From 3a11ba2918795821600b7113d0758415718d263a Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 11 Jun 2018 12:46:06 +0200 Subject: combine gui with rest --- api/api.json | 1098 +++++++++++++++++++++++++++++++++++++++++++++++++++ application.rb | 21 +- lib/aa.rb | 82 ++++ lib/api.rb | 9 + lib/compound.rb | 64 +++ lib/dataset.rb | 46 +++ lib/feature.rb | 29 ++ lib/lazar-rest.rb | 69 ++++ lib/model.rb | 38 ++ lib/nanoparticle.rb | 30 ++ lib/report.rb | 208 ++++++++++ lib/substance.rb | 30 ++ lib/swagger.rb | 6 + lib/validation.rb | 71 ++++ 14 files changed, 1799 insertions(+), 2 deletions(-) create mode 100644 api/api.json create mode 100644 lib/aa.rb create mode 100644 lib/api.rb create mode 100644 lib/compound.rb create mode 100644 lib/dataset.rb create mode 100644 lib/feature.rb create mode 100644 lib/lazar-rest.rb create mode 100644 lib/model.rb create mode 100644 lib/nanoparticle.rb create mode 100644 lib/report.rb create mode 100644 lib/substance.rb create mode 100644 lib/swagger.rb create mode 100644 lib/validation.rb diff --git a/api/api.json b/api/api.json new file mode 100644 index 0000000..9976569 --- /dev/null +++ b/api/api.json @@ -0,0 +1,1098 @@ +{ + "openapi": "3.0.0", + "x-orn-@id": "https://lazar.prod.openrisknet.org", + "x-orn-@type": "x-orn:Service", + "x-orn-@context": { + "@vocab": "http://openrisknet.org/schema#", + "x-orn": "http://openrisknet.org/schema#", + "x-orn-@id": "@id", + "x-orn-@type": "@type" + }, + "servers": [ + { + "url": "https://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": "info@in-silico.ch", + "url": "https://in-silico.ch" + }, + "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://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" + } + } + } + }, + "/model/{id}": { + "get": { + "x-orn-@type": "x-orn:Model", + "x-orn:path": "https://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": { + "$ref": "#/components/responses/404" + } + } + }, + "post": { + "x-orn-@type": "x-orn:Prediction", + "x-orn:path": "https://lazar.prod.openrisknet.org/model/{id}", + "x-orn:method": "Post", + "tags": [ + "model" + ], + "description": "Predict a compound or a nanoparticle", + "parameters": [ + { + "$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" + } + }, + "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": { + "$ref": "#/components/schemas/postmodel" + } + } + } + } + } + }, + "/report": { + "get": { + "x-orn-@type": "x-orn:Report", + "x-orn:path": "https://lazar.prod.openrisknet.org/report", + "x-orn:method": "Get", + "tags": [ + "report" + ], + "description": "Get a list of QMRF reports", + "parameters": [ + { + "$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": { + "$ref": "#/components/responses/500" + } + } + } + }, + "/report/{id}": { + "get": { + "x-orn-@type": "x-orn:Report", + "x-orn:path": "https://lazar.prod.openrisknet.org/report/{id}", + "x-orn:method": "Get", + "tags": [ + "report" + ], + "description": "Get QMRF for prediction model", + "parameters": [ + { + "$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://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://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://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://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://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://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://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://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://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://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://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://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": { + "$ref": "#/components/responses/500" + } + } + } + }, + "/compound/descriptor": { + "get": { + "x-orn-@type": "x-orn:Descriptor", + "x-orn:path": "https://lazar.prod.openrisknet.org/compound/descriptor", + "x-orn:method": "Get", + "tags": [ + "compound", + "descriptor" + ], + "description": "Get a list of all descriptors", + "parameters": [ + { + "$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": { + "$ref": "#/components/responses/500" + } + } + }, + "post": { + "x-orn-@type": "x-orn:Prediction", + "x-orn:path": "https://lazar.prod.openrisknet.org/compound/descriptor", + "x-orn:method": "Post", + "tags": [ + "compound", + "descriptor" + ], + "summary": "Descriptor calculation", + "description": "Calculate descriptors for a single compound as SMILES string", + "parameters": [ + { + "$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": { + "$ref": "#/components/responses/500" + } + }, + "requestBody": { + "description": "identifier and descriptor/s", + "required": true, + "content": { + "application/x-www-form-urlencoded": { + "x-orn:schema": "application/x-www-form-urlencoded", + "schema": { + "$ref": "#/components/schemas/postdescriptor" + } + } + } + } + } + }, + "/compound/descriptor/{descriptor}": { + "get": { + "x-orn-@type": "x-orn:Descriptor", + "x-orn:path": "https://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://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": { + "$ref": "#/components/responses/500" + } + } + } + }, + "/aa/authenticate": { + "post": { + "x-orn-@type": "x-orn:Authentication", + "x-orn:path": "https://lazar.prod.openrisknet.org/aa/authenticate", + "x-orn:method": "Post", + "tags": [ + "authentication" + ], + "summary": "Get token", + "description": "Authentication against OpenSSO. Returns authentication token. Requires\nUsername and Password.\n", + "operationId": "login", + "responses": { + "200": { + "$ref": "#/components/responses/200" + }, + "400": { + "$ref": "#/components/responses/400" + }, + "401": { + "$ref": "#/components/responses/401" + }, + "500": { + "$ref": "#/components/responses/500" + } + }, + "requestBody": { + "description": "username and password", + "required": true, + "content": { + "application/x-www-form-urlencoded": { + "x-orn:schema": "application/x-www-form-urlencoded", + "schema": { + "$ref": "#/components/schemas/postauth" + } + } + } + } + } + }, + "/aa/logout": { + "post": { + "x-orn-@type": "x-orn:Authentication", + "x-orn:path": "https://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" + } + }, + "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" + }, + { + "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" + }, + "password": { + "x-orn:property": "password", + "type": "string", + "format": "password" + } + } + }, + "postlogout": { + "type": "object", + "properties": { + "subjectid": { + "x-orn:property": "subjectid", + "type": "string" + } + } + } + }, + "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" + } + } + }, + "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" + } + } + } +} diff --git a/application.rb b/application.rb index 895b0c2..04e5352 100644 --- a/application.rb +++ b/application.rb @@ -26,10 +26,27 @@ error do haml :error end -get '/?' do - redirect to('/predict') +# https://github.com/britg/sinatra-cross_origin#responding-to-options +options "*" do + response.headers["Allow"] = "HEAD,GET,PUT,POST,DELETE,OPTIONS" + response.headers["Access-Control-Allow-Headers"] = "X-Requested-With, X-HTTP-Method-Override, Content-Type, Cache-Control, Accept" + 200 end +[ + "aa.rb", + "api.rb", + "compound.rb", + "dataset.rb", + "feature.rb", + "model.rb", + "nanoparticle.rb", + "report.rb", + "substance.rb", + "swagger.rb", + "validation.rb" +].each{ |f| require_relative "./lib/#{f}" } + get '/predict/?' do @models = OpenTox::Model::Validation.all @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/} diff --git a/lib/aa.rb b/lib/aa.rb new file mode 100644 index 0000000..6dfec4b --- /dev/null +++ b/lib/aa.rb @@ -0,0 +1,82 @@ +post "/aa/authenticate/?" do + mime_types = ["text/plain"] + bad_request_error "Mime type #{@accept} not supported here. Please request data as #{mime_types.join(', ')}." unless mime_types.include? @accept + bad_request_error "Please send formdata username." unless params[:username] + bad_request_error "Please send formdata password." unless params[:password] + case @accept + when "text/plain" + if OpenTox::Authorization.authenticate(params[:username], params[:password]) + return OpenTox::RestClientWrapper.subjectid + else + return nil + end + else + bad_request_error "'#{@accept}' is not a supported content type." + end +end + +post "/aa/logout/?" do + mime_types = ["text/plain"] + bad_request_error "Mime type #{@accept} not supported here. Please request data as #{mime_types.join(', ')}." unless mime_types.include? @accept + bad_request_error "Please send formdata subjectid." unless params[:subjectid] + case @accept + when "text/plain" + if OpenTox::Authorization.logout(params[:subjectid]) + return "Successfully logged out. \n" + else + return "Logout failed.