Merge branch 'develop' into feature/limit_tests

dockstore-integration-testing/src/test/java/io/dockstore/client/cli/SwaggerClientIT.java

@@ -53,6 +53,7 @@
 import io.swagger.client.api.UsersApi;
 import io.swagger.client.api.WorkflowsApi;
 import io.swagger.client.model.DescriptorLanguageBean;
+import io.swagger.client.model.Config;
 import io.swagger.client.model.DockstoreTool;
 import io.swagger.client.model.Entry;
 import io.swagger.client.model.MetadataV1;
@@ -822,6 +823,17 @@ public void testUploadZip() {
         Assert.assertEquals(1, updatedWorkflow.getWorkflowVersions().size());
     }
 
+    /**
+     * Test that the config endpoint doesn't fail and validates one random property
+     */
+    @Test
+    public void testConfig() {
+        final ApiClient webClient = getWebClient();
+        final MetadataApi metadataApi = new MetadataApi(webClient);
+        final Config config = metadataApi.getConfig();
+        Assert.assertEquals("read:org,user:email", config.getGitHubScope());
+    }
+
     /**
      * Tests workflow sharing/permissions.
      *

dockstore-integration-testing/src/test/resources/dockstore.yml

@@ -81,3 +81,32 @@ logging:
       timeZone: UTC
       target: stdout
       logFormat: # TODO
+
+uiConfig:
+  # Must end with a slash
+  discourseUrl: https://discuss.dockstore.org/
+  dnaStackImportUrl: https://app.dnastack.com/#/app/workflow/import/dockstore
+  fireCloudImportUrl: https://portal.firecloud.org/#import/dockstore
+  dnaNexusImportUrl: https://platform.dnanexus.com/panx/tools/import-workflow
+  terraImportUrl: https://app.terra.bio/#import-tool/dockstore
+
+  gitHubAuthUrl: https://github.com/login/oauth/authorize
+  gitHubRedirectPath: /auth/github.com
+  gitHubScope: read:org,user:email
+
+  quayIoAuthUrl: https://quay.io/oauth/authorize
+  quayIoRedirectPath: /auth/quay.io
+  quayIoScope: repo:read,user:read
+
+  bitBucketAuthUrl: https://bitbucket.org/site/oauth2/authorize
+
+  gitlabAuthUrl: https://gitlab.com/oauth/authorize
+  gitlabRedirectPath: /auth/gitlab.com
+  gitlabScope: api
+
+  googleScope: profile email
+
+  cwlVisualizerUri: https://view.commonwl.org
+
+  enableLaunchWithFireCloud: true
+

dockstore-webservice/src/main/java/io/dockstore/webservice/DockstoreWebserviceConfiguration.java

@@ -60,7 +60,7 @@ public class DockstoreWebserviceConfiguration extends Configuration {
     private String quayClientID;
 
     @NotEmpty
-    private List<String> githubClientID;
+    private String githubClientID;
 
     @NotEmpty
     private String googleClientID;
@@ -82,7 +82,7 @@ public class DockstoreWebserviceConfiguration extends Configuration {
     private String githubRedirectURI;
 
     @NotEmpty
-    private List<String> githubClientSecret;
+    private String githubClientSecret;
 
     @NotEmpty
     private String googleRedirectURI;
@@ -105,6 +105,10 @@ public class DockstoreWebserviceConfiguration extends Configuration {
 
     private List<String> externalGoogleClientIdPrefixes = new ArrayList<>();
 
+    @Valid
+    @NotNull
+    private UIConfig uiConfig;
+
     @JsonProperty("database")
     public DataSourceFactory getDataSourceFactory() {
         return database;
@@ -183,15 +187,15 @@ public void setHttpClientConfiguration(HttpClientConfiguration newHttpClient) {
      */
     @JsonProperty
     @JsonFormat(with = JsonFormat.Feature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
-    public List<String> getGithubClientID() {
+    public String getGithubClientID() {
         return githubClientID;
     }
 
     /**
      * @param githubClientID the githubClientID to set
      */
     @JsonProperty
-    public void setGithubClientID(List<String> githubClientID) {
+    public void setGithubClientID(String githubClientID) {
         this.githubClientID = githubClientID;
     }
 
