Projects, Files, Apps and Tasks execution with Seven Bridges API R Client

2024-07-02

Projects

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 collaborators.

All projects related operations can be accessed through the projects path from the Auth object. Projects is also a Resource R6 class which contains implementation of query(), get() and delete() methods for listing, fetching a single project and deleting a specific project. Besides those, there is also a custom method to create projects.

When you fetch a single project, it is represented as an object of the Project class containing all project information and additional methods that can be executed directly on the project such as: updating the project, project members management, listing project files, apps and tasks etc.

List all projects

The following call returns a Collection with a list of all projects you are a member of. Each project’s project_id and name will be printed. For full project information, you can access the items field in the Collection object and preview the list of projects.

# List and view your projects
all_my_projects <- a$projects$query()
View(all_my_projects$items)

If you want to list the projects owned by and accessible to a particular user, specify the owner argument as follows.

# List projects of particular user
a$projects$query(owner = "<username1>")
a$projects$query(owner = "<username2>")

Partial match project name

For a more friendly interface and convenient search, the sevenbridges2 package supports partial name matching. Set the name parameter in the query() method:

# List projects whose name contains 'demo'
a$projects$query(name = "demo")

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Filter by project creation date, modification date, and creator

Project creation date, modification date, and creator information is useful for quickly locating the project you need, especially when you want to follow the life cycle of a large number of projects and distinguish recent projects from old ones. To facilitate such needs, the fields created_by, created_on, and modified_on are returned in the project query calls. Since these fields cannot be passed to the query() function as parameters, you can use the helper code below in order to perform such action:

# Return all projects matching the name "wgs"
wgs_projects <- a$projects$query(name = "wgs")

# Filter by project creators
creators <- sapply(wgs_projects$items, "[[", "created_by")
wgs_projects$items[which(creators == "<some_username>")]

# Filter by project creation date
create_date <- as.Date(sapply(wgs_projects$items, "[[", "created_on"))
wgs_projects$items[which(as.Date(create_date) < as.Date("2019-01-01"))]

# Filter by project modification date
modify_date <- as.Date(sapply(wgs_projects$items, "[[", "modified_on"))
wgs_projects$items[which(as.Date(modify_date) < as.Date("2019-01-01"))]

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Create a new project

To create a new project, use the create() method on the Projects path. Users need to specify the following:

• name (required)
• billing_group (required)

Other parameters and settings are optional. You can find more information in the create() function documentation on ?Projects.

# Get billing group
billing_groups <- a$billing_groups$query()
billing_group <- a$billing_groups$get("<billing_id>")

# Create a project named 'API Testing'
a$projects$create(
  name = "API Testing", billing_group = billing_group,
  description = "Test for API"
)

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Get a single project

Let’s fetch the project we’ve just created by its ID. For this purpose, we can use Projects’ get() method. This method accepts only project ID which consists of:

• user’s username or division name (for Seven Bridges platform users that are part of some divisions) and
• project’s short name in lowercase with spaces replaced by dashes,

in the form of <your_username_or_division>/<project's-short-name>. This id can also be seen in the URL of the project on the UI.

# Fetch previously created project
p <- a$projects$get(id = "<your_username_or_division>/api-testing")

To print all details about the project, use detailed_print() method directly on the Project object:

# Print all project info
p$detailed_print()

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Delete a project

There are two ways to delete a project. One is from the projects path on the authentication object and the other one is to call the delete() method directly on the Project object you want to delete:

# Delete project using Auth$projects path
a$projects$delete(project = "<project_object_or_id>")

# Delete project directly from the project object
p$delete()

Please be careful when using this method and note that calling it will permanently delete the project from the platform.

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Edit an existing project

If you want to edit an existing project, you can do so by using the update() method on the Project object. As a project Admin you can use it to change the name, description, settings, tags or billing group of the project. For example, if you want to change the name and description of the project, you can do it in the following way:

# Update project
p$update(
  name = "Project with modified name",
  description = "This is the modified description."
)

Keep in mind that this modifies only the name of the project, not its short name. Therefore, after calling this method, the ID of the project will remain the same.

If something changes in the project in the Platform UI, you can refresh your Project object to fetch the changes, by reloading it with:

# Reload project object
p$reload()

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Project members management

List project members

This call returns a Collection with a list of members of the specified project. For each member, the response is wrapped into a Member class object containing:

• The member’s username, email, id, and type and
• The member’s permissions in the specified project.

# List project members
p$list_members()

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Add a member to a project

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 default values, which is read-only (only the read value will be set to TRUE).

Set permissions by creating a named list with copy, write, execute, admin, or read names and assign TRUE or FALSE values to them.

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

# Add project member
p$add_member(
  user = "<username_of_a_user_you_want_to_add>",
  permissions = list(write = TRUE, execute = TRUE)
)

── Member ─────────────────────────────────────────────────────────────────────
• type: USER
• email: new_user@velsera.com
• username: <username_of_a_user_you_want_to_add>
• id: <username_of_a_user_you_want_to_add>
• href: https://api.sbgenomics.com/v2/projects/<admin_username>/api-testing/members/<username_of_a_user_you_want_to_add>
• permissions:
  • write: TRUE
  • read: TRUE
  • copy: FALSE
  • execute: TRUE
  • admin: FALSE
  

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Get and modify a project member’s permissions

Sometimes you may just want to investigate a member’s permissions within a specified project or update them, and you can do that by calling the modify_member_permissions() method. For this method to work, the user calling it must have admin permissions in the project. For example, you may want to give write permissions to a project member:

# Modify project member's permissions
p$modify_member_permissions(
  user = "<username_of_a_user_of_interest>",
  permissions = list(copy = TRUE)
)

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Remove a project member

On the other hand, you can delete a member from the project in a similar way with the remove_member() operation:

# Remove a project member
p$remove_member(user = "<username_of_a_user_you_want_to_remove>")

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List project files

In order to list all files and folders (special type of files) within the specified project object, you can use the Project’s list_files() method.

