lazar-rest 1.0.0
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- checksums.yaml +7 -0
- data/.gitignore +13 -0
- data/.yardopts +5 -0
- data/ChangeLog +9 -0
- data/Gemfile +6 -0
- data/LICENSE +674 -0
- data/README.md +54 -0
- data/VERSION +1 -0
- data/api/api.json +1209 -0
- data/config.ru +5 -0
- data/lazar-rest.gemspec +26 -0
- data/lib/aa.rb +82 -0
- data/lib/api.rb +9 -0
- data/lib/compound.rb +64 -0
- data/lib/dataset.rb +47 -0
- data/lib/feature.rb +25 -0
- data/lib/lazar-rest.rb +37 -0
- data/lib/model.rb +50 -0
- data/lib/nanoparticle.rb +25 -0
- data/lib/report.rb +209 -0
- data/lib/substance.rb +25 -0
- data/lib/validation.rb +71 -0
- data/test/aa.rb +23 -0
- data/test/all.rb +5 -0
- data/test/api.rb +13 -0
- data/test/compound.rb +54 -0
- data/test/data/test_03_post_descriptor_file.result +152 -0
- data/test/descriptor.rb +48 -0
- data/test/model.rb +17 -0
- data/test/setup.rb +8 -0
- data/test/validation.rb +17 -0
- data/unicorn.rb +2 -0
- data/views/model_details.haml +121 -0
- metadata +176 -0
data/README.md
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# lazar-rest
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REST API webservice for lazar and nano-lazar.
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lazar (lazy structure–activity relationships) is a modular framework for read across predictions of chemical toxicities. Within the European Union’s FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data, interfaces to other eNanoMapper services (databases and ontologies) and a stable and user-friendly graphical interface for nanoparticle read-across predictions. **lazar-rest** provides a new Restful webservice to this developments.
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## Installation
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Download the code from github.
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```
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git clone https://github.com/opentox/lazar-rest.git
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```
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Install the required library gems with bundler
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```
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cd lazar-gem
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bundle install
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```
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In development environment use lazar and qsar-report library from source
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```ruby
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require "../lazar/lib/lazar.rb"
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require "../qsar-report/lib/qsar-report.rb"
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```
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In production environment change this to the following to have lazar and qsar-report library from ruby gem
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```ruby
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require "../lazar/lib/lazar.rb"
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require "../qsar-report/lib/qsar-report.rb"
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```
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start the service with unicorn on an assigned port
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```
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unicorn -p 8080 -D
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```
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(satrt without daemonize option *-D* for debugging)
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## Documentation
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* For full Swagger API documentation open /api/api.json with Swagger UI.
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* [RubyDoc.info Code documentation](http://www.rubydoc.info/gems/lazar-rest)
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## See also
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* [eNanoMapper at github](https://github.com/enanomapper)
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* [eNanoMapper webpage](http://enanomapper.net)
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* [lazar at github](https://github.com/opentox/lazar)
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* [QSAR-report gem at github](https://github.com/opentox/qsar-report)
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## Copyright
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Copyright (c) 2015-2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
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data/VERSION
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1.0.0
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data/api/api.json
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{
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"swagger": "2.0",
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"info": {
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"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",
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"version": "1.0.0",
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"title": "Lazar & Nano-Lazar REST Service",
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"contact": {
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"name": "in silico toxicology gmbh",
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"email": "service@in-silico.ch",
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"url": "www.in-silico.ch"
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},
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"license": {
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"name": "GNU GENERAL PUBLIC LICENSE",
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"url": "https://github.com/opentox/lazar-rest/blob/master/LICENSE"
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}
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},
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"host": "enm.in-silico.ch",
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"basePath": "/",
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"schemes": [
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"https"
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],
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"paths": {
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"/model": {
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"get": {
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"tags": [
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"model"
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],
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"description": "Get a list of all prediction models",
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"parameters": [
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"text/uri-list",
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"application/json"
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]
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"text/uri-list",
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"application/json"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"404": {
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"$ref": "#/responses/404"
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},
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"500": {
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"$ref": "#/responses/500"
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}
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}
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}
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},
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"/model/{id}": {
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"get": {
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"tags": [
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"model"
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],
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"description": "Get model representation",
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"parameters": [
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"application/json"
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]
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},
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{
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"$ref": "#/parameters/id"
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"application/json"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"403": {
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"$ref": "#/responses/403"
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},
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"404": {
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"$ref": "#/responses/404"
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}
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}
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},
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"post": {
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"tags": [
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"model"
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],
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"description": "Predict a compound or a nanoparticle",
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"parameters": [
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{
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"name": "identifier",
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"in": "formData",
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"description": "SMILES identifier or Nanoparticle URI or comma separated list of SMILES identifiers or Nanoparticle URI",
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"required": true,
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"type": "string"
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},
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{
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"$ref": "#/parameters/id"
