fileset
Fileset REST API ResourcesLink
Provides Flask-RESTful resources for managing filesets within the PlantDB server, allowing for the creation of filesets, management of their metadata, and listing of associated files. These resources interface with the underlying filesystem database (FSDB) to provide a standardized API for handling grouped data assets and their descriptive information.
Key FeaturesLink
- FilesetCreate - Create new filesets associated with specific scans, including initial metadata assignment and name sanitization.
- FilesetMetadata - Retrieve or update metadata for a specific fileset, supporting both full dictionary retrieval and specific key lookups.
- FilesetFiles - List and query files contained within a fileset, with support for fuzzy searching and filtering.
- Security - Integrated JWT validation via decorators to ensure authorized access to data modification endpoints.
Usage ExamplesLink
Hereafter is a minimal working example that:
- Creates a
Flaskapp - Sets up a local test database
- Registers the
FilesetMetadataresource to a REST API - Starts the app
>>> import logging
>>> from flask import Flask
>>> from flask_restful import Api
>>> from plantdb.server.api.fileset import FilesetMetadata
>>> from plantdb.commons.auth.session import JWTSessionManager
>>> from plantdb.commons.fsdb.core import FSDB
>>> from plantdb.commons.test_database import setup_test_database
>>> # Create a Flask application
>>> app = Flask(__name__)
>>> # Create a logger
>>> logger = logging.getLogger("plantdb.fileset")
>>> logger.setLevel(logging.INFO)
>>> # Initialize a test database with a JWTSessionManager
>>> db_path = setup_test_database('real_plant')
>>> mgr = JWTSessionManager()
>>> db = FSDB(db_path, session_manager=mgr)
>>> db.connect()
>>> # RESTful API and resource registration
>>> api = Api(app)
>>> api.add_resource(FilesetMetadata, "/fileset/<string:scan_id>/<string:fileset_id>/metadata", resource_class_kwargs={"db": db, "logger": logger})
>>> # Start the APP
>>> app.run(host='0.0.0.0', port=5000)
It may be used as follows (in another Python REPL):
>>> import requests
>>> # Retrieve metadata for the 'images' fileset in the 'real_plant' scan
>>> url = "http://127.0.0.1:5000/fileset/real_plant/images/metadata"
>>> response = requests.get(url)
>>> print(response.json())
{'metadata': {'channels': ['rgb'], 'object': {'age': '0', 'environment': 'Lyon indoor', 'experiment_id': 'calibration01', 'object': 'random objects'}, 'task_params': {'fileset_id': 'images', 'output_file_id': 'out', 'scan_id': ''}, 'workspace': {'x': [340, 440], 'y': [330, 410], 'z': [-180, 105]}}}
>>> # Retrieve a specific metadata key
>>> response = requests.get(url + "?key=channels")
>>> print(response.json())
{'metadata': ['rgb']}
Fileset
Link
Bases: Resource
Represents a Fileset resource in the application.
This class provides the functionality to create and manage filesets associated with scans.
Attributes:
| Name | Type | Description |
|---|---|---|
db |
FSDB
|
The database providing the resources to serve. |
logger |
Logger
|
The logger used to record operations and errors. |
Initialize the resource.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
FSDB
|
A database instance providing the resources to serve. |
required |
|
Logger
|
A logger instance to record operations and errors. |
None
|
Source code in plantdb/server/api/fileset.py
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post
Link
post(scan_id, fileset_id, **kwargs)
Create a new fileset associated with a scan.
This method handles POST requests to create a new fileset. It validates the input data, creates the fileset with the specified name, and associates it with the given scan ID. Optional metadata can be attached to the fileset.
Returns:
| Type | Description |
|---|---|
dict
|
Response containing a success message or error description. If successful, also returns the created fileset ID under 'id' key, as sanitization may have happened. |
int
|
HTTP status code (201, 400, 404, or 500) |
Notes
The request body accepts a JSON object containing:
- 'metadata' (dict): the new metadata
Raises:
| Type | Description |
|---|---|
Exception
|
Any unexpected errors during fileset creation are caught and returned as 500 error responses. |
Examples:
>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> import requests
>>> # Start by log in as 'admin'
>>> response = requests.post('http://127.0.0.1:5000/login', json={'username': 'admin', 'password': 'admin'})
>>> token = response.json()['access_token']
>>> # Create a new fileset with metadata:
>>> scan_id = 'real_plant'
>>> fileset_id = 'test_fileset'
>>> metadata = {'description': 'This is a test fileset'}
>>> url = f"http://127.0.0.1:5000/fileset/{scan_id}/{fileset_id}"
>>> response = requests.post(url, json={'metadata': metadata}, headers={'Authorization': 'Bearer ' + token})
>>> response = requests.post(url, json={'metadata': metadata})
>>> print(response.status_code)
201
>>> print(response.json())
{'message': "Fileset 'my_fileset' created successfully in 'real_plant'."}
Source code in plantdb/server/api/fileset.py
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FilesetFiles
Link
Bases: Resource
Resource for handling fileset files operations.
Attributes:
| Name | Type | Description |
|---|---|---|
db |
FSDB
|
The database providing the resources to serve. |
logger |
Logger
|
The logger used to record operations and errors. |
Initialize the resource.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
FSDB
|
A database instance providing the resources to serve. |
required |
|
Logger
|
A logger instance to record operations and errors. |
None
|
Source code in plantdb/server/api/fileset.py
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get
Link
get(scan_id, fileset_id, **kwargs)
List all files in a specified fileset.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
The ID of the scan containing the fileset. |
required |
|
str
|
The name of the fileset. |
required |
Returns:
| Type | Description |
|---|---|
dict
|
Response containing either: - On success (200): {'files': list of file information} - On error (404, 500): {'message': error description} |
int
|
HTTP status code (200, 404, or 500) |
Notes
This method retrieves the list of files contained in a fileset using the
list_files() method from plantdb.commons.fsdb.core.Fileset.