# List project files
p$list_files()

It will return a Collection object with the items field containing a list of returned File objects, along with pagination options.

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Create a folder within project Files

You are also able to create a folder within a project’s root Files directory using the create_folder() method. You have to specify the folder name which should not start with ’__’ or contain spaces.

# Create a folder within project files
p$create_folder(name = "My_new_folder")

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Get a project’s root folder object

Lastly, the project’s root directory with all your files is a folder itself, therefore you are able to get this folder as a File object too using get_root_folder().

# Get a project's root folder object
p$get_root_folder()

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List project’s apps, tasks and import jobs

We will just briefly mention that you can also list all project’s apps, tasks and import jobs (created for Volume imports) directly on the Project object, but more details about these topics will be explained in the upcoming chapters:

# List project's apps
p$list_apps()

# List project's tasks
p$list_tasks()

# List project's imports
p$list_imports()

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Create a new app and task within a project

Another shortcut is available on the Project object and that is creation of apps and tasks. More details about this topic will be provided in the next chapters.

Files, folders and metadata

All file-related operations can be accessed through the files path from the Auth object. Files also inherits Resource R6 class which contains an implementation of query(), get() and delete() methods for listing, fetching a single file/folder, and deleting a specific file/folder. Besides those, there are also custom methods to copy files/folders and create folders.

When you fetch single file/folder, it is represented as an object of File class. Note that class of both files and subdirectories is File. The difference between them is in the type parameter which is:

• File for files
• Folder for subdirectories.

File object contains all file/folder information and additional methods that can be executed directly on the object like updating, adding tags, setting metadata, copying or moving files, exporting to volumes etc.

List files

This call lists files and subdirectories in a specified project or directory within a project, with specified properties that you can access. The project or directory whose contents you want to list is specified as a parameter in the call.

The result will be a Collection class containing a list of File objects in the items field.

# List files in the project root directory
api_testing_files <- a$files$query(project = "project_object_or_id")
api_testing_files

[[1]]

── File ────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 61f3f9c6e6aad23247516bf30
• url: NA
• modified_on: 2023-04-15T08:54:32Z
• created_on: 2023-04-11T10:04:50Z
• project: <username_or_division>/api-testing
• size: 56 bytes
• name: Drop-seq_small_example.bam
• id: 643530c28345522d97313d17
• href: https://api.sbgenomics.com/v2/files/643530c28345522d97313d17

[[2]]

── File ────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 61f3f9c6e6aae54367516bf30
• url: NA
• modified_on: 2023-04-11T10:29:13Z
• created_on: 2023-04-11T10:29:13Z
• project: <username_or_division>/api-testing
• size: 56 bytes
• name: G20479.HCC1143.2_1Mreads.tar.gz
• id: 6435367943r4456ecb66cfb2
• href: https://api.sbgenomics.com/v2/files/6435367943r4456ecb66cfb2

Note that this call lists both files and subdirectories in the specified project or directory within a project, but not the contents of the subdirectories. To list the contents of a subdirectory, make a new call and specify the subdirectory as the parent parameter.

# List files in a subdirectory
a$files$query(parent = "<parent_directory_object_or_id>")

You can also try and find a file with specific:

1. Name - List the file with the specified name. Note that the name must be an exact complete string for the results to match.
2. Metadata - List only files that have the specified value in a metadata field. Note that multiple instances of the same metadata field are implicitly separated by the OR operation. Conversely, different metadata fields are implicitly separated by the AND operation.
3. Tag - List files containing the specified tag. Note that the tag must be an exact complete string for the results to match. The OR operation is performed between multiple tags.
4. Origin task - List only files produced by the task specified by the ID in this field.

# List files with these names
a$files$query(
  project = "<project_object_or_id",
  name = c("<file_name1>", "<file_name2>")
)

# List files with metadata fields sample_id and library values set
a$files$query(
  project = "<project_object_or_id>",
  metadata = list(
    "sample_id" = "<sample_id_value>",
    "library" = "<library_value>"
  )
)

# List files with this tag
a$files$query(project = "<project_object_or_id>", tag = c("<tag_value>"))

# List files from this task
a$files$query(project = "<project_object_or_id>", task = "<task_object_or_id>")

To combine everything in a more realistic example - the following code gives us all files in the user1/api-testing project that have sample_id metadata set to “Sample1” OR “Sample2”, AND the library id “EXAMPLE”, AND have either “hello” OR “world” tag:

# Query project files according to described criteria
my_files <- a$files$query(
  project = "user1/api-testing",
  metadata = list(
    sample_id = "Sample1",
    sample_id = "Sample2",
    library_id = "EXAMPLE"
  ),
  tag = c("hello", "world")
)

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List public data

To list publicly available files on the Seven Bridges Platform, set the project parameter to admin/sbg-public-data.

# Query public files
public_files <- a$files$query(project = "admin/sbg-public-data")

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Get a single file/folder

To return a specific file or folder, knowing their ID, you can use the get() method, same as for other resources. File id can also be extracted from the URL in the Platform’s visual interface.

