Merge pull request #143 from phenoscape/issue-132

Serve swagger directly from the server.
phenoscape · Aug 26, 2021 · 083b994 · 083b994
2 parents 85f90c5 + 5bc5225
commit 083b994
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Showing 14 changed files with 345 additions and 83 deletions.
diff --git a/src/main/resources/docs/favicon-16x16.png b/src/main/resources/docs/favicon-16x16.png
diff --git a/src/main/resources/docs/favicon-32x32.png b/src/main/resources/docs/favicon-32x32.png
diff --git a/src/main/resources/docs/index.html b/src/main/resources/docs/index.html
@@ -0,0 +1,61 @@
+<!-- HTML for static distribution bundle build -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8">
+    <title>Swagger UI</title>
+    <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,700|Source+Code+Pro:300,600|Titillium+Web:400,600,700" rel="stylesheet">
+    <link rel="stylesheet" type="text/css" href="./swagger-ui.css" >
+    <link rel="icon" type="image/png" href="./favicon-32x32.png" sizes="32x32" />
+    <link rel="icon" type="image/png" href="./favicon-16x16.png" sizes="16x16" />
+    <style>
+      html
+      {
+        box-sizing: border-box;
+        overflow: -moz-scrollbars-vertical;
+        overflow-y: scroll;
+      }
+
+      *,
+      *:before,
+      *:after
+      {
+        box-sizing: inherit;
+      }
+
+      body
+      {
+        margin:0;
+        background: #fafafa;
+      }
+    </style>
+  </head>
+
+  <body>
+    <div id="swagger-ui"></div>
+
+    <script src="./swagger-ui-bundle.js"> </script>
+    <script src="./swagger-ui-standalone-preset.js"> </script>
+    <script>
+    window.onload = function() {
+
+      // Build a system
+      const ui = SwaggerUIBundle({
+        url: "../docs/swagger.json",
+        dom_id: '#swagger-ui',
+        deepLinking: true,
+        presets: [
+          SwaggerUIBundle.presets.apis,
+          SwaggerUIStandalonePreset
+        ],
+        plugins: [
+          SwaggerUIBundle.plugins.DownloadUrl
+        ],
+        layout: "StandaloneLayout"
+      })
+
+      window.ui = ui
+    }
+  </script>
+  </body>
+</html>
diff --git a/src/main/resources/docs/oauth2-redirect.html b/src/main/resources/docs/oauth2-redirect.html
@@ -0,0 +1,67 @@
+<!doctype html>
+<html lang="en-US">
+<body onload="run()">
+</body>
+</html>
+<script>
+    'use strict';
+    function run () {
+        var oauth2 = window.opener.swaggerUIRedirectOauth2;
+        var sentState = oauth2.state;
+        var redirectUrl = oauth2.redirectUrl;
+        var isValid, qp, arr;
+
+        if (/code|token|error/.test(window.location.hash)) {
+            qp = window.location.hash.substring(1);
+        } else {
+            qp = location.search.substring(1);
+        }
+
+        arr = qp.split("&")
+        arr.forEach(function (v,i,_arr) { _arr[i] = '"' + v.replace('=', '":"') + '"';})
+        qp = qp ? JSON.parse('{' + arr.join() + '}',
+                function (key, value) {
+                    return key === "" ? value : decodeURIComponent(value)
+                }
+        ) : {}
+
+        isValid = qp.state === sentState
+
+        if ((
+          oauth2.auth.schema.get("flow") === "accessCode"||
+          oauth2.auth.schema.get("flow") === "authorizationCode"
+        ) && !oauth2.auth.code) {
+            if (!isValid) {
+                oauth2.errCb({
+                    authId: oauth2.auth.name,
+                    source: "auth",
+                    level: "warning",
+                    message: "Authorization may be unsafe, passed state was changed in server Passed state wasn't returned from auth server"
+                });
+            }
+
+            if (qp.code) {
+                delete oauth2.state;
+                oauth2.auth.code = qp.code;
+                oauth2.callback({auth: oauth2.auth, redirectUrl: redirectUrl});
+            } else {
+                let oauthErrorMsg
+                if (qp.error) {
+                    oauthErrorMsg = "["+qp.error+"]: " +
+                        (qp.error_description ? qp.error_description+ ". " : "no accessCode received from the server. ") +
+                        (qp.error_uri ? "More info: "+qp.error_uri : "");
+                }
+
+                oauth2.errCb({
+                    authId: oauth2.auth.name,
+                    source: "auth",
+                    level: "error",
+                    message: oauthErrorMsg || "[Authorization failed]: no accessCode received from the server"
+                });
+            }
+        } else {
+            oauth2.callback({auth: oauth2.auth, token: qp, isValid: isValid, redirectUrl: redirectUrl});
+        }
+        window.close();
+    }
+</script>
diff --git a/src/main/resources/docs/swagger-ui-bundle.js b/src/main/resources/docs/swagger-ui-bundle.js
diff --git a/src/main/resources/docs/swagger-ui-bundle.js.map b/src/main/resources/docs/swagger-ui-bundle.js.map
diff --git a/src/main/resources/docs/swagger-ui-standalone-preset.js b/src/main/resources/docs/swagger-ui-standalone-preset.js
diff --git a/src/main/resources/docs/swagger-ui-standalone-preset.js.map b/src/main/resources/docs/swagger-ui-standalone-preset.js.map
diff --git a/src/main/resources/docs/swagger-ui.css b/src/main/resources/docs/swagger-ui.css
diff --git a/src/main/resources/docs/swagger-ui.css.map b/src/main/resources/docs/swagger-ui.css.map
diff --git a/src/main/resources/docs/swagger-ui.js b/src/main/resources/docs/swagger-ui.js
diff --git a/src/main/resources/docs/swagger-ui.js.map b/src/main/resources/docs/swagger-ui.js.map
diff --git a/docs/json/swagger.json → src/main/resources/docs/swagger.json b/docs/json/swagger.json → src/main/resources/docs/swagger.json
@@ -1,8 +1,5 @@
 {
   "openapi" : "3.0.0",
-  "servers" : [ {
-    "url" : "https://kb.phenoscape.org/owlery"
-  } ],
   "info" : {
     "description" : "Owlery provides a web API for an [OWL API](http://owlapi.sourceforge.net)-based reasoner containing a configurable set of ontologies (a \"knowledgebase\"). ",
     "version" : "1.0.0",

diff --git a/src/main/scala/org/phenoscape/owlery/Main.scala b/src/main/scala/org/phenoscape/owlery/Main.scala
@@ -83,112 +83,115 @@ object Main extends HttpApp with App {
 
   def routes: Route = Route.seal {
     cors() {
-      pathPrefix("kbs") {
-        pathPrefix(Segment) { kbName =>
-          Owlery.kb(kbName) match {
-            case None     => reject
-            case Some(kb) =>
-              path("subclasses") {
-                objectAndPrefixParametersToClass { expression =>
-                  parameters("direct".?(false), "includeEquivalent".?(false), "includeNothing".?(false), "includeDeprecated".?(true)) { (direct, includeEquivalent, includeNothing, includeDeprecated) =>
-                    complete {
-                      kb.querySubClasses(expression, direct, includeEquivalent, includeNothing, includeDeprecated)
-                    }
-                  }
-                }
-              } ~
-                path("superclasses") {
+      pathPrefix("docs") {
+        getFromResourceDirectory("docs")
+      } ~
+        pathPrefix("kbs") {
+          pathPrefix(Segment) { kbName =>
+            Owlery.kb(kbName) match {
+              case None     => reject
+              case Some(kb) =>
+                path("subclasses") {
                   objectAndPrefixParametersToClass { expression =>
-                    parameters("direct".?(false), "includeEquivalent".?(false), "includeThing".?(false), "includeDeprecated".?(true)) { (direct, includeEquivalent, includeThing, includeDeprecated) =>
+                    parameters("direct".?(false), "includeEquivalent".?(false), "includeNothing".?(false), "includeDeprecated".?(true)) { (direct, includeEquivalent, includeNothing, includeDeprecated) =>
                       complete {
-                        kb.querySuperClasses(expression, direct, includeEquivalent, includeThing, includeDeprecated)
+                        kb.querySubClasses(expression, direct, includeEquivalent, includeNothing, includeDeprecated)
                       }
                     }
                   }
                 } ~
-                path("instances") {
-                  objectAndPrefixParametersToClass { expression =>
-                    parameters("direct".?(false), "includeDeprecated".?(true)) { (direct, includeDeprecated) =>
-                      complete {
-                        kb.queryInstances(expression, direct, includeDeprecated)
+                  path("superclasses") {
+                    objectAndPrefixParametersToClass { expression =>
+                      parameters("direct".?(false), "includeEquivalent".?(false), "includeThing".?(false), "includeDeprecated".?(true)) { (direct, includeEquivalent, includeThing, includeDeprecated) =>
+                        complete {
+                          kb.querySuperClasses(expression, direct, includeEquivalent, includeThing, includeDeprecated)
+                        }
                       }
                     }
-                  }
-                } ~
-                path("equivalent") {
-                  objectAndPrefixParametersToClass { expression =>
-                    parameters("includeDeprecated".?(true)) { includeDeprecated =>
-                      complete {
-                        kb.queryEquivalentClasses(expression, includeDeprecated)
+                  } ~
+                  path("instances") {
+                    objectAndPrefixParametersToClass { expression =>
+                      parameters("direct".?(false), "includeDeprecated".?(true)) { (direct, includeDeprecated) =>
+                        complete {
+                          kb.queryInstances(expression, direct, includeDeprecated)
+                        }
                       }
                     }
-                  }
-                } ~
-                path("satisfiable") {
-                  objectAndPrefixParametersToClass { expression =>
-                    complete {
-                      kb.isSatisfiable(expression)
+                  } ~
+                  path("equivalent") {
+                    objectAndPrefixParametersToClass { expression =>
+                      parameters("includeDeprecated".?(true)) { includeDeprecated =>
+                        complete {
+                          kb.queryEquivalentClasses(expression, includeDeprecated)
+                        }
+                      }
                     }
-                  }
-                } ~
-                path("types") {
-                  parameters("object", "prefixes".as[Map[String, String]].?(NoPrefixes)).as(PrefixedIndividualIRI) { preIRI =>
-                    parameters("direct".?(true), "includeThing".?(false), "includeDeprecated".?(true)) { (direct, includeThing, includeDeprecated) =>
+                  } ~
+                  path("satisfiable") {
+                    objectAndPrefixParametersToClass { expression =>
                       complete {
-                        kb.queryTypes(factory.getOWLNamedIndividual(preIRI.iri), direct, includeThing, includeDeprecated)
+                        kb.isSatisfiable(expression)
                       }
                     }
-                  }
-                } ~
-                path("extract") {
-                  post {
-                    parameters("type".as[ModuleType].?(ModuleType.STAR), "ontologies".as[Seq[IRI]].?(Seq.empty[IRI])) { (moduleType, fromIRIs) =>
-                      handleWith(kb.extractModuleForOntology(_, moduleType, fromIRIs.toSet))
-                    }
-                  }
-                } ~
-                path("sparql") {
-                  get {
-                    parameter("query".as[Query]) { query =>
-                      complete {
-                        kb.performSPARQLQuery(query)
+                  } ~
+                  path("types") {
+                    parameters("object", "prefixes".as[Map[String, String]].?(NoPrefixes)).as(PrefixedIndividualIRI) { preIRI =>
+                      parameters("direct".?(true), "includeThing".?(false), "includeDeprecated".?(true)) { (direct, includeThing, includeDeprecated) =>
+                        complete {
+                          kb.queryTypes(factory.getOWLNamedIndividual(preIRI.iri), direct, includeThing, includeDeprecated)
+                        }
                       }
                     }
                   } ~
+                  path("extract") {
                     post {
-                      parameter("query".as[Query].?(NullQuery)) {
-                        case NullQuery => handleWith(kb.performSPARQLQuery)
-                        case query     => complete {
+                      parameters("type".as[ModuleType].?(ModuleType.STAR), "ontologies".as[Seq[IRI]].?(Seq.empty[IRI])) { (moduleType, fromIRIs) =>
+                        handleWith(kb.extractModuleForOntology(_, moduleType, fromIRIs.toSet))
+                      }
+                    }
+                  } ~
+                  path("sparql") {
+                    get {
+                      parameter("query".as[Query]) { query =>
+                        complete {
                           kb.performSPARQLQuery(query)
                         }
                       }
-                    }
-                } ~
-                path("expand") {
-                  get {
-                    parameter("query".as[Query]) { query =>
-                      complete {
-                        kb.expandSPARQLQuery(query)
+                    } ~
+                      post {
+                        parameter("query".as[Query].?(NullQuery)) {
+                          case NullQuery => handleWith(kb.performSPARQLQuery)
+                          case query     => complete {
+                            kb.performSPARQLQuery(query)
+                          }
+                        }
                       }
-                    }
                   } ~
-                    post {
-                      handleWith(kb.expandSPARQLQuery)
+                  path("expand") {
+                    get {
+                      parameter("query".as[Query]) { query =>
+                        complete {
+                          kb.expandSPARQLQuery(query)
+                        }
+                      }
+                    } ~
+                      post {
+                        handleWith(kb.expandSPARQLQuery)
+                      }
+                  } ~
+                  pathEnd {
+                    complete {
+                      kb.summary
                     }
-                } ~
-                pathEnd {
-                  complete {
-                    kb.summary
                   }
-                }
-          }
-        } ~
-          pathEnd {
-            complete {
-              Owlery
             }
-          }
-      }
+          } ~
+            pathEnd {
+              complete {
+                Owlery
+              }
+            }
+        }
     }
   }