id of the files in your project will be different from their id in the Public Files repository.

Alternatively, you copy a single file as shown below.

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3.9.4 Delete file(s)

Note: The delete action only works for one file at a time. Be sure your file call returns a single file rather than a file list.

You can also delete a group of files or FilesList object, just be careful when using this function.

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3.9.5 Download files

To get the download information, please use the following:

To download directly from R, use the download call directly from a single File object.

I also created a download function for FilesList object to save your time, as follows:

To download all files from a project, use the following:

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3.9.6 Upload files via API

Seven Bridges platforms provide a few different methods for data import:

  • Import from FTP or HTTP with the web interface
  • The GUI uploader
  • The file upload API that you can directly call with the sevenbridges package
  • The command line uploader which can be involked with the sevenbridges package

Use the API client uploader by calling the project$upload function to upload a file, a file list, or a folder recursively or via a manifest file.

3.9.6.4 Upload files via defined manifest file

A manifest file is a file used to define metadata values for a set of files. It can be used when uploading files to the Platform to set their metadata.The supported file format for the manifest file is CSV, i.e. comma separated values. A CSV file contains a number of rows with columns which are separated with a comma. Format of manifest file is defined in the documentaion online

Some requirements:

  • The first row has to contain column names which are parsed as metadata fields (e.g. “sample”“,”library“”). When it’s not customized fields, we do converstion for meta fields like “sample_id” which need to be string.
  • The first column has to contain the names of the files which will be uploaded. In case the files are not in the same directory as the manifest file, you should also include a path to the files (e.g. ../filename.fastq).

We allow users to

  • choose to upload metadata or not.
  • choose to use subset style to upload only part of metadata
  • choose to use subset style to upload only part of files with filter

Please check couple examples below

## upload all fiels and all metadatas
p$upload(manifest_file = "~/manifest.csv")
## verbal = TRUE, print single file level progress
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE, verbal = TRUE)
## manifest_metadata = FALSE doens't attach any meta
p$upload(manifest_file = "~/manifest.csv", manifest_metadata = FALSE, overwrite = TRUE)
## filter fils first, upload only files that score < 0.5
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE, subset = score < 0.5)
## attach all meta except "bad_field" and "sample_id"
p$upload(manifest_file = "~/manifest.csv", overwrite = TRUE,
         subset = score < 0.5, select = -c(bad_field, sample_id))
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3.9.7 Upload files via command line uploader

As an alternative to API file uploading, we also offer an interface in the sevenbridges package for uploading (possibly large) files via the Java-based command line uploader.

The first step is to download the command line uploader. With get_uploader(), users can easily download the uploader to a local directory for a specified Seven Bridges platform, for example, the Cancer Genomics Cloud:

To list the available projects accessible from your account via the uploader, use cli_list_projects(), with your authentication token for that platform and the directory containing the uploader:

The function will return a character vector containing the available projects which you could upload files to, in the form of username/project-name.

Similarly, to list all the file tags in a project via the uploader, use cli_list_tags():

Eventually, use cli_upload() to upload local files to a project:

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3.9.8 Update a file

You can call the update() function from the Files object. Using this call, the following can be updated:

  • The file’s name.
  • The file’s metadata. The metadata is in the form of a list. Note that as this call overwrites all the metadata for a given file, please supply a full list of all the metadata for the file. Conversely, you can use the set_meta() function to patch but not overwrite the metadata for a file.

If no parameters were provided, this call will just get the details of that file and update the object itself.

== File ==
id : 56c7916ae4b03b56a7d7
name : sample.fastq
project : tengfei/demo-project

Show metadata

Update meta

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3.9.9 Metadata operations

Learn about metadata fields and their values for the relevant environment: [Seven Bridges Platform] [CGC].

Note that the name of a file is not the same as its ID. A file’s ID is a hexadecimal string automatically assigned to a file in a project. The file’s name is a human-readable string. For information, please see the API overview for the Seven Bridges Platform and for the CGC.

Get metadata

To get the metadata for a file, call the meta() function, as shown below.

Set metadata

Files from curated datasets on Seven Bridges environments have a defined set of metadata which is visible on the visual interface of each environment. However, you can also pass additional metadata for each file which is stored with your copy of the file in your project.

