Bundles
Alexis Lucattini edited this page Jun 4, 2023
·
2 revisions
Usage:
icav2 bundles <command> <args...>
Plugin Commands:
init Initialise a bundle
list List bundles
add-data Add data to a bundle
add-pipeline Add pipeline to a bundle
release Release a bundle
Flags:
-h, --help help for bundles
Global Flags:
-t, --access-token string JWT used to call rest service
-o, --output-format string output format (default "table")
-s, --server-url string server url to direct commands
-k, --x-api-key string api key used to call rest service
Use "icav2 bundles [command] --help" for more information about a command.
Initialise a bundle
Usage:
icav2 bundles init help
icav2 bundles init <bundle_name>
(--short-description <description)
(--input-yaml <bundle.yaml>)
[--region <region_id_or_city_name>]
[--json]
Description:
Initialise a bundle through a yaml file.
The yaml file contains the following keys:
* region: (optional)
* A string containing either the region id or city-name
* pipelines
* A list of pipeline ids or codes to add to the bundle
* Where each item in the list must contain one of the following keys
* pipeline_id
* pipeline_code
* data
* A list of data paths or ids to add to the bundle
* Where each item in the list must contain one of the following keys
* data_id (accessed by the Data/ endpoint by default) (iterates through available regions to find data id)
* data_uri (icav2://project-name-or-id/path-to-data/) (accessed from the projectdata endpoint)
* analyses :construction:
* A list of analysis ids to add to the bundle
* Where each item in the list must contain one of the following keys
* analysis_id (required)
* pipeline_only (optional boolean)
* data_only (optional boolean)
* inputs_only (optional boolean)
* outputs_only (optional boolean)
The yaml file may look like the following
region:
id: abcdefg
pipelines:
- pipeline-code: abcdeg
- pipeline-id: a1b2c3de-uuid
data:
- data-id: fil.12345567
- data-id: fol.12345678
- data-uri: icav2://playground/path-to-file/
- data-uri: icav2://playground/path-to-folder/
Options:
--short-description=<description> Required, a short description for the bundle
--region=<region_id_or_city_name> Optional, specify a region ID or city name if user has access to multiple regions
One may also specify the region id / city name in the input yaml.
--input-yaml=<file> Required, path to input yaml file
--json Return bundle as json object to stdout
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles init my-first-bundle --short-description "My very first bundle" --input-yaml file.yaml
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Use the <tab> command to get the list of available parameters
List all bundles
Usage:
icav2 bundles list help
icav2 bundles list [--bundle-name <name>]
[--status <status>]
[--creator=<creator_id_or_username>]
[--region <region_id_or_city_name>]
Description:
List available bundles
Options:
--status=<status> Optional, show only bundles by status (one of DRAFT, RELEASED, DEPRECATED)
--bundle-name=<name> Optional, show only bundles that match a certain bundle name
--creator=<creator_id_or_username> Optional, show only bundles that are created by this user
--region=<region_id_or_city_name> Optional, show only bundles of a certain region
--json Return bundle list as json list object to stdout (table by default)
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles release abcdefg.12345
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N/A
Use the 'release' command to set the bundle status to 'released'
Usage:
icav2 bundles release help
icav2 bundles release <bundle_id>
Description:
Release a bundle
Options:
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles release abcdefg.12345
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N/A
Add data to a bundle
Usage:
icav2 bundles add-data help
icav2 bundles add-data <bundle_id>
(--input-yaml=<bundle.yaml> | --data-id=<data_id> | --data-uri=)
Description:
Add data to a bundle
The yaml file may look like the following, in this subcommand however, we only look at the 'data' key
region:
id: abcdefg
pipelines:
- pipeline-code: abcdeg
- pipeline-id: a1b2c3de-uuid
data:
- data-id: fil.12345567
- data-id: fol.12345678
- data-uri: icav2://playground/path-to-file/
- data-uri: icav2://playground/path-to-folder/
Options:
--input-yaml=<file> Optional, path to input yaml file.
--data-id=<data-id> Optional, the data id to add to the bundle
--data-uri=<data-uri> Optional, the data uri to add to the bundle
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles add-data-to-bundle --input-yaml path-to-input.yaml
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N/A
Usage:
icav2 bundles add-pipeline help
icav2 bundles add-pipeline <bundle_id>
(--input-yaml=<bundle.yaml> | --pipeline-id=<pipeline_id> | --pipeline-code=<pipeline_code>)
Description:
Add a released pipeline to a bundle
The yaml file may look like the following, in this subcommand however, we only look at the 'pipelines' key
region:
id: abcdefg
pipelines:
- pipeline-code: abcdeg
- pipeline-id: a1b2c3de-uuid
data:
- data-id: fil.12345567
- data-id: fol.12345678
- data-uri: icav2://playground/path-to-file/
- data-uri: icav2://playground/path-to-folder/
Options:
--input-yaml=<file> Optional, path to input yaml file.
--pipeline-id=<pipeline-id> Optional, the pipeline id to add to the bundle
--pipeline-code=<pipeline-code> Optional, the pipeline code to add to the bundle
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles add-pipeline-to-bundle --input-yaml path-to-input.yaml
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:greentickmark:
icav2 bundles release --help
Usage:
icav2 bundles release help
icav2 bundles release <bundle_id>
Description:
Release a bundle
Options:
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles release abcdefg.12345
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:greentickmark:
icav2 bundles add-bundle-to-project --help
Usage:
icav2 bundles add-bundle-to-project help
icav2 bundles add-bundle-to-project <bundle_id>
(--input-yaml=<bundle.yaml> | --project=<project_name_or_id>)
Description:
Add bundle to a project. Bundle MUST be released
The input yaml may contain one of the following attributes:
Where the projects key is a list.
Each list attribute may be a string or a dict containing either the project_id, project_name or project key
projects:
- project: <project_name_or_id>
OR
- <project_name_or_id>
If you have only one project to link to, you wish to may specify the project on the commandline instead.
In order to add a bundle to a project, you will need admin access to the project.
Options:
--input-yaml=<file> Optional, path to input yaml file.
--project=<project_name_or_id Optional, the project to add the bundle to
Environment variables:
ICAV2_BASE_URL Optional, default set as https://ica.illumina.com/ica/rest
Example:
icav2 bundles add-bundle-to-project bundle1234 --input-yaml path-to-input.yaml
icav2 bundles add-bundle-to-project bundle1234 --project my-project
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:greentickmark: