Searching Data Objects

You can use the dx ls command to list the objects in your current project. You can learn which project and folder you are currently in by using the command dx pwd. Using glob patterns, you can broaden your search for objects by specifying filenames with wildcard characters such as * and ?. An asterisk (*) is used to represent zero or more characters in a string, and a question mark (?) represents exactly one character.

Searching Objects with Glob Patterns

Searching Objects in Your Current Folder

By listing objects in your current directory with the wildcard characters * and ?, you can search for objects with a filename using a glob pattern. Here we take folder "C. Elegans - Ce10/" in the public project "Reference Genome Files" (platform login required to access this link) and walk through these examples:

Printing the Current Working Directory

$ dx select "Reference Genome Files"
$ dx cd "C. Elegans - Ce10/"
$ dx pwd # Print current working directory
Reference Genome Files:/C. Elegans - Ce10

Listing Folders and/or Objects in a Folder

$ dx ls

Listing Objects Named Using a Pattern

$ dx ls ‘*.fa*’ # List objects with filenames of the pattern "*.fa*"
$ dx ls ce10.???-index.tar.gz # List objects with filenames of the pattern "ce10.???-index.tar.gz"

Searching Across Objects in the Current Project

If you wish to search the entire project with a filename pattern, you can utilize the command dx find data --name with the wildcard characters. Unless --path or --all-projects is specified, dx find data searches data under the current project. Below, we use the command dx find data in the public project "Reference Genome Files" (platform login required to access this link) using the --name option to specify the filename of objects that we're searching for.

$ dx find data --name "*.fa*.gz"
closed  2014-10-09 09:50:51 776.72 MB /M. musculus - mm10/mm10.fasta.gz (file-BQbYQPj0Z05ZzPpb1xf000Xy)
closed  2014-10-09 09:50:30 767.47 MB /M. musculus - mm9/mm9.fasta.gz (file-BQbYK6801fFJ9Fj30kf003PB)
closed  2014-10-09 09:49:27 49.04 MB /D. melanogaster - Dm3/dm3.fasta.gz (file-BQbYVf80yf3J9Fj30kf00PPk)
closed  2014-10-09 09:48:55 29.21 MB /C. Elegans - Ce10/ce10.fasta.gz (file-BQbY9Bj015pB7JJVX0vQ7vj5)
closed  2014-10-08 13:52:26 818.96 MB /H. Sapiens - GRCh37 - hs37d5 (1000 Genomes Phase II)/hs37d5.fa.gz (file-B6ZY7VG2J35Vfvpkj8y0KZ01)
closed  2014-10-08 13:51:31 876.79 MB /H. Sapiens - hg19 (UCSC)/ucsc_hg19.fa.gz (file-B6qq93v2J35fB53gZ5G0007K)
closed  2014-10-08 13:50:53 827.95 MB /H. Sapiens - hg19 (Ion Torrent)/ion_hg19.fa.gz (file-B6ZYPQv2J35xX095VZyQBq2j)
closed  2014-10-08 13:50:17 818.88 MB /H. Sapiens - GRCh38/GRCh38.no_alt_analysis_set.fa.gz (file-BFBv6J80634gkvZ6z100VGpp)
closed  2014-10-08 13:49:53 810.45 MB /H. Sapiens - GRCh37 - b37 (1000 Genomes Phase I)/human_g1k_v37.fa.gz (file-B6ZXxfG2J35Vfvpkj8y0KXF5)

Escaping Special Characters

As described above, if your file contains special characters in their filename, the special characters should be escaped when searching. Additionally, as a colon (:) is used to denote project names and a slash (/) is used to separate folder names on the platform, they are also special characters, so we will also need to escape these two characters when they appear in a data object's name. To escape any special characters, you will use a preceding backslash \.

Please note that while dx-toolkit itself requires a single \ to escape a colon or a slash, the syntax conventions in some shells may require you to escape the \ character itself by an extra backslash or by enclosing the argument in single quotes.

Searching Objects with Other Criteria

dx find data also allows you to search data using metadata fields, such as when the data was created, the data's tags, or the project the data exists in.

Searching Objects Created Within a Certain Period of Time

You can utilize the flags --created-after and --created-before to search for data objects created within a period of time.

