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swagger.yaml
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---
swagger: "2.0"
info:
description: "DeRegNet REST API\n"
version: "0.0.1"
title: "DeRegNet REST API"
contact:
email: "deregnet@informatik.uni-tuebingen.de"
license:
name: "BSD 3-clause"
url: "https://opensource.org/licenses/BSD-3-Clause"
host: "api.dereg.net"
basePath: "/"
tags:
- name: "graph"
description: "Uploading and retrieving networks for use with DeRegNet algorithms"
- name: "score"
description: "Upload node scores for use with DeRegNet algorithms"
- name: "nodeset"
description: "Endpoint for uploading node sets (i.e. gene sets, etc.)"
- name: "parameter_set"
description: "Administration of additional algorithm parameters"
- name: "run"
description: "Run DeRegNet algorithms"
- name: "subgraph"
description: "Access found subgraphs"
- name: "info"
description: "Help and Documentation"
schemes:
- "http"
- "https"
paths:
/graph:
post:
tags:
- "graph"
summary: "Allows to initiate GraphML upload"
description: "This Endpoint creates a Metadata-Object for a Graph.\nIt returns\
\ the endpoint that is to be called with the \nfile containing the graph as\
\ payload/body in the header-attribute \"location\"\n"
operationId: "post_graph"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: "body"
name: "initalGraphInfo"
description: "The intial Information required for creating a new graph"
required: false
schema:
$ref: "#/definitions/InitalGraphInfo"
responses:
200:
description: "Graph entity created"
schema:
$ref: "#/definitions/GraphInfo"
400:
description: "invalid input, object invalid"
409:
description: "an existing item already exists"
x-swagger-router-controller: "deregnet_rest.controllers.graph_controller"
/graph/{graph_id}:
get:
tags:
- "graph"
summary: "Retrieve information on a previously uploaded graph\n"
operationId: "get_graph"
produces:
- "application/json"
parameters:
- name: "graph_id"
in: "path"
description: "ID of graph to return"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/GraphInfo"
400:
description: "Invalid ID supplied"
404:
description: "Graph not found"
x-swagger-router-controller: "deregnet_rest.controllers.graph_controller"
post:
tags:
- "graph"
summary: "Uploads a GraphML file"
description: "Adds a Graph to the system. The Graph Object with name:graphname\
\ must already be created by issuing a POST Request to /graph with repsective\
\ payload\n"
operationId: "post_graphml"
consumes:
- "multipart/form-data"
parameters:
- name: "graph_id"
in: "path"
description: "The Name of the graph"
required: true
type: "string"
- name: "file_to_upload"
in: "formData"
description: "The file containing the graph"
required: true
type: "file"
responses:
201:
description: "item created"
400:
description: "invalid input, object invalid"
409:
description: "an item with that name already exists"
x-swagger-router-controller: "deregnet_rest.controllers.graph_controller"
delete:
tags:
- "graph"
summary: "Delete a previously uploaded network"
description: "Delete a previously uplaoded network"
operationId: "delete_graph"
produces:
- "application/json"
parameters:
- name: "graph_id"
in: "path"
description: "ID of the graph to be deleted"
required: true
type: "string"
responses:
400:
description: "Invalid ID supplied"
404:
description: "Graph not found"
x-swagger-router-controller: "deregnet_rest.controllers.graph_controller"
/graphs:
get:
tags:
- "graph"
summary: "List available previously uploaded graphs"
description: "Returns a list of all available graphs"
operationId: "get_graphs"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/GraphInfo"
x-swagger-router-controller: "deregnet_rest.controllers.graph_controller"
/score:
post:
tags:
- "score"
summary: "Upload a node score for use with DeRegNet algorithms"
operationId: "post_score"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: "body"
name: "body"
description: "Node scores to be uploaded for later use with a DeRegNet algorithm"
required: true
schema:
$ref: "#/definitions/Score"
responses:
200:
description: "Score upload successful"
schema:
$ref: "#/definitions/ScoreInfo"
405:
description: "Invalid input"
x-swagger-router-controller: "deregnet_rest.controllers.score_controller"
/scores:
get:
tags:
- "score"
summary: "List available previously uploaded node scores"
description: "Returns a list with all available node scores"
operationId: "get_scores"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/ScoreInfo"
x-swagger-router-controller: "deregnet_rest.controllers.score_controller"
/score/{score_id}:
get:
tags:
- "score"
summary: "Retrieve information on a previously uploaded score"
operationId: "get_score"
produces:
- "application/json"
parameters:
- name: "score_id"
in: "path"
description: "ID of node score to return"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/ScoreInfo"
400:
