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

Search Bar

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.