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Agent SDK

Agent-triggered flows​

Objects for triggering a Flow from an Agent can be found in agent_sdk for Agents v5.0+.

note

The agent_sdk is only available for Agents v5.0+. Prior to v5.0, these functions were included in ganymede_sdk.agent.

class FileWatcherResult​

FileWatcherResult is a dictionary of FileParam objects indexed by node name.param name.

  • param files: dict[str, fileParam | list[FileParam]] - Dictionary of FileParam objects indexed by node name.param name
  • param tags: list[UnappliedFileTag] | None - List of tags to be applied to all files

class TriggerFlowParams​

TriggerFlowParams specifies the inputs for the Flow executed when all files are observed. It includes the following parameters:

  • param single_file_params: dict[str, FileParam] | None - Dict of FileParam objects indexed by node name.param name. These parameters are used for Nodes that accept a single file as input.
  • param multi_file_params: dict[str, MultiFileParam] | None - Dict of MultiFileParam objects indexed by node name.param name. These parameters are used for Nodes that accept multiple files as input.
  • param benchling_tag: Tag | None - Additional parameters to be passed to flow. This parameter is used for inputs to the Input_Benchling node.
  • param additional_params: dict[str, str] | None - Additional parameters to be passed to flow. This parameter is used for inputs to the Input_Param node; the key is the name if the Node name for the input parameter, and the value is the string to pass into the Node.

class FileParam​

FileParam specifies files to be uploaded to Ganymede Cloud and their corresponding Flow parameters. These parameters are provided to the execute function once all files are detected.

  • param filename: str - Name of the file, e.g. "my_file.txt"
  • param content_type: str - Content type of the file, e.g. "text/plain". If not specified, the content type of the first file in the files dict will be used.
  • param body: bytes - File contents in bytes
  • param param: str - Name of parameter to be used in Flow, e.g. node_name.parameter_field_name
  • param parent_dir: str - Path within the Agent watch directory containing the file. For example. if C:/Users/username/watch_dir/ is being watched and C:/Users/username/watch_dir/abc/def/my_file.txt is found, then parent_dir would be "abc/def"
  • param upload_ts: str - Timestamp string in ISO format of when file was uploaded to the Agent watch directory, e.g. "2021-01-01T00:00:00Z"
  • param upload_path: str | None - Path in Ganymede storage where file will be uploaded
  • param tags: list[FileTag] | None - List of tags to be applied to the file
  • param bucket_name: str - Bucket associated with file
  • param files: str - Alternative method for specifying file contents, where the key is the filename and the value is the file body.

class MultiFileParam​

MultiFileParam is used for submitting multiple files to a single node. It includes the following parameters:

  • param files: str - Alternative method for specifying file contents, where the key is the filename and the value is the file body.
  • param content_type: str - Content type of file, e.g. "text/plain". If not specified, the content type of the first file in the files dict will be used.
  • param param: str - Name of parameter to be used in flow, e.g. node_name.parameter_field_name
  • param parent_dir: str - Path within Agent watch directory that contains file. For example. if C:/Users/username/watch_dir/ is being watched and C:/Users/username/watch_dir/abc/def/my_file.txt is found, then parent_dir would be "abc/def"
  • param upload_ts: str - Timestamp string in ISO format of when file was uploaded to Agent watch directory, e.g. "2021-01-01T00:00:00Z"
  • param upload_paths: list[str] | None - Path in Ganymede storage where file will be uploaded
  • param tags: list[FileTag] | None - List of tags to be applied to file
  • param bucket_name: str - Bucket associated with file

The MultiFileParam object contains a method for initiation from a list of FileParam objects as shown below. The content type of the object is assumed to take on the content type of the first item in the list.

# assume fp1 and fp2 are FileParam objects
m = agent_sdk.file_params_list_to_multi([fp1, fp2])

class NoOpFileTagParams​

NoOpFileTagParams is a used to specify that tags should be applied to a file, but that no Flow should be triggered upon file upload to Ganymede.

  • param files: list[FileParam | list[FileParam]] - List of FileParam objects to apply tags to

function fp​

fp returns a function that performs pattern matching against a file path. Specifically, the function returns callable[[str], bool] - a function that takes a file path and returns True if the file path matches the pattern, and False otherwise.

This function can be useful as a template for creating your own pattern matching functions.

  • param watch_dir: str - Directory to watch for files
  • param pattern: str - Glob pattern to match against the file path
  • param seconds_since_modification: int | None - if set, filters for files last modified within the number of seconds specified, by default None
  • param seconds_since_access: int | NOne - if set, filters for files last accessed within the number of seconds specified, by default None

function file_params_list_to_multi​

file_params_list_to_multi converts a list of FileParam objects to a MultiFileParam object.

  • param file_params: list[FileParam] - List of FileParam objects to convert to MultiFileParam

class FlowTag​

The FlowTag class is used to represent a tag that can be applied to a file. This class is not used for applying tags, but rather for interacting with tags already applied to files.

  • param tag_id: str - Name of the tag type applied to a file.
  • param display_tag: str - Value of the tag applied to a file.
  • param upload_ts: datetime - Timestamp of when tag was applied

function add_file_tag_to_fileparam​

add_file_tag_to_fileparam adds a Tag to a FileParam object, returning a FileParam | MultiFileParam object with the tag applied.

param file_param: FileParam | MultiFileParam - FileParam object to add Tag to param tag_type_id: str - Tag type of Tag to add param display_value: str - Value of Tag to add param tag_id: str | None - Optional Tag ID which can be used to reference the Tag in code param url: str | None - Optional URL to associate with the Tag

Checksum functions​

Agent utility functions are provided in agent_sdk for validating data integrity and interacting with file systems.