To set metadata but not overwrite all previously stored metadata, call the set_meta() function from the Files object. Unlike the update() function for the Files object, the set_meta() function doesn’t overwrite the metadata field. To overwrite the metadata field, use the update() function or pass the optional argument overwrite = TRUE for the set_meta() call.

Check details of each metadata field

You can use the Metadata() constructor to check the details of each metadata field. Simply call the function (name of the metadata) to display descriptions and enumerated itemts. Please pay attention to the suggested_values field.

As you can see, some metadata fields have suggested values. To construct the metadata, use Metadata() directly to pass the metadata fields and their values directly into the call. The call will perform the validation.

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3.9.10 Tag file(s)

You can tag your files with keywords or strings to make it easier to identify and organize files. Tags are different from metadata, and are more convenient and visible from the files list on the visual interface.

Add a new tag

To add a new tag, call the obj$add_tag() method for the File object with a single tag string or a list or vector of tags.

Overwrite the tags for a file

To completely overwrite the tags for a file, use the obj$set_tag() method, which contains the default argument overwrite = TRUE.

Let’s use a file called sample.bam and play with its tags.

Below, find convenient methods for FilesList. Let’s add the tag “s1” to a group files matching “Sample1” and add the tag “s2” to a group of files that match “s2”. Then, we will filter by these tags to obtain specific files.

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3.10 App

All Seven Bridges environments support the Common Workflow Language (CWL) natively to allow for reproducible and portable workflows and tools. In this section, we will work with apps, including tools and workflows, via the API using the sevenbridges R package.

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3.10.1 List all apps

This call lists all the apps available to you.

Search for an app by name

To search for a specific app by its name, pass a pattern for the name argument or provide a unique id as shown below.

List all apps in a project

To list all apps belonging to a specific project, use the project argument.

List all public apps

To list all public apps, use the visibility argument.

Search through all public apps in all locations

To search for a public app cross all locations, make the following call. Note that this may take a bit of time.

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3.10.2 Copy an app

This call copies the specified app to a specified project. The app should be one in a project that you can access, either an app which has been uploaded by a project member or a publicly availble app which has been copied to the project.

This call requires the following two arguments:

  • project: include the project id
  • name (optional): use this field to optionally re-name your app

You can also copy directly from the app object, as shown below.

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3.10.3 Get an app’s CWL description

This call returns the raw CWL of a specific app, including its raw CWL. The call differs from the call to GET details of an app in that it returns a JSON object that is the CWL.

The app should be one in a project that you can access, either an app which has been uploaded by a project member or a publicly availble app which has been copied to the project.

To get a specific revision, pass the revision argument.

Coming soon: converting apps to CWL objects

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3.10.4 Add CWL as an app

To add a CWL object as an app, use the app_add function call for a Project object. The following two parameters are required:

  • short_name: Project short names are based on the name you give to a project when you create it. Learn more about project short names on the Seven Bridges Platform or the CGC.
  • filename: The name of the JSON file containing the CWL.

Note: If you provide the same short_name, this will add a new revision.

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3.10.5 Describe CWL in R directly

This is introduced in another vignette (vignette("apps", "sevenbridges")).

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3.10.6 Create test or keep previous test for Tool

On sevenbridges platform, when you create or update your tools in the GUI, there is a test tab allow users to tweak the parameters and see what it looks like in your commandline simulatd terminal. To do this via R when you push your Tool object to your project, you need to provide “sbg:job” information like the example shown below

Or if you have created a test info on the platform or previously pushed one, and you want to keep the previous test setup. We provide a arguments called keep_test to allow you keep the previous revision’s test information.

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3.11 Task

3.11.2 Create a draft task

To create a draft task, you need to call the task_add function from the Project object. And you need to pass the following arguments:

  • name: The name for this task
  • description (optional): A description for this task
  • app: The app id
  • inputs: A list of inputs for this task
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3.11.3 Modify a task

Call the update function from a Task object to update the following:

  • name
  • description
  • inputs list. Note that you can only update the items you provided.
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3.11.4 Run a task

This call runs (“executes”) the specified task. Only tasks with a “DRAFT” status may be run.

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### Monitor a running task and set the hook function

To monitor a running task, call monitor from a Task object.

  • First argument, set the interval time to check the status
  • Rest arguments might be used for hook function

Get and set default a hook function for task status. Currently, failed tasks will break the monitoring.

Note: Hook function has to return TRUE (break monitoring) or FALSE (continuing) in the end.

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3.11.5 Abort a running task

This call aborts the specified task. Only tasks whose status is “RUNNING” may be aborted.

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3.11.7 Download all files from a completed task

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3.12 Volumes

Cloud storage providers come with their own interfaces, features and terminology. At a certain level, though, they all view resources as data objects organized in repositories. Authentication and operations are commonly defined on those objects and repositories, and while each cloud provider might call these things different names and apply different parameters to them, their basic behavior is the same.

Seven Bridges environments mediate access to these repositories using volumes. A volume is associated with a particular cloud storage repository that you have enabled Seven Bridges to read from (and, optionally, to write to). Currently, volumes may be created using two types of cloud storage repository: Amazon Web Services’ (AWS) S3 buckets and Google Cloud Storage (GCS) buckets.

A volume enables you to treat the cloud repository associated with it as external storage. You can ‘import’ files from the volume to your Seven Bridges environment to use them as inputs for computation. Similarly, you can write files from the Seven Bridges environment to your cloud storage by ‘exporting’ them to your volume.

Learn more about volumes on the Seven Bridges Platform and the CGC.

3.12.3 Get a volume’s detail

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3.12.4 Delete volume

This call deletes a volume you’ve created to refer to storage on Amazon Web Services or Google Cloud Storage.

Note that any files you’ve imported from your volume onto a Seven Bridges environment, known as an alias, will no longer be usable. If a new volume is created with the same volume_id as the deleted volume, aliases will point to files on the newly created volume instead (if those exist).

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3.12.6 Export file from project to volume

Important :

  • 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 a Seven Bridges environment. 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.
  • If this call is successful, the original project file will become an alias to the newly exported object on the volume. The source file will be deleted from the Seven Bridges environment and, if no more copies of this file exist, it will no longer count towards your total storage price on the Seven Bridges environment.

When testing please update your file in a project.

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3.13 Public Files and Apps

Seven Bridges hosts publicly accessible files and apps on its environments. The sevenbridges package provides two easy function calls from the Authentication object to search for and copy files and apps to a project.

3.14 Get Raw Response from httr

In the easy API, we return an object which contains the raw response from httr as a field. You can either call response() on that object or just use the field as is.

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3.15 Batch Operation on Project/Files/Tasks

Currently, users have to use lapply to do those operations themselves. It’s a simple implementation.

In this package, we implement delete and download for some objects like task, project, or file.

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4 Cheatsheet

Quick cheat sheet (in progress)

## Authentication
getToken()
a <- Auth(token = token)
a <- Auth(token = token, platform = "cgc")
a <- Auth(from = "env")
a <- Auth(from = "file", profile_name = "aws-us-tengfei")

## list API
a$api()

## Rate limits
a$rate_limit()

## Users
a$user()
a$user("tengfei")

## billing
a$billing()
a$billing(id = , breakdown = TRUE)
a$invoice()
a$invoice(id = "fake_id")

## Project
### create new project
a$project_new(name = , billing_group_id = , description = )
### list all project owned by you
a$project()
a$project(owner = "yintengfei")
### partial match
p <- a$project(name = , id = , exact = TRUE)
### delete
p$delete()
### update
p$update(name = , description = )
### members
p$member()
p$member_add(username = )
p$member(username = )$update(write = , copy = , execute = )
p$memeber(usrname = )$delete()

## file
### list all files in this project
p$file()
### list all public files
a$file(visibility = "public")
### copy
a$copyFile(c(fid, fid2), project = pid)
### delete
p$file(id = fid)$delete()
### download
p$file()[[1]]$download_url()
p$file(id = fid3)$download("~/Downloads/")
### download all
download(p$file())
### update a file
fl$update(name = , metadata = list(a = , b = , ...))
### meta
fl$meta()
fl$setMeta()
fl$setMeta(..., overwrite = TRUE)

## App
a$app()
### apps in a project
p$app()
p$app(name, id, revision = )
a$copy_app(aid, project = pid, name = )
### add
p$app_add(short_name = , filename =)

## Task
a$task()
a$task(name = , id = )
a$task(status = )

p$task()
p$task(name = , id = )
p$task(status = )

tsk <- p$task(name = , id = )
tsk$update()
tsk$abort()
tsk$run()
tsk$download()
tsk$detele()
tsk$getInputs()
tsk$monitor()

getTaskHook()
setTaskHook(status = , fun = )
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