$ dx find data --created-after 2017-02-22 --created-before 2017-02-25
closed  2017-02-27 19:14:51 3.90 GB  /H. Sapiens - hg19 (UCSC)/ucsc_hg19.hisat2-index.tar.gz (file-F2pJvF80Vzx54f69K4J8K5xy)
closed  2017-02-27 19:14:21 3.55 GB  /M. musculus - mm10/mm10.hisat2-index.tar.gz (file-F2pJqk00Vq161bzq44Vjvpf5)
closed  2017-02-27 19:13:57 3.51 GB  /M. musculus - mm9/mm9.hisat2-index.tar.gz (file-F2pJpKj0G0JxZxBZ4KJq0Q6B)
closed  2017-02-27 19:13:41 3.85 GB  /H. Sapiens - hg19 (Ion Torrent)/ion_hg19.hisat2-index.tar.gz (file-F2pJkp00BjBk99xz4Jk74V0y)
closed  2017-02-27 19:13:28 3.85 GB  /H. Sapiens - GRCh37 - b37 (1000 Genomes Phase I)/human_g1k_v37.hisat2-index.tar.gz (file-F2pJpy007bGBzj7X446PzxJJ)
closed  2017-02-27 19:13:02 3.90 GB  /H. Sapiens - GRCh37 - hs37d5 (1000 Genomes Phase II)/hs37d5.hisat2-index.tar.gz (file-F2pJpb000vFpzj7X446PzxF0)
closed  2017-02-27 19:12:31 3.91 GB  /H. Sapiens - GRCh38/GRCh38.no_alt_analysis_set.hisat2-index.tar.gz (file-F2pK5y00F8Bp9BYk4KX7Qb4P)
closed  2017-02-27 19:12:18 224.54 MB /D. melanogaster - Dm3/dm3.hisat2-index.tar.gz (file-F2pJP7j0QkbQ3ZqG269589pj)
closed  2017-02-27 19:11:56 139.76 MB /C. Elegans - Ce10/ce10.hisat2-index.tar.gz (file-F2pJK300KKz8bx1126Ky5b3P)

Searching Objects by Their Metadata

You can search for objects based on their metadata. An object's metadata can be set by performing the command dx tag or dx set_properties to respectively tag or setup key-value pairs to describe your data object. You can also set metadata while uploading data to the platform. To search by object tags, use the option --tag. This option can be repeated if the search requires multiple tags.

$ dx find data --tag sampleABC --tag batch123
closed  2017-01-01 09:00:00 6.08 GB  /Input/SRR504516_1.fastq.gz (file-xxxx)
closed  2017-01-01 09:00:00 5.82 GB  /Input/SRR504516_2.fastq.gz (file-wwww)

To search by object properties, use the option --property. This option can be repeated if the search requires multiple properties.

$ dx find data --property sequencing_providor=CRO_XYZ
closed  2017-01-01 09:00:00 8.06 GB  /Input/SRR504555_1.fastq.gz (file-qqqq)
closed  2017-01-01 09:00:00 8.52 GB  /Input/SRR504555_2.fastq.gz (file-rrrr)

Searching Objects in Another Project

You can search for an object living in a different project than your current working project by specifying a project and folder path with the flag --path. Below, we specify the project ID (project-BQfgzV80bZ46kf6pBGy00J38) of the public project "Exome Analysis Demo" (platform login required to access this link) as an example.

$ dx find data --name "*.fastq.gz"
 --path project-BQfgzV80bZ46kf6pBGy00J38:/Input
  closed  2014-10-03 12:04:16 6.08 GB  /Input/SRR504516_1.fastq.gz (file-B40jg7v8KfPy38kjz1vQ001y)
  closed  2014-10-03 12:04:16 5.82 GB  /Input/SRR504516_2.fastq.gz (file-B40jgYG8KfPy38kjz1vQ0020)

Searching Objects Across Projects with VIEW and Above Permissions

If you would like to search for data objects live in all projects in which you have VIEW and above permissions, you can use the --all-projects flag. Public projects are not shown in this search.

$ dx find data --name "SRR*_1.fastq.gz" --all-projects
closed  2017-01-01 09:00:00 6.08 GB  /Exome Analysis Demo/Input/SRR504516_1.fastq.gz (project-xxxx:file-xxxx)
closed  2017-07-01 10:00:00 343.58 MB /input/SRR064287_1.fastq.gz (project-yyyy:file-yyyy)
closed  2017-01-01 09:00:00 6.08 GB  /data/exome_analysis_demo/SRR504516_1.fastq.gz (project-zzzz:file-xxxx)

Scoping Within Projects

To describe data for small amounts of files (typically below 100), scope findDataObjects to only a project level.

The below is an example of code used to scope a project:

dx api system findDataObjects '{"scope": {"project": "project-xxxx"}, "describe":{"fields":{"state":true}}}'

See the API method system/findDataObjects for more information about usage.

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