Computing file checksums​

Ganymede provides functions to validate file integrity; these values can be used to verify the integrity of a file uploaded to cloud storage

function calculate_crc32c​

The function returns the CRC32C checksum of a file as a string encoded in utf-8.

  • param file_path: str - Path to file to generate checksum for
  • param blocksize: int | None - Block size to use for the checksum calculation. If not specified, the default block size is 2**20.

function calculate_md5​

The function returns the MD5 hash of a file as a string encoded in utf-8.

  • param file_path: str - Path to file to generate MD5 hash for

Examples​

# Before Agent v5.0
# from ganymede_sdk.agent.utils import calculate_md5, calculate_crc32c

from agent_sdk import calculate_md5, calculate_crc32c

file_path = "path/to/local/file"

# either md5 or crc32c can be used to validate the integrity of a file
md5 = calculate_md5(file_path)
crc32c = calculate_crc32c(file_path)

You can also calculate the checksum of a file uploaded to Ganymede Cloud by creating a a tempfile.TemporaryFile object, writing the file contents to it, and then calculating the checksum:

from agent_sdk import calculate_md5, calculate_crc32c
import os
import tempfile

data = b"Example data to calculate checksum"

with tempfile.NamedTemporaryFile(delete=False) as tmp_file:
    tmp_file.write(data)
    tmp_file_name = tmp_file.name

md5 = calculate_md5(tmp_file_name)
crc32c = calculate_crc32c(tmp_file_name)

os.remove(tmp_file_name)

File system utilities​

agent_sdk provides a number of convenience functions, which can be helpful to use with cron Agents that involve more complex logic prior to invoking a flow. Some examples of this are when a file is written to multiple times before being processed, or if there is a variable number of files being processed, such that the trigger for invoking a flow requires more than just the presence of a file.

class ScanResult​

ScanResult is a frozen dataclass stores file paths for files of interest. Two files are considered to be the same if they have the same relative_path amd modified_time.

  • param relative_path: str - Path to file
  • param modified_time: datetime - Datetime of when file was last modified

function list_files_recursive​

list_files_recursive returns a list of all filepaths in a directory and its subdirectories as a list[str].

  • param file_path: str - Path to directory to list files from

function matches_pattern​

matches_pattern returns True if a file path matches at least one of the specified regex patterns specified and False otherwise.

  • param filename: str - Name of file
  • param pattern: str | re.Pattern | list[re.Pattern] - Regex pattern or list of regex patterns to match against

function is_file_ready​

is_file_ready returns True if a file has the modified time is within the last interval_in_seconds seconds, or if the size of the file has changed in that same timespan; otherwise, it returns False.

  • param file_path: str - Path to file to watch
  • param threshold_seconds: float - Number of seconds to wait between checks, by default 0.1

function get_most_recent_modified_result​

get_most_recent_modified_result returns a ScanResult object referencing the most recently modified file in a directory, or None if no files are found.

  • param directory: Path - Path to directory to watch

function filter_by_age​

filter_by_age returns a list[str] of file paths that have not been modified within the last age_in_minutes minutes.

  • param scan_results: Iterable[ScanResult] - List of ScanResult objects
  • param age_in_minutes: int - Minimum age in minutes

function zip_directory​

zip_directory creates a zip file of a directory and its contents.

  • param directory: str - Path to directory to zip
  • param zip_file: str - Path to zip file to create

function scan_for_finished_files​

scan_for_finished_files scans a directory, returning paths to files with a modified date older than the specified number of minutes as a list[str].

  • param directory: str - Path to directory to scan
  • param age_in_minutes: int - Minimum age in minutes for files to be included in the results
  • param pattern: re.Pattern | list[re.Pattern] - Regex pattern to match files against; only files that match against at least one of the specified patterns will be included in results

Example​

You can use scan_for_finished_files to continuously scan a directory for files, uploading them to Ganymede Cloud for processing when they are older than a specified number of minutes. The Flow could query previously uploaded files using the list_files_recursive method to avoid uploading the same file multiple times.

Accessing Ganymede Cloud​

function read_sql_query​

read_sql_query returns a pandas DataFrame object containing the results of a SQL query run against the Ganymede DB.

  • param sql_query: str - SQL query to run

Example​

from agent_sdk.query import read_sql_query

df = read_sql_query('SELECT * FROM instrument_methods')

function get_secret​

get_secret returns the value of a secret stored in Ganymede.

  • param secret_name: str - Name of the secret to retrieve

Logging Methods​

Ganymede Agents (v5.0+) support user-defined logging messages in the agent_sdk, aligning with logging level for Agent messages. Each level corresponds with a separate method in agent_sdk.

from agent_sdk import internal, debug, info, activity, error

# log internal
internal('Display internal message')

# log debug
debug('Display debug message')

# log info
info('Display info message')

# log activity
activity('Display activity message')

# log error
error('Display error message')

In the UI, these log messages are viewable and filterable on the corresponding Connections page.

Notifications​

Ganymede Agents (v5.1.31+) support sending email notifications to users via the agent_sdk. Email addresses for notifications can be set in the Agent Connection configuration as shown below:

Configuring Connection Emails

function notify​

  • param msg: str - Message to send in notification