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authorgebele <gebele@in-silico.ch>2018-05-07 12:44:31 +0200
committergebele <gebele@in-silico.ch>2018-05-07 12:44:31 +0200
commit14e626e3b0e5dad90f772bfec575fdd73d1bd3a3 (patch)
tree3642f453cb5ad4f2bf24a2e679de828d45056917
parentfe7055073961d9de1caf03536359c1b9b2ad7fa0 (diff)
use orn uri
-rw-r--r--api/api.json2098
1 files changed, 1069 insertions, 1029 deletions
diff --git a/api/api.json b/api/api.json
index 23dd1cc..1a07c0d 100644
--- a/api/api.json
+++ b/api/api.json
@@ -1,1052 +1,1092 @@
{
- "swagger": "2.0",
- "info": {
- "description": "REST API webservice for lazar and nano-lazar. \n*lazar* (lazy structure–activity relationships) is a modular framework for predictive toxicology. With activated Authentication & Authorization, subjectid authorization token are obligatory for designated services.\n",
- "version": "1.1.0",
- "title": "Lazar & Nano-Lazar REST Service",
- "contact": {
- "name": "in silico toxicology gmbh",
- "email": "service@in-silico.ch",
- "url": "https://in-silico.ch"
- },
- "license": {
- "name": "GNU GENERAL PUBLIC LICENSE",
- "url": "https://github.com/opentox/lazar-rest/blob/master/LICENSE"
- }
+ "openapi": "3.0.0",
+ "x-orn-@id": "https://dg-lazar.prod.openrisknet.org",
+ "x-orn-@type": "x-orn:Service",
+ "servers": [
+ {
+ "url": "https://dg-lazar.prod.openrisknet.org/"
+ }
+ ],
+ "info": {
+ "description": "REST API webservice for lazar and nano-lazar. \n\n*lazar* (lazy structure–activity relationships) is a modular framework for\npredictive toxicology. With activated Authentication & Authorization,\nsubjectid authorization token are obligatory for designated services.\n",
+ "version": "1.1.0",
+ "title": "Lazar & Nano-Lazar REST Service",
+ "contact": {
+ "name": "in silico toxicology gmbh",
+ "email": "service@in-silico.ch",
+ "url": "https://in-silico.ch"
},
- "host": "api.in-silico.ch",
- "externalDocs": {
- "description": "See also *lazar-rest* documentation on Github\n",
- "url": "https://github.com/opentox/lazar-rest"
+ "license": {
+ "name": "GNU GENERAL PUBLIC LICENSE",
+ "url": "https://github.com/opentox/lazar-rest/blob/master/LICENSE"
+ }
+ },
+ "externalDocs": {
+ "description": "See also *lazar-rest* documentation on Github\n",
+ "url": "https://github.com/opentox/lazar-rest"
+ },
+ "paths": {
+ "/model": {
+ "get": {
+ "x-orn-@type": "x-orn:Model",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/model",
+ "x-orn:method": "Get",
+ "tags": [
+ "model"
+ ],
+ "description": "Get a list of all prediction models",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
},
- "basePath": "/",
- "schemes": [
- "https"
- ],
- "paths": {
- "/model": {
- "get": {
- "tags": [
- "model"
- ],
- "description": "Get a list of all prediction models",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/model/{id}": {
- "get": {
- "tags": [
- "model"
- ],
- "description": "Get model representation",
- "produces": [
- "application/json"
- ],
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- }
- }
- },
- "post": {
- "tags": [
- "model"
- ],
- "description": "Predict a compound or a nanoparticle",
- "consumes": [
- "multipart/form-data"
- ],
- "parameters": [
- {
- "name": "identifier",
- "in": "formData",
- "description": "SMILES identifier or Nanoparticle URI or comma separated list of SMILES identifiers or Nanoparticle URI",
- "required": true,
- "type": "string"
- },
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- }
- }
- }
- },
- "/report": {
- "get": {
- "tags": [
- "report"
- ],
- "description": "Get a list of QMRF reports",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/report/{id}": {
- "get": {
- "tags": [
- "report"
- ],
- "description": "Get QMRF for prediction model",
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/xml"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- }
- }
- }
- },
- "/dataset": {
- "get": {
- "tags": [
- "dataset"
- ],
- "description": "Get a list of all datasets",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/dataset/{id}": {
