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Commit 3924137d authored by Charles King's avatar Charles King
Browse files

SSR Comments

Fixes to address Comments from SSR on 2791 schema format
parent 66b1996e
...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
}, },
"uri": { "uri": {
"type": "object", "type": "object",
"description": "A Uniform Resource Identifer", "description": "Any of the four Resource Identifers defined at https://json-schema.org/latest/json-schema-validation.html#rfc.section.7.3.5",
"additionalProperties": false, "additionalProperties": false,
"required": [ "required": [
"uri" "uri"
...@@ -39,11 +39,12 @@ ...@@ -39,11 +39,12 @@
}, },
"access_time": { "access_time": {
"type": "string", "type": "string",
"description": "Time stamp of when the request for this data was submitted",
"format": "date-time" "format": "date-time"
}, },
"sha1_checksum": { "sha1_checksum": {
"type": "string", "type": "string",
"description": "hash function that produces a message digest", "description": "output of hash function that produces a message digest",
"pattern": "[A-Za-z0-9]+" "pattern": "[A-Za-z0-9]+"
} }
} }
...@@ -61,14 +62,14 @@ ...@@ -61,14 +62,14 @@
"type": "string", "type": "string",
"description": "Name of contributor", "description": "Name of contributor",
"examples": [ "examples": [
"Charles Hadley King" "Charles Darwin"
] ]
}, },
"affiliation": { "affiliation": {
"type": "string", "type": "string",
"description": "Organization the particular contributor is affiliated with", "description": "Organization the particular contributor is affiliated with",
"examples": [ "examples": [
"George Washington University" "HMS Beagle"
] ]
}, },
"email": { "email": {
...@@ -106,7 +107,7 @@ ...@@ -106,7 +107,7 @@
"type": "string", "type": "string",
"description": "Field to record author information. ORCID identifiers allow for the author to curate their information after submission. ORCID identifiers must be valid and must have the prefix ‘https://orcid.org/’", "description": "Field to record author information. ORCID identifiers allow for the author to curate their information after submission. ORCID identifiers must be valid and must have the prefix ‘https://orcid.org/’",
"examples": [ "examples": [
"https://orcid.org/0000-0003-1409-4549" "http://orcid.org/0000-0002-1825-0097"
], ],
"format": "uri" "format": "uri"
} }
...@@ -123,14 +124,14 @@ ...@@ -123,14 +124,14 @@
"type": "string", "type": "string",
"description": "Version of the IEEE-2791 specification used to define this document", "description": "Version of the IEEE-2791 specification used to define this document",
"examples": [ "examples": [
"https://w3id.org/2791/v1.2" "https://w3id.org/2791/"
], ],
"readOnly": true, "readOnly": true,
"format": "uri" "format": "uri"
}, },
"etag": { "etag": {
"type": "string", "type": "string",
"description": "A string-type, read-only value, protecting the object from internal or external alterations without proper validation generated with a SHA-256 hash function.", "description": "See https://tools.ietf.org/html/rfc7232#section-2.1 for full description. It is recommended that the ETag be deleted or updated if the object file is changed (except in cases using weak ETags in which the entirety of the change comprises a simple re-writing of the JSON).",
"examples": [ "examples": [
"5986B05969341343E77A95B4023600FC8FEF48B7E79F355E58B0B404A4F50995" "5986B05969341343E77A95B4023600FC8FEF48B7E79F355E58B0B404A4F50995"
], ],
...@@ -145,7 +146,7 @@ ...@@ -145,7 +146,7 @@
}, },
"extension_domain": { "extension_domain": {
"type": "array", "type": "array",
"description": "points to internal or external references to a script object that was used to perform computations for this IEEE-2791 Object instance.", "description": "An optional domain that contains user-defined fields.",
"items":{ "items":{
"required":[ "required":[
"extension_schema" "extension_schema"
......
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
"properties": { "properties": {
"script": { "script": {
"type": "array", "type": "array",
"description": "points to internal or external references to a script object that was used to perform computations for this IEEE-2791 Object instance.", "description": "points to a script object or objects that was used to perform computations for this IEEE-2791 Object instance.",
"items": { "items": {
"additionalProperties": false, "additionalProperties": false,
"properties": { "properties": {
...@@ -27,7 +27,7 @@ ...@@ -27,7 +27,7 @@
}, },
"script_driver": { "script_driver": {
"type": "string", "type": "string",
"description": "Specification of the kind of executable that can be launched in order to perform a sequence of commands described in the script in order to run the pipelin", "description": "Indication of the kind of executable that can be launched in order to perform a sequence of commands described in the script in order to run the pipelin",
"examples": [ "examples": [
"hive", "hive",
"cwl-runner", "cwl-runner",
......
