Search

Each Quilt stack includes an Elasticsearch cluster that indexes objects and packages as documents. The objects in Amazon S3 buckets connected to Quilt are synchronized to an Elasticsearch cluster, which provides Quilt's search and package listing features.

NOTE: This page is about full-text searching using Elasticsearch. For precise querying of specific fields, see the Queries page.

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

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.

NOTE: 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]/

ELASTICSEARCH tab

When you click into a specific bucket, you can access the Elasticsearch tab to run more complex queries. The Elasticsearch tab provides a more powerful search interface than the search bar, allowing you to specify the Elasticsearch index and query parameters.

catalog-es-queries-default

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)