{
"openapi": "3.0.0",
"sections": [
{
"title": "account",
"endpoints": [
{
"description": "Fetches the details for the account associated with the user agent.",
"method": "get",
"parameters": [],
"path": "/account",
"title": "Get an account",
"errors": [
{
"status": "401",
"description": "Requires Authorization"
}
],
"response": {
"example": {
"administrator_role": null,
"groups": [],
"handle": "bob",
"id": "test",
"last_password_change": "2015-10-06T20:00:00Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": {
"id": 5,
"name": "Technician"
},
"settings": {
"quick_analyze_workflow": "pathoscope_bowtie",
"show_ids": true,
"show_versions": true,
"skip_quick_analyze_dialog": true
}
},
"status": "200"
}
},
{
"description": "Updates the account associated with the user agent.\n\nProvide a ``password`` to update the account password. The ``old_password`` must\nalso be provided in the request.\n\nThe ``email`` address is not currently used, but will be in future releases.",
"example": {
"email": "[email protected]",
"old_password": "hello_world",
"password": "foo_bar_1"
},
"method": "patch",
"parameters": [
{
"description": "an email address",
"title": "Email",
"type": "string",
"name": "email",
"required": false
},
{
"description": "the old password for verification",
"title": "Old Password",
"type": "string",
"name": "old_password",
"required": false
},
{
"description": "the new password",
"title": "Password",
"type": "string",
"name": "password",
"required": false
}
],
"path": "/account",
"title": "Update an account",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "401",
"description": "Requires Authorization"
}
],
"response": {
"example": {
"administrator_role": null,
"email": "[email protected]",
"groups": [],
"handle": "bob",
"id": "test",
"last_password_change": "2015-10-06T20:00:00Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": {
"id": 6,
"name": "Technicians"
},
"settings": {
"quick_analyze_workflow": "pathoscope_bowtie",
"show_ids": true,
"show_versions": true,
"skip_quick_analyze_dialog": true
}
},
"status": "200"
}
},
{
"description": "Deletes all API keys registered for the account associated with the user agent.",
"method": "delete",
"parameters": [],
"path": "/account/keys",
"title": "Purge API keys",
"errors": []
},
{
"description": "Lists all API keys registered on the account associated with the user agent.",
"method": "get",
"parameters": [],
"path": "/account/keys",
"title": "List API keys",
"errors": [
{
"status": "401",
"description": "Requires authorization"
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new API key on the account associated with the user agent.\n\nThe new key value is returned in the response. **This is the only response\nfrom the server that will ever include the key**.",
"example": {
"name": "Foobar",
"permissions": {
"create_sample": true
}
},
"method": "post",
"parameters": [
{
"description": "a non-unique name for the API key",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"allOf": [
{
"$ref": "#/components/schemas/PermissionsUpdate"
}
],
"default": {
"cancel_job": null,
"create_ref": null,
"create_sample": null,
"modify_hmm": null,
"modify_subtraction": null,
"remove_file": null,
"remove_job": null,
"upload_file": null
},
"description": "an object describing the permissions the new key will have. Any unset permissions will default to false",
"title": "Permissions",
"name": "permissions",
"required": false
}
],
"path": "/account/keys",
"title": "Create an API key",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "401",
"description": "Requires authorization"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"groups": [],
"id": "foobar_0",
"key": "raw_key",
"name": "Foobar",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
}
},
"status": "201"
}
},
{
"description": "Removes an API key by its 'key id'.",
"method": "delete",
"parameters": [],
"path": "/account/keys/{key_id}",
"title": "Delete an API key",
"errors": []
},
{
"description": "Fetches the details for an API key registered on the account associated with\nthe user agent.",
"method": "get",
"parameters": [],
"path": "/account/keys/{key_id}",
"title": "Get an API key",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"groups": [],
"id": "foobar_0",
"name": "Foobar",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
}
},
"status": "200"
}
},
{
"description": "Updates the permissions an existing API key registered on the account\nassociated with the user agent.",
"example": {
"permissions": {
"modify_subtraction": true
}
},
"method": "patch",
"parameters": [
{
"allOf": [
{
"$ref": "#/components/schemas/PermissionsUpdate"
}
],
"description": "a permission update comprising an object keyed by permissions with boolean values",
"title": "Permissions",
"name": "permissions",
"required": false
}
],
"path": "/account/keys/{key_id}",
"title": "Update an API key",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "401",
"description": "Requires Authorization"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"groups": [],
"id": "foobar_0",
"name": "Foobar",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": true,
"remove_file": false,
"remove_job": false,
"upload_file": false
}
},
"status": "200"
}
},
{
"description": "Logs in using the passed credentials.\n\nThis creates a new session for the user with `username`. The session ID and\ntoken are returned in cookies.",
"example": {
"password": "p@ssword123",
"remember": false,
"username": "foobar"
},
"method": "post",
"parameters": [
{
"description": "account password",
"minLength": 1,
"title": "Password",
"type": "string",
"name": "password",
"required": true
},
{
"default": false,
"description": "value determining whether the session will last for 1 month or 1 hour",
"title": "Remember",
"type": "boolean",
"name": "remember",
"required": false
},
{
"description": "account username",
"minLength": 1,
"title": "Username",
"type": "string",
"name": "username",
"required": true
}
],
"path": "/account/login",
"title": "Login",
"errors": [
{
"status": "400",
"description": "Invalid input"
}
],
"response": {
"example": {
"reset": false
},
"status": "201"
}
},
{
"description": "Logs out the user by invalidating the session associated with the user agent. A\nnew unauthenticated session ID is returned in cookies.",
"method": "get",
"parameters": [],
"path": "/account/logout",
"title": "Logout",
"errors": [],
"response": {
"status": "204"
}
},
{
"description": "Resets the password for the account associated with the requesting session.",
"example": {
"password": "p@ssword123",
"reset_code": "4bcda8b3bcaf5f84cc6e26a3d23a6179f29d356e43c9ced1b6de0d8f4946555e"
},
"method": "post",
"parameters": [
{
"title": "Password",
"type": "string",
"name": "password",
"required": true
},
{
"title": "Reset Code",
"type": "string",
"name": "reset_code",
"required": true
}
],
"path": "/account/reset",
"title": "Reset password",
"errors": [
{
"status": "400",
"description": "Invalid input"
}
],
"response": {
"example": {
"login": false,
"reset": false
},
"status": "200"
}
},
{
"description": "Fetches the settings for the account associated with the user agent.",
"method": "get",
"parameters": [],
"path": "/account/settings",
"title": "Get account settings",
"errors": [
{
"status": "401",
"description": "Requires authorization"
}
],
"response": {
"example": {
"quick_analyze_workflow": "pathoscope_bowtie",
"show_ids": true,
"show_versions": true,
"skip_quick_analyze_dialog": true
},
"status": "200"
}
},
{
"description": "Updates the settings of the account associated with the user agent.",
"example": {
"show_ids": false
},
"method": "patch",
"parameters": [
{
"allOf": [
{
"$ref": "#/components/schemas/AnalysisWorkflow"
}
],
"description": "workflow to use for quick analysis",
"name": "quick_analyze_workflow",
"required": false
},
{
"description": "show document ids in client where possible",
"title": "Show Ids",
"type": "boolean",
"name": "show_ids",
"required": false
},
{
"description": "show document versions in client where possible",
"title": "Show Versions",
"type": "boolean",
"name": "show_versions",
"required": false
},
{
"description": "don’t show the quick analysis dialog",
"title": "Skip Quick Analyze Dialog",
"type": "boolean",
"name": "skip_quick_analyze_dialog",
"required": false
}
],
"path": "/account/settings",
"title": "Update account settings",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "401",
"description": "Requires Authorization"
}
],
"response": {
"example": {
"quick_analyze_workflow": "pathoscope_bowtie",
"show_ids": false,
"show_versions": true,
"skip_quick_analyze_dialog": true
},
"status": "200"
}
}
]
},
{
"title": "admin",
"endpoints": [
{
"description": "Starts an action with the given name.",
"example": {
"name": "relist_jobs"
},
"method": "put",
"parameters": [
{
"description": "the action to run",
"title": "Name",
"type": "string",
"name": "name",
"required": true
}
],
"path": "/admin/actions",
"title": "Initiate an action",
"errors": []
},
{
"description": "",
"method": "get",
"parameters": [],
"path": "/admin/roles",
"title": "List administrator roles",
"errors": [],
"response": {
"example": [
{
"description": "Manage who is an administrator and what they can do.",
"id": "full",
"name": "Full"
},
{
"description": "Manage instance settings and administrative messages.",
"id": "settings",
"name": "Settings"
},
{
"description": "Manage users in any space. Delete any space.",
"id": "spaces",
"name": "Spaces"
},
{
"description": "Create user accounts. Control activation of user accounts.",
"id": "users",
"name": "Users"
},
{
"description": "Provides ability to:\n - Create new spaces even if the `Free Spaces` setting is not enabled.\n - Manage HMMs and common references.\n - View all running jobs.\n - Cancel any job.\n ",
"id": "base",
"name": "Base"
}
],
"status": "200"
}
},
{
"description": "Returns a paginated list of users.",
"method": "get",
"parameters": [],
"path": "/admin/users",
"title": "Find users",
"errors": [],
"response": {
"example": {
"items": [
{
"active": true,
"administrator_role": "base",
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"force_reset": false,
"groups": [],
"handle": "leeashley",
"id": "TxWalSSn",
"last_password_change": "2023-03-20T22:46:26.151000Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": null
},
{
"active": true,
"administrator_role": "full",
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"force_reset": false,
"groups": [],
"handle": "zclark",
"id": "fb085f7f",
"last_password_change": "2023-03-20T22:46:26.151000Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": null
}
]
},
"status": "200"
}
},
{
"description": "Creates a new user.",
"method": "post",
"parameters": [
{
"default": true,
"description": "forces a password reset next time the user logs in",
"title": "Force Reset",
"type": "boolean",
"name": "force_reset",
"required": false
},
{
"description": "the unique handle for the user",
"minLength": 1,
"title": "Handle",
"type": "string",
"name": "handle",
"required": true
},
{
"description": "the password for the user",
"minLength": 1,
"title": "Password",
"type": "string",
"name": "password",
"required": true
}
],
"path": "/admin/users",
"title": "Create a user",
"errors": [
{
"status": "400",
"description": "Password does not meet length requirement"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"status": "201"
}
},
{
"description": "Fetches the details of a user.",
"method": "get",
"parameters": [],
"path": "/admin/users/{user_id}",
"title": "Get a user",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": {
"active": true,
"administrator_role": "base",
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"force_reset": false,
"groups": [],
"handle": "user_handle",
"id": "TxWalSSn",
"last_password_change": "2023-03-20T22:46:26.151000Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": null
},
"status": "200"
}
},
{
"description": "",
"method": "patch",
"parameters": [
{
"description": "deactivate a user",
"title": "Active",
"type": "boolean",
"name": "active",
"required": false
},
{
"description": "Forces a password reset next time the user logs in",
"title": "Force Reset",
"type": "boolean",
"name": "force_reset",
"required": false
},
{
"description": "Sets the IDs of groups the user belongs to",
"items": {
"anyOf": [
{
"type": "integer"
},
{
"type": "string"
}
]
},
"title": "Groups",
"type": "array",
"name": "groups",
"required": false
},
{
"description": "the new password",
"title": "Password",
"type": "string",
"name": "password",
"required": false
},
{
"description": "Sets the ID of the user's primary group",
"title": "Primary Group",
"type": "integer",
"name": "primary_group",
"required": false
}
],
"path": "/admin/users/{user_id}",
"title": "Update a user",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": {
"active": true,
"administrator_role": "base",
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"force_reset": false,
"groups": [],
"handle": "user_handle",
"id": "TxWalSSn",
"last_password_change": "2023-03-20T22:46:26.151000Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": null
},
"status": "200"
}
},
{
"description": "Updates the user's administrator role.",
"example": {
"role": "users",
"user_id": "foo"
},
"method": "put",
"parameters": [
{
"allOf": [
{
"$ref": "#/components/schemas/AdministratorRole"
}
],
"description": "the administrator role for the user",
"name": "role",
"required": false
}
],
"path": "/admin/users/{user_id}/role",
"title": "Set administrator role",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": {
"active": true,
"administrator_role": "base",
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"force_reset": false,
"groups": [],
"handle": "user_handle",
"id": "TxWalSSn",
"last_password_change": "2023-03-20T22:46:26.151000Z",
"permissions": {
"cancel_job": false,
"create_ref": false,
"create_sample": false,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": false,
"upload_file": false
},
"primary_group": null
},
"status": "200"
}
}
]
},
{
"title": "analyses",
"endpoints": [
{
"description": "Lists analyses based on a search `term`.\n\nThe response will only list analyses on which the user agent has read rights.",
"method": "get",
"parameters": [],
"path": "/analyses",
"title": "Find analyses",
"errors": [],
"response": {
"example": {
"documents": [
{
"created_at": "2022-08-15T17:42:35.979000Z",
"id": "ofv7rp4v",
"index": {
"id": "u3lm1rk8",
"version": 14
},
"job": {
"id": "us3toy8j"
},
"ready": true,
"reference": {
"id": "d19exr83",
"name": "New Plant Viruses"
},
"sample": {
"id": "7tu8c5m5"
},
"subtractions": [
{
"id": "1sk885at",
"name": "Vitis vinifera"
}
],
"updated_at": "2022-08-15T17:42:35.979000Z",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflow": "pathoscope_bowtie"
}
],
"found_count": 2621,
"page": 1,
"page_count": 105,
"per_page": 25,
"total_count": 2621
},
"status": "200"
}
},
{
"description": "Downloads analysis data in CSV or XSLX format. The returned format depends on\nthe extension included in the request path.",
"method": "get",
"parameters": [],
"path": "/analyses/documents/{analysis_id}.{extension}",
"title": "Download an analysis",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
},
{
"description": "Permanently deletes an analysis.",
"method": "delete",
"parameters": [],
"path": "/analyses/{analysis_id}",
"title": "Delete an analysis",
"errors": []
},
{
"description": "Fetches the details of an analysis.",
"method": "get",
"parameters": [],
"path": "/analyses/{analysis_id}",
"title": "Get an analysis",
"errors": [
{
"status": "400",
"description": "Parent sample does not exist"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2022-08-15T17:42:35.979000Z",
"files": [
{
"analysis": "ofv7rp4v",
"description": null,
"format": "tsv",
"id": 3145,
"name": "report.tsv",
"name_on_disk": "3145-report.tsv",
"size": 4120,
"uploaded_at": "2022-08-15T17:48:02.467000Z"
}
],
"id": "ofv7rp4v",
"index": {
"id": "u3lm1rk8",
"version": 14
},
"job": {
"id": "us3toy8j"
},
"ready": true,
"reference": {
"id": "d19exr83",
"name": "New Plant Viruses"
},
"results": {
"hits": [
{
"abbreviation": "GLRaV3",
"id": "6tli5mz3",
"isolates": [
{
"default": false,
"id": "qauxg1g9",
"sequences": [],
"source_name": "WA-MR",
"source_type": "isolate"
}
],
"length": 18671,
"name": "Grapevine leafroll-associated virus 3",
"version": 30
}
],
"read_count": 584,
"subtracted_count": 0
},
"sample": {
"id": "7tu8c5m5"
},
"subtractions": [
{
"id": "1sk885at",
"name": "Vitis vinifera"
}
],
"updated_at": "2022-08-15T17:42:35.979000Z",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflow": "pathoscope_bowtie"
},
"status": "200"
}
},
{
"description": "Downloads a file associated with an analysis. Some workflows retain key files\nafter the complete.",
"method": "get",
"parameters": [],
"path": "/analyses/{analysis_id}/files/{upload_id}",
"title": "Download an analysis file",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
},
{
"description": "BLASTs a sequence that is part of a NuVs result record. The resulting BLAST data\nwill be attached to that sequence.",
"method": "put",
"parameters": [],
"path": "/analyses/{analysis_id}/{sequence_index}/blast",
"title": "BLAST a NuVs contig",
"errors": [
{
"status": "400",
"description": "Parent sample does not exist"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Sequence not found"
},
{
"status": "409",
"description": "Analysis is still running"
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "groups",
"endpoints": [
{
"description": "Lists all user groups. The group IDs and names are included in the response.",