description: "Invalid ID supplied"
404:
description: "Node score not found"
x-swagger-router-controller: "deregnet_rest.controllers.score_controller"
delete:
tags:
- "score"
summary: "Delete a previously uploaded node score"
description: "Delete a previously uploaded node score"
operationId: "delete_score"
produces:
- "application/json"
parameters:
- name: "score_id"
in: "path"
description: "ID of the node score to be deleted"
required: true
type: "string"
responses:
201:
description: "Score successfully deleted"
400:
description: "Invalid ID supplied"
404:
description: "Node score not found"
x-swagger-router-controller: "deregnet_rest.controllers.score_controller"
/nodeset:
post:
tags:
- "nodeset"
summary: "Upload a node set for use with DeRegNet algorithms"
operationId: "post_nodeset"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: "body"
name: "body"
description: "Node set to be uploaded for later use with a DeRegNet algorithm"
required: true
schema:
$ref: "#/definitions/NodeSet"
responses:
200:
description: "Node set upload successful"
schema:
$ref: "#/definitions/NodeSetInfo"
405:
description: "Invalid input"
x-swagger-router-controller: "deregnet_rest.controllers.nodeset_controller"
/nodesets:
get:
tags:
- "nodeset"
summary: "List available previously uploaded node sets"
description: "Returns a list with information of all available node sets"
operationId: "get_nodesets"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/NodeSetInfo"
x-swagger-router-controller: "deregnet_rest.controllers.nodeset_controller"
/nodeset/{nodeset_id}:
get:
tags:
- "nodeset"
summary: "Retrieve information on a previously uploaded node set"
operationId: "get_nodeset"
produces:
- "application/json"
parameters:
- name: "nodeset_id"
in: "path"
description: "ID of node set to return"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/NodeSetInfo"
400:
description: "Invalid ID supplied"
404:
description: "Node set not found"
x-swagger-router-controller: "deregnet_rest.controllers.nodeset_controller"
delete:
tags:
- "nodeset"
summary: "Delete a previously uploaded node set"
description: "Deletes a node set"
operationId: "delete_nodeset"
parameters:
- name: "nodeset_id"
in: "path"
description: "ID of the node set to be deleted"
required: true
type: "string"
responses:
200:
description: "Node set successfully deleted"
400:
description: "Invalid ID supplied"
404:
description: "Node set not found"
x-swagger-router-controller: "deregnet_rest.controllers.nodeset_controller"
/parameter_set:
post:
tags:
- "parameter_set"
summary: "Upload a parameters collection for use with DeRegNet algorithms"
operationId: "post_parameter_set"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: "body"
name: "body"
description: "Parameters to be uploaded for later use with a DeRegNet algorithm"
required: true
schema:
$ref: "#/definitions/ParameterSet"
responses:
200:
description: "Parameter set successfully uploaded"
schema:
$ref: "#/definitions/ParameterSetInfo"
405:
description: "Invalid input"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/parameter_sets:
get:
tags:
- "parameter_set"
summary: "List available previously uploaded parameter collections"
description: "Returns a list with information about availabel parameter collections"
operationId: "get_parameter_sets"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/ParameterSetInfo"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/parameter_set/{parameter_set_id}:
get:
tags:
- "parameter_set"
summary: "Retrieve information on a previously uploaded score"
operationId: "get_parameter_set"
produces:
- "application/json"
parameters:
- name: "parameter_set_id"
in: "path"
description: "ID of parameter collection to retrieve information about"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/ParameterSetInfo"
400:
description: "Invalid ID supplied"
404:
description: "Parameter collection not found"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
delete:
tags:
- "parameter_set"
summary: "Delete a previously uploaded parameter collection"
description: "Deletes a parameter collection"
operationId: "delete_parameter_set"
produces:
- "application/json"
parameters:
- name: "parameter_set_id"
in: "path"
description: "ID of the parameter collection to be deleted"
required: true
type: "string"
responses:
200:
description: "Parameter set successfully deleted"
400:
description: "Invalid ID supplied"
404:
description: "Parameter collection not found"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/parameter_set/{parameter_set_id}/data:
get:
tags:
- "parameter_set"
summary: "Retrieve a parameter collection"
description: "Returns a parameter collection"
operationId: "get_parameter_set_data"
produces:
- "application/json"
parameters:
- name: "parameter_set_id"
in: "path"
description: "ID of the parameter collection to return"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/ParameterSet"