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"application/json"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"403": {
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"$ref": "#/responses/403"
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},
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"404": {
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"$ref": "#/responses/404"
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}
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}
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}
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},
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"/report": {
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"get": {
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"tags": [
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"report"
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],
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"description": "Get a list of QMRF reports",
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"parameters": [
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"text/uri-list",
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"application/json"
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]
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"text/uri-list",
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"application/json"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"404": {
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"$ref": "#/responses/404"
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},
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"500": {
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"$ref": "#/responses/500"
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}
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}
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}
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},
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"/report/{id}": {
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"get": {
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"tags": [
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"report"
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],
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"description": "Get a QMRF report prototype",
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"parameters": [
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"application/xml"
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]
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},
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{
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"$ref": "#/parameters/id"
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"application/xml"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"403": {
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"$ref": "#/responses/403"
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},
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"404": {
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"$ref": "#/responses/404"
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}
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}
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}
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},
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"/dataset": {
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"get": {
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"tags": [
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"dataset"
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],
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"description": "Get a list of all datasets",
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"parameters": [
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"text/uri-list",
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"application/json"
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]
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"text/uri-list",
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"application/json"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"404": {
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"$ref": "#/responses/404"
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},
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"500": {
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"$ref": "#/responses/500"
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}
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}
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}
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},
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"/dataset/{id}": {
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"get": {
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"tags": [
|
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"dataset"
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],
|
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"description": "Get dataset representation",
|
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"parameters": [
|