\n" + end + else + bad_request_error "'#{@accept}' is not a supported content type." + end +end + +module OpenTox + + AA = "https://opensso.in-silico.ch" + + module Authorization + #Authentication against OpenSSO. Returns token. Requires Username and Password. + # @param user [String] Username + # @param pw [String] Password + # @return [Boolean] true if successful + def self.authenticate(user, pw) + begin + res = RestClientWrapper.post("#{AA}/auth/authenticate",{:username=>user, :password => pw},{:subjectid => ""}).sub("token.id=","").sub("\n","") + if is_token_valid(res) + RestClientWrapper.subjectid = res + return true + else + bad_request_error "Authentication failed #{res.inspect}" + end + rescue + bad_request_error "Authentication failed #{res.inspect}" + end + end + + #Logout on opensso. Make token invalid. Requires token + # @param [String] subjectid the subjectid + # @return [Boolean] true if logout is OK + def self.logout(subjectid=RestClientWrapper.subjectid) + begin + out = RestClientWrapper.post("#{AA}/auth/logout", :subjectid => subjectid) + return true unless is_token_valid(subjectid) + rescue + return false + end + return false + end + + #Checks if a token is a valid token + # @param [String]subjectid subjectid from openSSO session + # @return [Boolean] subjectid is valid or not. + def self.is_token_valid(subjectid=RestClientWrapper.subjectid) + begin + return true if RestClientWrapper.post("#{AA}/auth/isTokenValid",:tokenid => subjectid) == "boolean=true\n" + rescue #do rescue because openSSO throws 401 + return false + end + return false + end + end +end \ No newline at end of file diff --git a/lib/api.rb b/lib/api.rb new file mode 100644 index 0000000..28e33df --- /dev/null +++ b/lib/api.rb @@ -0,0 +1,9 @@ +# route to swagger API file +get "/api/api.json" do + response['Content-Type'] = "application/json" + api_file = File.join("api", "api.json") + bad_request_error "API Documentation in Swagger JSON is not implemented." unless File.exists?(api_file) + api_hash = JSON.parse(File.read(api_file)) + api_hash["host"] = request.env['HTTP_HOST'] + return api_hash.to_json +end diff --git a/lib/compound.rb b/lib/compound.rb new file mode 100644 index 0000000..01ba036 --- /dev/null +++ b/lib/compound.rb @@ -0,0 +1,64 @@ +# Get a list of a single or all descriptors +# @param [Header] Accept one of text/plain, application/json +# @param [Path] Descriptor name or descriptor ID (e.G.: Openbabel.HBA1, 5755f8eb3cf99a00d8fedf2f) +# @return [text/plain, application/json] list of all prediction models +get "/compound/descriptor/?:descriptor?" do + case @accept + when "application/json" + return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} " unless params[:descriptor] + return PhysChem.find_by(:name => params[:descriptor]).to_json if PhysChem::DESCRIPTORS.include?(params[:descriptor]) + return PhysChem.find(params[:descriptor]).to_json if PhysChem.find(params[:descriptor]) + else + return PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor] + return PhysChem::DESCRIPTORS[params[:descriptor]] if PhysChem::DESCRIPTORS.include?(params[:descriptor]) + return "#{PhysChem.find(params[:descriptor]).name}: #{PhysChem.find(params[:descriptor]).description}" if PhysChem.find(params[:descriptor]) + end +end + +post "/compound/descriptor/?" do + bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor] + descriptors = params['descriptor'].split(',') + compound = Compound.from_smiles params[:identifier] + physchem_descriptors = [] + descriptors.each do |descriptor| + physchem_descriptors << PhysChem.find_by(:name => descriptor) + end + result = compound.calculate_properties physchem_descriptors + csv = (0..result.size-1).collect{|i| "\"#{physchem_descriptors[i].name}\",#{result[i]}"}.join("\n") + csv = "SMILES,\"#{params[:identifier]}\"\n#{csv}" if params[:identifier] + case @accept + when "text/csv","application/csv" + return csv + when "application/json" + result_hash = (0..result.size-1).collect{|i| {"#{physchem_descriptors[i].name}" => "#{result[i]}"}} + data = {"compound" => {"SMILES" => "#{params[:identifier]}"}} + data["compound"]["InChI"] = "#{compound.inchi}" if compound.inchi + data["compound"]["results"] = result_hash + return JSON.pretty_generate(data) + end +end + +get %r{/compound/(.+)} do |inchi| + bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/) + compound = Compound.from_inchi URI.unescape(inchi) + response['Content-Type'] = @accept + case @accept + when "application/json" + return JSON.pretty_generate JSON.parse(compound.to_json) + when "chemical/x-daylight-smiles" + return compound.smiles + when "chemical/x-inchi" + return compound.inchi + when "chemical/x-mdl-sdfile" + return compound.sdf + when "chemical/x-mdl-molfile" + when "image/png" + return compound.png + when "image/svg+xml" + return compound.svg + when "text/plain" + return "#{compound.names}\n" + else + return compound.inspect + end +end \ No newline at end of file diff --git a/lib/dataset.rb b/lib/dataset.rb new file mode 100644 index 0000000..7c74f39 --- /dev/null +++ b/lib/dataset.rb @@ -0,0 +1,46 @@ +# Get all datasets +get "/dataset/?" do + datasets = Dataset.all + case @accept + when "text/uri-list" + uri_list = datasets.collect{|dataset| uri("/dataset/#{dataset.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + datasets = JSON.parse datasets.to_json + list = [] + datasets.each{|d| list << uri("/dataset/#{d["_id"]["$oid"]}")} + return list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a dataset +get "/dataset/:id/?" do + dataset = Dataset.find :id => params[:id] + not_found_error "Dataset with id: #{params[:id]} not found." unless dataset + case @accept + when "application/json" + dataset.data_entries.each do |k, v| + dataset.data_entries[k][:URI] = uri("/substance/#{k}") + end + dataset[:URI] = uri("/dataset/#{dataset.id}") + dataset[:substances] = uri("/dataset/#{dataset.id}/substances") + dataset[:features] = uri("/dataset/#{dataset.id}/features") + return dataset.to_json + when "text/csv", "application/csv" + return dataset.to_csv + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a dataset attribute. One of compounds, nanoparticles, substances, features +get "/dataset/:id/:attribute/?" do + dataset = Dataset.find :id => params[:id] + not_found_error "Dataset with id: #{params[:id]} not found." unless dataset + attribs = ["compounds", "nanoparticles", "substances", "features"] + return "Attribute '#{params[:attribute]}' is not available. Choose one of #{attribs.join(', ')}." unless attribs.include? params[:attribute] + out = dataset.send("#{params[:attribute]}") + return out.to_json +end diff --git a/lib/feature.rb b/lib/feature.rb new file mode 100644 index 0000000..06a5b37 --- /dev/null +++ b/lib/feature.rb @@ -0,0 +1,29 @@ +# Get all Features +get "/feature/?" do + features = Feature.all + case @accept + when "text/uri-list" + uri_list = features.collect{|feature| uri("/feature/#{feature.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + features = JSON.parse features.to_json + list = [] + features.each{|f| list << uri("/feature/#{f["_id"]["$oid"]}")} + return list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a feature +get "/feature/:id/?" do + case @accept + when "application/json" + feature = Feature.find :id => params[:id] + not_found_error "Feature with id: #{params[:id]} not found." unless feature + feature[:URI] = uri("/feature/#{feature.id}") + return feature.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end diff --git a/lib/lazar-rest.rb b/lib/lazar-rest.rb new file mode 100644 index 0000000..255c52f --- /dev/null +++ b/lib/lazar-rest.rb @@ -0,0 +1,69 @@ +require "sinatra" +require "sinatra/reloader" +require 'sinatra/cross_origin' + +configure do + $logger = Logger.new(STDOUT) + enable :reloader #if development? + enable :cross_origin + disable :show_exceptions + disable :raise_errors +end + +#set :protection, :except => :frame_options + +# Environment setup from unicorn -E param +ENV["LAZAR_ENV"] = ENV["RACK_ENV"] +require "../lazar/lib/lazar.rb" +require "../qsar-report/lib/qsar-report.rb" +=begin +if ENV["LAZAR_ENV"] == "development" + require "../lazar/lib/lazar.rb" + require "../qsar-report/lib/qsar-report.rb" +else + require "lazar" + require "qsar-report" +end +=end + +include OpenTox + +before do + @accept = request.env['HTTP_ACCEPT'] + response['Content-Type'] = @accept +end + +not_found do + 400 + "Path '#{request.env["REQUEST_PATH"]}' not found.