- "get": {
- "tags": [
- "dataset"
- ],
- "description": "Get dataset representation",
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json",
- "text/csv"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/dataset/{id}/{attribute}": {
- "get": {
- "tags": [
- "dataset"
- ],
- "description": "Get dataset representation",
- "parameters": [
- {
- "name": "attribute",
- "in": "path",
- "description": "requested attribute",
- "required": true,
- "type": "string",
- "enum": [
- "compounds",
- "nanoparticles",
- "substances",
- "features"
- ]
- },
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/substance": {
- "get": {
- "tags": [
- "substance"
- ],
- "description": "Get a list of all substances",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/substance/{id}": {
- "get": {
- "tags": [
- "substance"
- ],
- "description": "Get substance representation",
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/nanoparticle": {
- "get": {
- "tags": [
- "nanoparticle"
- ],
- "description": "Get a list of all nanoparticles",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/nanoparticle/{id}": {
- "get": {
- "tags": [
- "nanoparticle"
- ],
- "description": "Get nanoparticle representation",
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/feature": {
- "get": {
- "tags": [
- "feature"
- ],
- "description": "Get a list of ids for all features",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/feature/{id}": {
- "get": {
- "tags": [
- "feature"
- ],
- "description": "Get feature representation",
- "parameters": [
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/validation": {
- "get": {
- "tags": [
- "validation"
- ],
- "description": "Get a list of all validation types",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/validation/{validationtype}": {
- "get": {
- "tags": [
- "validation"
- ],
- "description": "Get all validations of a validation type",
- "parameters": [
- {
- "$ref": "#/parameters/valtype"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/uri-list",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
- },
- "/validation/{validationtype}/{id}": {
- "get": {
- "tags": [
- "validation"
- ],
- "description": "Get validation representation",
- "parameters": [
- {
- "$ref": "#/parameters/valtype"
- },
- {
- "$ref": "#/parameters/id"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "403": {
- "$ref": "#/responses/403"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- }
+ "/model/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Model",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/model",
+ "x-orn:method": "Get",
+ "tags": [
+ "model"
+ ],
+ "description": "Get model representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ }
+ }
+ },
+ "post": {
+ "x-orn-@type": "x-orn:Prediction",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/model/{id}",
+ "x-orn:method": "Post",
+ "tags": [
+ "model"
+ ],
+ "description": "Predict a compound or a nanoparticle",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ }
},
- "/compound/descriptor": {
- "get": {
- "tags": [
- "compound",
- "descriptor"
- ],
- "description": "Get a list of all descriptors",
- "parameters": [
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/plain; charset=utf-8",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
- },
- "post": {
- "tags": [
- "compound",
- "descriptor"
- ],
- "summary": "Descriptor calculation",
- "description": "Calculate descriptors for a single compound as SMILES string <br> <strong>curl example:</strong> <pre>curl -Lk -X POST -i -H \"Accept:application/json\" -F \"identifier=O=C1NC(=O)NC=C1\" -F \"descriptor=Openbabel.MW,Openbabel.atoms\" https://api.in-silico.ch/compound/descriptor </pre>.",
- "consumes": [
- "multipart/form-data"
- ],
- "parameters": [
- {
- "name": "identifier",
- "in": "formData",
- "description": "SMILES identifier",
- "required": true,
- "type": "string"
- },
- {
- "name": "descriptor",
- "in": "formData",
- "description": "list of comma seperated descriptors",