# Get a single File object by ID
a$files$get(id = "<file_id>")

── File ────────────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 61f3f9c6e6aad8667516rf543
• url: NA
• modified_on: 2023-04-11T10:29:13Z
• created_on: 2023-04-11T10:29:13Z
• project: <username_or_division>/api-testing
• size: 56 bytes
• name: G20479.HCC1143.2_1Mreads.tar.gz
• id: 6435367997d934334fb66cfb2
• href: https://api.sbgenomics.com/v2/files/6435367997d934334fb66cfb2

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Delete a file

The delete action only works for one file at a time. It can be called from the Auth$files path and accepts the File object or ID of the file you want to delete.

# Delete a file
a$files$delete(file = "<file_object_or_id>")

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Copy files

The copy() method allows you to copy multiple files between projects at a time. It can also be called from the Auth$files path and accepts a list of File objects or their ids within the files parameter. Besides this, you have to specify the destination project too. The result will contain a printed response with information about the copied files - their destination names and ids.

# Fetch files by id to copy into the api-testing project
file1 <- a$files$get(id = "6435367997d9446ecb66cfb2")
file2 <- a$files$get(id = "6435367997d9446ecb66cgr2")

# Copy files to the project
a$files$copy(
  files = list(file1, file2),
  destination_project = "<username_or_division>/api-testing"
)

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Get details of multiple files

The bulk_get() method allows you to retrieve details for multiple files efficiently - in a single API call. This method accepts an argument, files, which can be either a list of File objects or a list of strings representing file IDs.

File ID can also be extracted from the URL in the Platform’s visual interface.

# Get details of multiple files by providing their IDs
a$files$bulk_get(files = list("<file_1_id>", "<file_2_id>"))

── 1 ──

── File ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 52e0ed0de4b069f418bc13c7
• modified_on: 2022-01-11T11:41:17Z
• created_on: 2016-06-17T16:43:52Z
• project: admin/sbg-public-data
• size: 2780048573 bytes
• name: mouse_mm10_ucsc.fasta
• id: 5772b6dc507c1752674486eb
• href: https://api.sbgenomics.com/v2/files/5772b6dc507c1752674486eb

── 2 ──

── File ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 52e0ed0de4b069f418bc13c7
• modified_on: 2022-01-11T11:41:17Z
• created_on: 2016-06-17T16:42:50Z
• project: admin/sbg-public-data
• size: 3189750467 bytes
• name: human_g1k_v37_decoy.fasta
• id: 5772b6d8507c1752674486e6
• href: https://api.sbgenomics.com/v2/files/5772b6d8507c1752674486e6

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Update details of multiple files

The bulk_update() method updates the details for multiple specified files. It requires a single argument, files, which should be a list of File objects.

Use this call to set new information for the files, thus replacing all existing information and erasing omitted parameters. For each of the specified files, the call sets a new name, new tags, and metadata.

When editing fields in the File objects you wish to update, keep the following in mind:

• The name field should be a string representing the new name of the file.
• The metadata field should be a named list of key-value pairs. The keys and values should be strings.
• The tags field should be an unnamed list of values.

The maximum number of files you can update the details for per call is 100.

# Get files
file_obj_1 <- a$files$get(id = "<file_1_ID>")
file_obj_2 <- a$files$get(id = "<file_2_ID>")

# Edit file_obj_1 fields
file_obj_1$name <- "new_file_1_name.txt"
file_obj_1$metadata <- list("new_metadata_field" = "123")
file_obj_1$tags <- list("bulk_update_tag")

# Edit file_obj_2 fields
file_obj_2$name <- "new_file_2_name.txt"
file_obj_2$metadata <- list("new_metadata_field" = "123")
file_obj_2$tags <- list("bulk_update_tag")

# Bulk update
a$files$bulk_update(files = list(file_obj_1, file_obj_2))

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Edit details of multiple files

The bulk_edit() method edits the details for multiple specified files. It requires a single argument, files, which should be a list of File objects.

Use this call to modify the existing information for the files or add new information while preserving omitted parameters. For each of the specified files, the call edits its name, tags, and metadata.

When editing fields in the File objects you wish to update, keep the following in mind:

• The name field should be a string representing the new name of the file.
• The metadata field should be a named list of key-value pairs. The keys and values should be strings.
• The tags field should be an unnamed list of values.

The maximum number of files you can edit the details for per call is 100.

# Get files
file_obj_1 <- a$files$get(id = "<file_1_ID>")
file_obj_2 <- a$files$get(id = "<file_2_ID>")

# Edit file_obj_1 fields
file_obj_1$name <- "new_file_1_name.txt"
file_obj_1$metadata <- list("new_metadata_field" = "123")
file_obj_1$tags <- list("bulk_edit_tag")

# Edit file_obj_2 fields
file_obj_2$name <- "new_file_2_name.txt"
file_obj_2$metadata <- list("new_metadata_field" = "123")
file_obj_2$tags <- list("bulk_edit_tag")

# Bulk edit
a$files$bulk_edit(files = list(file_obj_1, file_obj_2))

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Create a folder within the destination project or parent folder

To create a new folder on the Platform, use the Auth$files method create_folder(). It allows you to create a new folder on the Platform within the root folder of a specified destination project or the provided parent folder. Remember that you should provide either the destination project (as the project parameter) or the destination folder (as the parent parameter), not both.

# Option 1 - Using the project parameter

# Option 1.a (providing a Project object as the project parameter)
my_project <- a$projects$get(project = "<username_or_division>/api-testing")
demo_folder <- a$files$create_folder(
  name = "my_new_folder",
  project = my_project
)

# Option 1.b (providing a project's ID as the project parameter)
demo_folder <- a$files$create_folder(
  name = "my_new_folder",
  project = "<username_or_division>/api-testing"
)

Alternatively, you can provide the parent parameter to specify the destination where the new folder is going to be created. The parent parameter can be either a File object (must be of type folder) or an ID of the parent destination folder.