"method": "get",
"parameters": [],
"path": "/groups",
"title": "List groups",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Creates a new group with the given name.\n\nThe ``group_id`` parameter is deprecated and will no longer be accepted in a\nfuture major release. For now, ``group_id`` will be used as ``name`` if it is\nprovided.",
"example": {
"name": "Research"
},
"method": "post",
"parameters": [
{
"description": "a name for the group",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
}
],
"path": "/groups",
"title": "Create a group",
"errors": [
{
"status": "400",
"description": "Group already exists"
}
],
"response": {
"example": {
"id": "research",
"name": "Research",
"permissions": {
"cancel_job": true,
"create_ref": false,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": true,
"upload_file": true
},
"users": []
},
"status": "201"
}
},
{
"description": "Deletes a group by its 'group id'.",
"method": "delete",
"parameters": [],
"path": "/groups/{group_id}",
"title": "Delete a group",
"errors": []
},
{
"description": "Fetches the complete representation of a single user group including its\npermissions.",
"method": "get",
"parameters": [],
"path": "/groups/{group_id}",
"title": "Get a group",
"errors": [
{
"status": "404",
"description": "Group not found"
}
],
"response": {
"example": {
"id": "technicians",
"name": "technicians",
"permissions": {
"cancel_job": true,
"create_ref": false,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": true,
"upload_file": true
},
"users": [
{
"administrator": false,
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"handle": "leeashley",
"id": "7CtBo2yG"
}
]
},
"status": "200"
}
},
{
"description": "Updates a group's name or permissions.\n\nPermissions that are not included in the ``permissions`` object will retain\ntheir previous setting.",
"example": {
"name": "Managers",
"permissions": {
"create_ref": true
}
},
"method": "patch",
"parameters": [
{
"description": "a name for the group",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"allOf": [
{
"$ref": "#/components/schemas/PermissionsUpdate"
}
],
"description": "a permission update comprising an object keyed by permissions with boolean values",
"title": "Permissions",
"name": "permissions",
"required": false
}
],
"path": "/groups/{group_id}",
"title": "Update a group",
"errors": [
{
"status": "404",
"description": "Group not found"
}
],
"response": {
"example": {
"id": "technicians",
"name": "Managers",
"permissions": {
"cancel_job": true,
"create_ref": true,
"create_sample": true,
"modify_hmm": false,
"modify_subtraction": false,
"remove_file": false,
"remove_job": true,
"upload_file": true
},
"users": [
{
"administrator": false,
"b2c": null,
"b2c_display_name": null,
"b2c_family_name": null,
"b2c_given_name": null,
"b2c_oid": null,
"handle": "leeashley",
"id": "7CtBo2yG"
}
]
},
"status": "200"
}
}
]
},
{
"title": "history",
"endpoints": [
{
"description": "Returns a list of change documents.",
"method": "get",
"parameters": [],
"path": "/history",
"title": "List history",
"errors": [
{
"status": "422",
"description": "Invalid query"
}
],
"response": {
"example": [
{
"created_at": "2022-01-28T23:28:53.881000Z",
"description": "Removed Betaflexivirus from Camelia #1 (BFV_CAM1)",
"id": "1wfc5x6e.removed",
"index": {
"id": "s7frhn8n",
"version": 1
},
"method_name": "remove",
"otu": {
"id": "1wfc5x6e",
"name": "Betaflexivirus from Camelia #1",
"version": 4
},
"reference": {
"id": "pat6xdn3"
},
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
}
],
"status": "200"
}
},
{
"description": "Removes the change document with the given ``change_id`` and\nany subsequent changes.",
"method": "delete",
"parameters": [],
"path": "/history/{change_id}",
"title": "Delete a change document",
"errors": [
{
"status": "403",
"description": "Insufficient Rights"
},
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "Not unbuilt"
}
],
"response": {
"status": "204"
}
},
{
"description": "Fetches a specific change document by its ``change_id``.",
"method": "get",
"parameters": [],
"path": "/history/{change_id}",
"title": "Get a change document",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2022-01-28T23:28:53.881000Z",
"description": "Removed Betaflexivirus from Camelia #1 (BFV_CAM1)",
"diff": {
"_id": "1wfc5x6e",
"abbreviation": "BFV_CAM1",
"created_at": "2021-12-09T01:32:35.390000Z",
"imported": true,
"isolates": [
{
"default": false,
"id": "714d1ea9",
"sequences": [
{
"_id": "eukvplhn",
"accession": "16SP043_BFV_CAM1",
"definition": "Betaflexivirus, complete genome",
"host": "Camelia",
"isolate_id": "714d1ea9",
"otu_id": "1wfc5x6e",
"reference": {
"id": "pat6xdn3"
},
"remote": {
"id": "g84vd2rm"
},
"segment": "",
"sequence": "TTCAGAAATCAACTCAACCTGTTGTGAGTACCCATCACATCAAAGCAATGGCTTCAGTGATGATAAGAACTCCTATGGAAAAGTTTTTTTCAGCAAATGACAAGAATGATCAAAAAATAATTCTTACGTCTGGAGTGAATTATGTTAAAAAATTTTGTGATGAGCAGGGTTTACACTTTGCATACTCAGTGGATGAGAGGAAAAAGGCTGCACTGACCAATCTTGGCATTAATTTGCATCCAGTGCCCTTTTTACCTCATTCACACCCTTTTTGCAAAATTCTTGAAAATAACCAGCTCATCAACATCCTACCAGGGATATTAGGTAGTGGTAGATGGACATTTATGTCAATTAAAGAAGGAAAAGTAGAAAGTATTATAAAAAAAAGTGGAGGTGTAAATAATAATATTAGTTTAATTAATAGATGTATATGTGCAAAAGATTTTTCAAGGTATGATTTCACCCCTGAAGAAGTTGATTTGAGAACAAATGTTCTCTCTGAGGATCATTTATTTCCAGAGAATCTGATGAGAAGCCTCAAAGGGAAAAAGATTTTTATACATGATGAGGTTCATCACTGGAATTCAAAAATCATGATCAACTTTCTGGAGAAAGTCAAACCTAAGATAATCTTTTGTTCAGTCGTTTATCCGCCAGAATTATTGGCTGGAATATTGGAACCTCAAAATAAAAGTTTTTATGATTTTAAGGTTGATGGTGATAAATTATTTTTTTTTCCAGATGGCAATAGGAGTGAATTTTATGAGCAGCCAAAGGATCTTGGTTGGCTAATGCTTGCAAAGAAATTCAAGCTCAATGACTGCAATTACACTGTTAAATTAATCAGCAGCACTTACTGCCATCACTTATTTCAAATATCTAGAGGTGAGAAGATAACTGAATCAAAGAGATTCTTCTCAGACTTTGATACCATTGACCTCAAAGTTATACACAATGAGAGGTTCAGATACTACGATCACATCCCCATAAGAAGGGCACATCTTGAGAAAGTGTACACATACTTGATGTGTCTTAAAAAACCGGATGTTGAATCAGCCATTGCAAAACTACGCCAACTTATGGAGGATGAGCAGGACACCAGAGTTGTGGCTTTTTTCTGCAAATTTGCAAGGGATGTGATTGAGAAATTCAAGGGAAAGATACATCTGTATGAAACGGGGTGGTTGAGTCAAATTGGAGACAATTTCATACAGATGCTTCCAAATTTCTGGGGGAGGATATTGTCAAGGTGGCATGGATTGAATCTTTTTGACTTCTTGTTCAAGCTTGATAACTTGAGAATTGAGGTTGAGTTGATTGACGTGGATGCTGAGTACTCATCGAGAAGTGAGGTCCTTAAACGCTTGTTTAAGAAGGATCAATTTAGTGAAAATTTTGATGGGCTTAATGTTGAGTACCTCAGAACTATTGGTCTTGAGGTCGAGATGGATGACGCATGGAGCAAGGGTTTCTCATCAAAAAAAAATAACTCAATTCATGCCTGCATCTCAAAATTTGGTGTTGAGAGAGTATCCAGCAAGGCCTTTGAAAGTAAACTCATCTCAAGATTTCATCTCAAAGTTGGCATTCTTGCCTTACTGCACAGGAGAAATGGAAATGGGAAGTCCTTGTTGAAAGGAGCACCTGTGAACCCAGATTCTAAGCAGGAAAAGAAAGGTATTTTAATGATCAAGCTCAGGTCAGATGACAAGGTTGAATCATATCCAGAGCCTTTTTTCTTAAATTTGAGAAATTTTTCATCAAAAGAATGTCCATTTGAAGATTTACGATGGATGAGAGTTCATAACAAGATTTGGGGTGGAACTTTCGGCACCCCATTAATACCAAGTGACTCACCATTGGAAGGAGATGAGGATGTTGACGTTTGTGTCATGGTGGACGAATTAGGATATGATAATGATGTCCAAGATGAGCAATGTGTCAAAAATTTGGAAATTCTTGAGATGGATGAAATTTTGAATGATTCCAACCCCAATATGAATGTGACTTCAACTGAAGTCAAACAAGATGATAAAAGGGAAGATTGCCAGCTCAATTTGATTGAATCCAGCGAAGTGGAAACTTCCAAATTCATGTCAGAGCTTGAGGACTCTGTATATCTCAGTTTCCATGATGATGAAACATTTAATTACTCAAATGTGCCAATAATAGGAGATGGCAATTGTTTTTTTAGAGCCATTTGCATGTCAGTGCATGGAAATGACTTTGGTCATCTTGAAACTAGGAAAAAATTTTCTGAACATGCAAGAAAAATTGGATTCAAATTTAATGCTGAAATTGAGGAGGCAATCACCAAGGATGGCACTTTCTCTGACACATGGATGGTCAATCTCTTTGCAAATGTTATGAATGTTAGACTCTTCATTCATGAAACAGAGGATGGTCCTTACTATGAGATTCACCCAACAATCATCAAGTATGATGACCCCCCAGTGTTCACAGTTAGATTACTATTTAGGGACGCACACTTTACTCTTTTGAAAGAGGAAAAGAGTGAGACTTGTGAAACGCTTAAGAAAGAGTTTTTGATTGATTGGGGGGAGAATGAATTCAGAGCTCTTAATGAATTTGTTGACTTGATAGTGGCTGAGCAGCAAAGGTTCAAGGCCAATAACTTCAAATCAAGGAAGGCCTTCTTTTTCTCTGAGCACGAGGGCATTGACTATGGGCATGATAAAGTTAAGTACCATCGGAATCAGATTGATTCAATTGACAGTCTTCTGCCCAGAGGAATGAATTGTGGTTTCAATTCAATGCTTGTGCAGATCTACGCTGATGGTGCTGAATTGCCAATGCACAGAGATGATGAGAAGGTTTATGACAATGACAACATCCTTTCCATCAATCTCAGGGGAGACTGCAAATTCATAATTAATGAGTCAAAAAAAGGGGCTAGCAATGTCAGGTCAATTGAGATGAAGCAAGGGGCTTATATAGTAATGTTAAGTGGCTTTCAAAAAAAATTCAAACATGGGGTTTCTGAATGTAGAAATGGGCGTGTGAATGTCACATTCAGAAGGCATGTGAGAAGTATGAGGGGTCATGACTTGATTGATTTTGATCTTTCCAAAATTAAAAATGGGTGTTTAATAAGGTCAATTGCAAATGCTGAATGCAGAGGACTGAATCAAGTTGTCCAGGCCTTGATCAGAAAGGATAGAGCCTTTTGGAGTGATTGGATTCATTCAGGGCAGGGGGGGACGATAGATGATCTAGTCAAAGCTGCCACTGAACTTCATTTCTCATTTGATCTAATTACTGAAAAGGGGTGTGACTCTTTTAAAAATTCCGGGCCCAAATTCACATTCCAACTTAAAAATGGTCATTTTGAAAGTATTAATGAAAGACCTTCATGTGTGGAAATGACCTTCCTGAATATGAGATCAAAAGGAAAAAAAAGTGGGAAAGGCATTGAAAAGCTCAAGTTCGAGCACATGAATGAAACAAATTTTGAGATTGTCGGAGAATTTGCCGCAATCCTTAAAAGATCATTCATGGAGCGAACAACAGGTCTAATTCTCTCCGAATGTTATGGCTCTGCATGCAAGAATCTTGAAGATTTGCAAATAGATCCAAGCAGTCAATTTGAGAAGAGAATTGACTTTATCTGTGGCTTTGCGGGGTCAGGAAAGAGCTTTTCAATTCAGTGCAAACTTGCATCGGAGCCTAAAGCTGATTTCTTGGTTATATGTCCCAGGAATGAACTCAAAAAAGATTGGCTTGAAAAAATCAATTGCAGTGAGAAAAAAGTTAGGACATTTGAAGTAGCCTTAACGCTCAACCTTTCAAAGATTGAATTGATTGTGATAGATGAACTGGGCTTGTTTCCAAATGGGTATCTCGATTTGCTGTGTCTAATGCTAACAAACCAGGGCAATTACAATTGCCAAGTGGTATGTTTGTTCGACCCTTTACAAGCGAGGTACCACAGTGATCTTGATGATTCTCTTTTAGATTTTCAGCATGACTGTGATAGGCTGATTGCTGATTGTGAATATCTGTACCTTGCAGAAAGTAGGAGGTTATCAAGCAAGTTCTTTGGAGCTTTCTTTCCAGACATCCACCTGCACAATGAAGGGAAAGAAGATCTAAGCATAACAATATTTGATAGTGTTGTTGTGGCGATAAATGAAATGAAAAAGAAAGAAACTCCAATCGACTTGGTGCTGGTTGCCTCAAGAGATGAAAAAAAGGCGCTGGCAACATCTGTTCGAACATTAACATTTGGGGAAGCTCAAGGCCTCACAGTCAATTATGCTTGTATTGTACTCTCTGAGTACTCAGAAAAGCAAGACGACCTACGGTGGATGGTAGCACTGACAAGGGCAAGGATCAAAATAGTCTTTGTATGTATGTACAGGGGAGGTCCAAGTTGCTTTTTACAAAACAATACATCCAGGTTAATAGGTCTGTTTCTGAGACAATCACCCATGACTATAAACAGGATGAAATTGATGGTCAAGGGTGATTTGATACCTTTTAGAAAGACAATAGGTTGTTCAGATGAAATGGATAGAGAGGAGAGATTGGAAGGAGACCCTTTTCTTAAACCACTGATTTTTCTTGGTAGTAGGATCAATTCAGAACAGGTTGAAGTTCTGGAGCCAGAAGTTGTTGAACCAATTGAGATGACTCACATCCCATTACCCCCAAGCCATTTTGATCAAAGCATTAATTTTGACAGAATTAGAGCACGTGAGCATAGGGAGTTCAGGATGTATTCAATGTGTACAAAGCAGTTTTGTGAGGATTTTGAACATTCAAGAGCCTCGGGGAAGCAGATGACACCAGGTCCTATGAGATTCGAAGCAATCTACCCAAGACATAAAGCAGATGATGACCTGACCTTTTGGATGGCTGTCAAGAAGAGGTTGCGCTTTTCCGAGGAGTTTGTTGAAAGAGCAAAACTTAAAGAAGCAATGGGAGTTGGGGGTTTGTTGTATTCAAACTTCAAGGAGACATTGGGTTTGAAGTTCAATTGGGATCAGAAGCTCCTTGACGAGTGCGTCAATGACTTTGAAGAGAAGAAACTTAGCAAAAGCAAGGCAACTCTACAAGCTCATAGCTCAAGATCTGACTCAGACTGGAAATTGGATCATATCTTTCTGTTCATGAAATCCCAATTGTGCACAAAATTTGAAAAGCAGTATGTTGACGCAAAAGCCGGGCAAACATTGGCTTGTTTTGCACACTGCATTTTAGTCAAGTTTGCGCCTTATTGCAGATACATGGAAAAACAATTGAGAAATCAATTTCCAGATAACATATACATTCACTCAGGAAAGAACTTCAATGATCTTAATCAGTGGGTTAAAGAGAACATGAAGGGGAAGGAATGTATAGAGTCAGACTATGAAGCATTCGATGCGAGTCAAGATGAATACATACTGGCCTTTGAAATATGCCTCATGGAGGATATGGGGATGCCAACTTGGTTCATCAATGATTATATAGATCTTAAATGCACACTTGGGTGCAAATTGGGCCACTTTGCCATTATGAGATTCACTGGTGAGTTTAGCACCTTTCTATTCAACACATTGGCAAACATGGCCTTCACATATGCCAGATATGATTGTGATGCATCAACTCCAATTGCCTTTGCTGGAGATGACATGTGCATGCTTGACAATTGTGCCGAGACTGACAAATTCGAAGGAATTTTTGAGAAAATATCACTGAAGGCGAAGGTTTTGAGGTCATGTACACCTATGTTTTGTGGGTGGAATTTGTGCAAGTATGGAATCTTCAAGGAACCGGCTCTAGTTTATAATAGATTTATGGTTGCTCAGGAAAGGGGTAATGTAGAGGAGTGCCTTGAGAATTATGCAATAGAGGTTTCCTATGCTTACATGTTAGGTGAGAAGCTCTATGAATTTTTGAAAGAAGAAGAGAGAATTAACTATCATCAAAGCGTAGTGAGATTCATAATTAAAAGAGCATATAAACTCAAGACCAAAGTGCGGCTTCTGTACACCAGTGATGGCGAAAGCAATTAGAGTTAAGAGCCTCACCAATCGGCTAGAGGTTGACAAATCTCTGCTCAATTCAAATGAAGTCTCAGCTCTGTATGGTGGTGCCTTTGCACCACTAGTTTTTAAGGATGAGGTTAAAATGGTAATTCCTGGCAACCTACTGGGCGGGCCAATTCGTCTACAGGCAAACATACTCACAAAGTCAAGACTCGAAAAAATTCGCAGCCAAAAATTTAAAGGAAACTCATGTGCTTATCTGCATCTTGGGGTGGTCACCATTGTTATACAATCACTGCTGGTGTCTGGCAATGAAAATGTCAGAGGCAGGTGCTCATTGGTTGATCTTTCAAGGGGCTCTGAAATGACTGGGCTCATTGACAAATTCAAGTTCAGCTTTACTAAAAACGAACCTTTCGCTGCAAAAATGTTGACAATAAATGCAGCAATTGATATTGACTGCGAGGTGTCTGCTGGAAGTATTCAGGCTCTCCTTGAAGTTGAAGGCATTGATGTCAGATCTGAGAGGAGTGTTCTAGCCATCACCACTGGGATAACCTGTGTTCCAACTAACTCCATGGTAATGTTGCCAGGTCTGAAAAGAGAAACCCCGAAGTTTGCAATTGCGAATGTTTACAATGTTCCTGATGAAGATCCAACTGAATGCGAGGCGTTTAACAGATTATTTGGAGCCGCTAATCCAAAGTTGATTGATTTGGGTAGTGAGACTGTGTTGGAAGAAGGGAAGAGATTTGGCCTATGGGGACCTGTCGTTAAACCAGTACACAGAAGGAAGCTCGTGACAAAAGGCATTATCAAGGATCACATGAGCCAATTTATGTCAGGCCCTTCCAAAGATTTGAAAATAGAAGAAGGTTTGGAAAGGTCAAGCTCATTACGTGTTGAAAATGTCTGCGAAACTGGCAAAGAAGAGGCTGATACACGACGAAGTGTCGGAATGGATTTTCAGGAGTTTCGTGGACCAGATAATTCAATGGGGGTTGTTGCTGGTAAATGCTGGGAATCAGAGAGTTCAGCTGAATTTAAACCAACAGGAGCAGAAATCAAGAGTTCAGAACAGCAGACTCCGGACGATTTTTGGCAATATAGCAGATCACTCAGCAGGGCCAGCAACAGTGTACCCGTCAATCAGTGTAAGTTATCAGGTGATGAACATTCAGGGAATCGAAGGTGTTGCACAGATGGATGGAAATTTCAATCTGAGAACATTGGTGGAAAATCTGAAGACCTTCCTTCTGACCAGCCAGGATCCTCAGCTCAACACTGCAACATTAAGGGAGGTCTGCCGGAGCTTTGCAAACTACGCCCTTGAGTACTACATGGAAGACCCCGACAGGATGTCCAATCTAGCTGACAAAATGCCACAACTAGCTCTGCAGGCGAGGGAGGTCATGTTTGACTTTTCTGATGGAATAAGTCAGCAATATTTGAGGGGTTTTCCAATGAGGGCTAAGGTTATACAGGAATTGAATAGTAGGCTTCTGCAGTCCACTGGCACCAAGGCTGTGTTTGAAGCAAGGGGCACAGTTGAGTCCTCAGTTAATTTGATTGTTTAAGGAAACAATACAGGCTTTGTCATTTGAGTGCTGTGAGTTCAAATGATACCTTATAAGTCAGATTCATCTGCACAGGTAAGTTTCAACCTCTTTGTATTTAAAGAGTGGCCGAGTGAGTGTACGCTCATGTTCGGAGATTAGCTTCCCAGCTTTATCAAATATTATGACTTAAGTATTAATAGGGATGTCTTTTATGAAT"
}
],
"source_name": "16SP043",
"source_type": "internal"
},
{
"default": true,
"id": "950197de",
"sequences": [
{
"_id": "5oydqvv1",
"accession": "16SP042_BFV_CAM1_B",
"definition": "Betaflexivirus, complete genome",
"host": "Camelia",
"isolate_id": "950197de",
"otu_id": "1wfc5x6e",
"reference": {
"id": "pat6xdn3"
},
"remote": {
"id": "nkun91us"
},
"segment": "",
"sequence": "GTTGAAAATAATATTAGTGTAGTAAATACGAAAACAAACACACATAACTAACACTTGAACTTGAATTCATCTCCCAACGGTACCCATCAGTGTAAGTCCAATGGCATCAGTGATGATAAGAACCCCTCTGGAGAAATTCTTTTCTGCCAATGATAAGGCTGACCAAAAGGTCATCCTTACATCTGGAGTTAGTTATGTAAAAAAATATTGTGATGATAAAGGTCTGCATTTTGCCTATTACCTTGATGAAAGGAAGAAAAAGGCAATCACAGATCTTGGAATTAATTTGCATCCCGTACCCTTTCTGGCACATTCACACCCATTCTGTAAAGTTCTTGAAAACAATCAGCTTGTCAACATTTTGCCAGGTCTGCTTGGCTCAGGCAAATGGGTATTTATGTCCATTAAAGAAGGAAAGGTGGAGCAAATTATTAAAAAAAGTGGAGGAGTTGAAAATAATATTAGTGTAGTAAATAGATGTATATGTGCTAAGGATTTCTCTAGATACGACTTCACACCTAATGAGGTCGATATTCGGCGAAACTCCATTAAAGGTGACCACCTTTTTCCAGAAAATTTAATGCGGAGCCTTAAAGGAAAGAAAATCTTCATTCATGATGAAGTTCATCATTGGAATTCCAAGCAGATGATTGATTTTTTGGAAAGGGTTTCACCTACAATATTATATTGTTCAGTAGTTTACCCACCTGAGCTTTTGGGTGGGATCACCACCCCTCAAAATAAGACCTTTTATGATTTTAAAGTTGAAGGGGACAAACTTTATTTTTTTCCTGACGGTAATCGGAGTGAATTCTATGAACAACCTGCTGATCTCAAATGGTTGCTCATGGCTAAAAGGTTCATTTTGAAGGACTCTGAGTACACTGTCAAAATGCTCAGTAGCACTTATTGTCATCACCTTATCCAAATTTCAAAAGGGGCCAAAATCACGGAATCAAAACGGTTTTTCTCAAACTTTGATACCATTGATTTGAAGGTCATACACAAAGAAAGGTTTAGGTATTATGATGACATTCCAATTCGGAAACTGCACCTTGAGAAGGTTTACACTTATTTGATGTGTCTTAAAAAACCAGATGTTGAATCAGCCATTGCTAAGCTGAGGCAGCTTATGGAGGATGAACAAGACACAAGGGTTGTTGCCTTTTTTTGCAAATTTGCAAAGGATATAATTGACAGATTCAAAGGCAAAATACATCTTTATGAAACTGGATGGTTTGAGCACATTAAAGACTCATTTGTAAAGATGTTGCCCAACTTTTGGGGTAGATTGCTCTCAAGGTGGCACGGCGTTAATCTTTTCGAGTTTCTATTTAAGCTGGAATGCTTATGCATAGAGGTTGAATTGATTGACGTTGATTCTAGTTTCTCAGTCAAGGAATCCCTCAAGGATAGAGTTTTGGGCAGATCTGAGGGATGCAGTGCCGAGCTACAAAATTTGTATATGCAGGAGTTTGGTCCTTCAGCCATGCTAGAAGTAGGCTGGCATGGCAATCTTAAAAAGGTCATGAAGGATGTTGAAGAGAAAAACTTGATTAAAAATGGCAGATTATCCATCCGTGAAAAAGCATATTCTTCAAAGTTACTAAGCAGGTTCCATTTGAGAGTTGGAATTCTTAAGTATATTGGTGTTCAAAATAGAATAGGGGAAAGGAATGAGTTAAAACTTAGAACACCAATGATCAAGATGCACAATTCTGATGGCATTTACTCCTATCCAGAACCTGAATTCATCAGAGATGAGGGGTTCACCTCATTTGAATGTGAGTACAGCAACCTTAGGTGGCTGAATGTTCATAGAAACCTTTGGTTCAACAATTTGGAATTAGGGGTTGACGTTTGTGATGTTCATGAGCCACAAGTCACCAATTCTGAGGACTTGTCTTCCGCTGAAAACCTTTTAGAGGTCATTGAAGTGGATGATGAGTTCTTTCCCTCAAACATGAAAGAGACTGTTGAGGTGGCTAAAGAAACTGGTACTCTCAGAGAGAAAAGTGACCCTATGAGGCAAAGTTCATCTGAAGTTTTGGATGATGAGCTGATTCGTGAACTTGATGGATCTGTGACCATAATTCACAATTTTACAGAGGAGTTGTTGGTTAAAAAAGATGTGCTTGGAGATGGTAACTGCTTTTACAGAGCACTGAGGCTCAAATTAACTGGGAGTCAGGAGGGCCATGAGGAGGTCAGATTGAAATTTGCAAATCATGCTAGTCATATTGGCTTTAATTTGTCTACAAACATGAGAAATATGATCATCACGCCAGGTGTTTTTACTGAGACGTGGATGGTGAATCTTTTTGTGAATGTTATGAATATAGACATCATGATTCATGAGGACATGAGTGGCAATTACTACTCAATCAAACCCAACCTGATTCATTATGATGAAACCCCAAAAATCCAAATAAGATTGCTTTTTGAAAATTCTCACTTTGCATTGCTGGAGTCAGCAGACAAGTATGAAGAGAAAATGGATTTGGACTCCAAATCTTTTGAGGCAAAGTATCTCATTAAAAGTGGGTTTGGAGATTTTGAAGCTATTAGAACTTTAGTTGAAGATCTTGTCAGCAGGGTGAAAGAATACAAATTCAATGAGTTTAAAGGAAGGAGGGCTTATTTCTTCTCTGAAAATGAAAGCATTGATTATGCACATGGGAAGACCAAATATTTGAGAAATCAATTTGACTCTGTCAACGAATTACTTCCCATTGAATTGAAAGGGAAATTCAATGCCTTTCTGCTCCAAATTTTTGAAGAGGATGGAGAGATAGGGTTCCATAGAGACAATGAAGGTGTGTATGACAATGACAACATTCTTTCAATCAATCTCAATGGTTGTGCATCCTTCATGATTGAAGACTGTGGCAGCAAGGAAATCTATGAAATCAAAATGACTGATGGTTTATTCATTTCAATGCTTCCTGGATTTCAAAAGAAGTTCCGTCACGGTGTCACCAATTGTTCGTCAAAAAGAGTTAATATCACTTTCCGAAACCATGTTAGATCGGTCAATGGCAGGCCTGTAATTGAAATTGACCTTTCTGAAATAAGAAATGGTTGCATGCTTAGAGCAATAGCTGATGCTGAAAAGCGCAGCTTAGGGCAGGTTGTGCATGCATTATTTAAAAAAGATCGTGACTTTTGGAAGATGTGGATTTCAGAAGCAAAGGGTGGCACAATTGAAGATATGATGAAAGCAGCCATTGACCTCAAATTTTCATTCGAACTTTTGAGTGATGGCAAGTGTGAAATCTTTGGAACTTCAGGTCCAAAACTCAATTTCGAGTTAAAGGGGGGACACTTTTCAGTCATGGATTCAAGACCTTCATGTGTAGAGAGGACCTTCTTAAATTCAAACACCTCAAGGAGAGGGTCATCTAAACATTTGGGTGAGATGGACCTTGAATATTTGAATAATACCAACTTTGAAGCAAAGGGAATTTTTGCGAACCAACTCCAGATATCCTTTCTGGAACGTACTACTGGTCTAATTTTGTCAGAGGTTTACGGTTCAGCTGGGAAAAATTTGGAATTGGTTAAGATCAACAGGGAGAACATGATTGAAAAGGAAATTAATTTTATGTGTGGATTTGCAGGATCTGGGAAGAGTTATTCCTTACAACAGAGGGTTAAACAGAGCCTGGATGCTGAATTCCTCATAATATGCCCAAGAAATGAGCTCAAGAAGGATTGGTTGAGTAAGTTGAATTGCAATGAGAAAAAAGTGAGAACATTTGAAGTTGCATTAACTCTCAATTTATCCAAATTGGACTTGATAATTATTGATGAGCTTGGCCTTTTCCCAAATGGTTATCTAGATTTAATTTGCTATATGCTTGCGGATCAAGGTAATCATGACTGTAAGATCATGTGTCTGTTCGACCCTTTGCAATCTAGATACCATAGCGACCTAGACAACCATCTTTTGGATTTTGACCATGAATGCGACAGATTGATAGATGGTCTTGATTTTAACTATTTGATGGAGAGTAGGAGAATGTCCAAATCATTCTTTGGAGCCTTCTTTAGAGATGTAACTTTATACAACGAGGGTGATCAAAACTTCAAATTGGAGGTGTATGATTCAGTCATCGTTGCCATAAATGAAGGAAAGAAAAAGGGCATTGAGGTCGATCTGATACTAGTTGCATCCAGAGATGAGAAAAGAGCATTATCTTGTTCTGTCAATACATTGACATTTGGAGAAGCACAAGGTTTGACGGTGAACCATGCATGCATTGTGCTTTCAGAATATGCAGAGAAACAAGATGATTTCAGATGGATGGTCGCATTAACTAGGTCCAGAATAAAGGTCAGCTTTGCGGTCATGTACAGAGGTGGATTAGTGAGTTTTGTTCAAAATAACTCAGCAAGATTGATTGGCCTGTTTATGGCTCAATCACCACTAACCATCAATCGAATGCAATTAATGCTCAAAGGAAACATTAATCCATGCATCAGAAGTCTAGGATGCTCTGATGAGATGGACAGGGAAGAAAGGCTTGAGGGTGATCCCTTTCTAAAACCGCATATATACCTTGGCCAGAGGATCAATGCTGAAGAGTTTGAGGTTTTTGAGCCAGAAGTTGTTGAGCCAATTTGTAGAACGCATATTGAACTACCTCCTGAAAACTTTGATCAAAGCATCAACTTTGATTTAATTAGAGCGAGGGAGTTTCGGGAAATGCGGATTGGAGGTGAGACAACTAAACAATTTTGCGAAGACTTTGAGCATTCTAGAGCAAATGGAAAAAGAATGACTTCAGGTCCAATGAGGTATGAAGCAATATACCCTAGGCACAAAGCCGATGATGATGTGACCTTTTGGATGGCAGTCAAGAAAAGATTGAGATTTTCCGAGGAGCATGTTGAGAGGGCCAAATTGAAAGATGCATTTGGGGTCGGAGGCTTGTTATACGAAAATTTCAAAAGTAAAATGGGACTCAAATTCAACTGGGATCAACAACTTTTGGATGAATGTGTTAACGACTTTGAAGTCAAAAAACTGAGTAAAAGTAAAGCCACTTTGCAAGCTCACAGCTCCAGGTCTGATTCTGACTGGAAGATTGACAACATATTTCTCTTCATGAAATCACAATTGTGCACAAAGTATGAAAAGCAATATGTAGATGCGAAGGCTGGCCAAACGTTGGCGTGCTTTGCTCACATGGTGTTGGTCAAATTTGCGCCATATTGTAGGTATATGGAGAAGCAGTTAAGAAATCAATTTCCAGAGAACATTTATATACATTCAGGGAAGAACTTCAATGACCTTAATGACTGGGTTAAAAGGCATATGTCAGACAATGAATGCATTGAATCGGATTATGAAGCATTTGATGCATGTCAAGATGAGTATATATTGGCATTTGAGGTACTTCTCATGGAAGATATGGGTATGCCAAATTGGTTCATTAATGACTACATTGATCTTAAATGTACTTTGGGTTGCAAATTGGGCCACTTTGCGATCATGAGATTTACTGGTGAGTTTAGCACCTTTTTGTTCAACACCTTGGCAAACATGGCATTTACTTTTGCCAAATATGATTGTGATGGGAAAACACCAATTGCTTTTGCTGGAGATGATATGTGCATGCTTTCAAAATGTGATGAAATCTCAAAATTTGAGAGCGTCTTTGAGAAGATATCACTAAAAGCAAAGGTGGTAATCTCAAAAAATCCAATGTTTTGTGGGTGGAATCTGTGTAAGTATGGAATTTTCAAAGAACCTGCATTGGTGTACAACAGGTTCATGGTTGCAGAGGAAAGGGGAAATGTCAATGAATGCTTAGAAAATTATGCAATTGAAGTTTCCTATGCTTACATGTTAGGTGAGAAGCTCTATGAATTTTTGAAAGAAGAGGATAGGGTCAATTATCATCAAATTGTGGTCAGATACATTGTTAAACACATCGACAAACTCAAAACGAAGGTAAAGGTTCTGTTCTCAGGGAAAGATGTCTAAGGCTGTCAAAGTTAAAAGCCTTGTACAGAGATTGGAAGTTGACAGGTCGTTATTGAACTCAAATGAGATATCCGCTCTGTATGGGGGTGCATTTGCGCCATTGGTCTTTAAAGATGAGGTCAAGATGGTCATCCCTGGTAATCTATTGGGTGGTCCGATTTGTTTGCAAACAAACATTCTAACCAAGTCAAGGCTTGAAAAAATAAGAAGTCAGAAATTCAAAGGGAAGAGCTGTGCTTATTTGCATTTAGGCGTTGTGACAGTCGCTATTCAATCCTTATTAGTTTCCGGCAATGAGAAAATTAAGGGTAGATGCTCGCTTGTTGATTTATCCAGAGGGTCAGAGGAGACTGGCTTAATAGACAGATTCAAGTTTTGCTTCACAAAATCTGAACCTTTTGCTGCAAAAATGTTGACCATCAATGCTGCAATCGATATCGACTGTGATGTATCTGCAGGGAGCTTGCAAGCTCTGCTCGAAGTTGAGGGAATAGATATTCGAACTGAAAGGAGTGTGCTTGCAGTTACTACAGGTATAACGTGTGTGCCAACCAATTCCATGGTGATGCTCCCTGGTTTGAAGAGAGAGACTCCCAAATTCGCAATTGCAAATGTTTATAATGTTTCTGATGAGGACCCGGAAGAACATGCTGCTTTCAATTCATTATTCAGTGCAGCAAATCCAAAGCTGATCGATTTGGGCCAAGAATGCATTTTGGAGGAAGGAAAAAGATTTGGCTTTTGGGGTCCAATGGTTAAGCCAGTTCATAGAAGGAAATTAACAACTCGCGGCTTGATCAGAACTCATATGGATCAAATTATGTCTGGTCCTGGAAAAGATTTGAAAGAAGAAGGAAATTCAAAGTTGTCCAGATCATACTTATCAAGAAATGTCTGCGAAATTGGCAAAGAAGAGGCTCATCCACGACGAAGTGTCGGAATGGCTATGGAGGAGCTTTGTGGACCCAGAAAATTCGATGGGAGTTTGGTTGGTGAATGCAGCAAATCAGCGGGTTCAGTTAAATCTGAATCAGCAGGAGCAAAAATCAAGGGTGCAAGTGAGTCGCCTAAGATCTATTTTTGGGAACATAGCAGATCACTCGGCAGGTCCAGCAACCGTGTACCCGTCAATCAATGTAAGCTTTCAAACTCTGAACATTCAGGGAATAGAAGGAGTTGCACAGATGGATGGGAATTTCAATCTGAGAACACTTGTCGAAAATCTGAAGATGTTTCTGATAACGAGTCAGGATCAGCAGCTGAGCACTGCAACATTGAGGGAGGTTTGCCGGAGCTTTGCAAATTACGCCCTTGAGTATTACTTGGAAGACCCCGACAGAATGTCAAATCTCGCTGACAAAATGCCTCAATTGGCACTGCAGGCTAGAGAAGTTATGTTTGACTTTTCTGATGGCATTAGTCAGCAATTCATAAGGGGTTTTCCAATGAGGGCAAAGGTAATCCAGGAGTTGAATAGCAGGTTGTTACAGTCATCTGGGACAAAAGCTGTGTTTGAAGCAAGGGGCACAGTTGAGTCTTCAGTTAATTTGATTGTTTAAGGAAACAATACAGGCTTTGTCATTTGAGTGCTGTGAGTTCAAATGATACCTTATAAGTCGCTTGCGCACAGGTAAGTTTCTATACCTCTTTGTATTTAAAGAGGAGTCACTTCCTTTGGTAGAATTGCTTTAATTAGCAGTGGGCCGCCAAACAGTGCATTAAGTACTCCCCAACTAAGTAAAATATTATGATATAACTATTAATAGGGATGCCTTTTCAATATTTAGG"
}
],
"source_name": "16SP042_B",
"source_type": "internal"
},
{
"default": false,
"id": "eb4c1673",
"sequences": [
{
"_id": "yymkrcpy",
"accession": "16SP042_BFV_CAM1_A",
"definition": "Betaflexivirus, complete genome",
"host": "Camelia",
"isolate_id": "eb4c1673",
"otu_id": "1wfc5x6e",
"reference": {
"id": "pat6xdn3"
},
"remote": {
"id": "u7ni2w4n"
},
"segment": "",
"sequence": "ATCACAAAATACAACAACATAATTCAGAAACTAACTTAACCTGTCGTGAGTACCCATCACATCAAAGCAATGGCTTCAGTGATGATAAGAACTCCTATGGAAAAGTTTTTTTCAGCAAATGACAAGAATGATCAAAAGATCATTCTCACGTCTGGGGTGAATTATGTTAAAAGATTTTGTGATGAGCAGGGTTTACATTTTGCATACTCGGTGGATGAGAGGAAAAAGGCTGCACTGACCAATCTTGGTATTAATTTGCATCCAGTCCCCTTTCTACCTCATTCGCACCCTTTTTGCAAGATCCTTGAAAATAACCAGCTCATTAACATTTTACCAGGGATACTAGGTAGTGGTAGGTGGACGTTTATGTCAATTAAAGAAGGAAAAGTAGAAAGTATAATTAAAAAAAGCGGAGGTGTAAATAATAATATTAGTTTAATCAATAGATGTATATGCGCAAAGGATTTTTCAAGATATGACTTTACTCCCGAAGAGGTTGATTTGAGGACAAATGTCCTCTCTGAAGATCATTTATTTCCTGAAAATCTGATGAGGAGCCTCAAAGGAAAGAAAATATTCATACACGATGAGGTTCATCACTGGGATTCGAAAATTATGATCAACTTTTTAGAGAAAGTTAAACCGAAAATAATCTTTTGCTCAGTTGTTTATCCGCCAGAATTATTAGCTGGCATATTAGAACCTCAGAACAAGAGTTTTTATGACTTTAAGGTGGATGGTAATAAGTTATTCTTTTTCCCTGATGGTAATAGGAGTGAGTTTTATGAACAGCCAAAGGATCTCAGTTGGCTAATGCTCGCAAAAAGATTCAAACTTGATGATTGCAATTACACCGTCAAGTTGATCAGCAGCACCTATTGCCATCATCTGTTTCAAATATCCAGAGGGGAAAAAATAACGGAGTCAAAGAGATTCTTCTCAGACTTTGACACCATTGACCTCAAAGTTATACACAATGAGAGGTTTAGATACTACGATCACATTCCAATAAGAAGAGCACACCTTGAGAAAGTGTACACATATTTGATGTGCTTAAAGAAGCCTGATGTTGAATCGGCTATTGCAAAATTGCGCCAACTTATGGAGGATGAGCAGGACACCAGAGTTGTGGCCTTTTTCTGCAAATTTGCAAGGGATGTGATTGAGAAATTCAAGGGAAAGATACATCTGTATGAAACTGGATGGCTAAGTCAAATTGGAGACAATTTCATACAGATGCTTCCAAATTTTTGGGGGAGAATATTGTCAAGGTGGCATGGGCTTAATCTCTTTGATTTCCTATTTAAGCTTGACAATTTGAGAATTGAAGTTGAGCTGATTGACGTTGATGCAGAGTACTCATCAAGGAATGAGGTACTCAAACGTCTGTTCAAAAAAGACCAATTTGGTGAGAACCTCGATGGGCTAAACACTGAATACCTTAGGACCATTGGTCTTGAGGCTGAAATGGATAATGCATGGGGAAAAGGTTTCTCATCAAAGAAAGATAGCTCAATTCGTGCATGTGTCTCAAAATTTGGCATTGAGAGGGTCTCAAGTAAGGCTTTTCAGAGCAAGCTCGTCTCAAGATTCCATCTCAAAGTTGGAATTCTTGCCCTGCTACATGAGAGAAACAGGAATGAGAAGTTCTTACAAAAAGGGATGTCTGTTGATTTCAATTCCAAATCCCAAGAGAGAAGGGTTTTAATGATCAAGTTCAAGTCGGAGGATAGGGTTGACTCATATCCCGAACCCTTTTTCTTGAATTTGAGAAATTTTTCATCAAAAGAGTGTCCATTCGAGGATCTTAGATGGATGAAAGTGCATAATAAAATTTGGGGTGAAACTTTTTGCACTCCATTGATTCCAAATGAATTTCCATCAGAAAAAGATGAAGATATTGACGTCTGCAGCATTGTGGATGAGTCAGAATGTGATGACAGCAATCACGATGGGCAGTGTCTTGAAAACTCAGGGTCTTTTGGAATTAACAAGACCTCAGATGACCCAAACATTAATGTGGAAATAACTTCAATTGAGACCAGGCAGGGTGATGAAATCGATTGCCGGCTTAATTCAACTGAACCTAGTGAGGTGGAAACATCTGAATTCATGTCTGAGCTAGAGAATTCTGTGTATCTCAGCTTTCATGATGATGAAGTTTTCAATTATTCAAAGGTGCCAATAATAGGGGATGGCAATTGTTTCTTCAGAGCCATTTGTATGGCAGTGCATGGGAATGATCATGGTCACCTTGAAACTAGGAGGAAATTCTCTGAACATGCAAAGAGGATTGGATTCAAATTTAACGCTGAGATTGAGAAGGCAATTGTCGAGAGTGGAACTTTCTCTGACACATGGATGGTCAATCTCTTTGCAAATGTTATGAATGTTAGACTCTTCATTCATGAAACAGAGGATGGTCCTTACTATGAGATTCACCCAACAATCATCAAGTATGATGATCCCCCATTATTTTCAATTAGACTATTATTTGGGGATGCACACTTCACACTTTTGAGGGAAGTGGAAGGTGAATCATGTGAAAAACTTAAAGAAGAGTACATGATTGATTGGGGAGAGAACGAATTCAAGGTCCTCAATGAGTTTGTTGACTCAATAATGGACGAGCAGCATAGGTTCAAGGCTAACAATCTCAGGTCAAGAAAGGCTTTCTTCTTTTCTGAGCACGAGGGTATTGACTACGGGCATGATAAAGTTAAGTACCATCGGAATCAGATTGATTCAATTGACAGTCTTCTGCCCAGAGGAATGAATTGTGGTTTCAATTCAATGCTTGTGCAGGTGTACACTGATGGTGCTGAGCTACCAATGCATAAAGATGATGAGAAGGTCTACGACAATGACAACATTCTCTCTATCAATCTAAGGGGAAGCTGCAACTTCATAATTAATGAGTCAAAAAGAGGAGCTGACAATGCCAGATCAATTGAAATGAAGCCAGGGGCTTACATAGTGATGTTGAGTGGCTTCCAGAAAAAGTTCAAACATGGGGTTTCTGAATGTAGAAATGGGCGTGTGAATGTCACATTCAGAAGGCATGTGAGAAGTATGAGGGGTCATGACTTAATTGATTTTGATCTTTCCAAAATTAAAAATGGGTGTTTAATTAGGTCAATTGCAAATGCTGAATGCAGAGGACTGAATCAAGTTGTCCAGGCCTTGATTAGAAAGGACAGAACCTTCTGGAGTGATTGGATTCACTCAGGGCAGGGGGGAACAATAGATGATCTGGTTAAGGCCGCCACTGAGCTTCACTTCTCATTTGACTTAATCACTGAAAAAGGGTGTGAATCCTTCAAAAATTCTGGGCCAAAGTTCACATTCCAACTCAAAGATGGACATTTCGAAAGCATCAATGAAAGACCATCATGTGTGGAAATGACCTTCCTGAACATGAAATCAAAAGGAAGCAGCAAAGATAGGAGGAGCATTGGAAAGTTGAGGTTTGAACACATGAATGAAACCACTTTTGAGATCGTTGGAGAGTTTGCTGCAATCCTCAAAAGATCATTCATGGAGAGAACAACAGGTCTAATCCTCTCTGAATGTTATGGCTCAGCATGCAAGAACCTTGAAGACTTACAAATAGATCCAAACAGTCAATTTGAAAAAGAAATTGACTTCATATGTGGTTTTGCAGGATCCGGGAAAAGCTTTTCAATTCAATGCAAACTTGCATCGGAACCTAAAGCTGATTTCTTGGTTATATGTCCCAGGAATGAACTTAAAAAAGATTGGCTTGAAAAGGTCAATTGTAATGAGAAGAAAGTGAGGACATTTGAAGTGGCTCTGACACTAAATCTTTCAAAAATTGAACTGATCGTGATAGACGAGCTGGGCTTGTTTCCTAATGGATACCTCGATCTGCTGTGTCTAATGTTGATCAATCAAGGGAATTACTCCTGTCAGGTGATATGTTTGTTCGACCCCTTACAGGCAAGGTACCATAGCGATCTTGATGACTCCCTTCTGGATTTTCAACATGACTGTGATAGGTTGGTCACTGACTGTGAGTATCTGTACCTCGCAGAAAGCAGAAGATTGTCAAGCAAATTCTTTGGGGCCTTTTTCCCAGACATTCACCTACATAACGAGGGGAGGGAGGATTTTGGCATGACAATATATGACAGTGTTGTCGTGGCAGTGAATGAAATGAAGAAGAAGGAAACCCCGCTTGACTTGGTGCTGGTCGCTTCAAGGGATGAAAAAAAAGCATTGGCAACATCCGTTCGAACCTTGACATTTGGAGAAGCACAGGGGCTTACAGTGAACTACGCCTGCATTGTGCTCTCTGAATATTCAGAAAAGCAAGATGACTTACGATGGATGGTGGCGCTAACAAGGGCAAGGATCAAAATAATTTTTGTGTGCATGTATAGAGGTGGTTCAAGCTGCTTTCTACAAAACAATTCATCTAGGTTAATAGGTCTGTTCATGAGACAATCACCCATGACAATAAACAGGATGAAGCTGATGGTCAAGGGCGATTTGATACCTTTCAGAAAGACGATAGGTTGTTCGGACGAGGTGGATAGAGAAGAAAGGCTAGAAGGGGACCCCTTTCTCAAACCACTTATTTTCCTTGGAAGCAGGATCAACTCAGAGCAAGTTGAAGTGCTGGAGCCAGAAGTTGTTGAACCAATTGAAATGACGCATATTCCACTACCTCCAAGTCACTTTGATCAAAGCATCAATTTTGACAGAATCAGAGCTCGTGAGCACAGAGAATTCAAAATGAATTCAATGTGTACAAAACAGTTCTGTGAAGATTTTGAGCATTCAAAGGCCTCAGGAAAACAGATGACGTCAGGCCCTATGCGCTTCGAGGCAATTTACCCAAGACATAAAGCAGATGACGATCTCACCTTCTGGATGGCTGTTAAGAAGAGACTGCGTTTTTCTGAAGAGTTTGTTGAAAGGGCAAAACTCAAAGAGGCAATGGGGGTTGGAGGTCTGTTGTATTCCAATCTTAAAGAGACATTAAATTTGAAATTCAATTGGGATCAGAGCCTCCTTGACGAATGTGTCAATGACTTTGAAGAGAAGAAGCTTAGCAAAAGCAAGGCAACTCTACAAGCTCATAGCTCAAGATCTGACTCAGACTGGAAATTGGACCACATCTTTCTATTTATGAAATCTCAATTGTGTACAAAATATGAGAAGCAGTACGTAGACGCAAAAGCTGGACAGACATTGGCATGTTTTGCGCACTGCATTCTGGTTAAATTTGCACCCTACTGCAGATATATGGAAAAGCAATTGAGGAGTCAATTTCCGGATAACATATACATTCACTCAGGAAAGAACTTCAATGATCTTAATCAGTGGGTTAAAGAGAACATGAAGGGGAAGGAATGTATAGAGTCAGACTATGAAGCGTTCGATGCGAGTCAAGATGAATACATACTGGCCTTTGAGATATGCCTCATGGAGGATATGGGGATGCCAACTTGGTTCATCAATGATTATATAGACCTTAAATGCACACTCGGGTGCAAATTGGGCCATTTTGCCATTATGAGGTTCACTGGGGAGTTTAGCACCTTTCTATTCAACACACTGGCAAACATGGCCTTCACGTATGCCAGATATGATTGTGATGCATCAACTCCAATTGCCTTTGCTGGGGATGACATGTGCATGCTTGATAACTGTGCTGAAACTGACAAATTCGAAGGAATTTTTGAGAAAATATCACTGAAGGCGAAGGTTTTGAGGTCATGTACACCCATGTTTTGTGGGTGGAATTTATGTAAGCATGGGATCTTTAAGGAACCAGCTCTAGTTTACAACAGATTCATGGTGGCTCAGGAAAGAGGTAACGTGGAAGAATGCCTTGAGAACTACGCAATAGAGGTATCCTATGCTTACATGTTAGGTGAGAAGCTCTATGACTTTTTGAAAGAAGAAGAGAGGATTAACTACCATCAAAGTGTTGTGAGGTTCATAATCAAAAGAGCAGATAGACTTAAAACAAAGGTGCGACTTCTGTATACCAGTGATGGCAAAGGCAATTAGGGTCAAAAGTCTCACCAATCGATTGGAGGTTGACAAGTCTTTGCTCAACTCCAATGAGGTCTCAGCTTTGTACGGCGGCGCTTTCGCACCACTAGTATTCAAAGATGAAGTCAAAATGGTGATTCCTGGCAATCTATTAGGTGGGCCAATTCGTTTGCAAGCAAATATACTCACCAAATCGAGACTTGAGAAAATTCGCAGTCAGAAGTTCAAAGGGAATTCCTGTGCCTACCTGCATCTTGGGGTGGTTACTATTGTCATACAATCACTATTGGTGTCCGGAAATGAAAATGTCAAAGGCAGATGCTCACTGGTTGACCTCTCAAGAGGCTCCGAGATAACTGGGCTTATTGACAAATTCAAGTTTAGTTTTACCAAGAGTGAACCATTCGCAGCAAAGATGTTAACAATAAATGCAGCAATTGATATTGATTGCGAGGTATCTGCTGGGAGTATTCAAGCCCTTCTTGAGGTCGAGGGCATTGATGTAAGATCTGAAAGAAGTGTCTTAGCCATCACCACCGGCATAACCTGTATTCCAACCAACTCCATGGTGATGCTACCAGGCTTAAAGAGGGAAACCCCAAAATTTGCAATCGCAAATGTTTACAATGTTCCTGATGAAGACCCGATTGAATGCGAGGCATTCAATAGGCTGTTCGGAGCTGCCAATCCAAAATTGATCGACCTAGGTAGTGAAACTGTATTGGAAGAAGGGAAAAGGTTTGGTCTATGGGGCCCTGTTGTGAAACCAGTGCACAGGAGGAAGCTTGTAACAAAAGGCATCATTAAGGATCATATGAGCCAGATTATGTCAGGCCCTTCCAAAGTTTTGAAAATAGAAGAAGGCTTGAAGAGATCAAACTCATTACGTGTTGAAGATGTCTGCAAAACTAGCGAAGAAGAGGCTGATACACGACGAAGTTTCGGAATGGATTTTCAGGAGCTTCGTGGATCCGGAGAATTCAATGGGGGTTTGGTTGGTGAATGCTGGGAACCAAAGAGTTCAGCTGAATTTAAACCAACAGGAGCAAAAATCAAGAGTTCAAAACAGTCGACTCCGGACGATTTTTGGCAACATAGCAGATCACTCAGCAGGGCCAGCAACAGTGTACCCGTCAATCAGTGTAAGTTATCAAGTGATGAACATTCAGGGAATCGAGGGTGTTGCACAGATGGATGGAAATTTCAATCTGAGAACATTGGTGGAAAATCTGAAGACCTTCCTTCTGACCAGCCAGGATCCTCAGCTCAACACTGCAACATTAAGGGAGGTTTGCCGGAGCTTTGCAAACTACGCCCTTGAGTACTACATGGAAGACCCCGATAGAATGTCGAATCTAGCTGACAAAATGCCACAACTAGCTCTGCAGGCGAGGGAGGTTATGTTTGACTTTTCTGATGGAATAAGTCAGCAATATTTGAGGGGTTTTCCAATGAGGGCTAAGGTGATACAGGAATTGAATAGCAGGCTTCTGCAGTCCACTGGCACCAAGGCTGTGTTTGAAGCAAAGGGGACTATTGAGTCCTCAGTTAATTTGATAGTTTAGAAACTATCTAGGCTTTGTATGTTGAGTGCTAAAAGTTCAACATATACCTCATAAGTCAGATTTATCTGCTCAGGTAAGTTTCAACCTCTTTGTATTTAAAGAGTGGCCGAATGAGTGCATGCTCATGTTCGGAGACCAGCTTCCCAGCTTTATCAAATATTATGACTTAAGTATTAATAGGGATGTCTTTTATGAATATTTATG"
}
],
"source_name": "16SP042_A",
"source_type": "internal"
}
],
"issues": null,
"last_indexed_version": 0,
"lower_name": "betaflexivirus from camelia #1",
"name": "Betaflexivirus from Camelia #1",
"reference": {
"id": "pat6xdn3"
},
"remote": {
"id": "5ce8b98a"
},
"schema": [],
"user": {
"id": "igboyes"
},
"verified": true,
"version": 0
},
"id": "1wfc5x6e.removed",
"index": {
"id": "s7frhn8n",
"version": 1
},
"method_name": "remove",
"otu": {
"id": "1wfc5x6e",
"name": "Betaflexivirus from Camelia #1",
"version": "removed"
},
"reference": {
"id": "pat6xdn3"
},
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
},
"status": "200"
}
}
]
},
{
"title": "hmms",
"endpoints": [
{
"description": "Lists profile hidden Markov model (HMM) annotations that are used in Virtool for\nnovel virus prediction.\n\nProviding a search term will return HMMs with full or partial matches in the\n`names` attribute.\n\nEach HMM annotation is generated from numerous public viral protein sequences.\nThe top three most common names in the protein records are combined into the\n`names` attribute.",
"method": "get",
"parameters": [],
"path": "/hmms",
"title": "Find HMMs",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Lists the installation status of the HMM data. Contains the following\nfields:\n\n| Field | Type | Description |\n| :--------- | :------------ | :-------------------------------------------------------- |\n| `errors` | array[string] | An array of any errors in the HMM data |\n| `installed`| object | A description of the currently installed HMM release |\n| `task.id` | integer | The `id` the task responsible for installing the HMM data |\n| `release` | object | A description of the latest available release |\n\n**Installed HMM data cannot currently be updated**.",
"method": "get",
"parameters": [],
"path": "/hmms/status",
"title": "Get HMM status",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Fetches the latest release for the HMM data.",
"method": "get",
"parameters": [],
"path": "/hmms/status/release",
"title": "Get the latest HMM release",
"errors": [
{
"status": "502",
"description": "Cannot reach GitHub"
}
],
"response": {
"status": "200"
}
},
{
"description": "Lists all updates applied to the HMM collection.",
"method": "get",
"parameters": [],
"path": "/hmms/status/updates",
"title": "List updates",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Installs the latest official HMM database from GitHub.",
"method": "post",
"parameters": [],
"path": "/hmms/status/updates",
"title": "Install HMMs",
"errors": [
{
"status": "400",
"description": "Target release does not exist"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"status": "201"
}
},
{
"description": "Fetches the details for an HMM annotation.",
"method": "get",
"parameters": [],
"path": "/hmms/{hmm_id}",
"title": "Get an HMM",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "indexes",
"endpoints": [
{
"description": "Lists all existing indexes.",
"method": "get",
"parameters": [],
"path": "/indexes",
"title": "Find indexes",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Fetches the details for an index.",
"method": "get",
"parameters": [],
"path": "/indexes/{index_id}",
"title": "Get an index",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"change_count": 2,
"contributors": [
{
"count": 1,
"id": "fred"
},
{
"count": 3,
"id": "igboyes"
}
],
"created_at": "2015-10-06T20:00:00Z",
"files": [],
"has_files": true,
"id": "foo",
"job": {
"id": "foo"
},
"manifest": [],
"modified_otu_count": 2,
"otus": [
{
"change_count": 1,
"id": "kjs8sa99",
"name": "Foo"
},
{
"change_count": 3,
"id": "zxbbvngc",
"name": "Test"
}
],
"ready": false,
"reference": {
"id": "foo"
},
"user": {
"administrator": false,
"handle": "leeashley",
"id": "bf1b993c"
},
"version": 0
},
"status": "200"
}
},
{
"description": "Downloads files relating to a given index.",
"method": "get",
"parameters": [],
"path": "/indexes/{index_id}/files/{filename}",
"title": "Download index files",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
},
{
"description": "Lists history changes for a specific index.",
"method": "get",
"parameters": [],
"path": "/indexes/{index_id}/history",
"title": "List history",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": [
{
"created_at": "2022-01-28T23:28:53.881000Z",
"description": "Removed Betaflexivirus from Camelia #1 (BFV_CAM1)",
"id": "1wfc5x6e.removed",
"index": {
"id": "s7frhn8n",
"version": 1
},
"method_name": "remove",
"otu": {
"id": "1wfc5x6e",
"name": "Betaflexivirus from Camelia #1",
"version": 4
},
"reference": {
"id": "pat6xdn3"
},
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
}
],
"status": "200"
}
}
]
},
{
"title": "instance_message",
"endpoints": [
{
"description": "Fetches the active administrative instance message.",
"method": "get",
"parameters": [],
"path": "/instance_message",
"title": "Get the administrative instance message",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Updates the existing active administrative instance message.",
"method": "patch",
"parameters": [
{
"title": "Active",
"type": "boolean",
"name": "active",
"required": false
},
{
"$ref": "#/components/schemas/MessageColor",
"name": "color",
"required": false
},
{
"title": "Message",
"type": "string",
"name": "message",
"required": false
}
],
"path": "/instance_message",
"title": "Update the administrative instance message",
"errors": [
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "No active message set"
}
],
"response": {
"example": {
"active": true,
"color": "red",
"created_at": "2022-11-24T19:40:03.320000Z",
"id": 3,
"message": "Changed the third instance message",
"updated_at": "2022-11-24T19:40:03.320000Z",
"user": {
"administrator": true,
"handle": "ianboyes",
"id": "ian"
}
},
"status": "200"
}
},
{
"description": "Creates a new administrative instance message.",
"method": "put",
"parameters": [
{
"$ref": "#/components/schemas/MessageColor",
"name": "color",
"required": true
},
{
"title": "Message",
"type": "string",
"name": "message",
"required": true
}
],
"path": "/instance_message",
"title": "Create an administrative instance message",
"errors": [],
"response": {
"example": {
"active": true,
"color": "yellow",
"created_at": "2022-11-24T19:40:03.320000Z",
"id": 3,
"message": "Third instance message",
"updated_at": "2022-11-24T19:40:03.320000Z",
"user": {
"administrator": true,
"handle": "ianboyes",
"id": "ian"
}
},
"status": "200"
}
}
]
},
{
"title": "jobs",
"endpoints": [
{
"description": "Lists jobs on the instance.\n\nJobs can be filtered by their current ``state`` by providing desired states as\nquery parameters.\n\n**Archived jobs are not currently returned from the API**.",
"method": "get",
"parameters": [],
"path": "/jobs",
"title": "Find jobs",
"errors": [
{
"status": "400",
"description": "Invalid query"
}
],
"response": {
"status": "200"
}
},
{
"description": "Sets the archived field on job documents.",
"method": "patch",
"parameters": [
{
"$ref": "#/components/schemas/ArchiveJobSchema",
"name": "update",
"required": true
}
],
"path": "/jobs",
"title": "Update archived field",
"errors": [
{
"status": "400",
"description": "Invalid archived field"
}
],
"response": {
"status": "200"
}
},
{
"description": "Fetches the details for a job.",
"method": "get",
"parameters": [],
"path": "/jobs/{job_id}",
"title": "Get a job",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"acquired": true,
"archived": false,
"args": {
"analysis_id": "rr8iryfy",
"index_id": "u3lm1rk8",
"ref_id": "d19exr83",
"sample_id": "4eynwmic",
"sample_name": "21BP088",
"subtractions": [
"0nhpi36p"
]
},
"created_at": "2022-07-08T18:37:44.936000Z",
"id": "splu0pq3",
"progress": 100,
"rights": {
"analyses": {
"modify": [
"rr8iryfy"
],
"read": [
"rr8iryfy"
],
"remove": [
"rr8iryfy"
]
},
"indexes": {
"read": [
"u3lm1rk8"
]
},
"references": {
"read": [
"d19exr83"
]
},
"samples": {
"read": [
"4eynwmic"
]
},
"subtractions": {
"read": [
"0nhpi36p"
]
}
},
"stage": "",
"state": "complete",
"status": [
{
"error": null,
"progress": 0,
"stage": null,
"state": "waiting",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:37:44.936000Z"
},
{
"error": null,
"progress": 3,
"stage": null,
"state": "preparing",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:41:20.647000Z"
},
{
"error": null,
"progress": 16,
"stage": "eliminate_otus",
"state": "running",
"step_description": "Map sample reads to reference OTUs and discard.",
"step_name": "Eliminate Otus",
"timestamp": "2022-07-08T18:48:11.287000Z"
},
{
"error": null,
"progress": 33,
"stage": "eliminate_subtraction",
"state": "running",
"step_description": "Map remaining reads to the subtraction and discard.",
"step_name": "Eliminate Subtraction",
"timestamp": "2022-07-08T19:00:24.291000Z"
},
{
"error": null,
"progress": 50,
"stage": "reunite_pairs",
"state": "running",
"step_description": "Reunite paired reads after elimination.",
"step_name": "Reunite Pairs",
"timestamp": "2022-07-08T19:02:53.618000Z"
},
{
"error": null,
"progress": 66,
"stage": "assemble",
"state": "running",
"step_description": "Assemble reads using SPAdes.",
"step_name": "Assemble",
"timestamp": "2022-07-08T19:02:53.644000Z"
},
{
"error": null,
"progress": 83,
"stage": "process_fasta",
"state": "running",
"step_description": "Find ORFs in the assembled contigs.",
"step_name": "Process Fasta",
"timestamp": "2022-07-08T19:07:22.352000Z"
},
{
"error": null,
"progress": 100,
"stage": "vfam",
"state": "running",
"step_description": "Search for viral motifs in ORF translations.",
"step_name": "Vfam",
"timestamp": "2022-07-08T19:07:44.531000Z"
},
{
"error": null,
"progress": 100,
"stage": "",
"state": "complete",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T19:13:04.293000Z"
}
],
"user": {
"administrator": false,
"handle": "jonathan",
"id": "88yksx67"
},
"workflow": "nuvs"
},
"status": "200"
}
},
{
"description": "Cancels a job using its 'job id'.",
"method": "put",
"parameters": [],
"path": "/jobs/{job_id}/cancel",
"title": "Cancel a job",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "Not cancellable"
}
],
"response": {
"example": {
"acquired": true,
"archived": false,
"args": {
"analysis_id": "rr8iryfy",
"index_id": "u3lm1rk8",
"ref_id": "d19exr83",
"sample_id": "4eynwmic",
"sample_name": "21BP088",
"subtractions": [
"0nhpi36p"
]
},
"created_at": "2022-07-08T18:37:44.936000Z",
"id": "splu0pq3",
"progress": 100,
"rights": {
"analyses": {
"modify": [
"rr8iryfy"
],
"read": [
"rr8iryfy"
],
"remove": [
"rr8iryfy"
]
},
"indexes": {
"read": [
"u3lm1rk8"
]
},
"references": {
"read": [
"d19exr83"
]
},
"samples": {
"read": [
"4eynwmic"
]
},
"subtractions": {
"read": [
"0nhpi36p"
]
}
},
"stage": "",
"state": "complete",
"status": [
{
"error": null,
"progress": 0,
"stage": null,
"state": "waiting",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:37:44.936000Z"
},
{
"error": null,
"progress": 3,
"stage": null,
"state": "preparing",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:41:20.647000Z"
},
{
"error": null,
"progress": 16,
"stage": "eliminate_otus",
"state": "running",
"step_description": "Map sample reads to reference OTUs and discard.",
"step_name": "Eliminate Otus",
"timestamp": "2022-07-08T18:48:11.287000Z"
},
{
"error": null,
"progress": 33,
"stage": "eliminate_subtraction",
"state": "running",
"step_description": "Map remaining reads to the subtraction and discard.",
"step_name": "Eliminate Subtraction",
"timestamp": "2022-07-08T19:00:24.291000Z"
},
{
"error": null,
"progress": 50,
"stage": "reunite_pairs",
"state": "running",
"step_description": "Reunite paired reads after elimination.",
"step_name": "Reunite Pairs",
"timestamp": "2022-07-08T19:02:53.618000Z"
},
{
"error": null,
"progress": 66,
"stage": "assemble",
"state": "running",
"step_description": "Assemble reads using SPAdes.",
"step_name": "Assemble",
"timestamp": "2022-07-08T19:02:53.644000Z"
},
{
"error": null,
"progress": 83,
"stage": "process_fasta",
"state": "running",
"step_description": "Find ORFs in the assembled contigs.",
"step_name": "Process Fasta",
"timestamp": "2022-07-08T19:07:22.352000Z"
},
{
"error": null,
"progress": 100,
"stage": "vfam",
"state": "running",
"step_description": "Search for viral motifs in ORF translations.",
"step_name": "Vfam",
"timestamp": "2022-07-08T19:07:44.531000Z"
},
{
"error": null,
"progress": 100,
"stage": "",
"state": "complete",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T19:13:04.293000Z"
}
],
"user": {
"administrator": false,
"handle": "jonathan",
"id": "88yksx67"
},
"workflow": "nuvs"
},
"status": "200"
}
}
]
},
{
"title": "labels",
"endpoints": [
{
"description": "Lists all sample labels on the instance. Pagination is not supported; all labels\nare included in the response.",
"method": "get",
"parameters": [],
"path": "/labels",
"title": "List labels",
"errors": [
{
"status": "400",
"description": "Invalid query"
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new sample label.\n\nThe color must be a valid hexadecimal code.",
"example": {
"color": "#374151",
"description": "dsRNA/binding protein",
"name": "Binding protein"
},
"method": "post",
"parameters": [
{
"default": "#A0AEC0",
"description": "color of the label",
"title": "Color",
"type": "string",
"name": "color",
"required": false
},
{
"default": "",
"description": "description of the document",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "unique name for the label document",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
}
],
"path": "/labels",
"title": "Create a label",
"errors": [
{
"status": "400",
"description": "Invalid Input"
}
],
"response": {
"example": {
"color": "#374151",
"count": 0,
"description": "dsRNA/binding protein",
"id": 23,
"name": "Binding protein"
},
"status": "201"
}
},
{
"description": "Deletes an existing sample label.",
"method": "delete",
"parameters": [],
"path": "/labels/{label_id}",
"title": "Delete a label",
"errors": []
},
{
"description": "Fetches the details for a sample label.",
"method": "get",
"parameters": [],
"path": "/labels/{label_id}",
"title": "Get a label",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"color": "#6B7280",
"count": 0,
"description": "dsRNA/Ab",
"id": 22,
"name": "Ab"
},
"status": "200"
}
},
{
"description": "Updates an existing sample label.",
"example": {
"color": "#93C5FD",
"description": "Field samples from 2022 harvest",
"name": "Blueberry 2022"
},
"method": "patch",
"parameters": [
{
"description": "A hexadecimal color for the label",
"title": "Color",
"type": "string",
"name": "color",
"required": false
},
{
"description": "A longer description for the label",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "A short display name",
"title": "Name",
"type": "string",
"name": "name",
"required": false
}
],
"path": "/labels/{label_id}",
"title": "Update a label",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"color": "#93C5FD",
"count": 0,
"description": "Field samples from 2022 harvest",
"id": 22,
"name": "Blueberry 2022"
},
"status": "200"
}
}
]
},
{
"title": "ml",
"endpoints": [
{
"description": "Lists all available machine learning models.\n\nThe `last_checked_at` field is the time at which the list of models was last\nrefreshed from www.virtool.ca.",
"method": "get",
"parameters": [],
"path": "/ml",
"title": "List models",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Fetches the details of a machine learning model, including all of its releases.\n\nThe `releases` field comprises a list of all releases of the model that can be\ndownloaded.",
"method": "get",
"parameters": [],
"path": "/ml/{model_id}",
"title": "Get a model",
"errors": [
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Fetches the details of a machine learning model release.",
"method": "get",
"parameters": [],
"path": "/ml/{model_id}/releases/{release_id}",
"title": "Get a model release",
"errors": [
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Downloads the archived model release.",
"method": "get",
"parameters": [],
"path": "/ml/{model_id}/releases/{release_id}/model.tar.gz",
"title": "Download a model release",
"errors": [
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "otus",
"endpoints": [
{
"description": "Deletes and OTU and its associated isolates and sequences.",
"method": "delete",
"parameters": [],
"path": "/otus/{otu_id}",
"title": "Delete an OTU",
"errors": [
{
"status": "401",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "204"
}
},
{
"description": "Fetches the details of an OTU.\n\nA FASTA file containing all sequences in the OTU can be downloaded by appending\n`.fa` to the path.",
"method": "get",
"parameters": [],
"path": "/otus/{otu_id}",
"title": "Get an OTU",
"errors": [
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Checks to make sure the supplied OTU name and abbreviation don't already exist\nin the parent reference.",
"method": "patch",
"parameters": [
{
"title": "Abbreviation",
"type": "string",
"name": "abbreviation",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"items": {
"$ref": "#/components/schemas/OTUSegment"
},
"title": "Schema",
"type": "array",
"name": "schema",
"required": false
}
],
"path": "/otus/{otu_id}",
"title": "Update an OTU",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Lists all the isolates and sequences for an OTU.",
"method": "get",
"parameters": [],
"path": "/otus/{otu_id}/isolates",
"title": "List isolates",
"errors": []
},
{
"description": "Creates an isolate on the OTU specified by `otu_id`.",
"method": "post",
"parameters": [
{
"default": false,
"title": "Default",
"type": "boolean",
"name": "default",
"required": false
},
{
"default": "",
"title": "Source Name",
"type": "string",
"name": "source_name",
"required": false
},
{
"default": "",
"title": "Source Type",
"type": "string",
"name": "source_type",
"required": false
}
],
"path": "/otus/{otu_id}/isolates",
"title": "Create an isolate",
"errors": [
{
"status": "401",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "201"
}
},
{
"description": "Deletes an isolate using its 'otu id' and 'isolate id'.",
"method": "delete",
"parameters": [],
"path": "/otus/{otu_id}/isolates/{isolate_id}",
"title": "Delete an isolate",
"errors": []
},
{
"description": "Fetches the details of an isolate.\n\nA FASTA file containing all sequences in the isolate can be downloaded by\nappending `.fa` to the path.",
"method": "get",
"parameters": [],
"path": "/otus/{otu_id}/isolates/{isolate_id}",
"title": "Get an isolate",
"errors": [
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Updates an isolate using 'otu_id' and 'isolate_id'.",
"method": "patch",
"parameters": [
{
"title": "Source Name",
"type": "string",
"name": "source_name",
"required": false
},
{
"title": "Source Type",
"type": "string",
"name": "source_type",
"required": false
}
],
"path": "/otus/{otu_id}/isolates/{isolate_id}",
"title": "Update an isolate",
"errors": [
{
"status": "401",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Lists the sequences for an isolate.",
"method": "get",
"parameters": [],
"path": "/otus/{otu_id}/isolates/{isolate_id}/sequences",
"title": "List sequences",
"errors": [
{
"status": "401",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new sequence for an isolate identified by `otu_id` and `isolate_id`.",
"method": "post",
"parameters": [
{
"minLength": 1,
"title": "Accession",
"type": "string",
"name": "accession",
"required": true
},
{
"minLength": 1,
"title": "Definition",
"type": "string",
"name": "definition",
"required": true
},
{
"default": "",
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"title": "Segment",
"type": "string",
"name": "segment",
"required": false
},
{
"minLength": 1,
"pattern": "^[ATCGNRYKM]+$",
"title": "Sequence",
"type": "string",
"name": "sequence",
"required": true
},
{
"title": "Target",
"type": "string",
"name": "target",
"required": false
}
],
"path": "/otus/{otu_id}/isolates/{isolate_id}/sequences",
"title": "Create a sequence",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "201"
}
},
{
"description": "Deletes the specified sequence.",
"method": "delete",
"parameters": [],
"path": "/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}",
"title": "Delete a sequence",
"errors": []
},
{
"description": "Fetches the details for a sequence.\n\nA FASTA file containing the nucelotide sequence can be downloaded by appending\n`.fa` to the path.",
"method": "get",
"parameters": [],
"path": "/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}",
"title": "Get a sequence",
"errors": []
},
{
"description": "Updates a sequence using its 'otu id', 'isolate id' and 'sequence id'.",
"method": "patch",
"parameters": [
{
"minLength": 1,
"title": "Accession",
"type": "string",
"name": "accession",
"required": false
},
{
"minLength": 1,
"title": "Definition",
"type": "string",
"name": "definition",
"required": false
},
{
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"title": "Segment",
"type": "string",
"name": "segment",
"required": false
},
{
"minLength": 1,
"pattern": "^[ATCGNRYKM]+$",
"title": "Sequence",
"type": "string",
"name": "sequence",
"required": false
},
{
"title": "Target",
"type": "string",
"name": "target",
"required": false
}
],
"path": "/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}",
"title": "Update a sequence",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "401",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "refs",
"endpoints": [
{
"description": "Lists references that match the find term.",
"method": "get",
"parameters": [],
"path": "/refs",
"title": "Find references",
"errors": [],
"response": {
"example": {
"documents": [
{
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "New Plant Viruses",
"organism": "virus",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
}
],
"found_count": 2,
"official_installed": true,
"page": 1,
"page_count": 1,
"per_page": 25,
"total_count": 2
},
"status": "200"
}
},
{
"description": "Creates an empty reference.",
"example": {
"data_type": "genome",
"name": "Plant Viruses",
"organism": "viruses"
},
"method": "post",
"parameters": [
{
"description": "a valid ref_id that the new reference should be cloned from",
"title": "Clone From",
"type": "string",
"name": "clone_from",
"required": false
},
{
"default": "genome",
"description": "the sequence data type",
"title": "Data Type",
"type": "string",
"name": "data_type",
"required": false
},
{
"default": "",
"description": "a longer description for the reference",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "a valid file_id that the new reference should be imported from",
"title": "Import From",
"type": "string",
"name": "import_from",
"required": false
},
{
"default": "",
"description": "the virus name",
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"default": "",
"description": "the organism",
"title": "Organism",
"type": "string",
"name": "organism",
"required": false
},
{
"default": 11447367,
"description": "the id of the GitHub release to install",
"title": "Release Id",
"type": "string",
"name": "release_id",
"required": false
},
{
"description": "a valid GitHub slug to download and update the new reference from",
"title": "Remote From",
"type": "string",
"name": "remote_from",
"required": false
}
],
"path": "/refs",
"title": "Create a reference",
"errors": [
{
"status": "400",
"description": "Source reference does not exist"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "502",
"description": "Could not reach GitHub"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"contributors": [
{
"administrator": true,
"count": 6,
"handle": "reece",
"id": "hjol9wdt"
},
{
"administrator": true,
"count": 7906,
"handle": "mrott",
"id": "ihvze2u9"
},
{
"administrator": true,
"count": 1563,
"handle": "igboyes",
"id": "igboyes"
},
{
"administrator": true,
"count": 2483,
"handle": "jasper",
"id": "1kg24j7t"
}
],