- "required": true,
- "type": "string"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/csv",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
+ "requestBody": {
+ "description": "SMILES identifier or Nanoparticle URI or comma separated\nlist of SMILES identifiers or Nanoparticle URI\n",
+ "required": true,
+ "content": {
+ "application/x-www-form-urlencoded": {
+ "x-orn:schema": "application/x-www-form-urlencoded",
+ "schema": {
+ "$ref": "#/components/schemas/postmodel"
+ }
}
- },
- "/compound/descriptor/{descriptor}": {
- "get": {
- "tags": [
- "compound",
- "descriptor"
- ],
- "description": "Get a list of a descriptors",
- "parameters": [
- {
- "name": "descriptor",
- "in": "path",
- "description": "descriptor name or ID",
- "required": true,
- "type": "string"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "text/plain; charset=utf-8",
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "404": {
- "$ref": "#/responses/404"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
+ }
+ }
+ }
+ },
+ "/report": {
+ "get": {
+ "x-orn-@type": "x-orn:Report",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/report",
+ "x-orn:method": "Get",
+ "tags": [
+ "report"
+ ],
+ "description": "Get a list of QMRF reports",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/report/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Report",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/report/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "report"
+ ],
+ "description": "Get QMRF for prediction model",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ }
+ }
+ }
+ },
+ "/dataset": {
+ "get": {
+ "x-orn-@type": "x-orn:Dataset",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/dataset",
+ "x-orn:method": "Get",
+ "tags": [
+ "dataset"
+ ],
+ "description": "Get a list of all datasets",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/dataset/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Dataset",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/dataset/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "dataset"
+ ],
+ "description": "Get dataset representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/dataset/{id}/{attribute}": {
+ "get": {
+ "x-orn-@type": "x-orn:Dataset",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/dataset/{id}/{attribute}",
+ "x-orn:method": "Get",
+ "tags": [
+ "dataset"
+ ],
+ "description": "Get dataset representation",
+ "parameters": [
+ {
+ "name": "attribute",
+ "in": "path",
+ "description": "requested attribute",
+ "required": true,
+ "schema": {
+ "type": "string",
+ "enum": [
+ "compounds",
+ "nanoparticles",
+ "substances",
+ "features"
+ ]
}
+ },
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/substance": {
+ "get": {
+ "x-orn-@type": "x-orn:Substance",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/substance",
+ "x-orn:method": "Get",
+ "tags": [
+ "substance"
+ ],
+ "description": "Get a list of all substances",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/substance/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Substance",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/substance/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "substance"
+ ],
+ "description": "Get substance representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/nanoparticle": {
+ "get": {
+ "x-orn-@type": "x-orn:Nanoparticle",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/nanoparticle",
+ "x-orn:method": "Get",
+ "tags": [
+ "nanoparticle"
+ ],
+ "description": "Get a list of all nanoparticles",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/nanoparticle/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Nanoparticle",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/nanoparticle/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "nanoparticle"
+ ],
+ "description": "Get nanoparticle representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/feature": {
+ "get": {
+ "x-orn-@type": "x-orn:Feature",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/feature",
+ "x-orn:method": "Get",
+ "tags": [
+ "feature"
+ ],
+ "description": "Get a list of ids for all features",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/feature/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Feature",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/feature/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "feature"
+ ],
+ "description": "Get feature representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/validation": {
+ "get": {
+ "x-orn-@type": "x-orn:Validation",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/validation",
+ "x-orn:method": "Get",
+ "tags": [
+ "validation"
+ ],
+ "description": "Get a list of all validation types",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/validation/{validationtype}": {
+ "get": {
+ "x-orn-@type": "x-orn:Validation",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/validation/{validationtype}",
+ "x-orn:method": "Get",
+ "tags": [
+ "validation"
+ ],
+ "description": "Get all validations of a validation type",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/valtype"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/validation/{validationtype}/{id}": {
+ "get": {
+ "x-orn-@type": "x-orn:Validation",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/validation/{validationtype}/{id}",
+ "x-orn:method": "Get",
+ "tags": [
+ "validation"
+ ],
+ "description": "Get validation representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/valtype"
+ },
+ {
+ "$ref": "#/components/parameters/id"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "403": {
+ "$ref": "#/components/responses/403"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/compound/descriptor": {
+ "get": {
+ "x-orn-@type": "x-orn:Descriptor",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/compound/descriptor",
+ "x-orn:method": "Get",
+ "tags": [
+ "compound",
+ "descriptor"
+ ],
+ "description": "Get a list of all descriptors",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ },
+ "post": {
+ "x-orn-@type": "x-orn:Prediction",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/compound/descriptor",
+ "x-orn:method": "Post",
+ "tags": [
+ "compound",
+ "descriptor"
+ ],
+ "summary": "Descriptor calculation",
+ "description": "Calculate descriptors for a single compound as SMILES string",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
},
- "/compound/{InChI}": {
- "get": {
- "tags": [
- "compound"
- ],
- "description": "Get compound representation",
- "parameters": [
- {
- "$ref": "#/parameters/InChI"
- },
- {
- "$ref": "#/parameters/subjectid"
- }
- ],
- "produces": [
- "application/json",
- "chemical/x-daylight-smiles",
- "chemical/x-inchi",
- "chemical/x-mdl-sdfile",
- "chemical/x-mdl-molfile",
- "image/png",
- "image/svg+xml",
- "text/plain"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- }
- }
+ "requestBody": {
+ "description": "identifier and descriptor/s",
+ "required": true,
+ "content": {
+ "application/x-www-form-urlencoded": {
+ "x-orn:schema": "application/x-www-form-urlencoded",
+ "schema": {
+ "$ref": "#/components/schemas/postdescriptor"
+ }
}
- },
- "/api/api.json": {
- "get": {
- "tags": [
- "api"
- ],
- "description": "Get swagger api in JSON",
- "produces": [
- "application/json"
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
+ }
+ }
+ }
+ },
+ "/compound/descriptor/{descriptor}": {
+ "get": {
+ "x-orn-@type": "x-orn:Descriptor",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/compound/descriptor/{descriptor}",
+ "x-orn:method": "Get",
+ "tags": [
+ "compound",
+ "descriptor"
+ ],
+ "description": "Get informations about a single descriptor",
+ "parameters": [
+ {
+ "name": "descriptor",
+ "in": "path",
+ "description": "descriptor name or ID",
+ "required": true,
+ "schema": {
+ "type": "string"
}
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "404": {
+ "$ref": "#/components/responses/404"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/compound/{InChI}": {