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{
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"name": "accept",
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"in": "header",
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"description": "requested Content-Type",
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"required": true,
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"type": "string",
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"enum": [
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"application/json",
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"text/csv"
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]
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},
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{
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"$ref": "#/parameters/id"
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},
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{
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"$ref": "#/parameters/subjectid"
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}
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],
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"produces": [
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"application/json",
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"text/csv"
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],
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"responses": {
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"200": {
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"$ref": "#/responses/200"
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},
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"400": {
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"$ref": "#/responses/400"
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},
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"401": {
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"$ref": "#/responses/401"
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},
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"403": {
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"$ref": "#/responses/403"
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},
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"404": {
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"$ref": "#/responses/404"
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}
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}
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}
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},
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|
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"/dataset/{id}/{attribute}": {
|
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"get": {
|
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|
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"tags": [
|
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|
+
"dataset"
|
|
343
|
+
],
|
|
344
|
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"description": "Get dataset representation",
|
|
345
|
+
"parameters": [
|
|
346
|
+
{
|
|
347
|
+
"name": "accept",
|
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|
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"in": "header",
|
|
349
|
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"description": "requested Content-Type",
|
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350
|
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"required": true,
|
|
351
|
+
"type": "string",
|
|
352
|
+
"enum": [
|
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353
|
+
"application/json"
|
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354
|
+
]
|
|
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|
+
},
|
|
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|
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{
|
|
357
|
+
"name": "attribute",
|
|
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|
+
"in": "path",
|
|
359
|
+
"description": "requested attribute",
|
|
360
|
+
"required": true,
|
|
361
|
+
"type": "string",
|
|
362
|
+
"enum": [
|
|
363
|
+
"compounds",
|
|
364
|
+
"nanoparticles",
|
|
365
|
+
"substances",
|
|
366
|
+
"features"
|
|
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|
+
]
|
|
368
|
+
},
|
|
369
|
+
{
|
|
370
|
+
"$ref": "#/parameters/id"
|
|
371
|
+
},
|
|
372
|
+
{
|
|
373
|
+
"$ref": "#/parameters/subjectid"
|
|
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|
+
}
|
|
375
|
+
],
|
|
376
|
+
"produces": [
|
|
377
|
+
"application/json"
|
|
378
|
+
],
|
|
379
|
+
"responses": {
|
|
380
|
+
"200": {
|
|
381
|
+
"$ref": "#/responses/200"
|
|
382
|
+
},
|
|
383
|
+
"400": {
|
|
384
|
+
"$ref": "#/responses/400"
|
|
385
|
+
},
|
|
386
|
+
"401": {
|
|
387
|
+
"$ref": "#/responses/401"
|
|
388
|
+
},
|
|
389
|
+
"403": {
|
|
390
|
+
"$ref": "#/responses/403"
|
|
391
|
+
},
|
|
392
|
+
"404": {
|
|
393
|
+
"$ref": "#/responses/404"
|
|
394
|
+
}
|
|
395
|
+
}
|
|
396
|
+
}
|
|
397
|
+
},
|
|
398
|
+
"/substance": {
|
|
399
|
+
"get": {
|
|
400
|
+
"tags": [
|
|
401
|
+
"substance"
|
|
402
|
+
],
|
|
403
|
+