@@ -216,15 +220,15 @@ public void setGithubRedirectURI(String githubRedirectURI) {
      */
     @JsonProperty
     @JsonFormat(with = JsonFormat.Feature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
-    public List<String> getGithubClientSecret() {
+    public String getGithubClientSecret() {
         return githubClientSecret;
     }
 
     /**
      * @param githubClientSecret the githubClientSecret to set
      */
     @JsonProperty
-    public void setGithubClientSecret(List<String> githubClientSecret) {
+    public void setGithubClientSecret(String githubClientSecret) {
         this.githubClientSecret = githubClientSecret;
     }
 
@@ -378,6 +382,11 @@ public void setLimitConfig(LimitConfig limitConfig) {
         this.limitConfig = limitConfig;
     }
 
+    @JsonProperty
+    public UIConfig getUiConfig() {
+        return uiConfig;
+    }
+
     /**
      * This config defines values that define the webservice from the outside world.
      * Most notably, for swagger. But also to configure generated RSS paths and TRS paths
@@ -489,4 +498,186 @@ public void setWorkflowVersionLimit(int workflowVersionLimit) {
             this.workflowVersionLimit = workflowVersionLimit;
         }
     }
+
+    /**
+     * A subset of properties returned to the UI. Only a subset because some properties that will
+     * be used by the UI are also used by the web service and predate the existences of this class.
+     */
+    public static class UIConfig {
+
+        /**
+         * Must end with a slash
+         */
+        private String discourseUrl;
+
+        private String dnaStackImportUrl;
+        private String fireCloudImportUrl;
+        private String dnaNexusImportUrl;
+        private String terraImportUrl;
+
+        private String gitHubAuthUrl;
+        private String gitHubRedirectPath;
+        private String gitHubScope;
+
+        private String quayIoAuthUrl;
+        private String quayIoRedirectPath;
+        private String quayIoScope;
+
+        private String bitBucketAuthUrl;
+
+        private String gitlabAuthUrl;
+        private String gitlabRedirectPath;
+        private String gitlabScope;
+
+        private String googleScope;
+
+        private String cwlVisualizerUri;
+
+        private boolean enableLaunchWithFireCloud;
+
+
+        public String getDiscourseUrl() {
+            return discourseUrl;
+        }
+
+        public void setDiscourseUrl(String discourseUrl) {
+            this.discourseUrl = discourseUrl;
+        }
+
+        public String getDnaStackImportUrl() {
+            return dnaStackImportUrl;
+        }
+
+        public void setDnaStackImportUrl(String dnaStackImportUrl) {
+            this.dnaStackImportUrl = dnaStackImportUrl;
+        }
+
+        public String getFireCloudImportUrl() {
+            return fireCloudImportUrl;
+        }
+
+        public void setFireCloudImportUrl(String fireCloudImportUrl) {
+            this.fireCloudImportUrl = fireCloudImportUrl;
+        }
+
+        public String getDnaNexusImportUrl() {
+            return dnaNexusImportUrl;
+        }
+
+        public void setDnaNexusImportUrl(String dnaNexusImportUrl) {
+            this.dnaNexusImportUrl = dnaNexusImportUrl;
+        }
+
+        public String getTerraImportUrl() {
+            return terraImportUrl;
+        }
+
+        public void setTerraImportUrl(String terraImportUrl) {
+            this.terraImportUrl = terraImportUrl;
+        }
+
+        public String getGitHubAuthUrl() {
+            return gitHubAuthUrl;
+        }
+
+        public void setGitHubAuthUrl(String gitHubAuthUrl) {
+            this.gitHubAuthUrl = gitHubAuthUrl;
+        }
+
+        public String getGitHubRedirectPath() {
+            return gitHubRedirectPath;
+        }
+
+        public void setGitHubRedirectPath(String gitHubRedirectPath) {
+            this.gitHubRedirectPath = gitHubRedirectPath;
+        }
+
+        public String getGitHubScope() {
+            return gitHubScope;
+        }
+
+        public void setGitHubScope(String gitHubScope) {
+            this.gitHubScope = gitHubScope;
+        }
+
+        public String getQuayIoAuthUrl() {
+            return quayIoAuthUrl;
+        }
+
+        public void setQuayIoAuthUrl(String quayIoAuthUrl) {
+            this.quayIoAuthUrl = quayIoAuthUrl;
+        }
+
+        public String getQuayIoRedirectPath() {
+            return quayIoRedirectPath;
+        }
+
+        public void setQuayIoRedirectPath(String quayIoRedirectPath) {
+            this.quayIoRedirectPath = quayIoRedirectPath;
+        }
+
+        public String getQuayIoScope() {
+            return quayIoScope;
+        }
+
+        public void setQuayIoScope(String quayIoScope) {
+            this.quayIoScope = quayIoScope;
+        }
+
+        public String getBitBucketAuthUrl() {
+            return bitBucketAuthUrl;
+        }
+
+        public void setBitBucketAuthUrl(String bitBucketAuthUrl) {
+            this.bitBucketAuthUrl = bitBucketAuthUrl;
+        }
+
+        public String getGitlabAuthUrl() {
+            return gitlabAuthUrl;
+        }
+
+        public void setGitlabAuthUrl(String gitlabAuthUrl) {
+            this.gitlabAuthUrl = gitlabAuthUrl;
+        }
+
+        public String getGitlabRedirectPath() {
+            return gitlabRedirectPath;
+        }
+
+        public void setGitlabRedirectPath(String gitlabRedirectPath) {
+            this.gitlabRedirectPath = gitlabRedirectPath;
+        }
+
+        public String getGitlabScope() {
+            return gitlabScope;
+        }
+
+        public void setGitlabScope(String gitlabScope) {
+            this.gitlabScope = gitlabScope;
+        }
+
+        public String getGoogleScope() {
+            return googleScope;
+        }
+
+        public void setGoogleScope(String googleScope) {
+            this.googleScope = googleScope;
+        }
+
+        public String getCwlVisualizerUri() {
+            return cwlVisualizerUri;
+        }
+
+        public void setCwlVisualizerUri(String cwlVisualizerUri) {
+            this.cwlVisualizerUri = cwlVisualizerUri;
+        }
+
+        public boolean isEnableLaunchWithFireCloud() {
+            return enableLaunchWithFireCloud;
+        }
+
+        public void setEnableLaunchWithFireCloud(boolean enableLaunchWithFireCloud) {
+            this.enableLaunchWithFireCloud = enableLaunchWithFireCloud;
+        }
+    }
 }

