Search
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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 page.
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
.pptx
.xls, .xlsx
The search bar on every page in the catalog provides a convenient shortcut for searching objects and packages in an Amazon S3 bucket.
The following are all valid search parameters:
Fields
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
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
*
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]/
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.
Quilt Elasticsearch queries support the following keys:
NOTE: Quilt uses Elasticsearch 6.7 .
index — comma-separated list of indexes to search ()
filter_path — to reducing response nesting, ()
_source — boolean that adds or removes the _source field, or a list of fields to return ()
size — limits the number of hits ()
from — starting offset for pagination ()
body — the search query body as a JSON dictionary ()