# Option 2 - Using the parent parameter

# Option 2.a (providing a File (must be a folder) object as parent parameter)
my_parent_folder <- a$files$get(id = "<folder_id>")
demo_folder <- a$files$create_folder(
  name = "my_new_folder",
  parent = my_parent_folder
)

# Option 2.b (providing a file's (folder's) ID as project parameter)
demo_folder <- a$files$create_folder(
  name = "my_new_folder",
  parent = "<folder_id>"
)

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File object operations

Let’s see now all available operations on the File objects that can be called.

File print

File object has a regular print() method which gives you most important information about the file:

# Get some file
demo_file <- a$files$get(id = "<file_id>")

# Regular file print
demo_file$print()

── File ────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 61f3f9c6e6aad86675453ff30
• url: NA
• modified_on: 2023-04-15T08:54:32Z
• created_on: 2023-04-11T10:04:50Z
• project: <username_or_division>/api-testing
• size: 56 bytes
• name: Drop-seq_small_example.bam
• id: 643530c286c9522d9222213d17
• href: `https://api.sbgenomics.com/v2/files/643530c286c9522d9222213d17`

But if you want to see all the details about a file in a specific format, you can use the detailed_print() method:

# Pretty print
demo_file$detailed_print()

── File ────────────────────────────────────────────────────────────────────────────────────────────────────────
• type: file
• parent: 61f3f9c6e6aad86675453ff30
• url: NA
• modified_on: 2023-04-15T08:54:32Z
• created_on: 2023-04-11T10:04:50Z
• project: <username_or_division>/api-testing
• size: 56 bytes
• name: Drop-seq_small_example.bam
• id: 643530c286c9522d9222213d17
• href: `https://api.sbgenomics.com/v2/files/643530c286c9522d9222213d17`
• tags
  • tag_1: TEST
  • tag_2: SEQ
• metadata
  • reference_genome: GSM1629193_hg19_ERCC
  • investigation: GSM1629193
  • md5_sum: 6294fee8200b29e03d3dc464f9c46a9c
  • sbg_public_files_category: test
• storage
  • type: PLATFORM
  • hosted_on_locations: list("aws:us-east-1", "aws:us-west-2")

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Update file details

You can call the update() function on the File object. With this call, the following can be updated:

• The file’s name,
• The file’s metadata,
• The file’s tags.

Read more details about this method in our API documentation.

# Update file name
demo_file$update(name = "<new_name>")

# Update file metadata
demo_file$update(
  metadata = list("<metadata_field>" = "<metadata_field_value")
)

# Update file tags
demo_file$update(tags = list("<tag_value>"))

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Add tags to a file

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 in the visual interface.

You can tag your files using the add_tag() method. This method will automatically just add a new tag to a list of already existing ones, but you also have the option to set the overwrite parameter, which will erase old ones and set the new one.

# Add a new tag to a file
demo_file$add_tag(tags = list("new_tag"))

# Add a new tag to a file and overwrite old ones
demo_file$add_tag(tags = list("new_tag"), overwrite = TRUE)

# Delete all tags - just set tags to NULL
demo_file$add_tag(tags = NULL, overwrite = TRUE)

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Copy a single file between projects

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. If you don’t specify a new name, the file will retain its old name in the new project. To make this call, you should have the copy permission within the project you are copying from. This call returns the File object of the newly copied file.

# Copy a file to a new project and set a new name
demo_file$copy_to(
  project = "<destination_project_object_or_id>",
  name = "<new_name>"
)

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Get downloadable URL for a file

To get a URL that you can use to download the specified file, you can use the get_download_url() method. This will set the url parameter in the File object and can later be used to download the file.

# Get downloadable URL for a file
demo_file$get_download_url()

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Get a file’s metadata

Files from curated datasets on Seven Bridges environments have a defined set of metadata which is visible in the visual interface of each environment.

File object has the get_metadata() method which returns the metadata values for the specified file. This will pull and reload file’s metadata from the platform.

# Get file metadata
demo_file$get_metadata()

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Modify file metadata

You can also pass additional metadata for each file which is stored with your copy of the file in your project.

To modify a file’s metadata use the set_metadata() method. Here you can also use the overwrite parameter if you want to erase previous metadata fields and add a new one (by default it’s set to FALSE).

# Set file metadata
demo_file$set_metadata(
  metadata_fields = list("<metadata_field>" = "metadata_field_value"),
  overwrite = TRUE
)

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List folder contents

Directories can have multiple files/subdirectories inside. You can see them using the list_contents() method. Note that this operation will work only on File objects whose type is folder. The result will also be a Collection class object containing a list of File objects in the items field.

# List folder contents
demo_folder$list_contents()

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Move a file into a folder

This call moves a file from one folder to another. Moving folders is not allowed by the API. Moving of files is only allowed within the same project. Parent parameter must be a folder id or a File object whose type is folder. A file can also be renamed at the destination by setting the name argument.

# Move a file to a folder
demo_file$move_to_folder(
  parent = "<parent_file_object_or_id>",
  name = "Moved_file.txt"
)

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Download a file

File object has a download() method, which allows you to download that file to your local computer. You should provide the directory_path parameter, which specifies the destination directory to which your file will be downloaded. By default, this parameter is set to your current working directory. You can also set the new name for your resulting (downloaded) file by providing the filename parameter. Otherwise, the default name (the one stored in the name field of your File object) will be used.