dockstore-webservice/src/main/java/io/dockstore/webservice/api/Config.java

@@ -0,0 +1,58 @@
+package io.dockstore.webservice.api;
+
+import java.lang.reflect.InvocationTargetException;
+
+import io.dockstore.webservice.DockstoreWebserviceConfiguration;
+import io.swagger.annotations.ApiModel;
+import org.apache.commons.beanutils.BeanUtils;
+
+@ApiModel(description = "Configuration information for UI clients of the Dockstore webservice.")
+public final class Config extends DockstoreWebserviceConfiguration.UIConfig {
+
+    /**
+     * Properties that aren't in UIConfig
+     */
+
+    private String githubClientId;
+    private String quayIoClientId;
+    private String bitBucketClientId;
+    private String gitlabClientId;
+    private String googleClientId;
+
+
+    private Config() {
+    }
+
+    public static Config fromWebConfig(DockstoreWebserviceConfiguration webConfig)
+            throws InvocationTargetException, IllegalAccessException {
+        final Config config = new Config();
+        config.githubClientId = webConfig.getGithubClientID();
+        config.quayIoClientId = webConfig.getQuayClientID();
+        config.bitBucketClientId = webConfig.getBitbucketClientID();
+        config.gitlabClientId = webConfig.getGitlabClientID();
+        config.googleClientId = webConfig.getGoogleClientID();
+        BeanUtils.copyProperties(config, webConfig.getUiConfig());
+        return config;
+    }
+
+    public String getGithubClientId() {
+        return githubClientId;
+    }
+
+    public String getQuayIoClientId() {
+        return quayIoClientId;
+    }
+
+    public String getBitBucketClientId() {
+        return bitBucketClientId;
+    }
+
+    public String getGitlabClientId() {
+        return gitlabClientId;
+    }
+
+    public String getGoogleClientId() {
+        return googleClientId;
+    }
+
+}