\n" +end + +error do + response['Content-Type'] = "text/plain" + error = request.env['sinatra.error'] + body = error.message+"\n" + error.respond_to?(:http_code) ? code = error.http_code : code = 500 + halt code, body +end + +# https://github.com/britg/sinatra-cross_origin#responding-to-options +options "*" do + response.headers["Allow"] = "HEAD,GET,PUT,POST,DELETE,OPTIONS" + response.headers["Access-Control-Allow-Headers"] = "X-Requested-With, X-HTTP-Method-Override, Content-Type, Cache-Control, Accept" + 200 +end + +[ + "aa.rb", + "api.rb", + "compound.rb", + "dataset.rb", + "feature.rb", + "model.rb", + "nanoparticle.rb", + "report.rb", + "substance.rb", + "swagger.rb", + "validation.rb" +].each{ |f| require_relative f } + diff --git a/lib/model.rb b/lib/model.rb new file mode 100644 index 0000000..9fbd90f --- /dev/null +++ b/lib/model.rb @@ -0,0 +1,38 @@ + +# Get a list of all prediction models +# @param [Header] Accept one of text/uri-list, +# @return [text/uri-list] list of all prediction models +get "/model/?" do + models = Model::Validation.all + case @accept + when "text/uri-list" + uri_list = models.collect{|model| uri("/model/#{model.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + models = JSON.parse models.to_json + list = [] + models.each{|m| list << uri("/model/#{m["_id"]["$oid"]}")} + return list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +get "/model/:id/?" do + model = Model::Validation.find params[:id] + not_found_error "Model with id: #{params[:id]} not found." unless model + return model.to_json +end + + +post "/model/:id/?" do + identifier = params[:identifier].split(",") + compounds = identifier.collect{ |i| Compound.from_smiles i.strip } + model = Model::Validation.find params[:id] + batch = {} + compounds.each do |compound| + prediction = model.predict(compound) + batch[compound] = {:id => compound.id, :inchi => compound.inchi, :smiles => compound.smiles, :model => model, :prediction => prediction} + end + return batch.to_json +end diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb new file mode 100644 index 0000000..332493d --- /dev/null +++ b/lib/nanoparticle.rb @@ -0,0 +1,30 @@ +# Get all Nanoparticles +get "/nanoparticle/?" do + nanoparticles = Nanoparticle.all + case @accept + when "text/uri-list" + uri_list = nanoparticles.collect{|nanoparticle| uri("/nanoparticle/#{nanoparticle.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + nanoparticles = JSON.parse nanoparticles.to_json + nanoparticles.each_index do |idx| + nanoparticles[idx][:URI] = uri("/nanoparticle/#{nanoparticles[idx]["_id"]["$oid"]}") + end + return nanoparticles.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a nanoparticle +get "/nanoparticle/:id/?" do + case @accept + when "application/json" + nanoparticle = Nanoparticle.find :id => params[:id] + not_found_error "Nanoparticle with id: #{params[:id]} not found." unless nanoparticle + nanoparticle[:URI] = uri("/nanoparticle/#{nanoparticle.id}") + return nanoparticle.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end diff --git a/lib/report.rb b/lib/report.rb new file mode 100644 index 0000000..f576106 --- /dev/null +++ b/lib/report.rb @@ -0,0 +1,208 @@ +# Get a list of all possible reports to prediction models +# @param [Header] Accept one of text/uri-list, +# @return [text/uri-list] list of all prediction models +get "/report/?" do + models = Model::Validation.all + case @accept + when "text/uri-list" + uri_list = models.collect{|model| uri("/report/#{model.model_id}")} + return uri_list.join("\n") + "\n" + when "application/json" + models = JSON.parse models.to_json + list = [] + models.each{|m| list << uri("/report/#{m["model_id"]["$oid"]}")} + return list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +get "/report/:id/?" do + case @accept + when "application/xml" + model = Model::Lazar.find params[:id] + not_found_error "Model with id: #{params[:id]} not found." unless model + prediction_model = Model::Validation.find_by :model_id => params[:id] + validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") + + if File.directory?