Package index • quartzbio.edp

EDP connections

Set, get manage connections to EDP using profiles or environments variables

autoconnect(): tries to connect, using environment variables or the default profile

connect(): connect to the QuartzBio EDP API and return the connection

connect_with_profile(): connect to the QuartzBio EDP API using a saved profile

get_connection(): get the default connection if any

read_connection_profile(): read a connection profile

save_connection_profile(): save a connection profile

set_connection(): set the default connection

test_connection(): test a connection

params: shared roxygen params

Vaults, Files, Folders

Vaults, Files, Folders management Vaults and Objects

Vault_create(): creates a new EDP vault or updates an existing one.

Vault_update(): updates a vault

Folder_create(): creates a folder.

File_download(): utility function that downloads an EDP File into a local file

File_get_download_url(): fetches the download URL of a file.

File_query(): queries the content of a file.

File_read(): convenience function to download a file into memory, just a wrapper over File_download()

File_upload(): uploads a file Upload a file to a QuartzBio vault. Automatically uses multipart upload for files larger than the multipart_threshold. multipart_threshold (int): File size threshold for multipart upload (default: 64MB) multipart_chunksize (int): Size of each upload part (default: 64MB)

Datasets

Dataset_create(): creates a new Dataset.

Dataset_import(): imports data into an existing dataset

Dataset_load(): Dataset_load

Dataset_query(): queries data into a dataset.

Dataset_schema(): Get dataset schema

Fetching, Querying and Filtering

fetch_all(): fetch all the pages for a possibly incomplete paginated API result

fetch_next(): fetch the next page of data if any

fetch_prev(): fetch the previous page of data if any

delete() fetch() fetch_vaults(): deletes an object from EDP

Dataset_query(): queries data into a dataset.

File_query(): queries the content of a file.

filters(): parses the maths-like syntax of filters.

All Functions

Dataset(): fetches a dataset.

DatasetField(): fetches a field metadata of a dataset by ID or (datasetid, field_name)

DatasetField_create(): creates a new Dataset Field.

DatasetField_update(): updates an existing Dataset Field.

DatasetFields(): fetches the fields of a dataset.

Dataset_create(): creates a new Dataset.

Dataset_import(): imports data into an existing dataset

Dataset_query(): queries data into a dataset.

Datasets(): fetches a list of datasets.

File(): fetches a file by id, full_path or (vault_id, path)

File_download(): utility function that downloads an EDP File into a local file

File_get_download_url(): fetches the download URL of a file.

File_query(): queries the content of a file.

File_read(): convenience function to download a file into memory, just a wrapper over File_download()

File_upload(): uploads a file Upload a file to a QuartzBio vault. Automatically uses multipart upload for files larger than the multipart_threshold. multipart_threshold (int): File size threshold for multipart upload (default: 64MB) multipart_chunksize (int): Size of each upload part (default: 64MB)

Files(): fetches a list of files.

Folder(): fetches a folder by id, full_path or (vault_id, path)

Folder_create(): creates a folder.

Folders(): fetches a list of folders.

Multi_part_file_upload(): Function to support multi-part upload for files larger than multipart_threshold.

Object(): fetches an object.

Object_create(): creates an Object.

Object_update(): updates an Object.

Objects(): fetches a list of objects (files, folders, datasets)

Task(): fetches a task.

Task_wait_for_completion(): Waits for a task to be completed (or failed).

Tasks(): fetches a list of tasks.

User(): fetches user information.

Vault(): fetches a vault

Vault_create(): creates a new EDP vault or updates an existing one.

Vault_update(): updates a vault

Vaults(): fetches a list of vaults

autoconnect(): tries to connect, using environment variables or the default profile

configure_logger(): Configure log file and set the log-level

connect(): connect to the QuartzBio EDP API and return the connection

connect_with_profile(): connect to the QuartzBio EDP API using a saved profile

create_model_df_from_fields(): create a model data frame from a list of column names and some meta data fields.

dataset_export_to_parquet(): Initiate a Dataset export to parquet

edp_health_check(): edp_health_check

fetch_all(): fetch all the pages for a possibly incomplete paginated API result

fetch_next(): fetch the next page of data if any

fetch_prev(): fetch the previous page of data if any

filters(): parses the maths-like syntax of filters.

format_df_like_model(): Format a data frame like the model data frame

delete() fetch() fetch_vaults(): deletes an object from EDP

get_connection(): get the default connection if any

log_message(): Record a log message with the given log level

old_params: shared old roxygen params

params: shared roxygen params

quartzbio_shiny_auth(): New function for EDP auth of shiny app. Returns the updated session with EDP connection to be used in shiny app

read_connection_profile(): read a connection profile

save_connection_profile(): save a connection profile

set_connection(): set the default connection

test_connection(): test a connection

Legacy former solvebio API

Former solvebio api functions. Compatible with the new connection functions.

Annotator.annotate(): Annotate a data table/frame with additional fields.

Application.all(): Retrieve the metadata about all application on QuartzBio EDP available to the current user.

Application.create(): Application.create

Application.delete(): Application.delete

Application.retrieve(): Retrieve the metadata about a specific application QuartzBio EDP.

Application.update(): Application.update

Beacon.all(): Beacon.all

Beacon.create(): Beacon.create

Beacon.delete(): Beacon.delete

Beacon.query(): Beacon.query

Beacon.retrieve(): Beacon.retrieve

Beacon.update(): Beacon.update

BeaconSet.all(): BeaconSet.all

BeaconSet.create(): BeaconSet.create

BeaconSet.delete(): BeaconSet.delete

BeaconSet.query(): BeaconSet.query

BeaconSet.retrieve(): BeaconSet.retrieve

BeaconSet.update(): BeaconSet.update

Dataset.activity(): Dataset.activity

Dataset.all(): Retrieves the metadata about datasets on QuartzBio EDP.

Dataset.count(): Dataset.count

Dataset.create(): Dataset.create

Dataset.data(): Dataset.data

Dataset.delete(): Dataset.delete

Dataset.disable_global_beacon(): Dataset.disable_global_beacon

Dataset.enable_global_beacon(): Dataset.enable_global_beacon

Dataset.facets(): Dataset.facets

Dataset.fields(): Dataset.fields

Dataset.get_by_full_path(): Dataset.get_by_full_path

Dataset.get_global_beacon_status(): Dataset.get_global_beacon_status

Dataset.get_or_create_by_full_path(): Dataset.get_or_create_by_full_path

Dataset.query(): Dataset.query

Dataset.retrieve(): Dataset.retrieve

Dataset.template(): Dataset.template

Dataset.update(): Dataset.update

DatasetCommit.all(): DatasetCommit.all

DatasetCommit.delete(): DatasetCommit.delete

DatasetCommit.retrieve(): DatasetCommit.retrieve

DatasetExport.all(): DatasetExport.all

DatasetExport.create(): DatasetExport.create

DatasetExport.delete(): DatasetExport.delete

DatasetExport.get_download_url(): DatasetExport.get_download_url

DatasetExport.retrieve(): DatasetExport.retrieve

DatasetField.all(): DatasetField.all

DatasetField.create(): DatasetField.create

DatasetField.facets(): DatasetField.facets

DatasetField.retrieve(): DatasetField.retrieve

DatasetField.update(): DatasetField.update

DatasetImport.all(): DatasetImport.all

DatasetImport.create(): DatasetImport.create

DatasetImport.delete(): DatasetImport.delete

DatasetImport.retrieve(): DatasetImport.retrieve

DatasetMigration.all(): DatasetMigration.all

DatasetMigration.create(): DatasetMigration.create

DatasetMigration.delete(): DatasetMigration.delete

DatasetMigration.retrieve(): DatasetMigration.retrieve

DatasetTemplate.all(): DatasetTemplate.all

DatasetTemplate.create(): DatasetTemplate.create

DatasetTemplate.delete(): DatasetTemplate.delete

DatasetTemplate.retrieve(): DatasetTemplate.retrieve

DatasetTemplate.update(): DatasetTemplate.update

Dataset_load(): Dataset_load

Dataset_schema(): Get dataset schema

Expression.evaluate(): Evaluate a QuartzBio EDP expression.

GlobalSearch.facets(): GlobalSearch.facets

GlobalSearch.request(): GlobalSearch.request

GlobalSearch.search(): GlobalSearch.search

GlobalSearch.subjects(): GlobalSearch.subjects

GlobalSearch.subjects_count(): GlobalSearch.subjects_count

Object.all(): Retrieves the metadata about all objects on EDP accessible to the current user.

Object.create(): Object.create

Object.data(): Object.data

Object.delete(): Object.delete

Object.disable_global_beacon(): Object.disable_global_beacon

Object.enable_global_beacon(): Object.enable_global_beacon

Object.fields(): Object.fields

Object.get_by_full_path(): Object.get_by_full_path

Object.get_by_path(): Object.get_by_path

Object.get_download_url(): Object.get_download_url

Object.get_global_beacon_status(): Object.get_global_beacon_status

Object.get_or_upload_file(): Object.get_or_upload_file

Object.query(): Object.query

Object.retrieve(): Object.retrieve

Object.update(): Object.update

Object.upload_file(): Object.upload_file

SavedQuery.all(): SavedQuery.all

SavedQuery.create(): SavedQuery.create

SavedQuery.delete(): SavedQuery.delete

SavedQuery.retrieve(): SavedQuery.retrieve

SavedQuery.update(): SavedQuery.update

Task.all(): Task.all

Task.follow(): Task.follow

Task.retrieve(): Task.retrieve

User.retrieve(): Retrieves information about the current user

Vault.all(): Vault.all

Vault.create(): Vault.create

Vault.create_dataset(): Vault.create_dataset

Vault.create_folder(): Vault.create_folder

Vault.datasets(): Vault.datasets

Vault.delete(): Vault.delete

Vault.files(): Vault.files

Vault.folders(): Vault.folders

Vault.get_by_full_path(): Vault.get_by_full_path

Vault.get_or_create_by_full_path(): Vault.get_or_create_by_full_path

Vault.get_personal_vault(): Vault.get_personal_vault

Vault.objects(): Vault.objects

Vault.retrieve(): Vault.retrieve

Vault.search(): Vault.search

Vault.update(): Vault.update

login(): login

protectedServer(): protectedServer

protectedServerJS(): protectedServerUI