# Download a file
demo_file$download(directory_path = "/path/to/your/destination/folder")

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Get a file’s parent directory

Sometimes, it’s convenient to get the parent folder ID for a file or folder: This information is stored in the parent field of the File object.

# Get a file's parent directory
demo_file$parent

[1] "5bd7c53ee4b04b8fb1a9f454x"

This is essentially the root folder ID. Alternatively, to get the parent folder as an object, use:

# Get a folder object
parent_folder <- a$files$get(demo_file$parent)

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Delete a file/folder

User can delete files and folders using the delete() method directly on the File object. Please be aware that folder can only be deleted if it’s empty.

# Delete a file
demo_file$delete()

# Delete a folder
demo_folder$delete()

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Delete multiple files/folders

To delete multiple files in a single API call, use the bulk_delete() method. This method accepts either a list of File objects or a vector of strings (IDs) representing the files you intend to delete.

The method also works with folders. However, please note that a folder can only be deleted if it is empty.

# Delete two files by providing their IDs
a$files$delete(files = list("<file_1_ID>", "<file_2_ID>"))

# Delete two files by providing a list of File objects
file_object_1 <- a$files$get(id = "<file_1_ID>")
file_object_2 <- a$files$get(id = "<file_2_ID>")
a$files$delete(files = list(file_object_1, file_object_2))

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Reload a file

To keep your local File object up to date with the file on the platform, you can always call the reload() function:

# Reload file/folder objects
demo_file$reload()
demo_folder$reload()

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Apps

Following the same logic as with other Resource classes, all apps related operations are grouped under the Apps class, that can be accessed within Auth objects on the Auth$apps path. From here you can call operations to list all apps, fetch single app by its id, copy or create a new app.

When you operate with a single app, it is represented as an object of App class. The App object contains almost all app information and additional methods that can be executed directly on the object, such as getting or creating new app revisions, copying, syncing with the latest revision or creating tasks with this app, etc.

Note that we say almost all information, because we don’t return all fields by default for apps - the raw CWL field is excluded due to its size and speed of execution. Therefore, if you wish to fetch the raw CWL of an app, there is a separate method for this purpose that you can call on the App object (get_raw_cwl()).

List apps

You can list all apps available to you by calling the apps$query() method from the authentication object. The method has several parameters that allow you to search for apps in various places and by specified search terms.

Note that you can see all of the publicly available apps on the Seven Bridges Platform by setting the visibility parameter to public. If you omit this parameter (it will use the default value private), and you will see all your private apps, i.e. those in projects that you can access. Learn more about public apps in our documentation.

# Query public apps - set visibility parameter to "public"
a$apps$query(visibility = "public", limit = 10)

The same can be done for private apps. The following call will return all the apps available to you, i.e. all the apps that you have in your projects:

# Query private apps
my_apps <- a$apps$query()

Just to remind you that not all of the available apps are going to be returned, because the limit parameter is set to 50 by default. Since the result is a Collection object, you can navigate through results by calling next_page() and prev_page() or call all() to return all results.

# Load next 50 apps
my_apps$next_page()

Alternatively, you can query all the apps in a specific project by providing the project of interest using the project parameter. You can either use the Project object, or a project ID (string).

# Query apps within your project - set limit to 10
a$apps$query(project = "<project_object_or_its_ID>", limit = 10)

You can also use one or more search terms via the query_terms parameter to query all apps that are available to you. Search terms should relate to the following app details:

• name
• label
• toolkit
• toolkit version
• category
• tagline
• description

For example, to get public apps that contain the term “VCFtools” anywhere in the app details, you can make a call similar to this one:

# List public apps containing the term "VCFtools" in app's details
a$apps$query(visibility = "public", query_terms = list("VCFtools"), limit = 10)

For the query to return results, each term must match at least one of the fields that describe an app. For example, the first term can match the app’s name while the second one can match the app description. However, if any part of the search fails to match app details, the call will return an empty list.

Another useful option is to query apps by id. You can do so either for public apps, or for private apps (apps available to you). The following example illustrates how this can be done for public apps:

# List files in project root directory
a$apps$query(
  visibility = "public",
  id = "admin/sbg-public-data/vcftools-convert"
)

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List project apps

All available apps in a specific project can also be listed by calling the list_apps() method directly on the Project object. This method has the project and visibility arguments predefined, while all other parameters are identical to those presented in the apps$query() function.

# Get project
p <- a$projects$get("<username_or_division>/api-testing")

# List apps in the specified project
p$list_apps(limit = 10)

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Get app information

If you need information about a specific app, you can get it using the apps$get() method. Keep in mind that the app should be in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app. You should provide the id of the app of interest, and optionally its revision. If no revision is specified, the latest one will be used.

# Get a public App object
bcftools_app <- a$apps$get(id = "admin/sbg-public-data/bcftools-call-1-15-1")

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Copy an app

To copy an app to a specified destination project, you can use the apps$copy() method.

Keep in mind that the app should be in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app.

Destination project (project parameter) should be provided either as an object of the Project class, or as an ID of the target project of interest.

You might want to set the new name that the app will have in the target project. To do so, use the name parameter. If the app’s name will not change, omit the name parameter.

Keep in mind that there are different strategies for copying the apps on the platform:

• clone : copy all revisions; get updates from the same app as the copied app (default)
• direct: copy latest revision; get updates from the copied app
• clone_direct: copy all revisions; get updates from the copied app
• transient: copy latest revision; get updates from the same app as the copied app

Learn more about copy strategies in our public API documentation.

