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Working with a Bucket
Quilt allows you to create, read, and write packages both on your local filesystem and on S3 buckets configured to work with Quilt3. For convenience, we provide a simple API for working with S3 buckets that serves as an alternative to boto3.
To connect to an S3
Bucket:import quilt3
b = quilt3.Bucket("s3://quilt-example")
This requires that the bucket is configured to work with Quilt 3. Unless this bucket is public, you will also first need to log into the catalog that controls this bucket:
# only need to run this once
# ie quilt3.config('https://your-catalog-homepage/')
quilt3.config('https://open.quiltdata.com/')
# follow the instructions to finish login
quilt3.login()
To see the contents of a
Bucket, use keys:# returns a list of objects in the bucket
b.keys()
To download a file or folder from a bucket use
fetch:# b.fetch("path/to/directory", "path/to/local")
b.fetch("aleksey/hurdat/", "./aleksey/")
b.fetch("README.md", "./read.md")
100%|██████████| 4.07M/4.07M [00:13<00:00, 304kB/s]
100%|██████████| 1.55k/1.55k [00:01<00:00, 972B/s]
You can write data to a bucket.
# put a file to a bucket
b.put_file("read.md", "./read.md")
# or put everything in a directory at once
b.put_dir("stuff", "./aleksey")
Note that
set operations on a Package are put operations on a Bucket.# always be careful when deleting
# delete a fle
b.delete("read.md")
# delete a directory
b.delete_dir("stuff/")
You can search for individual objects using
search.Note that this feature is currently only supported for buckets backed by a Quilt catalog instance. Before performing a search you must first configure a connection to that instance using
quilt3.config.# for example
quilt3.config(navigator_url="https://open.quiltdata.com")
<QuiltConfig at '/Users/gregezema/Library/Application Support/Quilt/config.yml' {
"navigator_url": "https://open.quiltdata.com",
"default_local_registry": "file:///Users/gregezema/Library/Application%20Support/Quilt/packages",
"default_remote_registry": null,
"default_install_location": null,
"registryUrl": "https://open-registry.quiltdata.com",
"telemetry_disabled": false,
"s3Proxy": "https://open-s3-proxy.quiltdata.com",
"apiGatewayEndpoint": "https://sttuv8u2u4.execute-api.us-east-1.amazonaws.com/prod",
"binaryApiGatewayEndpoint": "https://ap8tbn363c.execute-api.us-east-1.amazonaws.com/prod",
"default_registry_version": 1
}>
Quilt supports unstructured search:
# returns all files containing the word "thor"
b.search("thor")
{'took': 16,
'timed_out': False,
'_shards': {'total': 5, 'successful': 5, 'skipped': 0, 'failed': 0},
'hits': {'total': 10,
'max_score': 5.5741544,
'hits': [{'_index': 'quilt-example-reindex-v8bc2377',
'_type': '_doc',
'_id': 'dima/node_modules2/highlight.js/README.md:KOGAC2bPIY9o7vQ3d3ryrD04VpGPmaH2',
'_score': 5.5741544,
'_source': {'size': 19316,
'comment': '',
'version_id': 'KOGAC2bPIY9o7vQ3d3ryrD04VpGPmaH2',
'last_modified': '2019-12-12T01:33:15+00:00',
'updated': '2019-12-12T01:33:15.209387',
'key': 'dima/node_modules2/highlight.js/README.md'}},
{'_index': 'quilt-example-reindex-v8bc2377',
'_type': '_doc',
'_id': 'akarve/amazon-reviews/camera-reviews.parquet:yoLoCR6tdnqE141f5F4EvbFbn2J12AJt',
'_score': 0.080087036,
'_source': {'user_meta': {},
'size': 100764599,
'comment': '',
'version_id': 'yoLoCR6tdnqE141f5F4EvbFbn2J12AJt',
'last_modified': '2019-10-08T02:53:01+00:00',
'updated': '2019-10-08T02:53:31.040985',
'key': 'akarve/amazon-reviews/camera-reviews.parquet'}}]}}
As well as structured search on metadata (note that this feature is experimental):
# returns all files annotated {'name': 'thor'}
b.search("user_meta.name:'thor'")
{'took': 0,
'timed_out': False,
'_shards': {'total': 5, 'successful': 5, 'skipped': 0, 'failed': 0},
'hits': {'total': 0, 'max_score': None, 'hits': []}}