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"description": "",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "Plant Viruses",
"organism": "viruses",
"otu_count": 2102,
"restrict_source_types": false,
"source_types": [
"isolate",
"strain"
],
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
},
"users": [
{
"administrator": true,
"build": true,
"handle": "igboyes",
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Deletes a reference and its associated OTUs, history, and indexes. Deleting a\nreference does not break dependent analyses and other resources.",
"method": "delete",
"parameters": [],
"path": "/refs/{ref_id}",
"title": "Delete a reference",
"errors": []
},
{
"description": "Fetches the details of a reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}",
"title": "Get a reference",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "New Plant Viruses",
"organism": "virus",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Updates an existing reference.",
"example": {
"internal_control": "ah4m5jqz",
"name": "Regulated Pests",
"organism": "phytoplasma"
},
"method": "patch",
"parameters": [
{
"description": "a longer description for the reference",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "set the OTU identified by the passed id as the internal control for the reference",
"title": "Internal Control",
"type": "string",
"name": "internal_control",
"required": false
},
{
"description": "the virus name",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"description": "the organism",
"title": "Organism",
"type": "string",
"name": "organism",
"required": false
},
{
"description": "option to restrict source types",
"title": "Restrict Source Types",
"type": "boolean",
"name": "restrict_source_types",
"required": false
},
{
"description": "source types",
"items": {
"minLength": 1,
"type": "string"
},
"title": "Source Types",
"type": "array",
"name": "source_types",
"required": false
},
{
"description": "list of target sequences",
"items": {
"$ref": "#/components/schemas/ReferenceTargetRequest"
},
"title": "Targets",
"type": "array",
"name": "targets",
"required": false
}
],
"path": "/refs/{ref_id}",
"title": "Update a reference",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": "ah4m5jqz",
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "Regulated Pests",
"organism": "phytoplasma",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Lists all groups that have access to the reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/groups",
"title": "List groups",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 5,
"modify": false,
"modify_otu": false,
"remove": false
}
],
"status": "200"
}
},
{
"description": "Adds a group to the reference. Groups can view, use, and modify the reference.",
"example": {
"group_id": 2,
"modify_otu": true
},
"method": "post",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "the id of the group to add",
"title": "Group Id",
"type": "integer",
"name": "group_id",
"required": true
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
}
],
"path": "/refs/{ref_id}/groups",
"title": "Add a group",
"errors": [
{
"status": "400",
"description": "Bad request"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 5,
"modify": false,
"modify_otu": true,
"remove": false
}
],
"status": "201"
}
},
{
"description": "Deletes a group from the reference.",
"method": "delete",
"parameters": [],
"path": "/refs/{ref_id}/groups/{group_id}",
"title": "Delete a group",
"errors": []
},
{
"description": "Fetches the details of a group that has access to the reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/groups/{group_id}",
"title": "Get a group",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 4,
"modify": false,
"modify_otu": false,
"remove": false
},
"status": "200"
}
},
{
"description": "Updates the access rights a group has on the reference.",
"example": {
"build": true,
"modify": true
},
"method": "patch",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
}
],
"path": "/refs/{ref_id}/groups/{group_id}",
"title": "Update a group",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"build": true,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 4,
"modify": true,
"modify_otu": false,
"remove": false
},
"status": "200"
}
},
{
"description": "Lists changes made to OTUs in the reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/history",
"title": "List history",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"documents": [
{
"created_at": "2022-01-28T23:28:53.881000Z",
"description": "Removed Betaflexivirus from Camelia #1 (BFV_CAM1)",
"id": "1wfc5x6e.removed",
"index": {
"id": "s7frhn8n",
"version": 1
},
"method_name": "remove",
"otu": {
"id": "1wfc5x6e",
"name": "Betaflexivirus from Camelia #1",
"version": "removed"
},
"reference": {
"id": "pat6xdn3"
},
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
}
],
"found_count": 1419,
"page": 1,
"page_count": 710,
"per_page": 1,
"total_count": 1419
},
"status": "200"
}
},
{
"description": "Lists indexes that have been created for the reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/indexes",
"title": "List indexes",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"change_count": 12,
"documents": [
{
"change_count": 4,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "bar",
"job": {
"id": "bar"
},
"modified_otu_count": 3,
"ready": false,
"reference": {
"id": "bar"
},
"user": {
"administrator": false,
"handle": "leeashley",
"id": "bf1b993c"
},
"version": 1
},
{
"change_count": 2,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "foo",
"job": {
"id": "foo"
},
"modified_otu_count": 2,
"ready": false,
"reference": {
"id": "foo"
},
"user": {
"administrator": false,
"handle": "leeashley",
"id": "bf1b993c"
},
"version": 0
}
],
"found_count": 2,
"modified_otu_count": 3,
"page": 1,
"page_count": 1,
"per_page": 25,
"total_count": 2,
"total_otu_count": 123
},
"status": "200"
}
},
{
"description": "Starts a job to rebuild the otus Bowtie2 index on disk.\n\nDoes a check to make sure there are no unverified OTUs in the collection\nand updates otu history to show the version and id of the new index.",
"method": "post",
"parameters": [],
"path": "/refs/{ref_id}/indexes",
"title": "Create an index",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"change_count": 0,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "fb085f7f",
"job": {
"id": "bf1b993c"
},
"modified_otu_count": 0,
"ready": false,
"reference": {
"id": "foo"
},
"user": {
"administrator": false,
"handle": "bob",
"id": "test"
},
"version": 9
},
"status": "201"
}
},
{
"description": "Lists OTUs by name or abbreviation. Results are paginated.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/otus",
"title": "Find OTUs",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"documents": [
{
"abbreviation": "ABTV",
"id": "k77wgf8x",
"name": "Abaca bunchy top virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 18
},
{
"abbreviation": "AbBV",
"id": "7hpwj4yh",
"name": "Abutilon Brazil virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 4
},
{
"abbreviation": "",
"id": "p9ohme8k",
"name": "Abutilon golden mosaic Yucatan virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AbMBoV",
"id": "qrspg5w3",
"name": "Abutilon mosaic Bolivia virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 6
},
{
"abbreviation": "AbMoBrV",
"id": "yb7kpm43",
"name": "Abutilon mosaic Brazil virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 4
},
{
"abbreviation": "AbMV",
"id": "8540rw7b",
"name": "Abutilon mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 9
},
{
"abbreviation": "",
"id": "3zwrpu3y",
"name": "Abutilon yellow mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AcLV",
"id": "30n6qo2x",
"name": "Aconitum latent virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "",
"id": "x5qw901r",
"name": "Actinidia chlorotic ringspot associated virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 5
},
{
"abbreviation": "",
"id": "ss6bios9",
"name": "Actinidia emaravirus 2",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 13
},
{
"abbreviation": "",
"id": "nn5gt7db",
"name": "Actinidia seed borne latent virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "xo3khtnd",
"name": "Actinidia virus 1",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
},
{
"abbreviation": "AVA",
"id": "qg8optks",
"name": "Actinidia virus A",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AVB",
"id": "fnhtwiux",
"name": "Actinidia virus B",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AVX",
"id": "5uh1jzzk",
"name": "Actinidia virus X",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AYV1",
"id": "7ag9wwrr",
"name": "Actinidia yellowing virus 1",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AYV2",
"id": "f87f3cs7",
"name": "Actinidia yellowing virus 2",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "e2xpkmgy",
"name": "Adonis mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "3ly2pqbk",
"name": "Aeonium ringspot virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 0
},
{
"abbreviation": "",
"id": "3xa1dbt0",
"name": "African cassava mosaic Burkina Faso virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 5
},
{
"abbreviation": "ACMV",
"id": "0ommwgyh",
"name": "African cassava mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 9
},
{
"abbreviation": "",
"id": "iyw0y3ta",
"name": "African eggplant mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "set9w2zc",
"name": "African eggplant yellowing virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AOPRV",
"id": "taecz4c9",
"name": "African oil palm ringspot virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
},
{
"abbreviation": "",
"id": "zgsytbul",
"name": "Agave tequilana leaf virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
}
],
"found_count": 2102,
"modified_count": 1,
"page": 1,
"page_count": 85,
"per_page": 25,
"total_count": 2102
},
"status": "200"
}
},
{
"description": "Creates an OTU.",
"method": "post",
"parameters": [
{
"default": "",
"title": "Abbreviation",
"type": "string",
"name": "abbreviation",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"items": {
"$ref": "#/components/schemas/OTUSegment"
},
"title": "Schema",
"type": "array",
"name": "schema",
"required": false
}
],
"path": "/refs/{ref_id}/otus",
"title": "Create OTU",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "201"
}
},
{
"description": "Fetches the latest remote reference update from GitHub.\n\nAlso updates the reference document. This is the only way of doing so without\nwaiting for an automatic refresh every 10 minutes.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/release",
"title": "Get latest update",
"errors": [],
"response": {
"example": {
"body": "#### Changed\r\n- add new isolates to Cucurbit chlorotic yellows virus",
"content_type": "application/gzip",
"download_url": "https://github.com/virtool/ref-plant-viruses/releases/download/v0.1.2/reference.json.gz",
"etag": "W/\"b7e8a7fb0fbe0cade0d6a86c9e0d4549\"",
"filename": "reference.json.gz",
"html_url": "https://github.com/virtool/ref-plant-viruses/releases/tag/v0.1.2",
"id": 11449913,
"name": "v0.1.2",
"newer": true,
"published_at": "2018-06-12T21:52:33Z",
"retrieved_at": "2018-06-14T19:52:17.465000Z",
"size": 3699729
},
"status": "200"
}
},
{
"description": "Lists all updates made to the reference.",
"method": "get",
"parameters": [],
"path": "/refs/{ref_id}/updates",
"title": "List updates",
"errors": [],
"response": {
"example": [
{
"body": "#### Fixed\r\n- fixed uploading to GitHub releases in `.travis.yml`",
"created_at": "2018-06-14T18:37:54.242000Z",
"filename": "reference.json.gz",
"html_url": "https://github.com/virtool/ref-plant-viruses/releases/tag/v0.1.1",
"id": 11447367,
"name": "v0.1.1",
"published_at": "2018-06-12T19:20:57Z",
"ready": true,
"size": 3695872,
"user": {
"id": "igboyes"
}
}
],
"status": "200"
}
},
{
"description": "Updates the reference to the last version of the linked remote reference.",
"method": "post",
"parameters": [],
"path": "/refs/{ref_id}/updates",
"title": "Update a reference",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"body": "The release consists of a gzipped JSON file containing:\r\n\r\n- a `data_type` field with value _genome_\r\n- an `organism` field with value _virus_\r\n- the `version` name (eg. *v0.2.0*)\r\n- a timestamp with the key `created_at`\r\n- virus data compatible for import into Virtool v2.0.0+\r\n\r\nScripts have been updated to follow upcoming convention changes in Virtool v3.0.0.",
"content_type": "application/gzip",
"download_url": "https://github.com/virtool/virtool-database/releases/download/v0.3.0/reference.json.gz",
"etag": "W/\"ef123d746a33f88ee44203d3ca6bc2f7\"",
"filename": "reference.json.gz",
"html_url": "https://api.github.com/repos/virtool/virtool-database/releases/10742520",
"id": 10742520,
"name": "v0.3.0",
"newer": true,
"published_at": "2018-04-26T19:35:33Z",
"retrieved_at": "2018-04-14T19:52:17.465000Z",
"size": 3709091
},
"status": "201"
}
},
{
"description": "Adds a user to the reference. Users can view, use, and modify the reference.",
"example": {
"modify_otu": true,
"user_id": "sidney"
},
"method": "post",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
},
{
"description": "the id of the user to add",
"title": "User Id",
"type": "string",
"name": "user_id",
"required": true
}
],
"path": "/refs/{ref_id}/users",
"title": "Add a user",
"errors": [
{
"status": "400",
"description": "Bad request"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "201"
}
},
{
"description": "Removes a user from the reference.",
"method": "delete",
"parameters": [],
"path": "/refs/{ref_id}/users/{user_id}",
"title": "Remove a user",
"errors": []
},
{
"description": "Updates the access rights a user has on the reference.",
"example": {
"build": true,
"modify": true
},
"method": "patch",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
}
],
"path": "/refs/{ref_id}/users/{user_id}",
"title": "Update a user",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"build": true,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 4,
"modify": true,
"modify_otu": false,
"remove": false
},
"status": "200"
}
}
]
},
{
"title": "samples",
"endpoints": [
{
"description": "Lists samples, filtering by data passed as URL parameters.",
"method": "get",
"parameters": [],
"path": "/samples",
"title": "Find samples",
"errors": [
{
"status": "400",
"description": "Invalid query"
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new sample with the given name, labels and subtractions.",
"method": "post",
"parameters": [
{
"items": {},
"maxItems": 2,
"minItems": 1,
"title": "Files",
"type": "array",
"name": "files",
"required": true
},
{
"title": "Group",
"type": "integer",
"name": "group",
"required": false
},
{
"default": "",
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"default": "",
"title": "Isolate",
"type": "string",
"name": "isolate",
"required": false
},
{
"items": {},
"title": "Labels",
"type": "array",
"name": "labels",
"required": false
},
{
"allOf": [
{
"$ref": "#/components/schemas/LibraryType"
}
],
"default": "normal",
"name": "library_type",
"required": false
},
{
"default": "",
"title": "Locale",
"type": "string",
"name": "locale",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"default": "",
"title": "Notes",
"type": "string",
"name": "notes",
"required": false
},
{
"items": {},
"title": "Subtractions",
"type": "array",
"name": "subtractions",
"required": false
}
],
"path": "/samples",
"title": "Create a sample",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Malus domestica",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [],
"library_type": "normal",
"locale": "",
"name": "HX8",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "201"
}
},
{
"description": "Removes a sample document and all associated analyses.",
"method": "delete",
"parameters": [],
"path": "/samples/{sample_id}",
"title": "Delete a sample",
"errors": []
},
{
"description": "Fetches the details for a sample.",
"method": "get",
"parameters": [],
"path": "/samples/{sample_id}",
"title": "Get a sample",
"errors": [
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Malus domestica",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [],
"library_type": "normal",
"locale": "",
"name": "HX8",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "200"
}
},
{
"description": "Updates a sample using its 'sample id'.",
"example": {
"host": "Tobacco",
"labels": [
1,
5,
6
],
"name": "Tobacco mosaic viru"
},
"method": "patch",
"parameters": [
{
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"title": "Isolate",
"type": "string",
"name": "isolate",
"required": false
},
{
"items": {},
"title": "Labels",
"type": "array",
"name": "labels",
"required": false
},
{
"title": "Locale",
"type": "string",
"name": "locale",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"title": "Notes",
"type": "string",
"name": "notes",
"required": false
},
{
"items": {},
"title": "Subtractions",
"type": "array",
"name": "subtractions",
"required": false
}
],
"path": "/samples/{sample_id}",
"title": "Update a sample",
"errors": [
{
"status": "400",
"description": "Sample name is already in use"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Tobacco",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [
1,
5,
6
],
"library_type": "normal",
"locale": "",
"name": "Tobacco mosaic viru",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "200"
}
},
{
"description": "Lists the analyses associated with the given `sample_id`.",
"method": "get",
"parameters": [],
"path": "/samples/{sample_id}/analyses",