...@@ -42,6 +42,7 @@ ...@@ -42,6 +42,7 @@
"type": "string", "type": "string",
"title": "mediatype", "title": "mediatype",
"description": "https://www.iana.org/assignments/media-types/", "description": "https://www.iana.org/assignments/media-types/",
"default": "application/octet-stream",
"examples": [ "examples": [
"text/csv" "text/csv"
], ],
......
...@@ -18,8 +18,7 @@ ...@@ -18,8 +18,7 @@
"description": "Specific variables for the computational workflow", "description": "Specific variables for the computational workflow",
"examples": [ "examples": [
"seed" "seed"
], ]
"pattern": "^(.*)$"
}, },
"value": { "value": {
"type": "string", "type": "string",
...@@ -27,8 +26,7 @@ ...@@ -27,8 +26,7 @@
"title": "value", "title": "value",
"examples": [ "examples": [
"14" "14"
], ]
"pattern": "^(.*)$"
}, },
"step": { "step": {
"type": "string", "type": "string",
......
...@@ -52,7 +52,7 @@ ...@@ -52,7 +52,7 @@
"type": "string", "type": "string",
"description": "Optional free text comment by reviewer", "description": "Optional free text comment by reviewer",
"examples": [ "examples": [
"Approved by GW staff. Waiting for approval from FDA Reviewer" "Approved by research institution staff. Waiting for approval from regulator"
] ]
}, },
"status": { "status": {
...@@ -71,7 +71,7 @@ ...@@ -71,7 +71,7 @@
} }
}, },
"derived_from": { "derived_from": {
"description": "value of `ieee2791_id` field of another IEEE-2791 Object", "description": "value of `ieee2791_id` field of another IEEE-2791 that this object is partially or fully derived from",
"$ref": "2791object.json#/definitions/ieee2791_id" "$ref": "2791object.json#/definitions/ieee2791_id"
}, },
"obsolete_after": { "obsolete_after": {
......
...@@ -3,15 +3,14 @@ ...@@ -3,15 +3,14 @@
"$id": "https://w3id.org/2791/usability_domain.json", "$id": "https://w3id.org/2791/usability_domain.json",
"type": "array", "type": "array",
"title": "Usability Domain", "title": "Usability Domain",
"description": "Author-defined usability domain of the IEEE-2791 Object. This field is to aid in search-ability and provide a specific description of the function of the object. It is recommended that a novel use of the IEEE-2791 Object could result in the creation of a new entry with a new usability domain", "description": "Author-defined usability domain of the IEEE-2791 Object. This field is to aid in search-ability and provide a specific description of the function of the object.",
"items": { "items": {
"type": "string", "type": "string",
"description": "Free text values that can accept template language to indicate values from the external_references", "description": "Free text values that can be used to provide scientific reasoning and purpose for the experiment",
"examples": [ "examples": [
"Identify baseline single nucleotide polymorphisms SNPs [SO:0000694], insertions [so:SO:0000667], and deletions [so:SO:0000045] that correlate with reduced ledipasvir [pubchem.compound:67505836] antiviral drug efficacy in Hepatitis C virus subtype 1 [taxonomy:31646]", "Identify baseline single nucleotide polymorphisms SNPs [SO:0000694], insertions [so:SO:0000667], and deletions [so:SO:0000045] that correlate with reduced ledipasvir [pubchem.compound:67505836] antiviral drug efficacy in Hepatitis C virus subtype 1 [taxonomy:31646]",
"Identify treatment emergent amino acid substitutions [so:SO:0000048] that correlate with antiviral drug treatment failure", "Identify treatment emergent amino acid substitutions [so:SO:0000048] that correlate with antiviral drug treatment failure",
"Determine whether the treatment emergent amino acid substitutions [so:SO:0000048] identified correlate with treatment failure involving other drugs against the same virus", "Determine whether the treatment emergent amino acid substitutions [so:SO:0000048] identified correlate with treatment failure involving other drugs against the same virus"
"GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
] ]
} }
} }
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