The following example demonstrates how can you copy the previously created bcftools_app to a project:

# Copy an app to a project
app_copy <- a$apps$copy(bcftools_app,
  project = "<project_object_or_its_ID>",
  name = "New_app_name"
)

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Create new app

The apps$create() method allows you to add an app using raw CWL.

The raw CWL can be provided either through the raw parameter, or by using the file_path parameter. Keep in mind that these two parameters should not be used together.

If you choose to use the raw parameter, make sure to provide a list containing raw CWL for the app you are about to create. To generate such a list, you might want to load an existing JSON / YAML file. In case that your CWL file is in JSON format, please use the fromJSON function from the jsonlite package to minimize potential problems with parsing the JSON file. If you want to load a CWL file in YAML format, it is highly recommended to use the read_yaml function from the yaml package.

Make sure to set the raw_format parameter to match the type of the provided raw CWL file (JSON / YAML). By default, this parameter is set to JSON.

# Load the JSON file
file_json <- jsonlite::read_json("/path/to/your/raw_cwl_in_json_format.cwl")

# Create app from raw CWL (JSON)
new_app_json <- a$apps$create(
  project = "<destination_project_object_or_its_ID>",
  raw = file_json,
  name = "New_app_json",
  raw_format = "JSON"
)

If you opt for the file_path parameter instead, you should provide a path to a file containing the raw CWL for the app (JSON or YAML).

# Create an app from raw CWL (YAML)
new_app_yaml <- a$apps$create(
  project = "<destination_project_object_or_its_ID>",
  from_path = "/path/to/your/raw_cwl_in_yaml_format.cwl",
  name = "New_app_yaml",
  raw_format = "YAML"
)

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Create an app in a project

The app can also be directly created on a Project object by invoking create_app(). Except for the predefined project parameter, the create_app() has the same other parameters as apps$create().

# Load the JSON file
file_json <- jsonlite::read_json("/path/to/your/raw_cwl_in_json_format.cwl")

# Get project
p <- a$projects$get("<username_or_division>/api-testing")

# Create app from raw CWL (JSON) in specified project
p$create_app(
  raw = file_json,
  name = "New_app_json",
  raw_format = "JSON"
)

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App object operations

Once you’ve fetched the App object, you’ll see that it also has various useful methods within itself.

The following actions are available for an App object:

• print
• input_matrix
• output_matrix
• get_revision
• create_revision
• copy
• sync
• create_task
• reload

Print an app

The print method prints the app details to the console.

# Fetch the first app from project's apps
p <- a$projects$get("<username_or_division>/api-testing")
my_apps <- p$list_apps()
my_new_app <- my_apps$items[[1]]

# Print app's details
my_new_app$print()

── App ──────────────────────────────────────────────────────────────────────────────────────────────────────
• revision: 0
• name: BCFtools Call
• project: <username_or_division>/api-testing
• id: <username_or_division>/api-testing/new_app_json
• href: https://api.sbgenomics.com/v2/apps/<username_or_division>/api-testing/new_app_json/0

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Get an app’s raw CWL

If the app’s raw field is empty, just call the reload() method, to fetch app’s raw CWL.

Preview app’s inputs and expected outputs

Usually, for most of the tasks, some inputs should be defined, which are required by the app. Information about which inputs are required or optional to be set for the app is stored in its CWL. However, we have provided a utility function input_matrix() on the App object that can parse this information and return the app’s input matrix for you. This way, users will know how to construct the list of inputs (how to name them and make them available within files) when creating the task.

NOTE that id field in the data frame is the name you should use when specifying task inputs.

# Get app's inputs details
my_new_app$input_matrix()

id                                      label           required    type
in_variants                      Input Mpileup VCF file     TRUE      File
regions_file                          Regions from file    FALSE     File?
output_name                           Output file name    FALSE   string?
output_type                                Output type    FALSE      enum
regions                         Regions for processing    FALSE string[]?
...

Besides id and label describing the input, you can see whether the input is required or not and which type is expected. For most of the inputs, if you notice that type field contains ‘?’, it means that the field is optional.

There is another utility operation on the App object to list expected outputs of an app or task. This information can be received by calling the output_matrix() method:

# Get app's outputs details
my_new_app$output_matrix()

                     id                    label      type
1        summary_metrics          Summary Metrics      File
2  out_filtered_variants      Output filtered VCF     File?
3            html_report              HTML report     File?
...

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Get an app revision

To obtain a particular revision of an app, use the get_revision() method and set the revision parameter to the number of the version you want to get.

Keep in mind that there is another important parameter that can be set for this method. If the in_place parameter is set to TRUE, the current app object will be replaced with the new one for specified app revision. By default, this parameter is set to FALSE.

# Get an app revision
my_app <- a$apps$get(id = "<username_or_division>/api-testing/new_app_json/0")
my_app$print()

── App ──────────────────────────────────────────────────────────────────────────────────────────────────────
• latest_revision: 1
• copy_of: admin/sbg-public-data/bcftools-call-1-15-1/0
• revision: 0
• name: BCFtools Call
• project: <username_or_division>/api-testing
• id: <username_or_division>/api-testing/new_app_json
• href: https://api.sbgenomics.com/v2/apps/<username_or_division>/api-testing/new_app_json/0

# Get an app revision
my_app$get_revision(revision = 1)

# Get an app revision and update the object
my_app$get_revision(revision = 1, in_place = TRUE)

── App ──────────────────────────────────────────────────────────────────────────────────────────────────────
• latest_revision: 1
• copy_of: admin/sbg-public-data/bcftools-call-1-15-1/0
• revision: 1
• name: BCFtools Call
• project: <username_or_division>/api-testing
• id: <username_or_division>/api-testing/new_app_json
• href: https://api.sbgenomics.com/v2/apps/<username_or_division>/api-testing/new_app_json/1

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Create an app revision

The create_revision() method allows you to create a new revision for an existing app.

The raw CWL can be provided either through the raw parameter, or by using the file_path parameter. Keep in mind that these two parameters should not be used together.

If you choose to use the raw parameter, make sure to provide a list containing raw CWL for the app revision you are about to create. To generate such a list, you might want to load an existing JSON / YAML file. In case that your CWL file is in JSON format, please use the fromJSON function from the jsonlite package to minimize potential problems with parsing the JSON file. If you want to load a CWL file in YAML format, it is highly recommended to use the read_yaml function from the yaml package.

Make sure to set the raw_format parameter to match the type of the provided raw CWL file (JSON / YAML). By default, this parameter is set to JSON.

Using in_place parameter will overwrite the current app object with new app revision information.

# Create an app revision from a file
raw_cwl_as_list <- jsonlite::read_json(
  path = "/path/to/your/raw_cwl_in_json_format.cwl"
)
my_app$create_revision(raw = raw_cwl_as_list, in_place = TRUE)

If you opt for the file_path parameter instead, you should provide a path to a file containing the raw CWL for the app (JSON or YAML).

# Create a new revision for an existing app
my_app$create_revision(
  from_path = "/path/to/your/raw_cwl_in_json_format.cwl",
  in_place = TRUE
)

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Copy an app

An app can be copied to a specified destination project directly from an app’s object too, by calling its own copy()method.

Destination project (project parameter) should be provided either as an object of the Project class, or as an ID of the target project of interest.

You can set the new name that the app will have in the target project with the name parameter. Keep in mind that are different strategies for copying apps on the platform:

• clone : copy all revisions; get updates from the same app as the copied app (default)
• direct: copy latest revision; get updates from the copied app
• clone_direct: copy all revisions; get updates from the copied app
• transient: copy latest revision; get updates from the same app as the copied app

Learn more about copy strategies in our public API documentation.

# Copy app
copied_app <- my_app$copy(
  project = "<destination_project_object_or_its_ID>",
  name = "New_app_name"
)

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Sync a copied app

To synchronize a copied app with the source app from which it has been copied, so it uses the latest revision, you can call the sync() method. The App object will be overwritten with the latest app.

# Sync a copied app to the latest revision created
copied_app$sync()

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Reload an app

To keep your local App object up to date with the app on the platform, you can always call the reload() function:

# Reload an app object
my_app$reload()

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Tasks

All task related operations are grouped under the Tasks class within the authentication object, which also inherits the Resource class and implements query(), get() and delete() operations for listing tasks, fetching single task and deleting tasks. Besides these, users are able to create new tasks with the create() operation from this Auth$tasks path.

Furthermore, users can retrieve details for multiple tasks with a single API call using the bulk_get() method, also available from Auth$tasks.

When you operate with a single task, it is represented as an object of the Task class. The Task object contains all task information and additional methods that can be executed directly on the object such as running, aborting, cloning, updating, deleting the task, etc.

List tasks

As mentioned above, you can list your tasks by calling the tasks$query() method from the authentication object. The method has many additional query parameters that could allow you to search for tasks by specific criteria such as: status, parent, project, created_from, created_to, started_from, started_to, ended_from, ended_to, order_by, order, origin_id.

Let’s list all tasks that were completed:

# Query all tasks
a$tasks$query()

# Query tasks by their status
a$tasks$query(status = "COMPLETED", limit = 5)

To list all the tasks in a project, use the following.

# Find the project and pass it in the project parameter
p <- a$projects$query(id = "<project_id>")
a$tasks$query(project = p)

# Alternatively you can list all tasks directly from the Project object
p <- a$projects$get(id = "<project_id>")
p$list_tasks()

Similar to previous query methods, here you will also get the Collection object where resulting tasks will be stored in the items fields and you can use pagination to navigate through results.

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Get single task information

In order to retrieve information about a single task of interest, you can get it using the tasks$get() method using its id as parameter.

# Get specific task by ID
a$tasks$get(id = "<task_id>")

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Get details of multiple tasks

To retrieve details of multiple tasks in a single API call, use the tasks$bulk_get() method.

The tasks$bulk_get() method allows you to retrieve details of multiple tasks efficiently - in a single API call. This method accepts a single argument, tasks, which can be either a list of Task objects or a list of strings representing task IDs.

Task ID can be extracted from the URL in the Platform’s visual interface.

# Get details of multiple tasks by providing their IDs
a$tasks$bulk_get(tasks = list("<task_1_id>", "task_2_id"))

# Get details of multiple tasks by providing Task objects
task_obj_1 <- a$tasks$get("<task_1_id>")
task_obj_2 <- a$tasks$get("<task_2_id>")
a$tasks$bulk_get(tasks = list(task_obj_1, task_obj_2))

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Create a draft task

To create a new draft task, you can use the tasks$create method. The method accepts various arguments such as: in which project to create a task, which app and its revision to use, task name, description, which inputs it requires, batching options, execution settings, etc.

However, we can create a draft task by only defining the project and the app that will be run, since all other parameters are optional:

# Create a draft task
draft_task <- a$tasks$create(
  project = "<project_object_or_id>",
  app = "<app_object_or_id>"
)

This will create an empty task, without any parameter defined. User has the option to set execution settings by using execution_settings parameter, and also to define usage of interruptible instances through use_interruptible_instances parameter.

# Create task with execution settings and with use of interruptible instances
execution_settings <- list(
  "instance_type" = "c4.2xlarge;ebs-gp2;2000",
  "max_parallel_instances" = 2,
  "use_memoization" = TRUE,
  "use_elastic_disk" = FALSE
)
task_exec_settings <- a$tasks$create(
  project = "<project_object_or_id>",
  app = "<app_object_or_id>",
  execution_settings = execution_settings,
  use_interruptible_instances = FALSE,
)

To run the app immediately after it was created we have action parameter, which when set to run will start the analysis task when it’s created.

# Create and run task
task_exec_settings <- a$tasks$create(
  project = "<project_object_or_id>",
  app = "<app_object_or_id>",
  input = "<inputs>",
  action = "run"
)

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Create a batch task

To run tasks in batch mode we have batch, batch_input and batch_by parameters. The batch parameter defines whether to run a batch task or not, while batch_input and batch_by define the input by which the task will be batched and by which criteria, respectively.

The example below shows the format of creating a batch task for an input file named ‘reads’, with batch criteria set to the ‘sample_id’ metadata field:

# Create a draft task
batch_task <- a$tasks$create(
  project = "<project_object_or_id>",
  app = "<app_object_or_id>",
  inputs = list(
    "reads" = "<reads_file_object_or_id>",
    "reference" = "<reference_file_object_or_id>"
  ),
  batch = TRUE,
  batch_input = "reads",
  batch_by = list(
    type = "CRITERIA",
    criteria = list("metadata.sample_id")
  )
)

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Task operations

Once you’ve fetched the Task object, you can execute various operations directly on it.

Print task

To print all task details, call the print() method directly on the Task object:

# Print task details
draft_task$print()

── Task ─────────────────────────────────────────────────────────────────────
• batch: FALSE
• end_time: 2023-11-22T16:58:16Z
• start_time: 2023-11-22T16:51:35Z
• executed_by: <username>
• created_by: <username>
• app: <username_or_division>/api-testing/rna-seq-alignment-star/0
• project: <username_or_division>/api-testing
• description: STAR test 2
• status: COMPLETED
• name: Star-alignment-task
• id: 66f7a639-85fb-4594-aa93-d435ra37fb1b
• href: https://api.sbgenomics.com/v2/tasks/66f7a639-85fb-4594-aa93-d435ra37fb1b

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Run a task

To actually start the execution of a created draft task, use the task object’s run() function. You can modify input parameters values for: in_place - set to FALSE if you wish to store response in new task object, batch - this is used for tasks that are already batch tasks and this option allows the users to switch the batch mode off, use_interruptible_instances - This field can be TRUE or FALSE. Set this field to TRUE to allow the use of spot instances.

Only tasks with a DRAFT status may be run.

# Run a task
draft_task$run(in_place = TRUE)

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Abort a task

Users can abort the task execution by calling the abort() function. It immediately stops the execution and puts it into ABORT status. Only tasks whose status is RUNNING may be aborted.

# Abort a task
draft_task$abort()

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Clone a task

In order to copy a task, the user can clone it. Once cloned, the task can either be in DRAFT mode or immediately run, by setting the run parameter to TRUE.

# Clone a task
cloned_task <- draft_task$clone_task()

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Get execution details

If users would like to explore or debug the logs of task execution, they can use the get_execution_details() function. It returns execution details of the specified task and breaks down the information into the task’s distinct jobs. A job is a single subprocess carried out in a task. The information returned by this call is broadly similar to the one that can be found in the task stats and logs provided on the Platform. Task execution details include the following information:

• The name of the command line job that executed
• The start time of the job
• End time of the job (if it completed)
• The status of the job (DONE, FAILED, or RUNNING)
• Information on the computational instance that the job was run on, including the provider ID, the type of instance used and the cloud service provider
• A link that can be used to download the standard error logs for the job
• SHA hash of the Docker image (‘checksum’).

# Get execution details of the task
details <- draft_task$get_execution_details()

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List batch children

This operation retrieves child tasks for a batch task. It works just like the tasks$query() function, so you can set query parameters such as status, created_from, created_to, started_from, started_to, ended_from, ended_to, origin, and order to narrow down the search.

# List batch children
children_tasks <- batch_task$list_batch_children()

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Update task

Users can use the update() method to change the details of the specified task, including its name, description, and inputs. Note that you can only modify tasks with a task status of DRAFT. Tasks which are RUNNING, QUEUED, ABORTED, COMPLETED or FAILED cannot be modified in order to enable the reproducibility of analyses.

There are two things to note if you are editing a batch task:

• If you want to change the input on which to batch and the batch criteria, you need to specify the batch_input and batch_by parameters together in the same function call.
• If you want to disable batching on a task, set batch to false. Or, you can also set the parameters batch_input and batch_by to NULL.

# Update task
draft_task$update(
  description = "New description",
  batch_by = list(
    type = "CRITERIA",
    criteria = list("metadata.diagnosis")
  ),
  inputs = list("in_reads" = "<some_other_file_object_or_id>")
)

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Rerun a task

Users can also rerun the task which will actually clone the original task for them and start the execution immediately.

# Rerun task
draft_task$rerun()

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Reload task

In order to refresh the Task object and get the up to date info about its status, you can always call the reload() function:

# Reload task object
draft_task$reload()

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Delete task

Lastly, the task can be deleted using delete() method directly on the Task object too:

# Delete task
draft_task$delete()

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