("#{File.dirname(__FILE__)}/../../lazar") + lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip + lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}" + else + lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}" + end + + report = OpenTox::QMRFReport.new + + # QSAR Identifier Title 1.1 + report.value "QSAR_title", "Lazar model for #{prediction_model.species} #{prediction_model.endpoint}" + + # Software coding the model 1.3 + report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :description => "lazar Lazy Structure- Activity Relationships", :number => "1", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware + + # Date of QMRF 2.1 + report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}" + + # QMRF author(s) and contact details 2.1 + report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} + report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor + + # Model developer(s) and contact details 2.5 + report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} + report.ref_catalog :model_authors, :authors_catalog, :modelauthor + + # Date of model development and/or publication 2.6 + report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}" + + # Reference(s) to main scientific papers and/or software package 2.7 + report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz, Guetlein, Rautenberg, Vorgrimmler, Gebele and Helma (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} + report.ref_catalog :references, :publications_catalog, :publications_catalog_1 + + # Reference(s) to main scientific papers and/or software package 2.7 + report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Maunz A and Helma C (2008) Prediction of chemical toxicity with local support vector regression and activity-specific kernels. SAR & QSAR in Environmental Research 19 (5-6), 413-431", :url => "http://dx.doi.org/10.1080/10629360802358430"} + report.ref_catalog :references, :publications_catalog, :publications_catalog_2 + + # Species 3.1 + report.value "model_species", prediction_model.species + + # Endpoint 3.2 + report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""} + report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1 + + # Endpoint Units 3.4 + report.value "endpoint_units", "#{prediction_model.unit}" + + model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','') + + # Type of model 4.1 + report.value "algorithm_type", "#{model_type}" + + # Explicit algorithm 4.2 + report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.algorithms["similarity"]["method"].gsub('_',' ').titleize}#{(model.algorithms["similarity"][:min] ? ' with similarity > ' + model.algorithms["similarity"][:min].to_s : '')}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1 + report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3 + if model.algorithms["prediction"] + pred_algorithm_params = (model.algorithms["prediction"][:method] == "rf" ? "random forest" : model.algorithms["prediction"][:method]) + end + report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.algorithms["prediction"].to_s.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"} + report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2 + + # Descriptors in the model 4.3 + if model.algorithms["descriptors"][:type] + report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.algorithms["descriptors"][:type]}", :publication_ref => "", :units => ""} + report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1 + end + + # Descriptor selection 4.4 + report.value "descriptors_selection", "#{model.algorithms["feature_selection"].gsub('_',' ')} #{model.algorithms["feature_selection"].collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.algorithms["feature_selection"] + + # Algorithm and descriptor generation 4.5 + report.value "descriptors_generation", "exhaustive breadth first search for paths in chemical graphs (simplified MolFea algorithm)" + + # Software name and version for descriptor generation 4.6 + report.change_catalog :software_catalog, :software_catalog_2, {:name => "lazar, submitted version: #{lazar_commit}", :description => "simplified MolFea algorithm", :number => "2", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :descriptors_generation_software, :software_catalog, :software_catalog_2 + + # Chemicals/Descriptors ratio 4.7 + report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)" + + # Description of the applicability domain of the model 5.1 + report.value "app_domain_description", " +

+ The applicability domain (AD) of the training set is characterized by + the confidence index of a prediction (high confidence index: close to + the applicability domain of the training set/reliable prediction, low + confidence: far from the applicability domain of the + trainingset/unreliable prediction). The confidence index considers (i) + the similarity and number of neighbors and (ii) contradictory examples + within the neighbors. A formal definition can be found in Helma 2006. +

+

+ The reliability of predictions decreases gradually with increasing + distance from the applicability domain (i.e. decreasing confidence index) +

+ + " + + # Method used to assess the applicability domain 5.2 + report.value "app_domain_method", "see Helma 2006 and Maunz 2008" + + # Software name and version for applicability domain assessment 5.3 + report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} + report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3 + + # Limits of applicability 5.4 + report.value "applicability_limits", "Predictions with low confidence index, unknown substructures and neighbors that might act by different mechanisms" + + # Availability of the training set 6.1 + report.change_attributes "training_set_availability", {:answer => "Yes"} + + # Available information for the training set 6.2 + report.change_attributes "training_set_data", {:cas => "Yes", :chemname => "Yes", :formula => "Yes", :inchi => "Yes", :mol => "Yes", :smiles => "Yes"} + + # Data for each descriptor variable for the training set 6.3 + report.change_attributes "training_set_descriptors", {:answer => "No"} + + # Data for the dependent variable for the training set 6.4 + report.change_attributes "dependent_var_availability", {:answer => "All"} + + # Other information about the training set 6.5 + report.value "other_info", "#{prediction_model.source}" + + # Pre-processing of data before modelling 6.6 + report.value "preprocessing", (model.class == OpenTox::Model::LazarRegression ? "-log10 transformation" : "none") + + # Robustness - Statistics obtained by leave-many-out cross-validation 6.9 + if prediction_model.repeated_crossvalidation + crossvalidations = prediction_model.crossvalidations + out = haml File.read(validation_template), :layout=> false, :locals => {:model => prediction_model} + report.value "lmo", out + end + + # Mechanistic basis of the model 8.1 + report.value "mechanistic_basis"," +

+ Compounds with similar structures (neighbors) are assumed to have + similar activities as the query compound. For the determination of + activity specific similarities only statistically relevant subtructures + (paths) are used. For this reason there is a priori no bias towards + specific mechanistic hypothesis. +

+ + " + + # A priori or a posteriori mechanistic interpretation 8.2 + report.value "mechanistic_basis_comments","a posteriori for individual predictions" + + # Other information about the mechanistic interpretation 8.3 + report.value "mechanistic_basis_info","

Hypothesis about biochemical mechanisms can be derived from individual + predictions by inspecting neighbors and relevant fragments.

+

Neighbors are compounds that are similar in respect to a certain + endpoint and it is likely that compounds with high similarity act by + similar mechanisms as the query compound. Links at the webinterface + prove an easy access to additional experimental data and literature + citations for the neighbors and the query structure.

+

Activating and deactivating parts of the query compound are highlighted + in red and green on the webinterface. Fragments that are unknown (or too + infrequent for statistical evaluation are marked in yellow and + additional statistical information about the individual fragments can be + retrieved. Please note that lazar predictions are based on neighbors and + not on fragments. Fragments and their statistical significance are used + for the calculation of activity specific similarities.

" + + # Bibliography 9.2 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 + report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Helma (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} + report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 + + # output + response['Content-Type'] = "application/xml" + return report.to_xml + else + bad_request_error "Mime type #{@accept} is not supported." + end + +end diff --git a/lib/substance.rb b/lib/substance.rb new file mode 100644 index 0000000..fef1b7e --- /dev/null +++ b/lib/substance.rb @@ -0,0 +1,30 @@ +# Get all substances +get "/substance/?" do + substances = Substance.all + case @accept + when "text/uri-list" + uri_list = substances.collect{|substance| uri("/substance/#{substance.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + substances = JSON.parse substances.to_json + substances.each_index do |idx| + substances[idx][:URI] = uri("/substance/#{substances[idx]["_id"]["$oid"]}") + end + return substances.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a substance +get "/substance/:id/?" do + case @accept + when "application/json" + substance = Substance.find :id => params[:id] + not_found_error "Substance with id: #{params[:id]} not found." unless substance + substance[:URI] = uri("/substance/#{substance.id}") + return substance.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end diff --git a/lib/swagger.rb b/lib/swagger.rb new file mode 100644 index 0000000..efe1c9d --- /dev/null +++ b/lib/swagger.rb @@ -0,0 +1,6 @@ +get "/" do + response['Content-Type'] = "text/html" + index_file = File.join(ENV['HOME'],"swagger-ui/dist/index.html") + bad_request_error "API Documentation in Swagger JSON is not implemented." unless File.exists?(index_file) + File.read(index_file) +end diff --git a/lib/validation.rb b/lib/validation.rb new file mode 100644 index 0000000..fad8a44 --- /dev/null +++ b/lib/validation.rb @@ -0,0 +1,71 @@ +# All available validation types +VALIDATION_TYPES = ["repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation"] + +# Get a list of ayll possible validation types +# @param [Header] Accept one of text/uri-list, application/json +# @return [text/uri-list] URI list of all validation types +get "/validation/?" do + uri_list = VALIDATION_TYPES.collect{|validationtype| uri("/validation/#{validationtype}")} + case @accept + when "text/uri-list" + return uri_list.join("\n") + "\n" + when "application/json" + return uri_list.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get a list of all validations +# @param [Header] Accept one of text/uri-list, application/json +# @param [Path] Validationtype One of "repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation" +# @return [text/uri-list] list of all validations of a validation type +get "/validation/:validationtype/?" do + bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] + case params[:validationtype] + when "repeatedcrossvalidation" + validations = Validation::RepeatedCrossValidation.all + when "leaveoneout" + validations = Validation::LeaveOneOut.all + when "crossvalidation" + validations = Validation::CrossValidation.all + when "regressioncrossvalidation" + validations = Validation::RegressionCrossValidation.all + end + + case @accept + when "text/uri-list" + uri_list = validations.collect{|validation| uri("/validation/#{params[:validationtype]}/#{validation.id}")} + return uri_list.join("\n") + "\n" + when "application/json" + validations = JSON.parse validations.to_json + validations.each_index do |idx| + validations[idx][:URI] = uri("/validation/#{params[:validationtype]}/#{validations[idx]["_id"]["$oid"]}") + end + return validations.to_json + else + bad_request_error "Mime type #{@accept} is not supported." + end +end + +# Get validation representation +get "/validation/:validationtype/:id/?" do + bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] + case params[:validationtype] + when "repeatedcrossvalidation" + validation = Validation::RepeatedCrossValidation.find params[:id] + when "leaveoneout" + validation = Validation::LeaveOneOut.find params[:id] + when "crossvalidation" + validation = Validation::CrossValidation.find params[:id] + when "regressioncrossvalidation" + validation = Validation::RegressionCrossValidation.find params[:id] + end + + not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation + #model[:URI] = uri("/model/#{model.id}") + #model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id] + #model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id + #model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id + return validation.to_json +end -- cgit v1.2.3