"description": "Get a list of all substances",
|
|
404
|
+
"parameters": [
|
|
405
|
+
{
|
|
406
|
+
"name": "accept",
|
|
407
|
+
"in": "header",
|
|
408
|
+
"description": "requested Content-Type",
|
|
409
|
+
"required": true,
|
|
410
|
+
"type": "string",
|
|
411
|
+
"enum": [
|
|
412
|
+
"text/uri-list",
|
|
413
|
+
"application/json"
|
|
414
|
+
]
|
|
415
|
+
},
|
|
416
|
+
{
|
|
417
|
+
"$ref": "#/parameters/subjectid"
|
|
418
|
+
}
|
|
419
|
+
],
|
|
420
|
+
"produces": [
|
|
421
|
+
"text/uri-list",
|
|
422
|
+
"application/json"
|
|
423
|
+
],
|
|
424
|
+
"responses": {
|
|
425
|
+
"200": {
|
|
426
|
+
"$ref": "#/responses/200"
|
|
427
|
+
},
|
|
428
|
+
"400": {
|
|
429
|
+
"$ref": "#/responses/400"
|
|
430
|
+
},
|
|
431
|
+
"401": {
|
|
432
|
+
"$ref": "#/responses/401"
|
|
433
|
+
},
|
|
434
|
+
"404": {
|
|
435
|
+
"$ref": "#/responses/404"
|
|
436
|
+
},
|
|
437
|
+
"500": {
|
|
438
|
+
"$ref": "#/responses/500"
|
|
439
|
+
}
|
|
440
|
+
}
|
|
441
|
+
}
|
|
442
|
+
},
|
|
443
|
+
"/substance/{id}": {
|
|
444
|
+
"get": {
|
|
445
|
+
"tags": [
|
|
446
|
+
"substance"
|
|
447
|
+
],
|
|
448
|
+
"description": "Get substance representation",
|
|
449
|
+
"parameters": [
|
|
450
|
+
{
|
|
451
|
+
"name": "accept",
|
|
452
|
+
"in": "header",
|
|
453
|
+
"description": "requested Content-Type",
|
|
454
|
+
"required": true,
|
|
455
|
+
"type": "string",
|
|
456
|
+
"enum": [
|
|
457
|
+
"application/json"
|
|
458
|
+
]
|
|
459
|
+
},
|
|
460
|
+
{
|
|
461
|
+
"$ref": "#/parameters/id"
|
|
462
|
+
},
|
|
463
|
+
{
|
|
464
|
+
"$ref": "#/parameters/subjectid"
|
|
465
|
+
}
|
|
466
|
+
],
|
|
467
|
+
"produces": [
|
|
468
|
+
"application/json"
|
|
469
|
+
],
|
|
470
|
+
"responses": {
|
|
471
|
+
"200": {
|
|
472
|
+
"$ref": "#/responses/200"
|
|
473
|
+
},
|
|
474
|
+
"400": {
|
|
475
|
+
"$ref": "#/responses/400"
|
|
476
|
+
},
|
|
477
|
+
"401": {
|
|
478
|
+
"$ref": "#/responses/401"
|
|
479
|
+
},
|
|
480
|
+
"403": {
|
|
481
|
+
"$ref": "#/responses/403"
|
|
482
|
+
},
|
|
483
|
+
"404": {
|
|
484
|
+
"$ref": "#/responses/404"
|
|
485
|
+
}
|
|
486
|
+
}
|
|
487
|
+
}
|
|
488
|
+
},
|
|
489
|
+
"/nanoparticle": {
|
|
490
|
+
"get": {
|
|
491
|
+
"tags": [
|
|
492
|
+
"nanoparticle"
|
|
493
|
+
],
|
|
494
|
+
"description": "Get a list of all nanoparticles",
|
|
495
|
+
"parameters": [
|
|
496
|
+
{
|
|
497
|
+
"name": "accept",
|
|
498
|
+
"in": "header",
|
|
499
|
+
"description": "requested Content-Type",
|
|
500
|
+
"required": true,
|
|
501
|
+
"type": "string",
|
|
502
|
+
"enum": [
|
|
503
|
+
"text/uri-list",
|
|
504
|
+
"application/json"
|
|
505
|
+
]
|
|
506
|
+
},
|
|
507
|
+
{
|
|
508
|
+
"$ref": "#/parameters/subjectid"
|
|
509
|
+
}
|
|
510
|
+
],
|
|
511
|
+
"produces": [
|
|
512
|
+
"text/uri-list",
|
|
513
|
+
"application/json"
|
|
514
|
+
],
|
|
515
|
+
"responses": {
|
|
516
|
+
"200": {
|
|
517
|
+
"$ref": "#/responses/200"
|
|
518
|
+
},
|
|
519
|
+
"400": {
|
|
520
|
+
"$ref": "#/responses/400"
|
|
521
|
+
},
|
|
522
|
+
"401": {
|
|
523
|
+
"$ref": "#/responses/401"
|
|
524
|
+
},
|
|
525
|
+
"404": {
|
|
526
|
+
"$ref": "#/responses/404"
|
|
527
|
+
},
|
|
528
|
+
"500": {
|
|
529
|
+
"$ref": "#/responses/500"
|
|
530
|
+
}
|
|
531
|
+
}
|
|
532
|
+
}
|
|
533
|
+
},
|
|
534
|
+
"/nanoparticle/{id}": {
|
|
535
|
+
"get": {
|
|
536
|
+
"tags": [
|
|
537
|
+
"nanoparticle"
|
|
538
|
+
],
|
|
539
|
+
"description": "Get nanoparticle representation",
|
|
540
|
+
"parameters": [
|
|
541
|
+
{
|
|
542
|
+
"name": "accept",
|
|
543
|
+
"in": "header",
|
|
544
|
+
"description": "requested Content-Type",
|
|
545
|
+
"required": true,
|
|
546
|
+
"type": "string",
|
|
547
|
+
"enum": [
|
|
548
|
+
"application/json"
|
|
549
|
+
]
|
|
550
|
+
},
|
|
551
|
+
{
|
|
552
|
+
"$ref": "#/parameters/id"
|
|
553
|
+
},
|
|
554
|
+
{
|
|
555
|
+
"$ref": "#/parameters/subjectid"
|
|
556
|
+
}
|
|
557
|
+
],
|
|
558
|
+
"produces": [
|
|
559
|
+
"application/json"
|
|
560
|
+
],
|
|
561
|
+
"responses": {
|
|
562
|
+
"200": {
|
|
563
|
+
"$ref": "#/responses/200"
|
|
564
|
+
},
|
|
565
|
+
"400": {
|
|
566
|
+
"$ref": "#/responses/400"
|
|
567
|
+
},
|
|
568
|
+
"401": {
|
|
569
|
+
"$ref": "#/responses/401"
|
|
570
|
+
},
|
|
571
|
+
"403": {
|
|
572
|
+
"$ref": "#/responses/403"
|
|
573
|
+
},
|
|
574
|
+
"404": {
|
|
575
|
+
"$ref": "#/responses/404"
|
|
576
|
+
}
|
|
577
|
+
}
|
|
578
|
+
}
|
|
579
|
+
},
|
|
580
|
+
"/feature": {
|
|
581
|
+
"get": {
|
|
582
|
+
"tags": [
|
|
583
|
+
"feature"
|
|
584
|
+
],
|
|
585
|
+
"description": "Get a list of all features",
|
|
586
|
+
"parameters": [
|
|
587
|
+
{
|
|
588
|
+
"name": "accept",
|
|
589
|
+
"in": "header",
|
|
590
|
+
"description": "requested Content-Type",
|
|
591
|
+
"required": true,
|
|
592
|
+
"type": "string",
|
|
593
|
+
"enum": [
|
|
594
|
+
"text/uri-list",
|
|
595
|
+
"application/json"
|
|
596
|
+
]
|
|
597
|
+
}
|
|
598
|
+
],
|
|
599
|
+
"produces": [
|
|
600
|
+
"text/uri-list",
|
|
601
|
+
"application/json"
|
|
602
|
+
],
|
|
603
|
+
"responses": {
|
|
604
|
+
"200": {
|
|
605
|
+
"$ref": "#/responses/200"
|
|
606
|
+
},
|
|
607
|
+
"400": {
|
|
608
|
+
"$ref": "#/responses/400"
|
|
609
|
+
},
|
|
610
|
+
"401": {
|
|
611
|
+
"$ref": "#/responses/401"
|
|
612
|
+
},