400:
description: "Invalid ID supplied"
404:
description: "Parameter collection not found"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/parameter_set/default:
get:
tags:
- "parameter_set"
summary: "Retrieve the defaul parameter collection"
description: "Returns the default parameter collection"
operationId: "get_parameter_set_default"
produces:
- "application/json"
parameters: []
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/ParameterSetInfo"
400:
description: "Invalid ID supplied"
404:
description: "Parameter collection not found"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/parameter_set/default/data:
get:
tags:
- "parameter_set"
summary: "Retrieve information on a previously uploaded score"
operationId: "get_parameter_set_default_data"
produces:
- "application/json"
parameters: []
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/ParameterSet"
400:
description: "Invalid ID supplied"
404:
description: "Parameter collection not found"
x-swagger-router-controller: "deregnet_rest.controllers.parameter_set_controller"
/run:
post:
tags:
- "run"
summary: "Run average score DeRegNet algorithm"
operationId: "post_run"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: "body"
name: "body"
description: "All data needed to run the algorithm"
required: true
schema:
$ref: "#/definitions/RunInput"
responses:
200:
description: "Run posted successfully"
schema:
$ref: "#/definitions/RunInfo"
405:
description: "Invalid input"
x-swagger-router-controller: "deregnet_rest.controllers.run_controller"
/runs:
get:
tags:
- "run"
summary: "List current and past runs"
description: "Returns a single pet"
operationId: "get_runs"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/RunInfo"
x-swagger-router-controller: "deregnet_rest.controllers.run_controller"
/run/{run_id}:
get:
tags:
- "run"
summary: "Retrieve the status of a previously submitted run"
description: "Returns a single pet"
operationId: "get_run"
produces:
- "application/json"
parameters:
- name: "run_id"
in: "path"
description: "ID of pet to return"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/RunInfo"
400:
description: "Invalid ID supplied"
404:
description: "Run not found"
x-swagger-router-controller: "deregnet_rest.controllers.run_controller"
delete:
tags:
- "run"
summary: "Cancel an active run, you cannot delete finished runs"
description: "Cancel a run"
operationId: "delete_run"
produces:
- "application/json"
parameters:
- name: "run_id"
in: "path"
description: "ID of the run to be deleted"
required: true
type: "string"
responses:
201:
description: "Run successfully canceled"
400:
description: "Invalid ID supplied"
404:
description: "Run not found"
405:
description: "Run already finished"
x-swagger-router-controller: "deregnet_rest.controllers.run_controller"
/subgraphs:
get:
tags:
- "subgraph"
summary: "List available found subgraphs"
description: "Returns a single pet"
operationId: "get_subgraphs"
produces:
- "application/json"
parameters:
- name: "skip"
in: "query"
description: "number of records to skip for pagination"
required: false
type: "integer"
default: 0
minimum: 0
format: "int32"
- name: "limit"
in: "query"
description: "maximum number of records to return"
required: false
type: "integer"
default: 1000
maximum: 1000
minimum: 1
format: "int32"
responses:
200:
description: "successful operation"
schema:
type: "array"
items:
$ref: "#/definitions/SubgraphInfo"
x-swagger-router-controller: "deregnet_rest.controllers.subgraph_controller"
/subgraph/{subgraph_id}:
get:
tags:
- "subgraph"
summary: "Retrieve the information about a subgraph"
description: "Returns a single pet"
operationId: "get_subgraph"
produces:
- "application/json"
parameters:
- name: "subgraph_id"
in: "path"
description: "ID of subgraph about which to retrieve information"
required: true
type: "string"
responses:
200:
description: "successful operation"
schema:
$ref: "#/definitions/SubgraphInfo"
400:
description: "Invalid ID supplied"
404:
description: "Subgraph not found"
x-swagger-router-controller: "deregnet_rest.controllers.subgraph_controller"
delete:
tags:
- "subgraph"
summary: "Delete a previously found subgraph"
description: "Deletes a subgraph"
operationId: "delete_subgraph"
produces:
- "application/json"
parameters:
- name: "subgraph_id"
in: "path"
description: "ID of the order that needs to be deleted"
required: true
type: "string"
responses:
201:
description: "Subgraph successfully deleted"
400:
description: "Invalid ID supplied"
404:
description: "Subgraph not found"
x-swagger-router-controller: "deregnet_rest.controllers.subgraph_controller"
/subgraph/{subgraph_id}/{filetype}:
get:
tags:
- "subgraph"
summary: "Download a subgraph"
description: "With this GET Request you will retrieve a subgraph \n"
operationId: "download_subgraph_as"
produces:
- "application/octet-stream"
parameters:
- name: "subgraph_id"
in: "path"