+ "get": {
+ "x-orn-@type": "x-orn:Compound",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/compound/{InChI}",
+ "x-orn:method": "Get",
+ "tags": [
+ "compound"
+ ],
+ "description": "Get compound representation",
+ "parameters": [
+ {
+ "$ref": "#/components/parameters/InChI"
+ },
+ {
+ "$ref": "#/components/parameters/subjectid"
+ }
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ }
+ }
+ }
+ },
+ "/api/api.json": {
+ "get": {
+ "tags": [
+ "api"
+ ],
+ "description": "Get swagger api in JSON",
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
+ }
+ }
+ },
+ "/aa/authenticate": {
+ "post": {
+ "x-orn-@type": "x-orn:Authentication",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/aa/authenticate",
+ "x-orn:method": "Post",
+ "tags": [
+ "authentication"
+ ],
+ "summary": "Get token",
+ "description": "Authentication against OpenSSO. Returns authentication token. Requires\nUsername and Password.\n",
+ "operationId": "login",
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
},
- "/aa/authenticate": {
- "post": {
- "tags": [
- "authentication"
- ],
- "summary": "Get token",
- "description": "Authentication against OpenSSO. Returns authentication token. Requires Username and Password.",
- "operationId": "login",
- "consumes": [
- "text/plain; charset=utf-8",
- "multipart/form-data"
- ],
- "produces": [
- "text/plain; charset=utf-8"
- ],
- "parameters": [
- {
- "in": "formData",
- "name": "username",
- "description": "username",
- "required": true,
- "type": "string"
- },
- {
- "in": "formData",
- "name": "password",
- "description": "password",
- "required": true,
- "type": "string",
- "format": "password"
- }
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
+ "requestBody": {
+ "description": "username and password",
+ "required": true,
+ "content": {
+ "application/x-www-form-urlencoded": {
+ "x-orn:schema": "application/x-www-form-urlencoded",
+ "schema": {
+ "$ref": "#/components/schemas/postauth"
+ }
}
+ }
+ }
+ }
+ },
+ "/aa/logout": {
+ "post": {
+ "x-orn-@type": "x-orn:Authentication",
+ "x-orn:path": "https://dg-lazar.prod.openrisknet.org/aa/logout",
+ "x-orn:method": "Post",
+ "description": "Devalidates a token. Requires Subjectid.",
+ "summary": "Destroy token",
+ "operationId": "logout",
+ "tags": [
+ "authentication"
+ ],
+ "responses": {
+ "200": {
+ "$ref": "#/components/responses/200"
+ },
+ "400": {
+ "$ref": "#/components/responses/400"
+ },
+ "401": {
+ "$ref": "#/components/responses/401"
+ },
+ "500": {
+ "$ref": "#/components/responses/500"
+ }
},
- "/aa/logout": {
- "post": {
- "description": "Devalidates a token. Requires Subjectid.",
- "summary": "Destroy token",
- "operationId": "logout",
- "tags": [
- "authentication"
- ],
- "consumes": [
- "text/plain; charset=utf-8",
- "multipart/form-data"
- ],
- "produces": [
- "text/plain; charset=utf-8"
- ],
- "parameters": [
- {
- "in": "formData",
- "name": "subjectid",
- "description": "subjectid",
- "required": true,
- "type": "string"
- }
- ],
- "responses": {
- "200": {
- "$ref": "#/responses/200"
- },
- "400": {
- "$ref": "#/responses/400"
- },
- "401": {
- "$ref": "#/responses/401"
- },
- "500": {
- "$ref": "#/responses/500"
- }
- }
+ "requestBody": {
+ "required": true,
+ "content": {
+ "application/x-www-form-urlencoded": {
+ "x-orn:schema": "application/x-www-form-urlencoded",
+ "schema": {
+ "$ref": "#/components/schemas/postlogout"
+ }
}
+ }
}
+ }
+ }
+ },
+ "tags": [
+ {
+ "name": "api",
+ "description": "Swagger API representation in JSON"
},
- "parameters": {
- "id": {
- "name": "id",
- "in": "path",
- "description": "id",
- "required": true,
- "type": "string"
- },
- "InChI": {
- "name": "InChI",
- "in": "path",
- "description": "InChI String",
- "required": true,
- "type": "string"
- },
- "valtype": {
- "name": "validationtype",
- "in": "path",
- "description": "validation type",
- "required": true,
- "type": "string"
- },
- "subjectid": {
- "in": "header",
- "name": "subjectid",
- "description": "authorization token",
- "required": false,
+ {
+ "name": "algorithm",
+ "description": "Algorithm"
+ },
+ {
+ "name": "authentication",
+ "description": "minimal Authentication service"
+ },
+ {
+ "name": "compound",
+ "description": "Compound"
+ },
+ {
+ "name": "dataset",
+ "description": "Dataset"
+ },
+ {
+ "name": "descriptor",
+ "description": "Descriptor"
+ },
+ {
+ "name": "feature",
+ "description": "Feature"
+ },
+ {
+ "name": "model",
+ "description": "Lazar Model Service"
+ },
+ {
+ "name": "nanoparticle",
+ "description": "Nanoparticle"
+ },
+ {
+ "name": "report",
+ "description": "QMRF Reporting"
+ },
+ {
+ "name": "substance",
+ "description": "Substance"
+ },
+ {
+ "name": "validation",
+ "description": "Validation"
+ }
+ ],
+ "components": {
+ "schemas": {
+ "postmodel": {
+ "type": "object",
+ "properties": {
+ "identifier": {
+ "x-orn:property": "identifier",
+ "type": "string",
+ "example": "O=C1NC(=O)NC=C1"
+ }
+ }
+ },
+ "postdescriptor": {
+ "type": "object",
+ "properties": {
+ "identifier": {
+ "x-orn:property": "identifier",
+ "type": "string",
+ "example": "O=C1NC(=O)NC=C1"
+ },
+ "descriptor": {
+ "x-orn:property": "descriptor",
+ "type": "string",
+ "example": "Openbabel.MW,Openbabel.atoms"
+ }
+ }
+ },
+ "postauth": {
+ "type": "object",
+ "properties": {
+ "username": {
+ "x-orn:property": "username",
"type": "string"
- },
- "subjectidRequired": {
- "in": "header",
- "name": "subjectid",
- "description": "authorization token",
- "required": true,
+ },
+ "password": {
+ "x-orn:property": "password",
+ "type": "string",
+ "format": "password"
+ }
+ }
+ },
+ "postlogout": {
+ "type": "object",
+ "properties": {
+ "subjectid": {
+ "x-orn:property": "subjectid",
"type": "string"
+ }
}
+ }
},
- "responses": {
- "200": {
- "description": "OK"
- },
- "400": {
- "description": "Bad Request"
- },
- "401": {
- "description": "Unauthorized"
- },
- "403": {
- "description": "Forbidden"
- },
- "404": {
- "description": "Resource Not Found"
- },
- "500": {
- "description": "Server Error"
+ "parameters": {
+ "id": {
+ "name": "id",
+ "in": "path",
+ "description": "id",
+ "required": true,
+ "schema": {
+ "type": "string"
+ }
+ },
+ "InChI": {
+ "name": "InChI",
+ "in": "path",
+ "description": "InChI String",
+ "required": true,
+ "schema": {
+ "type": "string"
}
+ },
+ "valtype": {
+ "name": "validationtype",
+ "in": "path",
+ "description": "validation type",
+ "required": true,
+ "schema": {
+ "type": "string"
+ }
+ },
+ "subjectid": {
+ "in": "header",
+ "name": "subjectid",
+ "description": "authorization token",
+ "required": false,
+ "schema": {
+ "type": "string"
+ }
+ },
+ "subjectidRequired": {
+ "in": "header",
+ "name": "subjectid",
+ "description": "authorization token",
+ "required": true,
+ "schema": {
+ "type": "string"
+ }
+ }
},
- "tags": [
- {
- "name": "api",
- "description": "Swagger API representation in JSON"
- },
- {
- "name": "algorithm",
- "description": "Algorithm"
- },
- {
- "name": "authentication",
- "description": "minimal Authentication service"
- },
- {
- "name": "compound",
- "description": "Compound"
- },
- {
- "name": "dataset",
- "description": "Dataset"
- },
- {
- "name": "descriptor",
- "description": "Descriptor"
- },
- {
- "name": "feature",
- "description": "Feature"
- },
- {
- "name": "model",
- "description": "Lazar Model Service"
- },
- {
- "name": "nanoparticle",
- "description": "Nanoparticle"
- },
- {
- "name": "report",
- "description": "QMRF Reporting"
- },
- {
- "name": "substance",
- "description": "Substance"
- },
- {
- "name": "validation",
- "description": "Validation"
+ "responses": {
+ "200": {
+ "description": "OK",
+ "content": {
+ "application/json": {
+ "x-orn:returns": "application/json",
+ "schema": {
+ "type": "object"
+ }
+ }
}
- ]
+ },
+ "400": {
+ "description": "Bad Request"
+ },
+ "401": {
+ "description": "Unauthorized"
+ },
+ "403": {
+ "description": "Forbidden"
+ },
+ "404": {
+ "description": "Resource Not Found"
+ },
+ "500": {
+ "description": "Server Error"
+ }
+ }
+ }
}