|
|
613
|
+
"404": {
|
|
614
|
+
"$ref": "#/responses/404"
|
|
615
|
+
},
|
|
616
|
+
"500": {
|
|
617
|
+
"$ref": "#/responses/500"
|
|
618
|
+
}
|
|
619
|
+
}
|
|
620
|
+
}
|
|
621
|
+
},
|
|
622
|
+
"/feature/{id}": {
|
|
623
|
+
"get": {
|
|
624
|
+
"tags": [
|
|
625
|
+
"feature"
|
|
626
|
+
],
|
|
627
|
+
"description": "Get feature representation",
|
|
628
|
+
"parameters": [
|
|
629
|
+
{
|
|
630
|
+
"name": "acept",
|
|
631
|
+
"in": "header",
|
|
632
|
+
"description": "requested Content-Type",
|
|
633
|
+
"required": true,
|
|
634
|
+
"type": "string",
|
|
635
|
+
"enum": [
|
|
636
|
+
"application/json"
|
|
637
|
+
]
|
|
638
|
+
},
|
|
639
|
+
{
|
|
640
|
+
"$ref": "#/parameters/id"
|
|
641
|
+
}
|
|
642
|
+
],
|
|
643
|
+
"produces": [
|
|
644
|
+
"application/json"
|
|
645
|
+
],
|
|
646
|
+
"responses": {
|
|
647
|
+
"200": {
|
|
648
|
+
"$ref": "#/responses/200"
|
|
649
|
+
},
|
|
650
|
+
"400": {
|
|
651
|
+
"$ref": "#/responses/400"
|
|
652
|
+
},
|
|
653
|
+
"401": {
|
|
654
|
+
"$ref": "#/responses/401"
|
|
655
|
+
},
|
|
656
|
+
"403": {
|
|
657
|
+
"$ref": "#/responses/403"
|
|
658
|
+
},
|
|
659
|
+
"404": {
|
|
660
|
+
"$ref": "#/responses/404"
|
|
661
|
+
}
|
|
662
|
+
}
|
|
663
|
+
}
|
|
664
|
+
},
|
|
665
|
+
"/validation": {
|
|
666
|
+
"get": {
|
|
667
|
+
"tags": [
|
|
668
|
+
"validation"
|
|
669
|
+
],
|
|
670
|
+
"description": "Get a list of all validation types",
|
|
671
|
+
"parameters": [
|
|
672
|
+
{
|
|
673
|
+
"name": "accept",
|
|
674
|
+
"in": "header",
|
|
675
|
+
"description": "requested Content-Type",
|
|
676
|
+
"required": true,
|
|
677
|
+
"type": "string",
|
|
678
|
+
"enum": [
|
|
679
|
+
"text/uri-list",
|
|
680
|
+
"application/json"
|
|
681
|
+
]
|
|
682
|
+
}
|
|
683
|
+
],
|
|
684
|
+
"produces": [
|
|
685
|
+
"text/uri-list",
|
|
686
|
+
"application/json"
|
|
687
|
+
],
|
|
688
|
+
"responses": {
|
|
689
|
+
"200": {
|
|
690
|
+
"$ref": "#/responses/200"
|
|
691
|
+
},
|
|
692
|
+
"400": {
|
|
693
|
+
"$ref": "#/responses/400"
|
|
694
|
+
},
|
|
695
|
+
"401": {
|
|
696
|
+
"$ref": "#/responses/401"
|
|
697
|
+
},
|
|
698
|
+
"404": {
|
|
699
|
+
"$ref": "#/responses/404"
|
|
700
|
+
},
|
|
701
|
+
"500": {
|
|
702
|
+
"$ref": "#/responses/500"
|
|
703
|
+
}
|
|
704
|
+
}
|
|
705
|
+
}
|
|
706
|
+
},
|
|
707
|
+
"/validation/{validationtype}": {
|
|
708
|
+
"get": {
|
|
709
|
+
"tags": [
|
|
710
|
+
"validation"
|
|
711
|
+
],
|
|
712
|
+
"description": "Get all validations of a validation type",
|
|
713
|
+
"parameters": [
|
|
714
|
+
{
|
|
715
|
+
"name": "accept",
|
|
716
|
+
"in": "header",
|
|
717
|
+
"description": "requested Content-Type",
|
|
718
|
+
"required": true,
|
|
719
|
+
"type": "string",
|
|
720
|
+
"enum": [
|
|
721
|
+
"text/uri-list",
|
|
722
|
+
"application/json"
|
|
723
|
+
]
|
|
724
|
+
},
|
|
725
|
+
{
|
|
726
|
+
"$ref": "#/parameters/valtype"
|
|
727
|
+
},
|
|
728
|
+
{
|
|
729
|
+
"$ref": "#/parameters/subjectid"
|
|
730
|
+
}
|
|
731
|
+
],
|
|
732
|
+
"produces": [
|
|
733
|
+
"text/uri-list",
|
|
734
|
+
"application/json"
|
|
735
|
+
],
|
|
736
|
+
"responses": {
|
|
737
|
+
"200": {
|
|
738
|
+
"$ref": "#/responses/200"
|
|
739
|
+
},
|
|
740
|
+
"400": {
|
|
741
|
+
"$ref": "#/responses/400"
|
|
742
|
+
},
|
|
743
|
+
"401": {
|
|
744
|
+
"$ref": "#/responses/401"
|
|
745
|
+
},
|
|
746
|
+
"403": {
|
|
747
|
+
"$ref": "#/responses/403"
|
|
748
|
+
},
|
|
749
|
+
"404": {
|
|
750
|
+
"$ref": "#/responses/404"
|
|
751
|
+
}
|
|
752
|
+
}
|
|
753
|
+
}
|
|
754
|
+
},
|
|
755
|
+
"/validation/{validationtype}/{id}": {
|
|
756
|
+
"get": {
|
|
757
|
+
"tags": [
|
|
758
|
+
"validation"
|
|
759
|
+
],
|
|
760
|
+
"description": "Get validation representation",
|
|
761
|
+
"parameters": [
|
|
762
|
+
{
|
|
763
|
+
"name": "accept",
|
|
764
|
+
"in": "header",
|
|
765
|
+
"description": "requested Content-Type",
|
|
766
|
+
"required": true,
|
|
767
|
+
"type": "string",
|
|
768
|
+
"enum": [
|
|
769
|
+
"application/json"
|
|
770
|
+
]
|
|
771
|
+
},
|
|
772
|
+
{
|
|
773
|
+
"$ref": "#/parameters/valtype"
|
|
774
|
+
},
|
|
775
|
+
{
|
|
776
|
+
"$ref": "#/parameters/id"
|
|
777
|
+
},
|
|
778
|
+
{
|
|
779
|
+
"$ref": "#/parameters/subjectid"
|
|
780
|
+
}
|
|
781
|
+
],
|
|
782
|
+
"produces": [
|
|
783
|
+
"application/json"
|
|
784
|
+
],
|
|
785
|
+
"responses": {
|
|
786
|
+
"200": {
|
|
787
|
+
"$ref": "#/responses/200"
|
|
788
|
+
},
|
|
789
|
+
"400": {
|
|
790
|
+
"$ref": "#/responses/400"
|
|
791
|
+
},
|
|
792
|
+
"401": {
|
|
793
|
+
"$ref": "#/responses/401"
|
|
794
|
+
},
|
|
795
|
+
"403": {
|
|
796
|
+
"$ref": "#/responses/403"
|
|
797
|
+
},
|
|
798
|
+
"404": {
|
|
799
|
+
"$ref": "#/responses/404"
|
|
800
|
+
}
|
|
801
|
+
}
|
|
802
|
+
}
|
|
803
|
+
},
|
|
804
|
+
"/compound/descriptor": {
|
|
805
|
+
"get": {
|
|
806
|
+
"tags": [
|
|
807
|
+
"compound",
|
|
808
|
+
"descriptor"
|
|
809
|
+
],
|
|
810
|
+
"description": "Get a list of all descriptors",
|
|
811
|
+
"parameters": [
|
|
812
|
+
{
|
|
813
|
+
"name": "accept",
|
|
814
|
+
"in": "header",
|
|
815
|
+
"description": "requested Content-Type",
|
|
816
|
+
"required": true,
|
|
817
|
+
"type": "string",
|
|
818
|
+
"enum": [
|
|
819
|
+
"text/plain",
|
|
820
|
+
"application/json"
