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Search & query

Quilt provides support for queries in the Elasticsearch DSL, as well as SQL queries in Athena.

Elasticsearch

The objects in Amazon S3 buckets connected to Quilt are synchronized to an Elasticsearch cluster, which provides Quilt's search features.
Quilt uses Elasticsearch 6.7 (docs).

Indexing

Quilt maintains a near-realtime index of the objects in your S3 bucket in Elasticsearch. Each bucket corresponds to one or more Elasticsearch indexes. As objects are mutated in S3, Quilt uses an event-driven system (via SNS and SQS) to update Elasticsearch.
There are two types of indexing in Quilt:
  • shallow indexing includes object metadata (such as the file name and size)
  • deep indexing includes object contents. Quilt supports deep indexing for the following file extensions:
    • .csv, .html, .json, .md, .rmd, .rst, .tab, .txt, .tsv (plain-text formats)
    • .fcs (FlowJo)
    • .ipynb (Jupyter notebooks)
    • .parquet
    • .pdf
    • .pptx
    • .xls, .xlsx
By default, Quilt indexes a limited number of bytes per document for specified file formats (100KB). Both the max number of bytes per document and which file formats to deep index can be customized per Bucket in the Catalog Admin settings.
Example of Admin Bucket indexing options
The search bar on every page in the catalog provides a convenient shortcut for searching objects and packages in an Amazon S3 bucket.
Quilt uses Elasticsearch 6.7 query string syntax.
The following are all valid search parameters:
Fields
Syntax
Description
Example
comment
Package comment
comment:TODO
content
Object content
content:Hello
ext
Object extension
ext:*.fastq.gz
handle
Package name
handle:examples\/metadata
hash
Package hash
hash:3192ac1*
key
Object key
key:phase*
key_text
Analyzed object key
key:"phase"
last_modified
Last modified date
last_modified:[2022-02-04 TO 2022-02-20]
metadata
Package metadata
metadata:dapi
size
Object size in bytes
size:>=4096
version_id
Object version id
version_id:t.LVVCx*
pointer_file
Package revision tag in S3; either "latest" or a timestamp
pointer_file:latest
package_stats.total_files
Package total files
package_stats.total_files:>100
package_stats.total_bytes
Package total bytes
package_stats.total_bytes:<100
workflow.id
Package workflow ID
workflow.id:verify-metadata
Logical operators and grouping
Syntax
Description
Example
AND
Conjunction
a AND b
OR
Disjunction
a OR b
NOT
Negation
NOT a
_exists_
Matches any non-null value for the given field
_exists_: content
()
Group terms
(a AND b) NOT c
Wildcard and regular expressions
Syntax
Description
Example
*
Zero or more characters, avoid leading * (slows performance)
ext:config.y*ml
?
Exactly one character
ext:React.?sx
//
Regular expression (slows performance)
content:/lmnb[12]/

QUERIES > ELASTICSEARCH tab

Quilt Elasticsearch queries support the following keys:
  • index — comma-separated list of indexes to search (learn more)
  • filter_path — to reducing response nesting, (learn more)
  • _source — boolean that adds or removes the _source field, or a list of fields to return (learn more)
  • size — limits the number of hits (learn more)
  • from — starting offset for pagination (learn more)
  • body — the search query body as a JSON dictionary (learn more)
Saved queries
You can provide pre-canned queries for your users by providing a configuration file at s3://YOUR_BUCKET/.quilt/queries/config.yaml:
version: "1"
queries:
query-1:
name: My first query
description: Optional description
url: s3://BUCKET/.quilt/queries/query-1.json
query-2:
name: Second query
url: s3://BUCKET/.quilt/queries/query-2.json
The Quilt catalog displays your saved queries in a drop-down for your users to select, edit, and execute.

Athena

You can park reusable Athena Queries in the Quilt catalog so that your users can run them. You must first set up you an Athena workgroup and Saved queries per AWS's Athena documentation.

Configuration

You can hide the "Queries" tab by setting ui > nav > queries: false (learn more).

Basics

"Run query" executes the selected query and waits for the result.