Input and Output Domain - Revision history

Lorikrammer: /* Input and Output Domain (io_domain) */

2026-04-14T20:59:15Z

Input and Output Domain (io_domain)

← Older revision		Revision as of 20:59, 14 April 2026
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	== Input and Output Domain (''io_domain'') ==		== Input and Output Domain (''io_domain'') ==
	This section defines the io_domain part of the [[~~Bco-domains~~\|BCO]]. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here].		This section defines the io_domain part of the [[BCO Domains\|BCO]]. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here].

	This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can reside in the system performing the computation or any other accessible system. Just like the fields of the parametric domain, these fields are expected to vary depending on the specific BCO implementation and can refer to named input-output arguments of underlying pipelines. Please refer to the documentation of individual scripts and specific BCO descriptions for further details.		This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can reside in the system performing the computation or any other accessible system. Just like the fields of the parametric domain, these fields are expected to vary depending on the specific BCO implementation and can refer to named input-output arguments of underlying pipelines. Please refer to the documentation of individual scripts and specific BCO descriptions for further details.

Lorikrammer at 20:48, 14 April 2026

2026-04-14T20:48:25Z

← Older revision		Revision as of 20:48, 14 April 2026
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	'''Go back to [[~~Bco-domains\|~~BCO Domains]].'''		'''Go back to [[BCO Domains]].'''

	== Input and Output Domain (''io_domain'') ==		== Input and Output Domain (''io_domain'') ==

Lorikrammer: /* "Mediatype" Field Definition */

2026-02-10T21:34:32Z

"Mediatype" Field Definition

← Older revision		Revision as of 21:34, 10 February 2026
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	'''Go back to [[Bco-domains\|BCO Domains]].'''		'''Go back to [[Bco-domains\|BCO Domains]].'''

	== Input and Output Domain ~~\| "~~io_domain" ==		== Input and Output Domain (''io_domain'') ==
	This section defines the io_domain part of the [[Bco-domains\|BCO]]. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here].		This section defines the io_domain part of the [[Bco-domains\|BCO]]. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here].

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	\|}		\|}

	== Input Subdomain ~~\| “input_subdomain”~~ ==		== Input Subdomain (''input_subdomain'') ==
	This field records the references and input files for the entire pipeline. Each input file is listed as a uri object. This allows the author to be very specific about a particular type of input file if they so choose. For example, reference files have common names, and adding the common name here, in addition to the uri would make this more readable and understandable (eg, "HCV reference version..." or "human reference GRCH38"). For data integration workflows, the input files can be a table downloaded from a specific source which is then filtered for modification using rules described in the BCO.		This field records the references and input files for the entire pipeline. Each input file is listed as a uri object. This allows the author to be very specific about a particular type of input file if they so choose. For example, reference files have common names, and adding the common name here, in addition to the uri would make this more readable and understandable (eg, "HCV reference version..." or "human reference GRCH38"). For data integration workflows, the input files can be a table downloaded from a specific source which is then filtered for modification using rules described in the BCO.

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	},		},

	== Output Subdomain ~~\| “output_subdomain”~~ ==		== Output Subdomain (''output_subdomain'') ==
	This field records the outputs for the entire pipeline. Each output object is represented as a URI with the addition of a ''mediatype'' object. In the output domain, the URI and mediatype objects are both '''required'''. As mentioned in the ''URI Object and Field'' section, within the URI object, the ''URI field'' is '''required''' but ''filename'', ''access_time'', and ''sha1_checksum'' are not required.		This field records the outputs for the entire pipeline. Each output object is represented as a URI with the addition of a ''mediatype'' object. In the output domain, the URI and mediatype objects are both '''required'''. As mentioned in the ''URI Object and Field'' section, within the URI object, the ''URI field'' is '''required''' but ''filename'', ''access_time'', and ''sha1_checksum'' are not required.
	"output_subdomain": [		"output_subdomain": [
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	]		]

	=== "Mediatype" Field ~~Definition~~ ===		=== Mediatype Field ===
	The mediatype field is defined in the output domain. It is not required for the input domain. The official list of accepted media types can be found in the description within the definition. The definition can be found in the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json IEEE io schema] below:		The mediatype field is defined in the output domain. It is not required for the input domain. The official list of accepted media types can be found in the description within the definition. The definition can be found in the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json IEEE io schema] below:
	"output_subdomain": {		"output_subdomain": {

Lorikrammer: Created page with "'''Go back to BCO Domains.''' == Input and Output Domain | "io_domain" == This section defines the io_domain part of the BCO. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here]. This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can resid..."

2026-02-10T20:31:08Z

Created page with "'''Go back to BCO Domains.''' == Input and Output Domain | "io_domain" == This section defines the io_domain part of the BCO. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here]. This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can resid..."

New page

'''Go back to [[Bco-domains|BCO Domains]].'''

== Input and Output Domain | "io_domain" ==
This section defines the io_domain part of the [[Bco-domains|BCO]]. The IEEE io domain schema can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json here].

This represents the list of global input and output files created by the computational workflow, excluding the intermediate files. These fields are pointers to objects that can reside in the system performing the computation or any other accessible system. Just like the fields of the parametric domain, these fields are expected to vary depending on the specific BCO implementation and can refer to named input-output arguments of underlying pipelines. Please refer to the documentation of individual scripts and specific BCO descriptions for further details.

Condensed example:
"io_domain": {
"input_subdomain": [
],
"output_subdomain": [
]
}
{| class="wikitable"
|+Required Components of the IO Domain
!Subdomain
!Object
!Field
!Status
|-
|input_subdomain
|
|
|'''REQUIRED'''
|-
|
|uri
|
|'''REQUIRED'''
|-
|
|
|filename
|NOT REQUIRED
|-
|
|
|uri
|'''REQUIRED'''
|-
|
|
|access_time
|NOT REQUIRED
|-
|
|
|sha1_checksum
|NOT REQUIRED
|-
|output_subdomain
|
|
|'''REQUIRED'''
|-
|
|uri
|
|'''REQUIRED'''
|-
|
|
|filename
|NOT REQUIRED
|-
|
|
|uri
|'''REQUIRED'''
|-
|
|
|access_time
|NOT REQUIRED
|-
|
|
|sha1_checksum
|NOT REQUIRED
|-
|
|mediatype
|
|'''REQUIRED'''
|}

== Input Subdomain | “input_subdomain” ==
This field records the references and input files for the entire pipeline. Each input file is listed as a uri object. This allows the author to be very specific about a particular type of input file if they so choose. For example, reference files have common names, and adding the common name here, in addition to the uri would make this more readable and understandable (eg, "HCV reference version..." or "human reference GRCH38"). For data integration workflows, the input files can be a table downloaded from a specific source which is then filtered for modification using rules described in the BCO.

The URI object and the URI field are both '''required'''.

"input_subdomain": [
{
"uri": {
"filename": "Hepatitis C virus genotype 1",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus type 1b complete genome",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
}
]

=== URI Object and Field ===
'''The IO domain includes a required ''URI object''. Within the ''URI object'' is a required ''URI field''.''' The URI field must be included in both the input and output subdomains. Filename, access_time, and sha1_checksum are all optional. These optional values are up to the discretion of the author and the reviewer.
The URI object is defined at the top-level schema because it is used in multiple domains and defines each of its fields as well. See the URI field definition in the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/2791object.json?ref_type=heads IEEE top-level schema] below.
"definitions": {
"object_id": {
"type": "string",
"description": "A unique identifier that should be applied to each IEEE-2791 Object instance, generated and assigned by a IEEE-2791 database engine. IDs should never be reused"
},
"uri": {
"type": "object",
"description": "Any of the four Resource Identifers defined at <nowiki>https://tools.ietf.org/html/draft-handrews-json-schema-validation-01#section-7.3.5</nowiki>",
"additionalProperties": false,
"required": [
"uri"
],
"properties": {
"filename": {
"type": "string"
},
"uri": {
"type": "string",
"format": "uri"
},
"access_time": {
"type": "string",
"description": "Time stamp of when the request for this data was submitted",
"format": "date-time"
},
"sha1_checksum": {
"type": "string",
"description": "output of hash function that produces a message digest",
"pattern": "[A-Za-z0-9]+"
}
}
},

== Output Subdomain | “output_subdomain” ==
This field records the outputs for the entire pipeline. Each output object is represented as a URI with the addition of a ''mediatype'' object. In the output domain, the URI and mediatype objects are both '''required'''. As mentioned in the ''URI Object and Field'' section, within the URI object, the ''URI field'' is '''required''' but ''filename'', ''access_time'', and ''sha1_checksum'' are not required.
"output_subdomain": [
{
"uri": {
"filename": "Example Domain csv file",
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
},
"mediatype": "text/csv"
},
{
"uri": {
"uri": "http://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24T09:40:17-0500"
},
"mediatype": "text/tsv"
}
]

=== "Mediatype" Field Definition ===
The mediatype field is defined in the output domain. It is not required for the input domain. The official list of accepted media types can be found in the description within the definition. The definition can be found in the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/blob/master/io_domain.json IEEE io schema] below:
"output_subdomain": {
"type": "array",
"title": "output_subdomain",
"description": "A record of the outputs for the entire pipeline.",
"items": {
"type": "object",
"title": "The Items Schema",
"required": [
"mediatype",
"uri"
],
"properties": {
"mediatype": {
"type": "string",
"title": "mediatype",
"description": "https://www.iana.org/assignments/media-types/",
"default": "application/octet-stream",
"examples": [
"text/csv"
],
"pattern": "^(.*)$"
},
"uri": {
"$ref": "2791object.json#/definitions/uri"
}
}
}
}