"title": "Get analyses",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
},
{
"description": "Starts an analysis job for a given sample.",
"method": "post",
"parameters": [
{
"title": "Ml",
"type": "integer",
"name": "ml",
"required": false
},
{
"title": "Ref Id",
"type": "string",
"name": "ref_id",
"required": true
},
{
"items": {
"type": "string"
},
"title": "Subtractions",
"type": "array",
"name": "subtractions",
"required": false
},
{
"$ref": "#/components/schemas/AnalysisWorkflow",
"name": "workflow",
"required": true
}
],
"path": "/samples/{sample_id}/analyses",
"title": "Start analysis job",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2022-05-21T01:28:55.441000Z",
"id": "m9ktiz0i",
"index": {
"id": "9c5u6wsq",
"version": 13
},
"job": {
"id": "bt8nwg9z"
},
"ready": true,
"reference": {
"id": "d19exr83",
"name": "New Plant Viruses"
},
"sample": {
"id": "9zn468u9"
},
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"updated_at": "2022-05-21T01:28:55.441000Z",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflow": "pathoscope_bowtie"
},
"status": "201"
}
},
{
"description": "Updates the rights settings for the specified sample document.",
"example": {
"group": "administrator",
"group_read": true,
"group_write": true
},
"method": "patch",
"parameters": [
{
"title": "All Read",
"type": "boolean",
"name": "all_read",
"required": false
},
{
"title": "All Write",
"type": "boolean",
"name": "all_write",
"required": false
},
{
"anyOf": [
{
"type": "integer"
},
{
"type": "string"
}
],
"title": "Group",
"name": "group",
"required": false
},
{
"title": "Group Read",
"type": "boolean",
"name": "group_read",
"required": false
},
{
"title": "Group Write",
"type": "boolean",
"name": "group_write",
"required": false
}
],
"path": "/samples/{sample_id}/rights",
"title": "Update rights settings",
"errors": [
{
"status": "400",
"description": "Group does not exist"
},
{
"status": "403",
"description": "Must be administrator or sample owner"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": "administrator",
"group_read": true,
"group_write": true,
"hold": true,
"host": "virus",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [
1,
5,
6
],
"library_type": "normal",
"locale": "",
"name": "foo",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "200"
}
}
]
},
{
"title": "settings",
"endpoints": [
{
"description": "Fetches the complete application settings.",
"method": "get",
"parameters": [],
"path": "/settings",
"title": "Get settings",
"errors": [],
"response": {
"example": {
"default_source_types": [
"isolate",
"strain"
],
"enable_api": true,
"enable_sentry": true,
"hmm_slug": "virtool/virtool-hmm",
"minimum_passsword_length": 8,
"sample_all_read": false,
"sample_all_write": true,
"sample_group": "force_choice",
"sample_group_read": true,
"sample_group_write": true,
"sample_unique_names": true
},
"status": "200"
}
},
{
"description": "Updates the application settings.",
"method": "patch",
"parameters": [
{
"items": {},
"title": "Default Source Types",
"type": "array",
"name": "default_source_types",
"required": false
},
{
"default": false,
"title": "Enable Api",
"type": "boolean",
"name": "enable_api",
"required": false
},
{
"default": true,
"title": "Enable Sentry",
"type": "boolean",
"name": "enable_sentry",
"required": false
},
{
"default": "virtool/virtool-hmm",
"title": "Hmm Slug",
"type": "string",
"name": "hmm_slug",
"required": false
},
{
"default": 8,
"title": "Minimum Password Length",
"type": "integer",
"name": "minimum_password_length",
"required": false
},
{
"default": true,
"title": "Sample All Read",
"type": "boolean",
"name": "sample_all_read",
"required": false
},
{
"default": false,
"title": "Sample All Write",
"type": "boolean",
"name": "sample_all_write",
"required": false
},
{
"default": "none",
"title": "Sample Group",
"type": "string",
"name": "sample_group",
"required": false
},
{
"default": true,
"title": "Sample Group Read",
"type": "boolean",
"name": "sample_group_read",
"required": false
},
{
"default": false,
"title": "Sample Group Write",
"type": "boolean",
"name": "sample_group_write",
"required": false
}
],
"path": "/settings",
"title": "Update settings",
"errors": [
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"example": {
"default_source_types": [
"strain"
],
"enable_api": true,
"enable_sentry": true,
"hmm_slug": "virtool/virtool-hmm",
"minimum_passsword_length": 12,
"sample_all_read": false,
"sample_unique_names": true
},
"status": "200"
}
}
]
},
{
"title": "spaces",
"endpoints": [
{
"description": "Get a list of all spaces that the requesting user is a member or owner of.",
"method": "get",
"parameters": [],
"path": "/spaces",
"title": "List spaces",
"errors": [],
"response": {
"example": [
{
"description": "The default space.",
"id": 0,
"name": "Space 0"
}
],
"status": "200"
}
},
{
"description": "Fetches the complete representation of a space.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}",
"title": "Get a space",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"created_by": "test",
"description": "",
"id": 0,
"members": [
{
"administrator": true,
"handle": "bob",
"id": "test",
"label": null,
"project": null,
"reference": null,
"role": "owner",
"sample": null,
"subtraction": null,
"upload": null
}
],
"name": "Space 0",
"updated_at": "2015-10-06T20:00:00Z"
},
"status": "200"
}
},
{
"description": "Changes the name or description of a space.",
"example": {
"name": "My Space"
},
"method": "patch",
"parameters": [
{
"description": "the description for the space",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "the unique display name for the space",
"title": "Name",
"type": "string",
"name": "name",
"required": false
}
],
"path": "/spaces/{space_id}",
"title": "Update a space",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"created_by": "test",
"description": "",
"id": 0,
"members": [
{
"administrator": true,
"handle": "bob",
"id": "test",
"label": null,
"project": null,
"reference": null,
"role": "owner",
"sample": null,
"subtraction": null,
"upload": null
}
],
"name": "My Space",
"updated_at": "2015-10-06T20:00:00Z"
},
"status": "201"
}
},
{
"description": "Lists all sample labels on the instance. Pagination is not supported; all labels\nare included in the response.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/labels",
"title": "List labels",
"errors": [
{
"status": "400",
"description": "Invalid query"
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new sample label.\n\nThe color must be a valid hexadecimal code.",
"example": {
"color": "#374151",
"description": "dsRNA/binding protein",
"name": "Binding protein"
},
"method": "post",
"parameters": [
{
"default": "#A0AEC0",
"description": "color of the label",
"title": "Color",
"type": "string",
"name": "color",
"required": false
},
{
"default": "",
"description": "description of the document",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "unique name for the label document",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
}
],
"path": "/spaces/{space_id}/labels",
"title": "Create a label",
"errors": [
{
"status": "400",
"description": "Invalid Input"
}
],
"response": {
"example": {
"color": "#374151",
"count": 0,
"description": "dsRNA/binding protein",
"id": 23,
"name": "Binding protein"
},
"status": "201"
}
},
{
"description": "Deletes an existing sample label.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/labels/{label_id}",
"title": "Delete a label",
"errors": []
},
{
"description": "Fetches the details for a sample label.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/labels/{label_id}",
"title": "Get a label",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"color": "#6B7280",
"count": 0,
"description": "dsRNA/Ab",
"id": 22,
"name": "Ab"
},
"status": "200"
}
},
{
"description": "Updates an existing sample label.",
"example": {
"color": "#93C5FD",
"description": "Field samples from 2022 harvest",
"name": "Blueberry 2022"
},
"method": "patch",
"parameters": [
{
"description": "A hexadecimal color for the label",
"title": "Color",
"type": "string",
"name": "color",
"required": false
},
{
"description": "A longer description for the label",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "A short display name",
"title": "Name",
"type": "string",
"name": "name",
"required": false
}
],
"path": "/spaces/{space_id}/labels/{label_id}",
"title": "Update a label",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"color": "#93C5FD",
"count": 0,
"description": "Field samples from 2022 harvest",
"id": 22,
"name": "Blueberry 2022"
},
"status": "200"
}
},
{
"description": "Lists the members of a space and their roles.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/members",
"title": "List members",
"errors": [],
"response": {
"example": {
"available_roles": [
{
"description": "Full control over space a and all resources and members.\n- Remove or add members.\n- Cancel any job.",
"id": "owner",
"name": "Owner"
},
{
"description": "Access a space.",
"id": "member",
"name": "Member"
},
{
"description": "Create, edit, or delete labels.",
"id": "label_manager",
"name": "Label_manager"
},
{
"description": "Create, edit, or delete projects.",
"id": "project_manager",
"name": "Project_manager"
},
{
"description": "Create or edit projects.",
"id": "project_editor",
"name": "Project_editor"
},
{
"description": "View projects.",
"id": "project_viewer",
"name": "Project_viewer"
},
{
"description": "Edit, build, contribute to (modify otus), or delete any reference. Modify access\ncontrol and settings for any reference.",
"id": "reference_manager",
"name": "Reference_manager"
},
{
"description": "Edit, build, and contribute to any reference.",
"id": "reference_builder",
"name": "Reference_builder"
},
{
"description": "Edit or contribute to any reference.",
"id": "reference_editor",
"name": "Reference_editor"
},
{
"description": "Create, edit, or delete (modify) OTUs in any reference.",
"id": "reference_contributor",
"name": "Reference_contributor"
},
{
"description": "View any and use any reference.",
"id": "reference_viewer",
"name": "Reference_viewer"
},
{
"description": "Create, edit, or delete samples.",
"id": "sample_manager",
"name": "Sample_manager"
},
{
"description": "Create or edit samples.",
"id": "sample_editor",
"name": "Sample_editor"
},
{
"description": "Analyze samples.",
"id": "sample_analyzer",
"name": "Sample_analyzer"
},
{
"description": "View samples.",
"id": "sample_viewer",
"name": "Sample_viewer"
},
{
"description": "Create, edit, or delete subtractions.",
"id": "subtraction_manager",
"name": "Subtraction_manager"
},
{
"description": "Edit subtractions.",
"id": "subtraction_editor",
"name": "Subtraction_editor"
},
{
"description": "View or use subtractions.",
"id": "subtraction_viewer",
"name": "Subtraction_viewer"
},
{
"description": "Create, use, or delete uploads.",
"id": "upload_manager",
"name": "Upload_manager"
},
{
"description": "View or use uploads.",
"id": "upload_viewer",
"name": "Upload_viewer"
}
],
"items": [
{
"administrator": true,
"handle": "bob",
"id": "test",
"label": null,
"project": null,
"reference": null,
"role": "owner",
"sample": null,
"subtraction": null,
"upload": null
}
]
},
"status": "200"
}
},
{
"description": "Removes a member from the space.\nThey will no longer have access to any data in the space.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/members/{member_id}",
"title": "Remove a member",
"errors": []
},
{
"description": "Changes the roles of the space member.",
"example": {
"role": "member"
},
"method": "patch",
"parameters": [
{
"$ref": "#/components/schemas/SpaceLabelRole",
"name": "label",
"required": false
},
{
"$ref": "#/components/schemas/SpaceProjectRole",
"name": "project",
"required": false
},
{
"$ref": "#/components/schemas/SpaceReferenceRole",
"name": "reference",
"required": false
},
{
"$ref": "#/components/schemas/SpaceRole",
"name": "role",
"required": false
},
{
"$ref": "#/components/schemas/SpaceSampleRole",
"name": "sample",
"required": false
},
{
"$ref": "#/components/schemas/SpaceSubtractionRole",
"name": "subtraction",
"required": false
},
{
"$ref": "#/components/schemas/SpaceUploadRole",
"name": "upload",
"required": false
}
],
"path": "/spaces/{space_id}/members/{member_id}",
"title": "Update a member",
"errors": [
{
"status": "404",
"description": "User not found"
}
],
"response": {
"example": [
{
"administrator": true,
"handle": "bob",
"id": "test",
"label": null,
"project": null,
"reference": null,
"role": "member",
"sample": null,
"subtraction": null,
"upload": null
}
],
"status": "200"
}
},
{
"description": "Lists references that match the find term.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs",
"title": "Find references",
"errors": [],
"response": {
"example": {
"documents": [
{
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "New Plant Viruses",
"organism": "virus",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
}
],
"found_count": 2,
"official_installed": true,
"page": 1,
"page_count": 1,
"per_page": 25,
"total_count": 2
},
"status": "200"
}
},
{
"description": "Creates an empty reference.",
"example": {
"data_type": "genome",
"name": "Plant Viruses",
"organism": "viruses"
},
"method": "post",
"parameters": [
{
"description": "a valid ref_id that the new reference should be cloned from",
"title": "Clone From",
"type": "string",
"name": "clone_from",
"required": false
},
{
"default": "genome",
"description": "the sequence data type",
"title": "Data Type",
"type": "string",
"name": "data_type",
"required": false
},
{
"default": "",
"description": "a longer description for the reference",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "a valid file_id that the new reference should be imported from",
"title": "Import From",
"type": "string",
"name": "import_from",
"required": false
},
{
"default": "",
"description": "the virus name",
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"default": "",
"description": "the organism",
"title": "Organism",
"type": "string",
"name": "organism",
"required": false
},
{
"default": 11447367,
"description": "the id of the GitHub release to install",
"title": "Release Id",
"type": "string",
"name": "release_id",
"required": false
},
{
"description": "a valid GitHub slug to download and update the new reference from",
"title": "Remote From",
"type": "string",
"name": "remote_from",
"required": false
}
],
"path": "/spaces/{space_id}/refs",
"title": "Create a reference",
"errors": [
{
"status": "400",
"description": "Source reference does not exist"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "502",
"description": "Could not reach GitHub"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"contributors": [
{
"administrator": true,
"count": 6,
"handle": "reece",
"id": "hjol9wdt"
},
{
"administrator": true,
"count": 7906,
"handle": "mrott",
"id": "ihvze2u9"
},
{
"administrator": true,
"count": 1563,
"handle": "igboyes",
"id": "igboyes"
},
{
"administrator": true,
"count": 2483,
"handle": "jasper",
"id": "1kg24j7t"
}
],
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"description": "",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "Plant Viruses",
"organism": "viruses",
"otu_count": 2102,
"restrict_source_types": false,
"source_types": [
"isolate",
"strain"
],
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
},
"users": [
{
"administrator": true,
"build": true,
"handle": "igboyes",
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Deletes a reference and its associated OTUs, history, and indexes. Deleting a\nreference does not break dependent analyses and other resources.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}",
"title": "Delete a reference",
"errors": []
},
{
"description": "Fetches the details of a reference.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}",
"title": "Get a reference",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": null,
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "New Plant Viruses",
"organism": "virus",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Updates an existing reference.",
"example": {
"internal_control": "ah4m5jqz",
"name": "Regulated Pests",
"organism": "phytoplasma"
},
"method": "patch",
"parameters": [
{
"description": "a longer description for the reference",
"title": "Description",
"type": "string",
"name": "description",
"required": false
},
{
"description": "set the OTU identified by the passed id as the internal control for the reference",
"title": "Internal Control",
"type": "string",
"name": "internal_control",
"required": false
},
{
"description": "the virus name",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"description": "the organism",
"title": "Organism",
"type": "string",
"name": "organism",
"required": false
},
{
"description": "option to restrict source types",
"title": "Restrict Source Types",
"type": "boolean",
"name": "restrict_source_types",
"required": false
},
{
"description": "source types",
"items": {
"minLength": 1,
"type": "string"
},
"title": "Source Types",
"type": "array",
"name": "source_types",
"required": false
},
{
"description": "list of target sequences",
"items": {
"$ref": "#/components/schemas/ReferenceTargetRequest"
},
"title": "Targets",
"type": "array",
"name": "targets",
"required": false
}
],
"path": "/spaces/{space_id}/refs/{ref_id}",
"title": "Update a reference",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"cloned_from": {
"id": "pat6xdn3",
"name": "Plant Viruses"
},
"created_at": "2022-01-28T23:42:48.321000Z",
"data_type": "genome",
"groups": [
{
"build": false,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": "sidney",
"modify": false,
"modify_otu": false,
"remove": false
}
],
"id": "d19exr83",
"internal_control": "ah4m5jqz",
"latest_build": {
"created_at": "2022-07-05T17:41:51.857000Z",
"has_json": false,
"id": "u3lm1rk8",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"version": 14
},
"name": "Regulated Pests",
"organism": "phytoplasma",
"otu_count": 2102,
"task": {
"id": 331
},
"unbuilt_change_count": 4,
"user": {
"id": "igboyes"
},
"users": [
{
"build": true,
"id": "igboyes",
"modify": true,
"modify_otu": true,
"remove": true
}
]
},
"status": "200"
}
},
{
"description": "Lists changes made to OTUs in the reference.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/history",
"title": "List history",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"documents": [
{
"created_at": "2022-01-28T23:28:53.881000Z",
"description": "Removed Betaflexivirus from Camelia #1 (BFV_CAM1)",
"id": "1wfc5x6e.removed",
"index": {
"id": "s7frhn8n",
"version": 1
},
"method_name": "remove",
"otu": {
"id": "1wfc5x6e",
"name": "Betaflexivirus from Camelia #1",
"version": "removed"
},
"reference": {
"id": "pat6xdn3"
},
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
}
],
"found_count": 1419,
"page": 1,
"page_count": 710,
"per_page": 1,
"total_count": 1419
},
"status": "200"
}
},
{
"description": "Lists indexes that have been created for the reference.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/indexes",
"title": "List indexes",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"change_count": 12,
"documents": [
{
"change_count": 4,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "bar",
"job": {
"id": "bar"
},
"modified_otu_count": 3,
"ready": false,
"reference": {
"id": "bar"
},
"user": {
"administrator": false,
"handle": "leeashley",
"id": "bf1b993c"
},
"version": 1
},
{
"change_count": 2,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "foo",
"job": {
"id": "foo"
},
"modified_otu_count": 2,
"ready": false,
"reference": {
"id": "foo"
},
"user": {
"administrator": false,
"handle": "leeashley",
"id": "bf1b993c"
},
"version": 0
}
],
"found_count": 2,
"modified_otu_count": 3,
"page": 1,
"page_count": 1,
"per_page": 25,
"total_count": 2,
"total_otu_count": 123
},
"status": "200"
}
},
{
"description": "Starts a job to rebuild the otus Bowtie2 index on disk.\n\nDoes a check to make sure there are no unverified OTUs in the collection\nand updates otu history to show the version and id of the new index.",
"method": "post",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/indexes",
"title": "Create an index",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"change_count": 0,
"created_at": "2015-10-06T20:00:00Z",
"has_files": true,
"id": "fb085f7f",
"job": {
"id": "bf1b993c"
},
"modified_otu_count": 0,
"ready": false,
"reference": {
"id": "foo"
},
"user": {
"administrator": false,
"handle": "bob",
"id": "test"
},
"version": 9
},
"status": "201"
}
},
{
"description": "Lists OTUs by name or abbreviation. Results are paginated.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/otus",
"title": "Find OTUs",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"documents": [
{
"abbreviation": "ABTV",
"id": "k77wgf8x",
"name": "Abaca bunchy top virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 18
},
{
"abbreviation": "AbBV",
"id": "7hpwj4yh",
"name": "Abutilon Brazil virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 4
},
{
"abbreviation": "",
"id": "p9ohme8k",
"name": "Abutilon golden mosaic Yucatan virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AbMBoV",
"id": "qrspg5w3",
"name": "Abutilon mosaic Bolivia virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 6
},
{
"abbreviation": "AbMoBrV",
"id": "yb7kpm43",
"name": "Abutilon mosaic Brazil virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 4
},
{
"abbreviation": "AbMV",
"id": "8540rw7b",
"name": "Abutilon mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 9
},
{
"abbreviation": "",
"id": "3zwrpu3y",
"name": "Abutilon yellow mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AcLV",
"id": "30n6qo2x",
"name": "Aconitum latent virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "",
"id": "x5qw901r",
"name": "Actinidia chlorotic ringspot associated virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 5
},
{
"abbreviation": "",
"id": "ss6bios9",
"name": "Actinidia emaravirus 2",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 13
},
{
"abbreviation": "",
"id": "nn5gt7db",
"name": "Actinidia seed borne latent virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "xo3khtnd",
"name": "Actinidia virus 1",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
},
{
"abbreviation": "AVA",
"id": "qg8optks",
"name": "Actinidia virus A",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AVB",
"id": "fnhtwiux",
"name": "Actinidia virus B",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AVX",
"id": "5uh1jzzk",
"name": "Actinidia virus X",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 1
},
{
"abbreviation": "AYV1",
"id": "7ag9wwrr",
"name": "Actinidia yellowing virus 1",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AYV2",
"id": "f87f3cs7",
"name": "Actinidia yellowing virus 2",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "e2xpkmgy",
"name": "Adonis mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "3ly2pqbk",
"name": "Aeonium ringspot virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 0
},
{
"abbreviation": "",
"id": "3xa1dbt0",
"name": "African cassava mosaic Burkina Faso virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 5
},
{
"abbreviation": "ACMV",
"id": "0ommwgyh",
"name": "African cassava mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 9
},
{
"abbreviation": "",
"id": "iyw0y3ta",
"name": "African eggplant mosaic virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "",
"id": "set9w2zc",
"name": "African eggplant yellowing virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 3
},
{
"abbreviation": "AOPRV",
"id": "taecz4c9",
"name": "African oil palm ringspot virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
},
{
"abbreviation": "",
"id": "zgsytbul",
"name": "Agave tequilana leaf virus",
"reference": {
"id": "d19exr83"
},
"verified": true,
"version": 2
}
],
"found_count": 2102,
"modified_count": 1,
"page": 1,
"page_count": 85,
"per_page": 25,
"total_count": 2102
},
"status": "200"
}
},
{
"description": "Creates an OTU.",
"method": "post",
"parameters": [
{
"default": "",
"title": "Abbreviation",
"type": "string",
"name": "abbreviation",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"items": {
"$ref": "#/components/schemas/OTUSegment"
},
"title": "Schema",
"type": "array",
"name": "schema",
"required": false
}
],
"path": "/spaces/{space_id}/refs/{ref_id}/otus",
"title": "Create OTU",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"status": "201"
}
},
{
"description": "Lists all updates made to the reference.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/updates",
"title": "List updates",
"errors": [],
"response": {
"example": [
{
"body": "#### Fixed\r\n- fixed uploading to GitHub releases in `.travis.yml`",
"created_at": "2018-06-14T18:37:54.242000Z",
"filename": "reference.json.gz",
"html_url": "https://github.com/virtool/ref-plant-viruses/releases/tag/v0.1.1",
"id": 11447367,
"name": "v0.1.1",
"published_at": "2018-06-12T19:20:57Z",
"ready": true,
"size": 3695872,
"user": {
"id": "igboyes"
}
}
],
"status": "200"
}
},
{
"description": "Updates the reference to the last version of the linked remote reference.",
"method": "post",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/updates",
"title": "Update a reference",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"body": "The release consists of a gzipped JSON file containing:\r\n\r\n- a `data_type` field with value _genome_\r\n- an `organism` field with value _virus_\r\n- the `version` name (eg. *v0.2.0*)\r\n- a timestamp with the key `created_at`\r\n- virus data compatible for import into Virtool v2.0.0+\r\n\r\nScripts have been updated to follow upcoming convention changes in Virtool v3.0.0.",
"content_type": "application/gzip",
"download_url": "https://github.com/virtool/virtool-database/releases/download/v0.3.0/reference.json.gz",
"etag": "W/\"ef123d746a33f88ee44203d3ca6bc2f7\"",
"filename": "reference.json.gz",
"html_url": "https://api.github.com/repos/virtool/virtool-database/releases/10742520",
"id": 10742520,
"name": "v0.3.0",
"newer": true,
"published_at": "2018-04-26T19:35:33Z",
"retrieved_at": "2018-04-14T19:52:17.465000Z",
"size": 3709091
},
"status": "201"
}
},
{
"description": "Adds a user to the reference. Users can view, use, and modify the reference.",
"example": {
"modify_otu": true,
"user_id": "sidney"
},
"method": "post",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
},
{
"description": "the id of the user to add",
"title": "User Id",
"type": "string",
"name": "user_id",
"required": true
}
],
"path": "/spaces/{space_id}/refs/{ref_id}/users",
"title": "Add a user",
"errors": [
{
"status": "400",
"description": "Bad request"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "201"
}
},
{
"description": "Removes a user from the reference.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/refs/{ref_id}/users/{user_id}",
"title": "Remove a user",
"errors": []
},
{
"description": "Updates the access rights a user has on the reference.",
"example": {
"build": true,
"modify": true
},
"method": "patch",
"parameters": [
{
"description": "allow members to build new indexes for the reference",
"title": "Build",
"type": "boolean",
"name": "build",
"required": false
},
{
"description": "allow members to modify the reference metadata and settings",
"title": "Modify",
"type": "boolean",
"name": "modify",
"required": false
},
{
"description": "allow members to modify the reference’s member OTUs",
"title": "Modify Otu",
"type": "boolean",
"name": "modify_otu",
"required": false
},
{
"description": "allow members to remove the reference",
"title": "Remove",
"type": "boolean",
"name": "remove",
"required": false
}
],
"path": "/spaces/{space_id}/refs/{ref_id}/users/{user_id}",
"title": "Update a user",
"errors": [
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"build": true,
"created_at": "2022-06-10T20:00:34.129000Z",
"id": 4,
"modify": true,
"modify_otu": false,
"remove": false
},
"status": "200"
}
},
{
"description": "Lists samples, filtering by data passed as URL parameters.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/samples",
"title": "Find samples",
"errors": [
{
"status": "400",
"description": "Invalid query"
}
],
"response": {
"status": "200"
}
},
{
"description": "Creates a new sample with the given name, labels and subtractions.",
"method": "post",
"parameters": [
{
"items": {},
"maxItems": 2,
"minItems": 1,
"title": "Files",
"type": "array",
"name": "files",
"required": true
},
{
"title": "Group",
"type": "integer",
"name": "group",
"required": false
},
{
"default": "",
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"default": "",
"title": "Isolate",
"type": "string",
"name": "isolate",
"required": false
},
{
"items": {},
"title": "Labels",
"type": "array",
"name": "labels",
"required": false
},
{
"allOf": [
{
"$ref": "#/components/schemas/LibraryType"
}
],
"default": "normal",
"name": "library_type",
"required": false
},
{
"default": "",
"title": "Locale",
"type": "string",
"name": "locale",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"default": "",
"title": "Notes",
"type": "string",
"name": "notes",
"required": false
},
{
"items": {},
"title": "Subtractions",
"type": "array",
"name": "subtractions",
"required": false
}
],
"path": "/spaces/{space_id}/samples",
"title": "Create a sample",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Malus domestica",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [],
"library_type": "normal",
"locale": "",
"name": "HX8",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "201"
}
},
{
"description": "Removes a sample document and all associated analyses.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/samples/{sample_id}",
"title": "Delete a sample",
"errors": []
},
{
"description": "Fetches the details for a sample.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/samples/{sample_id}",
"title": "Get a sample",
"errors": [
{
"status": "403",
"description": ""
},
{
"status": "404",
"description": ""
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Malus domestica",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [],
"library_type": "normal",
"locale": "",
"name": "HX8",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "200"
}
},
{
"description": "Updates a sample using its 'sample id'.",
"example": {
"host": "Tobacco",
"labels": [
1,
5,
6
],
"name": "Tobacco mosaic viru"
},
"method": "patch",
"parameters": [
{
"title": "Host",
"type": "string",
"name": "host",
"required": false
},
{
"title": "Isolate",
"type": "string",
"name": "isolate",
"required": false
},
{
"items": {},
"title": "Labels",
"type": "array",
"name": "labels",
"required": false
},
{
"title": "Locale",
"type": "string",
"name": "locale",
"required": false
},
{
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"title": "Notes",
"type": "string",
"name": "notes",
"required": false
},
{
"items": {},
"title": "Subtractions",
"type": "array",
"name": "subtractions",
"required": false
}
],
"path": "/spaces/{space_id}/samples/{sample_id}",
"title": "Update a sample",
"errors": [
{
"status": "400",
"description": "Sample name is already in use"
},
{
"status": "403",
"description": "Insufficient rights"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"all_read": false,
"all_write": false,
"artifacts": [],
"created_at": "2022-05-20T23:48:00.901000Z",
"format": "fastq",
"group": {
"id": 4,
"name": "Sidney"
},
"group_read": true,
"group_write": true,
"hold": true,
"host": "Tobacco",
"id": "9zn468u9",
"is_legacy": false,
"isolate": "",
"labels": [
1,
5,
6
],
"library_type": "normal",
"locale": "",
"name": "Tobacco mosaic viru",
"notes": "",
"nuvs": false,
"paired": true,
"pathoscope": true,
"quality": {
"bases": [
[
36,
37,
37,
37,
37,
37
],
[
36,
37,
37,
37,
37,
37
]
],
"composition": [
[
29,
18,
15,
36.5
],
[
25.5,
19,
31.5,
22
]
],
"count": 94601674,
"encoding": "Sanger / Illumina 1.9\n",
"gc": 43,
"length": [
150,
150
],
"sequences": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
18,
298
]
},
"reads": [
{
"download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
"id": 713,
"name": "reads_1.fq.gz",
"name_on_disk": "reads_1.fq.gz",
"sample": "9zn468u9",
"size": 3540467819,
"upload": null,
"uploaded_at": "2022-05-21T00:10:27.418000Z"
},
{
"download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
"id": 714,
"name": "reads_2.fq.gz",
"name_on_disk": "reads_2.fq.gz",
"sample": "9zn468u9",
"size": 3321721014,
"upload": null,
"uploaded_at": "2022-05-21T00:11:10.743000Z"
}
],
"ready": true,
"subtractions": [
{
"id": "0nhpi36p",
"name": "Malus domestica"
}
],
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
},
"workflows": {
"aodp": "incompatible",
"nuvs": "none",
"pathoscope": "none"
}
},
"status": "200"
}
},
{
"description": "Lists subtractions by their `name` or `nickname` by providing a `term` as a\nquery parameter. Partial matches are supported.\n\nSupports pagination unless the `short` query parameter is set. In this case, an\narray of objects containing the `id` and `name` of every subtraction is\nreturned.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/subtractions",
"title": "Find subtractions",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Creates a new subtraction.\n\nA job is started to build the data necessary to make the subtraction usable in\nanalyses. The subtraction is usable when the `ready` property is `true`.",
"example": {
"name": "Foobar",
"nickname": "foo",
"upload_id": 1234
},
"method": "post",
"parameters": [
{
"description": "A unique name for the host (eg. Arabidopsis)",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"default": "",
"description": "A nickname of the host",
"title": "Nickname",
"type": "string",
"name": "nickname",
"required": false
},
{
"description": "The unique id of the file",
"title": "Upload Id",
"type": "integer",
"name": "upload_id",
"required": true
}
],
"path": "/spaces/{space_id}/subtractions",
"title": "Create a subtraction",
"errors": [
{
"status": "400",
"description": "Upload does not exist"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"deleted": false,
"file": {
"id": 1234,
"name": "test_upload"
},
"files": [],
"id": "abc123",
"linked_samples": [],
"name": "Foobar",
"nickname": "foo",
"ready": false,
"user": {
"administrator": false,
"handle": "bob",
"id": "test"
}
},
"status": "201"
}
},
{
"description": "Deletes an existing subtraction.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/subtractions/{subtraction_id}",
"title": "Delete a subtraction",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "Has linked samples"
}
],
"response": {
"status": "204"
}
},
{
"description": "Fetches the details of a subtraction.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/subtractions/{subtraction_id}",
"title": "Get a subtraction",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"count": 9,
"created_at": "2021-12-21T23:52:13.185000Z",
"deleted": false,
"file": {
"id": 58,
"name": "arabidopsis_thaliana_+_plastids.fa.gz"
},
"files": [
{
"download_url": "/subtractions/q0ek30si/files/subtraction.1.bt2",
"id": 39,
"name": "subtraction.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.2.bt2",
"id": 37,
"name": "subtraction.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.3.bt2",
"id": 42,
"name": "subtraction.3.bt2",
"size": 3275,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.4.bt2",
"id": 40,
"name": "subtraction.4.bt2",
"size": 30000958,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.fa.gz",
"id": 36,
"name": "subtraction.fa.gz",
"size": 36160657,
"subtraction": "q0ek30si",
"type": "fasta"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.1.bt2",
"id": 41,
"name": "subtraction.rev.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.2.bt2",
"id": 38,
"name": "subtraction.rev.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
}
],
"gc": {
"a": 0.319,
"c": 0.18,
"g": 0.18,
"n": 0.002,
"t": 0.319
},
"id": "q0ek30si",
"linked_samples": [
{
"id": "2izth91q",
"name": "21BP074"
},
{
"id": "noni4fpk",
"name": "21BP075"
},
{
"id": "o3ldvwpm",
"name": "22SP001-M"
},
{
"id": "gobtw98t",
"name": "22SP001-R"
}
],
"name": "Arabidopsis thaliana",
"nickname": "",
"ready": true,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
},
"status": "200"
}
},
{
"description": "Updates the name or nickname of an existing subtraction.",
"example": {
"name": "Arabidopsis",
"nickname": "Thale cress"
},
"method": "patch",
"parameters": [
{
"description": "A unique name for the host",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"description": "A nickname for the host",
"title": "Nickname",
"type": "string",
"name": "nickname",
"required": false
}
],
"path": "/spaces/{space_id}/subtractions/{subtraction_id}",
"title": "Update a subtraction",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"count": 9,
"created_at": "2021-12-21T23:52:13.185000Z",
"deleted": false,
"file": {
"id": 58,
"name": "arabidopsis_thaliana_+_plastids.fa.gz"
},
"files": [
{
"download_url": "/subtractions/q0ek30si/files/subtraction.1.bt2",
"id": 39,
"name": "subtraction.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.2.bt2",
"id": 37,
"name": "subtraction.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.3.bt2",
"id": 42,
"name": "subtraction.3.bt2",
"size": 3275,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.4.bt2",
"id": 40,
"name": "subtraction.4.bt2",
"size": 30000958,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.fa.gz",
"id": 36,
"name": "subtraction.fa.gz",
"size": 36160657,
"subtraction": "q0ek30si",
"type": "fasta"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.1.bt2",
"id": 41,
"name": "subtraction.rev.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.2.bt2",
"id": 38,
"name": "subtraction.rev.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
}
],
"gc": {
"a": 0.319,
"c": 0.18,
"g": 0.18,
"n": 0.002,
"t": 0.319
},
"id": "q0ek30si",
"linked_samples": [
{
"id": "2izth91q",
"name": "21BP074"
},
{
"id": "noni4fpk",
"name": "21BP075"
},
{
"id": "o3ldvwpm",
"name": "22SP001-M"
},
{
"id": "gobtw98t",
"name": "22SP001-R"
}
],
"name": "Arabidopsis",
"nickname": "Thale cress",
"ready": true,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
},
"status": "200"
}
},
{
"description": "Lists JSON details of all files uploaded to the instance.",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/uploads",
"title": "List uploads",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Accepts file uploads as multipart requests. The request should contain a single\nfield ``file`` containing the file data.\n\nA file ``name`` and ``type`` must be included in the query string.",
"method": "post",
"parameters": [],
"path": "/spaces/{space_id}/uploads",
"title": "Upload a file",
"errors": [
{
"status": "401",
"description": "Requires authorization"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2022-01-22T17:28:21.491000Z",
"id": 106,
"name": "MPI19_L3_2.fq.gz",
"name_on_disk": "106-MPI19_L3_2.fq.gz",
"ready": true,
"removed": false,
"removed_at": null,
"reserved": true,
"size": 3356803271,
"type": "reads",
"uploaded_at": "2022-01-22T17:31:59.801000Z",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
}
},
"status": "201"
}
},
{
"description": "Deletes an upload using its 'upload id'.",
"method": "delete",
"parameters": [],
"path": "/spaces/{space_id}/uploads/{upload_id}",
"title": "Delete an upload",
"errors": [
{
"status": "401",
"description": "Requires authorization"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "204"
}
},
{
"description": "Downloads a previously uploaded file.\n\nHeaders:\n Content-Disposition: attachment; filename=<name>\n Content-Type: application/octet-stream",
"method": "get",
"parameters": [],
"path": "/spaces/{space_id}/uploads/{upload_id}",
"title": "Download an upload",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "subtractions",
"endpoints": [
{
"description": "Lists subtractions by their `name` or `nickname` by providing a `term` as a\nquery parameter. Partial matches are supported.\n\nSupports pagination unless the `short` query parameter is set. In this case, an\narray of objects containing the `id` and `name` of every subtraction is\nreturned.",
"method": "get",
"parameters": [],
"path": "/subtractions",
"title": "Find subtractions",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Creates a new subtraction.\n\nA job is started to build the data necessary to make the subtraction usable in\nanalyses. The subtraction is usable when the `ready` property is `true`.",
"example": {
"name": "Foobar",
"nickname": "foo",
"upload_id": 1234
},
"method": "post",
"parameters": [
{
"description": "A unique name for the host (eg. Arabidopsis)",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": true
},
{
"default": "",
"description": "A nickname of the host",
"title": "Nickname",
"type": "string",
"name": "nickname",
"required": false
},
{
"description": "The unique id of the file",
"title": "Upload Id",
"type": "integer",
"name": "upload_id",
"required": true
}
],
"path": "/subtractions",
"title": "Create a subtraction",
"errors": [
{
"status": "400",
"description": "Upload does not exist"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"example": {
"created_at": "2015-10-06T20:00:00Z",
"deleted": false,
"file": {
"id": 1234,
"name": "test_upload"
},
"files": [],
"id": "abc123",
"linked_samples": [],
"name": "Foobar",
"nickname": "foo",
"ready": false,
"user": {
"administrator": false,
"handle": "bob",
"id": "test"
}
},
"status": "201"
}
},
{
"description": "Deletes an existing subtraction.",
"method": "delete",
"parameters": [],
"path": "/subtractions/{subtraction_id}",
"title": "Delete a subtraction",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "Has linked samples"
}
],
"response": {
"status": "204"
}
},
{
"description": "Fetches the details of a subtraction.",
"method": "get",
"parameters": [],
"path": "/subtractions/{subtraction_id}",
"title": "Get a subtraction",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"count": 9,
"created_at": "2021-12-21T23:52:13.185000Z",
"deleted": false,
"file": {
"id": 58,
"name": "arabidopsis_thaliana_+_plastids.fa.gz"
},
"files": [
{
"download_url": "/subtractions/q0ek30si/files/subtraction.1.bt2",
"id": 39,
"name": "subtraction.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.2.bt2",
"id": 37,
"name": "subtraction.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.3.bt2",
"id": 42,
"name": "subtraction.3.bt2",
"size": 3275,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.4.bt2",
"id": 40,
"name": "subtraction.4.bt2",
"size": 30000958,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.fa.gz",
"id": 36,
"name": "subtraction.fa.gz",
"size": 36160657,
"subtraction": "q0ek30si",
"type": "fasta"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.1.bt2",
"id": 41,
"name": "subtraction.rev.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.2.bt2",
"id": 38,
"name": "subtraction.rev.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
}
],
"gc": {
"a": 0.319,
"c": 0.18,
"g": 0.18,
"n": 0.002,
"t": 0.319
},
"id": "q0ek30si",
"linked_samples": [
{
"id": "2izth91q",
"name": "21BP074"
},
{
"id": "noni4fpk",
"name": "21BP075"
},
{
"id": "o3ldvwpm",
"name": "22SP001-M"
},
{
"id": "gobtw98t",
"name": "22SP001-R"
}
],
"name": "Arabidopsis thaliana",
"nickname": "",
"ready": true,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
},
"status": "200"
}
},
{
"description": "Updates the name or nickname of an existing subtraction.",
"example": {
"name": "Arabidopsis",
"nickname": "Thale cress"
},
"method": "patch",
"parameters": [
{
"description": "A unique name for the host",
"minLength": 1,
"title": "Name",
"type": "string",
"name": "name",
"required": false
},
{
"description": "A nickname for the host",
"title": "Nickname",
"type": "string",
"name": "nickname",
"required": false
}
],
"path": "/subtractions/{subtraction_id}",
"title": "Update a subtraction",
"errors": [
{
"status": "400",
"description": "Invalid input"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"count": 9,
"created_at": "2021-12-21T23:52:13.185000Z",
"deleted": false,
"file": {
"id": 58,
"name": "arabidopsis_thaliana_+_plastids.fa.gz"
},
"files": [
{
"download_url": "/subtractions/q0ek30si/files/subtraction.1.bt2",
"id": 39,
"name": "subtraction.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.2.bt2",
"id": 37,
"name": "subtraction.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.3.bt2",
"id": 42,
"name": "subtraction.3.bt2",
"size": 3275,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.4.bt2",
"id": 40,
"name": "subtraction.4.bt2",
"size": 30000958,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.fa.gz",
"id": 36,
"name": "subtraction.fa.gz",
"size": 36160657,
"subtraction": "q0ek30si",
"type": "fasta"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.1.bt2",
"id": 41,
"name": "subtraction.rev.1.bt2",
"size": 44200803,
"subtraction": "q0ek30si",
"type": "bowtie2"
},
{
"download_url": "/subtractions/q0ek30si/files/subtraction.rev.2.bt2",
"id": 38,
"name": "subtraction.rev.2.bt2",
"size": 30000964,
"subtraction": "q0ek30si",
"type": "bowtie2"
}
],
"gc": {
"a": 0.319,
"c": 0.18,
"g": 0.18,
"n": 0.002,
"t": 0.319
},
"id": "q0ek30si",
"linked_samples": [
{
"id": "2izth91q",
"name": "21BP074"
},
{
"id": "noni4fpk",
"name": "21BP075"
},
{
"id": "o3ldvwpm",
"name": "22SP001-M"
},
{
"id": "gobtw98t",
"name": "22SP001-R"
}
],
"name": "Arabidopsis",
"nickname": "Thale cress",
"ready": true,
"user": {
"administrator": true,
"handle": "igboyes",
"id": "igboyes"
}
},
"status": "200"
}
},
{
"description": "Downloads a Bowtie2 index or FASTA file for the given subtraction.\n\nFiles are attached to the subtraction as part of the creation job. They aren't\navailable for download until the job has completed and the `ready` field is\n`true`.",
"method": "get",
"parameters": [],
"path": "/subtractions/{subtraction_id}/files/{filename}",
"title": "Download a subtraction file",
"errors": [
{
"status": "400",
"description": ""
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "tasks",
"endpoints": [
{
"description": "Lists all tasks active on the instance. Pagination is not\nsupported.",
"method": "get",
"parameters": [],
"path": "/tasks",
"title": "List all tasks",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Fetches the details of a task.",
"method": "get",
"parameters": [],
"path": "/tasks/{task_id}",
"title": "Retrieve a task",
"errors": [
{
"status": "400",
"description": ""
}
],
"response": {
"example": {
"complete": true,
"context": {
"user_id": "virtool"
},
"created_at": "2021-11-24T19:40:03.320000Z",
"error": null,
"file_size": null,
"id": 2,
"progress": 100,
"step": "remove_referenced_otus",
"type": "delete_reference"
},
"status": "200"
}
}
]
},
{
"title": "uploads",
"endpoints": [
{
"description": "Lists JSON details of all files uploaded to the instance.",
"method": "get",
"parameters": [],
"path": "/uploads",
"title": "List uploads",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Accepts file uploads as multipart requests. The request should contain a single\nfield ``file`` containing the file data.\n\nA file ``name`` and ``type`` must be included in the query string.",
"method": "post",
"parameters": [],
"path": "/uploads",
"title": "Upload a file",
"errors": [
{
"status": "401",
"description": "Requires authorization"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"example": {
"created_at": "2022-01-22T17:28:21.491000Z",
"id": 106,
"name": "MPI19_L3_2.fq.gz",
"name_on_disk": "106-MPI19_L3_2.fq.gz",
"ready": true,
"removed": false,
"removed_at": null,
"reserved": true,
"size": 3356803271,
"type": "reads",
"uploaded_at": "2022-01-22T17:31:59.801000Z",
"user": {
"administrator": true,
"handle": "mrott",
"id": "ihvze2u9"
}
},
"status": "201"
}
},
{
"description": "Deletes an upload using its 'upload id'.",
"method": "delete",
"parameters": [],
"path": "/uploads/{upload_id}",
"title": "Delete an upload",
"errors": [
{
"status": "401",
"description": "Requires authorization"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "204"
}
},
{
"description": "Downloads a previously uploaded file.\n\nHeaders:\n Content-Disposition: attachment; filename=<name>\n Content-Type: application/octet-stream",
"method": "get",
"parameters": [],
"path": "/uploads/{upload_id}",
"title": "Download an upload",
"errors": [
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
}
]
},
{
"title": "users",
"endpoints": [
{
"description": "Find all Virtool users.\n\nThe ``active`` query parameter can be used to filter users by their active\nstatus.\n\nThe ``find`` query parameter can be used to filter users by partial matches to\ntheir handles.",
"method": "get",
"parameters": [],
"path": "/users",
"title": "Find users",
"errors": [],
"response": {
"status": "200"
}
},
{
"description": "Creates a new user.",
"method": "post",
"parameters": [
{
"default": true,
"description": "forces a password reset next time the user logs in",
"title": "Force Reset",
"type": "boolean",
"name": "force_reset",
"required": false
},
{
"description": "the unique handle for the user",
"minLength": 1,
"title": "Handle",
"type": "string",
"name": "handle",
"required": true
},
{
"description": "the password for the user",
"minLength": 1,
"title": "Password",
"type": "string",
"name": "password",
"required": true
}
],
"path": "/users",
"title": "Create a user",
"errors": [
{
"status": "400",
"description": "Password does not meet length requirement"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"status": "201"
}
},
{
"description": "Creates the first user for the instance. This endpoint will not succeed more\nthan once.\n\nAfter calling this endpoint, authenticate as the first user and use those\ncredentials to continue interacting with the API.",
"method": "put",
"parameters": [
{
"description": "the unique handle for the user",
"minLength": 1,
"title": "Handle",
"type": "string",
"name": "handle",
"required": true
},
{
"description": "the password for the user",
"minLength": 1,
"title": "Password",
"type": "string",
"name": "password",
"required": true
}
],
"path": "/users/first",
"title": "Create a first user",
"errors": [
{
"status": "400",
"description": "Bad request"
},
{
"status": "403",
"description": "Not permitted"
}
],
"response": {
"status": "201"
}
},
{
"description": "Fetches the details for a user.",
"method": "get",
"parameters": [],
"path": "/users/{user_id}",
"title": "Retrieve a user",
"errors": [
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
}
],
"response": {
"status": "200"
}
},
{
"description": "Updates and existing user with the provided parameters. Users cannot modify\ntheir own administrative status.",
"method": "patch",
"parameters": [
{
"description": "make a user active or not",
"title": "Active",
"type": "boolean",
"name": "active",
"required": false
},
{
"description": "forces a password reset next time the user logs in",
"title": "Force Reset",
"type": "boolean",
"name": "force_reset",
"required": false
},
{
"description": "sets the IDs of groups the user belongs to",
"items": {
"anyOf": [
{
"type": "integer"
},
{
"type": "string"
}
]
},
"title": "Groups",
"type": "array",
"name": "groups",
"required": false
},
{
"description": "the new password",
"title": "Password",
"type": "string",
"name": "password",
"required": false
},
{
"description": "set the ID of the user's primary group",
"title": "Primary Group",
"type": "integer",
"name": "primary_group",
"required": false
}
],
"path": "/users/{user_id}",
"title": "Update a user",
"errors": [
{
"status": "400",
"description": "Bad request"
},
{
"status": "403",
"description": "Not permitted"
},
{
"status": "404",
"description": "Not found"
},
{
"status": "409",
"description": "User is not member of group"
}
],
"response": {
"status": "200"
}
},
{
"description": "Lists all roles that a user has on the space.",
"method": "get",
"parameters": [],
"path": "/users/{user_id}/permissions",
"title": "List user roles",
"errors": [],
"response": {
"example": [
"create_ref",
"create_sample"
],
"status": "200"
}
},
{
"description": "Removes a permission for a user.",
"method": "delete",
"parameters": [],
"path": "/users/{user_id}/permissions/{role}",
"title": "Delete user permission",
"errors": [],
"response": {
"example": true,
"status": "200"
}
},
{
"description": "Adds a role for a user.",
"method": "put",
"parameters": [],
"path": "/users/{user_id}/permissions/{role}",
"title": "Add user role",
"errors": [],
"response": {
"example": true,
"status": "200"
}
}
]
}
],
"sectionTitles": [
"account",
"admin",
"analyses",
"groups",
"history",
"hmms",
"indexes",
"instance_message",
"jobs",
"labels",
"ml",
"otus",
"refs",
"samples",
"settings",
"spaces",
"subtractions",
"tasks",
"uploads",
"users"
],
"version": "1.0.0"
}