|
|
821
|
+
]
|
|
822
|
+
}
|
|
823
|
+
],
|
|
824
|
+
"produces": [
|
|
825
|
+
"text/plain",
|
|
826
|
+
"application/json"
|
|
827
|
+
],
|
|
828
|
+
"responses": {
|
|
829
|
+
"200": {
|
|
830
|
+
"$ref": "#/responses/200"
|
|
831
|
+
},
|
|
832
|
+
"400": {
|
|
833
|
+
"$ref": "#/responses/400"
|
|
834
|
+
},
|
|
835
|
+
"401": {
|
|
836
|
+
"$ref": "#/responses/401"
|
|
837
|
+
},
|
|
838
|
+
"404": {
|
|
839
|
+
"$ref": "#/responses/404"
|
|
840
|
+
},
|
|
841
|
+
"500": {
|
|
842
|
+
"$ref": "#/responses/500"
|
|
843
|
+
}
|
|
844
|
+
}
|
|
845
|
+
},
|
|
846
|
+
"post": {
|
|
847
|
+
"tags": [
|
|
848
|
+
"compound",
|
|
849
|
+
"descriptor"
|
|
850
|
+
],
|
|
851
|
+
"summary": "Descriptor calculation",
|
|
852
|
+
"description": "Calculate descriptors for a single compound as SMILES string <br> <strong>curl example:</strong> <pre>curl -Lk -X POST -i -H \"accept:application/json\" -F \"identifier=O=C1NC(=O)NC=C1\" -F \"descriptor=Openbabel.MW,JoeLib.LogP\" https://enm.in-silico.ch/compound/descriptor </pre>.",
|
|
853
|
+
"parameters": [
|
|
854
|
+
{
|
|
855
|
+
"name": "accept",
|
|
856
|
+
"in": "header",
|
|
857
|
+
"description": "requested Content-Type",
|
|
858
|
+
"required": true,
|
|
859
|
+
"type": "string",
|
|
860
|
+
"enum": [
|
|
861
|
+
"text/csv",
|
|
862
|
+
"application/json"
|
|
863
|
+
],
|
|
864
|
+
"default": "text/csv"
|
|
865
|
+
},
|
|
866
|
+
{
|
|
867
|
+
"name": "identifier",
|
|
868
|
+
"in": "formData",
|
|
869
|
+
"description": "SMILES identifier",
|
|
870
|
+
"required": true,
|
|
871
|
+
"type": "string"
|
|
872
|
+
},
|
|
873
|
+
{
|
|
874
|
+
"name": "descriptor",
|
|
875
|
+
"in": "formData",
|
|
876
|
+
"description": "array of descriptors",
|
|
877
|
+
"required": true,
|
|
878
|
+
"type": "array",
|
|
879
|
+
"items": {
|
|
880
|
+
"type": "string"
|
|
881
|
+
}
|
|
882
|
+
},
|
|
883
|
+
{
|
|
884
|
+
"$ref": "#/parameters/subjectid"
|
|
885
|
+
}
|
|
886
|
+
],
|
|
887
|
+
"produces": [
|
|
888
|
+
"text/csv",
|
|
889
|
+
"application/json"
|
|
890
|
+
],
|
|
891
|
+
"responses": {
|
|
892
|
+
"200": {
|
|
893
|
+
"$ref": "#/responses/200"
|
|
894
|
+
},
|
|
895
|
+
"400": {
|
|
896
|
+
"$ref": "#/responses/400"
|
|
897
|
+
},
|
|
898
|
+
"401": {
|
|
899
|
+
"$ref": "#/responses/401"
|
|
900
|
+
},
|
|
901
|
+
"404": {
|
|
902
|
+
"$ref": "#/responses/404"
|
|
903
|
+
},
|
|
904
|
+
"500": {
|
|
905
|
+
"$ref": "#/responses/500"
|
|
906
|
+
}
|
|
907
|
+
}
|
|
908
|
+
}
|
|
909
|
+
},
|
|
910
|
+
"/compound/descriptor/{descriptor}": {
|
|
911
|
+
"get": {
|
|
912
|
+
"tags": [
|
|
913
|
+
"compound",
|
|
914
|
+
"descriptor"
|
|
915
|
+
],
|
|
916
|
+
"description": "Get a list of a descriptors",
|
|
917
|
+
"parameters": [
|
|
918
|
+
{
|
|
919
|
+
"name": "accept",
|
|
920
|
+
"in": "header",
|
|
921
|
+
"description": "requested Content-Type",
|
|
922
|
+
"required": true,
|
|
923
|
+
"type": "string",
|
|
924
|
+
"enum": [
|
|
925
|
+
"text/plain",
|
|
926
|
+
"application/json"
|
|
927
|
+
]
|
|
928
|
+
},
|
|
929
|
+
{
|
|
930
|
+
"name": "descriptor",
|
|
931
|
+
"in": "path",
|
|
932
|
+
"description": "descriptor name or ID",
|
|
933
|
+
"required": true,
|
|
934
|
+
"type": "string"
|
|
935
|
+
}
|
|
936
|
+
],
|
|
937
|
+
"produces": [
|
|
938
|
+
"text/plain",
|
|
939
|
+
"application/json"
|
|
940
|
+
],
|
|
941
|
+
"responses": {
|
|
942
|
+
"200": {
|
|
943
|
+
"$ref": "#/responses/200"
|
|
944
|
+
},
|
|
945
|
+
"400": {
|
|
946
|
+
"$ref": "#/responses/400"
|
|
947
|
+
},
|
|
948
|
+
"401": {
|
|
949
|
+
"$ref": "#/responses/401"
|
|
950
|
+
},
|
|
951
|
+
"404": {
|
|
952
|
+
"$ref": "#/responses/404"
|
|
953
|
+
},
|
|
954
|
+
"500": {
|
|
955
|
+
"$ref": "#/responses/500"
|
|
956
|
+
}
|
|
957
|
+
}
|
|
958
|
+
}
|
|
959
|
+
},
|
|
960
|
+
"/compound/{InChI}": {
|
|
961
|
+
"get": {
|
|
962
|
+
"tags": [
|
|
963
|
+
"compound"
|
|
964
|
+
],
|
|
965
|
+
"description": "Get compound representation",
|
|
966
|
+
"parameters": [
|
|
967
|
+
{
|
|
968
|
+
"$ref": "#/parameters/InChI"
|
|
969
|
+
},
|
|
970
|
+
{
|
|
971
|
+
"name": "accept",
|
|
972
|
+
"in": "header",
|
|
973
|
+
"description": "requested Content-type",
|
|
974
|
+
"required": true,
|
|
975
|
+
"type": "string",
|
|
976
|
+
"enum": [
|
|
977
|
+
"application/json",
|
|
978
|
+
"chemical/x-daylight-smiles",
|
|
979
|
+
"chemical/x-inchi",
|
|
980
|
+
"chemical/x-mdl-sdfile",
|
|
981
|
+
"chemical/x-mdl-molfile",
|
|
982
|
+
"image/png",
|
|
983
|
+
"image/svg+xml",
|
|
984
|
+
"text/plain"
|
|
985
|
+
]
|
|
986
|
+
}
|
|
987
|
+
],
|
|
988
|
+
"produces": [
|
|
989
|
+
"application/json",
|
|
990
|
+
"chemical/x-daylight-smiles",
|
|
991
|
+
"chemical/x-inchi",
|
|
992
|
+
"chemical/x-mdl-sdfile",
|
|
993
|
+
"chemical/x-mdl-molfile",
|
|
994
|
+
"image/png",
|
|
995
|
+
"image/svg+xml",
|
|
996
|
+
"text/plain"
|
|
997
|
+
],
|
|
998
|
+
"responses": {
|
|
999
|
+
"200": {
|
|
1000
|
+
"$ref": "#/responses/200"
|
|
1001
|
+
},
|
|
1002
|
+
"400": {
|
|
1003
|
+
"$ref": "#/responses/400"
|
|
1004
|
+
}
|
|
1005
|
+
}
|
|
1006
|
+
}
|
|
1007
|
+
},
|
|
1008
|
+
"/api/api.json": {
|
|
1009
|
+
"get": {
|
|
1010
|
+
"tags": [
|
|
1011
|
+
"api"
|
|
1012
|
+
],
|
|
1013
|
+
"description": "Get swagger api in JSON",
|
|
1014
|
+
"produces": [
|
|
1015
|
+
"application/json"
|
|
1016
|
+
],
|
|
1017
|
+
"responses": {
|
|
1018
|
+
"200": {
|
|
1019
|
+
"$ref": "#/responses/200"
|
|
1020
|
+
},
|
|
1021
|
+
"400": {
|
|
1022
|
+
"$ref": "#/responses/400"
|
|
1023
|
+
},
|
|
1024
|
+
"500": {
|
|
1025
|
+
"$ref": "#/responses/500"
|
|
1026
|
+
}
|
|
1027
|
+
}
|
|
1028
|
+
}
|
|
1029
|
+
},
|
|
1030
|
+
"/aa/authenticate": {
|
|
1031
|
+
"post": {
|
|
1032
|
+
"tags": [
|
|
1033
|
+
"authentication"
|
|
1034
|
+
],
|
|
1035
|
+
"description": "Authentication against OpenSSO. Returns token. Requires Username and Password.",
|
|
1036
|
+
"operationId": "login",
|
|
1037
|
+
"consumes": [
|
|
1038
|
+
"text/plain"
|
|
1039
|
+
],
|
|
1040
|
+
"produces": [
|
|
1041
|
+
"text/plain"
|
|
1042
|
+
],
|
|
1043
|
+
"parameters": [
|
|
1044
|
+
{
|
|
1045
|
+
"in": "formData",
|
|
1046
|
+
"name": "username",
|
|
1047
|
+
"description": "username",
|
|
1048
|
+
"required": true,
|
|
1049
|
+
"type": "string"
|
|
1050
|
+
},
|
|
1051
|
+
{
|
|
1052
|
+
"in": "formData",
|
|
1053
|
+
"name": "password",
|
|
1054
|
+
"description": "password",
|
|
1055
|
+
"required": true,
|
|
1056
|
+
"type": "string",
|
|
1057
|
+
"format": "password"
|
|
1058
|
+
}
|
|
1059
|
+
],
|
|
1060
|
+
"responses": {
|
|
1061
|
+
"200": {
|
|
1062
|
+
"$ref": "#/responses/200"
|
|
1063
|
+
},
|
|
1064
|
+
"400": {
|
|
1065
|
+
"$ref": "#/responses/400"
|
|
1066
|
+
},
|
|
1067
|
+
"401": {
|
|
1068
|
+
"$ref": "#/responses/401"
|
|
1069
|
+
}
|
|
1070
|
+
}
|
|
1071
|
+
}
|
|
1072
|
+
},
|
|
1073
|
+
"/aa/logout": {
|
|
1074
|
+
"post": {
|
|
1075
|
+
"description": "Devalidates a token. Requires Subjectid.",
|
|
1076
|
+
"operationId": "logout",
|
|
1077
|
+
"tags": [
|
|
1078
|
+
"authentication"
|
|
1079
|
+
],
|
|
1080
|
+
"consumes": [
|
|
1081
|
+
"text/plain"
|
|
1082
|
+
],
|
|
1083
|
+
"produces": [
|
|
1084
|
+
"text/plain"
|
|
1085
|
+
],
|
|
1086
|
+
"parameters": [
|
|
1087
|
+
{
|
|
1088
|
+
"in": "formData",
|
|
1089
|
+
"name": "subjectid",
|
|
1090
|
+
"description": "subjectid",
|
|
1091
|
+
"required": true,
|
|
1092
|
+
"type": "string"
|
|
1093
|
+
}
|
|
1094
|
+
],
|
|
1095
|
+
"responses": {
|
|
1096
|
+
"200": {
|
|
1097
|
+
"$ref": "#/responses/200"
|
|
1098
|
+
},
|
|
1099
|
+
"400": {
|
|
1100
|
+
"$ref": "#/responses/400"
|
|
1101
|
+
},
|
|
1102
|
+
"401": {
|
|
1103
|
+
"$ref": "#/responses/401"
|
|
1104
|
+
}
|
|
1105
|
+
}
|
|
1106
|
+
}
|
|
1107
|
+
}
|
|
1108
|
+
},
|
|
1109
|
+
"parameters": {
|
|
1110
|
+
"id": {
|
|
1111
|
+
"name": "id",
|
|
1112
|
+
"in": "path",
|
|
1113
|
+
"description": "id",
|
|
1114
|
+
"required": true,
|
|
1115
|
+
"type": "string"
|
|
1116
|
+
},
|
|
1117
|
+
"InChI": {
|
|
1118
|
+
"name": "InChI",
|
|
1119
|
+
"in": "path",
|
|
1120
|
+
"description": "InChI String",
|
|
1121
|
+
"required": true,
|
|
1122
|
+
"type": "string"
|
|
1123
|
+
},
|
|
1124
|
+
"valtype": {
|
|
1125
|
+
"name": "validationtype",
|
|
1126
|
+
"in": "path",
|
|
1127
|
+
"description": "validation type",
|
|
1128
|
+
"required": true,
|
|
1129
|
+
"type": "string"
|
|
1130
|
+
},
|
|
1131
|
+
"subjectid": {
|
|
1132
|
+
"in": "header",
|
|
1133
|
+
"name": "subjectid",
|
|
1134
|
+
"description": "authorization token",
|
|
1135
|
+
"required": false,
|
|
1136
|
+
"type": "string"
|
|
1137
|
+
}
|
|
1138
|
+
},
|
|
1139
|
+
"responses": {
|
|
1140
|
+
"200": {
|
|
1141
|
+
"description": "OK"
|
|
1142
|
+
},
|
|
1143
|
+
"400": {
|
|
1144
|
+
"description": "Bad Request"
|
|
1145
|
+
},
|
|
1146
|
+
"401": {
|
|
1147
|
+
"description": "Unauthorized"
|
|
1148
|
+
},
|
|
1149
|
+
"403": {
|
|
1150
|
+
"description": "Forbidden"
|
|
1151
|
+
},
|
|
1152
|
+
"404": {
|
|
1153
|
+
"description": "Resource Not Found"
|
|
1154
|
+
},
|
|
1155
|
+
"500": {
|
|
1156
|
+
"description": "Server Error"
|
|
1157
|
+
}
|
|
1158
|
+
},
|
|
1159
|
+
"tags": [
|
|
1160
|
+
{
|
|
1161
|
+
"name": "algorithm",
|
|
1162
|
+
"description": "Algorithm"
|
|
1163
|
+
},
|
|
1164
|
+
{
|
|
1165
|
+
"name": "api",
|
|
1166
|
+
"description": "Swagger API representation in JSON"
|
|
1167
|
+
},
|
|
1168
|
+
{
|
|
1169
|
+
"name": "authentication",
|
|
1170
|
+
"description": "minimal Authentication service"
|
|
1171
|
+
},
|
|
1172
|
+
{
|
|
1173
|
+
"name": "descriptor",
|
|
1174
|
+
"description": "Descriptor"
|
|
1175
|
+
},
|
|
1176
|
+
{
|
|
1177
|
+
"name": "model",
|
|
1178
|
+
"description": "Lazar Model Service"
|
|
1179
|
+
},
|
|
1180
|
+
{
|
|
1181
|
+
"name": "compound",
|
|
1182
|
+
"description": "Compound"
|
|
1183
|
+
},
|
|
1184
|
+
{
|
|
1185
|
+
"name": "dataset",
|
|
1186
|
+
"description": "Dataset"
|
|
1187
|
+
},
|
|
1188
|
+
{
|
|
1189
|
+
"name": "validation",
|
|
1190
|
+
"description": "Validation"
|
|
1191
|
+
},
|
|
1192
|
+
{
|
|
1193
|
+
"name": "substance",
|
|
1194
|
+
"description": "Substance"
|
|
1195
|
+
},
|
|
1196
|
+
{
|
|
1197
|
+
"name": "nanoparticle",
|
|
1198
|
+
"description": "Nanoparticle"
|
|
1199
|
+
},
|
|
1200
|
+
{
|
|
1201
|
+
"name": "feature",
|
|
1202
|
+
"description": "Feature"
|
|
1203
|
+
},
|
|
1204
|
+
{
|
|
1205
|
+
"name": "report",
|
|
1206
|
+
"description": "QMRF Reporting"
|
|
1207
|
+
}
|
|
1208
|
+
]
|
|
1209
|
+
}
|