description: "The Name of the graph"
required: true
type: "string"
- name: "filetype"
in: "path"
description: "File type of file to be downloaded"
required: true
type: "string"
enum:
- "graphml"
- "sif"
- "gmt"
- "grp"
responses:
201:
description: "file download ok"
400:
description: "invalid input, object invalid"
409:
description: "an existing item already exists"
x-swagger-router-controller: "deregnet_rest.controllers.subgraph_controller"
definitions:
GraphInfo:
type: "object"
required:
- "id"
- "num_edges"
- "num_nodes"
- "time_of_upload"
properties:
name:
type: "string"
description: "Name of the graph"
description:
type: "string"
description: "Description of the graph"
num_nodes:
type: "integer"
description: "Number of nodes in the graph"
num_edges:
type: "integer"
description: "Number of edges in the graph"
id:
type: "string"
description: "Id of the graph"
time_of_upload:
type: "string"
description: "Time of upload"
example:
time_of_upload: "time_of_upload"
name: "name"
description: "description"
id: "id"
num_nodes: 0
num_edges: 6
InitalGraphInfo:
type: "object"
properties:
description:
type: "string"
description: "Description of the graph"
name:
type: "string"
description: "Name of the graph"
node_id_attr:
type: "string"
description: "Node attribute containing node ids"
example:
node_id_attr: "node_id_attr"
name: "name"
description: "description"
Score:
type: "object"
required:
- "node_ids"
- "score_values"
properties:
description:
type: "string"
description: "Description of the score"
node_ids:
type: "array"
items:
type: "string"
score_values:
type: "array"
items:
type: "number"
example:
score_values:
- 0.80082819046101150206595775671303272247314453125
- 0.80082819046101150206595775671303272247314453125
description: "description"
node_ids:
- "node_ids"
- "node_ids"
ScoreInfo:
type: "object"
required:
- "id"
- "size"
- "time_of_upload"
properties:
description:
type: "string"
description: "Description of the score"
size:
type: "integer"
description: "Number of scored nodes"
id:
type: "string"
description: "Id of the score object"
time_of_upload:
type: "string"
description: "Time of upload"
example:
size: 0
time_of_upload: "time_of_upload"
description: "description"
id: "id"
NodeSet:
type: "object"
required:
- "nodes"
properties:
description:
type: "string"
description: "Description of the node set"
nodes:
type: "array"
items:
type: "string"
example:
nodes:
- "nodes"
- "nodes"
description: "description"
NodeSetInfo:
type: "object"
required:
- "id"
- "size"
- "time_of_upload"
properties:
description:
type: "string"
description: "Description of the score"
size:
type: "integer"
description: "Number of scored nodes"
id:
type: "string"
description: "Id of the score object"
time_of_upload:
type: "string"
description: "Time of upload"
example:
size: 0
time_of_upload: "time_of_upload"
description: "description"
id: "id"
RunInput:
type: "object"
required:
- "graph_id"
properties:
description:
type: "string"
description: "Description of run"
parameter_set_id:
type: "string"
description: "Id of a parameter set to run the algorithm with"
parameter_set:
$ref: "#/definitions/ParameterSet"
graph_id:
type: "string"
description: "Id of graph underlying the run"
score_id:
type: "string"
description: "Id of node score used in the run"
receptors_id:
type: "string"
description: "Id of a node set acting as receptors in the run"
terminals_id:
type: "string"
description: "Id of a node set acting as terminals in the run"
exclude_id:
type: "string"
description: "Id of a node set of nodes to be excluded from the subgraphs\n"
include_id:
type: "string"
description: "Id of a node set of nodes to be included in the subgraphs\n"
root:
type: "string"
description: "Node id of a fixed root node"
description: "All data and parameters the algorithm needs / can accept to run"
example:
include_id: "include_id"
terminals_id: "terminals_id"
parameter_set_id: "parameter_set_id"
score_id: "score_id"
root: "root"
description: "description"
receptors_id: "receptors_id"
exclude_id: "exclude_id"
parameter_set:
model_sense: "max"
default_score: 0.80082819046101150206595775671303272247314453125
time_limit: 0
num_suboptimal: 0
flip_orientation: true
max_overlap: 14.6581298050294517310021547018550336360931396484375
gap_cut: 0.59621339166831821554382031536079011857509613037109375
min_size: 0
abs_values: true
max_size: 0
algorithm: "dta"
graph_id: "graph_id"
RunInfo:
type: "object"
required:
- "done"
- "id"
- "post_time"
- "run_input"
- "started"
properties:
description:
type: "string"
description: "Description of the run"
id:
type: "string"
description: "Id of the score object"
post_time:
type: "string"
description: "Time of initial run post"
started:
type: "boolean"
description: "Whether the run has already started"
done:
type: "boolean"
description: "Whether the run is completed"
subgraph_ids:
type: "array"
items:
type: "string"
run_input: