{

"basePath": "",

"consumes": [

"application/json"

],

"definitions": {

"Category": {

"properties": {

"create_date": {

"description": "ISO8601 formatted create date",

"format": "date-time",

"type": "string"

},

"links": {

"$ref": "#/definitions/CategoryLinks"

},

"name": {

"description": "The name of a category within in an organization",

"type": "string"

},

"organization": {

"description": "The name of a organization that owns this category",

"type": "string"

}

},

"type": "object"

},

"CategoryLinks": {

"properties": {

"organization": {

"description": "Organization that owns this category",

"type": "string"

},

"self": {

"description": "Templates for this category",

"type": "string"

}

},

"type": "object"

},

"Error": {

"properties": {

"code": {

"description": "HTTP status code",

"example": 200,

"type": "integer"

},

"error": {

"$ref": "#/definitions/InnerError"

},

"message": {

"type": "string"

}

},

"type": "object"

},

"InnerError": {

"properties": {

"description": {

"type": "string"

},

"request_id": {

"type": "string"

},

"type": {

"type": "string"

}

},

"type": "object"

},

"Organization": {

"properties": {

"create_date": {

"description": "ISO8601 formatted create date",

"format": "date-time",

"type": "string"

},

"links": {

"$ref": "#/definitions/OrganizationLinks"

},

"name": {

"description": "Globally unique name for an organization",

"type": "string"

},

"protected": {

"description": "Is this organization only writable by admin?",

"type": "boolean"

}

},

"type": "object"

},

"OrganizationLinks": {

"properties": {

"self": {

"description": "Categories for this organization",

"type": "string"

}

},

"type": "object"

},

"PerspectiveLinks": {

"properties": {

"name": {

"description": "name of the perspective",

"type": "string"

},

"ref": {

"description": "link to resource",

"type": "string"

}

},

"type": "object"

},

"Query": {

"properties": {

"args": {

"description": "Arguments passed to the template (only if template query)",

"type": "object"

},

"available": {

"description": "Are results for this query available",

"type": "boolean"

},

"complete_date": {

"description": "ISO8601 formatted complete date",

"format": "date-time",

"type": "string"

},

"date_submitted": {

"description": "ISO8601 formatted submit date (for backwards-compatibility)",

"format": "date-time",

"type": "string"

},

"details": {

"description": "Additional information about the query",

"type": "object"

},

"error": {

"description": "Error information about the query if it FAILED. Includes 'description' and 'type' string keys",

"type": "object"

},

"id": {

"type": "integer"

},

"links": {

"allOf": [

{

"$ref": "#/definitions/QueryLinks"

}

],

"description": "The URLs to the resources related to this query"

},

"progress": {

"description": "Progress information for running job",

"type": "object"

},

"project_name": {

"description": "The project into which the query was submitted",

"type": "string"

},

"query": {

"description": "The query string that was executed (if any)",

"type": "string"

},

"query_id": {

"description": "Unique ID of this query",

"type": "integer"

},

"relations": {

"description": "Virtual relations associated with the query",

"type": "object"

},

"results": {

"description": "Results, equal or less than requested rows, normally null. To get the rest, query the result endpoint.",

"type": "object"

},

"start_date": {

"description": "ISO8601 formatted start date",

"format": "date-time",

"type": "string"

},

"stats": {

"allOf": [

{

"$ref": "#/definitions/QueryStats"

}

],

"description": "Various stats about the query"

},

"status": {

"description": "The current status of the query",

"enum": [

"PENDING",

"RUNNING",

"DONE",

"CANCELLING",

"CANCELLED",

"FAILED"

],

"example": "PENDING",

"type": "string"

},

"submit_date": {

"description": "ISO8601 formatted submit date",

"format": "date-time",

"type": "string"

},

"template_name": {

"description": "The template associated with this query (if any)",

"type": "string"

},

"user_name": {

"description": "The user that submitted the query",

"type": "string"

}

},

"type": "object"

},

"QueryLinks": {

"properties": {

"perspectives": {

"items": {

"$ref": "#/definitions/PerspectiveLinks"

},

"type": "array"

},

"result": {

"description": "Fully qualified URL of the results for the query, once it is finished",

"type": "string"

},

"self": {

"description": "Fully qualified URL of the template query resource itself",

"type": "string"

}

},

"type": "object"

},

"QueryStats": {

"properties": {

"column_count": {

"description": "Number of columns in results",

"type": "integer"

},

"end_timestamp": {

"description": "Unix timestamp when the GOR Server finished running the query",

"type": "integer"

},

"line_count": {

"description": "Number of lines in results",

"type": "integer"

},

"size_bytes": {

"description": "Size of the results in bytes",

"type": "integer"

},

"start_timestamp": {

"description": "Unix timestamp when the GOR Server started running the query",

"type": "integer"

},

"submit_timestamp": {

"description": "Unix timestamp when the query was submitted to the GOR Server",

"type": "integer"

}

},

"type": "object"

},

"RenderedTemplate": {

"properties": {

"query": {

"description": "rendered template query",

"type": "string"

}

},

"type": "object"

},

"SimpleQuery": {

"properties": {

"links": {

"allOf": [

{

"$ref": "#/definitions/QueryLinks"

}

],

"description": "The URLs to the resources related to this query"

},

"project_name": {

"description": "The project into which the query was submitted",

"type": "string"

},

"query_id": {

"description": "Unique ID of this query",

"type": "integer"

},

"status": {

"description": "The current status of the query",

"enum": [

"PENDING",

"RUNNING",

"DONE",

"CANCELLING",

"CANCELLED",

"FAILED"

],

"example": "PENDING",

"type": "string"

},

"submit_date": {

"description": "ISO8601 formatted submit date",

"format": "date-time",

"type": "string"

},

"user_name": {

"description": "The user that submitted the query",

"type": "string"

}

},

"type": "object"

},

"Template": {

"properties": {

"arguments": {

"description": "Defined arguments this query template accepts",

"type": "object"

},

"category": {

"description": "The category that this template belongs to",

"type": "string"

},

"column_metadata": {

"description": "The package version of the query template",

"type": "string"

},

"create_date": {

"description": "ISO8601 formatted create date",

"format": "date-time",

"type": "string"

},

"file_contents": {

"description": "The raw contents of the query template YAML file",

"type": "string"

},

"full_name": {

"description": "The globally unique name of a query template",

"type": "string"

},

"id": {

"description": "Unique ID for this template",

"type": "string"

},

"links": {

"$ref": "#/definitions/TemplateLinks"

},

"list_description": {

"description": "The description of a query template",

"type": "string"

},

"min_ref_data_version": {

"description": "Minimum reference data version for this template",

"type": "string"

},

"name": {

"description": "The unique name of a query template within a given category",

"type": "string"

},

"organization": {

"description": "The organization that this template belongs to",

"type": "string"

},

"perspectives": {

"description": "Available perspectives for this query template",

"type": "object"

},

"user": {

"description": "The user that created this template",

"type": "string"

},

"version": {

"description": "Version info for this query template",

"type": "string"

}

},

"type": "object"

},

"TemplateLinks": {

"properties": {

"category": {

"description": "Category that this template is in",

"type": "string"

},

"execute": {

"description": "Endpoint for executing the template",

"type": "string"

},

"organization": {

"description": "Organization that owns the category",

"type": "string"

},

"render": {

"description": "Endpoint for rendering the template",

"type": "string"

},

"self": {

"description": "The Template Resource",

"type": "string"

}

},

"type": "object"

},

"TemplateSimple": {

"properties": {

"category": {

"description": "The category that this template belongs to",

"type": "string"

},

"create_date": {

"description": "ISO8601 formatted create date",

"format": "date-time",

"type": "string"

},

"full_name": {

"description": "The globally unique name of a query template",

"type": "string"

},

"id": {

"description": "Unique ID for this template",

"type": "string"

},

"links": {

"$ref": "#/definitions/TemplateLinks"

},

"list_description": {

"description": "The description of a query template",

"type": "string"

},

"name": {

"description": "The unique name of a query template within a given category",

"type": "string"

},

"organization": {

"description": "The organization that this template belongs to",

"type": "string"

},

"version": {

"description": "Version info for this query template",

"type": "string"

}

},

"type": "object"

}

},

"info": {

"description": "GOR Query API executes and manages GOR queries, query templates, and templated queries (queries executed from a rendered template).\n\nGOR query results can be returned as JSON or raw tab-formatted values.\n \nOnce a query is complete, its GOR results can be retrieved. If the Accept HTTP header is 'application/json' then JSON is returned. Otherwise raw tab-separated values are returned (TSV, 'application/tab-separated-values').\n\nThe JSON output is a somewhat freeform object-in-object list-of-maps structure:\n\n\n [{'column1': 'value-l1c1', 'column2': 'value-l1c1'}, {'column1': 'value-l1c1', 'column2': 'value-l1c1'}]\nIf the Accept header is 'application/json+compact' then the JSON follows the following format:\n{ 'header': ['column1', 'column2'], 'data: { [[value-l1c1','value-l1c1'], [value-l1c1','value-l1c1']] }}\nFor information on how queries or templates work,or information on the YAML data required to create new templates, please refer to CSA/GOR manuals or the documentation in the GOR Developer Console in your instance.",

"title": "GOR Query API",

"version": "1.9.0"

},

"paths": {

"/api/query/": {

"get": {

"description": "Get information about the service and currently authenticated user, if available.\n\n\n\nThe *json_limit* constant defines how many lines of query results may be returned in a single request.\nIf a result is longer than that then pagination kicks in.",

"operationId": "get_root",

"responses": {

"200": {

"description": "Success"

}

},

"summary": "API Information",

"tags": [

"root"

]

}

},

"/api/query/query/": {

"get": {

"operationId": "get_queries",

"parameters": [

{

"description": "Project to view",

"in": "query",

"name": "project",

"type": "string"

},

{

"description": "Filter queries by status",

"in": "query",

"name": "status",

"type": "string"

},

{

"description": "User ID of the submitter",

"in": "query",

"name": "user_id",

"type": "integer"

},

{

"description": "User name of the submitter",

"in": "query",

"name": "user_name",

"type": "string"

},

{

"default": 50,

"description": "Number of results to return",

"in": "query",

"name": "limit",

"type": "integer"

},

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"items": {

"$ref": "#/definitions/SimpleQuery"

},

"type": "array"

}

}

},

"tags": [

"query"

]

},

"post": {

"description": "The query is validated and submitted to the GOR server for execution.\nResults are delivered in a dedicated results endpoint under here.",

"operationId": "post_queries",

"parameters": [

{

"description": "The GOR Query we want executed (e.g. ``\"gor #dbsnp# | top 100\"``)",

"in": "query",

"name": "query",

"required": true,

"type": "string"

},

{

"description": "The name of the project the query should be executed on",

"in": "query",

"name": "project",

"required": true,

"type": "string"

},

{

"default": "default",

"description": "The type of the job being run, for queue routing purposes",

"in": "query",

"name": "type",

"type": "string"

},

{

"description": "The file that the query results should be saved in (must start with user_data/)",

"in": "query",

"name": "persist",

"type": "string"

},

{

"collectionFormat": "multi",

"description": "Virtual relations to be resolved within the query",

"in": "query",

"items": {

"type": "string"

},

"name": "relations",

"type": "array"

},

{

"description": "Number of seconds to wait for query to complete before returning PENDING",

"in": "query",

"name": "wait",

"type": "number"

},

{

"description": "Number of rows to return from this call. wait must be larger than zero",

"in": "query",

"name": "results",

"type": "integer"

},

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"201": {

"description": "Success",

"schema": {

"$ref": "#/definitions/Query"

}

},

"400": {

"description": "Unauthorized"

},

"401": {

"description": "Unauthorized"

},

"403": {

"description": "Forbidden"

},

"404": {

"description": "Not found.",

"schema": {

"$ref": "#/definitions/Error"

}

}

},

"summary": "Submit a GOR query",

"tags": [

"query"

]

}

},

"/api/query/query/{query_id}": {

"delete": {

"operationId": "delete_query",

"parameters": [

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"$ref": "#/definitions/Query"

}

},

"401": {

"description": "Unauthorized"

},

"403": {

"description": "Forbidden"

},

"404": {

"description": "Not found.",

"schema": {

"$ref": "#/definitions/Error"

}

}

},

"summary": "Cancels a running query",

"tags": [

"query"

]

},

"get": {

"operationId": "get_query",

"parameters": [

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"$ref": "#/definitions/Query"

}

},

"401": {

"description": "Unauthorized"

},

"403": {

"description": "Forbidden"

},

"404": {

"description": "Not found.",

"schema": {

"$ref": "#/definitions/Error"

}

}

},

"summary": "Check the status of a query",

"tags": [

"query"

]

},

"parameters": [

{

"description": "The ID of a query that has been submitted to GOR",

"in": "path",

"name": "query_id",

"required": true,

"type": "integer"

}

]

},

"/api/query/query/{query_id}/result": {

"get": {

"description": "Once a query is complete, its GOR results can be retrieved. If the Accept HTTP header is 'application/json',\nthen JSON is returned. Otherwise raw tab-separated values are returned. As JSON, each line will be returned as\na key-value object-in-object format approximately like this:\n\n [{\"column1\": \"value-l1c1\", \"column2\": \"value-l1c1\"},\n {\"column1\": \"value-l1c1\", \"column2\": \"value-l1c1}]\n\nPlease note that in JSON format there is a limit on how many lines can be returned at a time.\nIn that case results will include pagination links (\"next\").",

"operationId": "get_result",

"parameters": [

{

"description": "GOR query filter to apply to results",

"in": "query",

"name": "perspective",

"type": "string"

},

{

"description": "GOR query filter to apply to results",

"in": "query",

"name": "filter",

"type": "string"

},

{

"default": 100,

"description": "Maximum number of rows to return",

"in": "query",

"name": "limit",

"type": "integer"

},

{

"default": 0,

"description": "Number of rows to skip",

"in": "query",

"name": "offset",

"type": "integer"

},

{

"description": "Comma separated list of columns to sort on, including direction. Example: `POS asc,Chrom desc`",

"in": "query",

"name": "sort",

"type": "string"

},

{

"default": false,

"description": "Skip the header, used for paging",

"in": "query",

"name": "skipheader",

"type": "boolean"

}

],

"produces": [

"application/json",

"application/json+compact",

"text/tab-separated-values"

],

"responses": {

"200": {

"description": "Sucessful. Results in JSON/TSV format; See above."

},

"401": {

"description": "Unauthorized"

},

"403": {

"description": "Forbidden"

},

"404": {

"description": "Not found. Query not found, or no results exist yet. See error message.",

"schema": {

"$ref": "#/definitions/Error"

}

}

},

"summary": "Gets the results of a completed query",

"tags": [

"query"

]

},

"parameters": [

{

"description": "The ID of a query that has been submitted to GOR",

"in": "path",

"name": "query_id",

"required": true,

"type": "string"

}

]

},

"/api/query/templates/": {

"get": {

"operationId": "get_templates",

"parameters": [

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"items": {

"$ref": "#/definitions/Organization"

},

"type": "array"

}

}

},

"summary": "Return a list of organizations",

"tags": [

"templates"

]

},

"post": {

"description": "Assumes the organization and category come from the yaml string\nand creates the resources as needed.\n\nFor information on YAML data to create new templates, please refer to CSA/GOR manuals or the documentation\navailable in the GOR Developer Console in your instance.",

"operationId": "post_templates",

"parameters": [

{

"description": "The query template represented as a YAML string. See above.",

"in": "query",

"name": "yaml",

"required": true,

"type": "string"

},

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"$ref": "#/definitions/TemplateSimple"

}

}

},

"summary": "Receives and stores a new template from YAML",

"tags": [

"templates"

]

}

},

"/api/query/templates/{organization}/": {

"delete": {

"operationId": "delete_categories",

"responses": {

"200": {

"description": "Success"

}

},

"summary": "Delete an organization including all categories and templates",

"tags": [

"templates"

]

},

"get": {

"operationId": "get_categories",

"parameters": [

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"items": {

"$ref": "#/definitions/Category"

},

"type": "array"

}

}

},

"summary": "Return a list of categories",

"tags": [

"templates"

]

},

"parameters": [

{

"in": "path",

"name": "organization",

"required": true,

"type": "string"

}

]

},

"/api/query/templates/{organization}/{category}/": {

"delete": {

"operationId": "delete_actual_templates",

"responses": {

"200": {

"description": "Success"

}

},

"summary": "Delete a category including all templates",

"tags": [

"templates"

]

},

"get": {

"operationId": "get_actual_templates",

"parameters": [

{

"description": "An optional fields mask",

"format": "mask",

"in": "header",

"name": "X-Fields",

"type": "string"

}

],

"responses": {

"200": {

"description": "Success",

"schema": {

"items": {

"$ref": "#/definitions/TemplateSimple"

},

"type": "array"

}

}

},

"summary": "Return all templates in this category",

"tags": [

"templates"

]

},

"parameters": [

{

"in": "path",

"name": "organization",

"required": true,

"type": "string"

},

{

"in": "path",

"name": "category",

"required": true,

"type": "string"

}

]

},

"/api/query/templates/{organization}/{category}/{name}/": {

"delete": {

"operationId": "delete_template_by_name",

"responses": {

"200": {

"description": "Success"

}

},

"summary": "Delete a template",

"tags": [

"templates"

]

},

"get": {

"operationId": "get_template_by_name",

"produces": [

"application/json",

"text/plain"

],

"responses": {

"200": {

"description": "Success",

"schema": {

"$ref": "#/definitions/Template"

}

}

},

"summary": "Return a single template which satisfies the criteria",

"tags": [

"templates"

]

},

"parameters": [

{

"in": "path",

"name": "organization",

"required": true,

"type": "string"

},

{

"in": "path",

"name": "category",

"required": true,

"type": "string"

},

{

"in": "path",

"name": "name",

"required": true,

"type": "string"

}