See Also
plantdb.commons.fsdb.core.Fileset.list_files
Examples:
>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> import requests
>>> # List files in a fileset:
>>> url = f"http://127.0.0.1:5000/fileset/real_plant/images/files"
>>> response = requests.get(url)
>>> print(response.status_code)
200
>>> print(response.json())
{'files': ['00000_rgb', '00001_rgb', '00002_rgb', '00003_rgb', '00004_rgb', '00005_rgb', '00006_rgb', '00007_rgb', '00008_rgb', '00009_rgb', '00010_rgb', '00011_rgb', '00012_rgb', '00013_rgb', '00014_rgb', '00015_rgb', '00016_rgb', '00017_rgb', '00018_rgb', '00019_rgb', '00020_rgb', '00021_rgb', '00022_rgb', '00023_rgb', '00024_rgb', '00025_rgb', '00026_rgb', '00027_rgb', '00028_rgb', '00029_rgb', '00030_rgb', '00031_rgb', '00032_rgb', '00033_rgb', '00034_rgb', '00035_rgb', '00036_rgb', '00037_rgb', '00038_rgb', '00039_rgb', '00040_rgb', '00041_rgb', '00042_rgb', '00043_rgb', '00044_rgb', '00045_rgb', '00046_rgb', '00047_rgb', '00048_rgb', '00049_rgb', '00050_rgb', '00051_rgb', '00052_rgb', '00053_rgb', '00054_rgb', '00055_rgb', '00056_rgb', '00057_rgb', '00058_rgb', '00059_rgb']}
Source code in plantdb/server/api/fileset.py
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FilesetMetadata
Link
Bases: Resource
A REST resource for managing fileset metadata operations.
This class provides HTTP endpoints for retrieving and updating metadata associated with filesets within a scan. It supports both complete metadata retrieval and specific key lookups, as well as partial and full metadata updates.
Attributes:
| Name | Type | Description |
|---|---|---|
db |
FSDB
|
The database providing the resources to serve. |
logger |
Logger
|
The logger used to record operations and errors. |
Notes
All fileset names are sanitized before processing to ensure they contain only alphanumeric characters, underscores, dashes, or periods.
Initialize the resource.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
FSDB
|
A database instance providing the resources to serve. |
required |
|
Logger
|
A logger instance to record operations and errors. |
None
|
Source code in plantdb/server/api/fileset.py
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get
Link
get(scan_id, fileset_id, **kwargs)
Retrieve metadata for a specified fileset.
This method retrieves the metadata dictionary for a fileset. Optionally, it can return the value for a specific metadata key.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
The ID of the scan containing the fileset. |
required |
|
str
|
The name of the fileset. |
required |
Returns:
| Type | Description |
|---|---|
Union[dict, Any]
|
Without a 'key' URL parameter, it returns the complete metadata dictionary. If a 'key' URL parameter is provided, it returns the value for that key. |
Raises:
| Type | Description |
|---|---|
FilesetNotFoundError
|
If the specified fileset doesn't exist. |
KeyError
|
If the specified key doesn't exist in the metadata. |
Notes
In the URL, you can use the key parameter to retrieve specific metadata keys.
Examples:
>>> # Start a test REST API server first:
>>> # $ fsdb_rest_api --test
>>> import requests
>>> # Get all metadata:
>>> url = "http://127.0.0.1:5000/fileset/real_plant/images/metadata"
>>> response = requests.get(url)
>>> metadata = response.json()['metadata']
>>> print(metadata['channels'])
['rgb']
>>> # Get a specific metadata key:
>>> response = requests.get(url+"?key=channels")
>>> print(response.json()['metadata'])
['rgb']
Source code in plantdb/server/api/fileset.py
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post
Link
post(scan_id, fileset_id, **kwargs)
Update metadata for a specified fileset.
This method handles updating metadata for a fileset within a scan. It supports both full metadata replacement and partial updates of specific key-value pairs.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
|
str
|
Unique identifier for the scan containing the fileset |
required |
|
str
|
Name of the fileset to update metadata for |
required |
Returns:
| Type | Description |
|---|---|
dict
|
Response dictionary with either: |
int
|
HTTP status code (200 for success, 4xx/5xx for errors) |
Raises:
| Type | Description |
|---|---|
Exception
|
Any unexpected errors during metadata update will be caught, logged, and returned as a 500 error response. |
Notes
The request body accepts a JSON object containing:
- 'metadata' (dict): the new metadata
Examples:
>>> import requests
>>> # Start by log in as 'admin'
>>> response = requests.post('http://127.0.0.1:5000/login', json={'username': 'admin', 'password': 'admin'})
>>> token = response.json()['access_token']
>>> # Get all metadata:
>>> url = "http://127.0.0.1:5000/fileset/real_plant/images/metadata"
>>> response = requests.get(url)
>>> metadata = response.json()['metadata']
>>> # Update the original metadata dictionary and upload it to the database:
>>> metadata['object']['description'] = 'Test plant scan images'
>>> response = requests.post(url, json={'metadata': metadata}, headers={'Authorization': 'Bearer ' + token})
>>> print(response.ok)
True
>>> print(response.json()['metadata']['object']['description'])
Test plant scan images
>>> # Replace metadata:
>>> metadata_update = {"metadata": {"description": "Brand new description", "version": "2.0"}, "replace": True}
>>> response = requests.post(url, json=metadata_update)
>>> print(response.json())
Source code in plantdb/server/api/fileset.py
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