Add oncokb-curation API client and remove oncokb-transcript

oncokbTranscriptApiClient/build.gradle → oncokbCurationApiClient/build.gradle

@@ -3,8 +3,8 @@ apply plugin: 'eclipse'
 apply plugin: 'java'
 apply plugin: 'com.diffplug.spotless'
 
-group = 'org.oncokb.oncokb-transcript.client'
-version = '0.0.1-SNAPSHOT'
+group = 'org.oncokb.oncokb-curation.client'
+version = '1.0.0-SNAPSHOT'
 
 buildscript {
     repositories {
@@ -89,7 +89,7 @@ if(hasProperty('target') && target == 'android') {
     publishing {
         publications {
             maven(MavenPublication) {
-               artifactId = 'oncokbTranscriptApiClient'
+               artifactId = 'oncokbCurationApiClient'
                from components.java
             }
         }

oncokbTranscriptApiClient/build.sbt → oncokbCurationApiClient/build.sbt

@@ -1,8 +1,8 @@
 lazy val root = (project in file(".")).
   settings(
-    organization := "org.oncokb.oncokb-transcript.client",
-    name := "oncokbTranscriptApiClient",
-    version := "0.0.1-SNAPSHOT",
+    organization := "org.oncokb.oncokb-curation.client",
+    name := "oncokbCurationApiClient",
+    version := "1.0.0-SNAPSHOT",
     scalaVersion := "2.11.4",
     scalacOptions ++= Seq("-feature"),
     javacOptions in compile ++= Seq("-Xlint:deprecation"),

oncokbCurationApiClient/docs/AccountResourceApi.md

@@ -0,0 +1,179 @@
+# AccountResourceApi
+
+All URIs are relative to *http://beta.curation.oncokb.dev.aws.mskcc.org*
+
+Method | HTTP request | Description
+------------- | ------------- | -------------
+[**getAccount**](AccountResourceApi.md#getAccount) | **GET** /api/account | 
+[**getFirebaseToken**](AccountResourceApi.md#getFirebaseToken) | **GET** /api/account/firebase-token | 
+[**isAuthenticated**](AccountResourceApi.md#isAuthenticated) | **GET** /api/authenticate | 
+
+
+<a name="getAccount"></a>
+# **getAccount**
+> UserDTO getAccount()
+
+
+
+### Example
+```java
+// Import classes:
+import org.oncokb.oncokb_curation.ApiClient;
+import org.oncokb.oncokb_curation.ApiException;
+import org.oncokb.oncokb_curation.Configuration;
+import org.oncokb.oncokb_curation.models.*;
+import org.oncokb.oncokb_curation.client.AccountResourceApi;
+
+public class Example {
+  public static void main(String[] args) {
+    ApiClient defaultClient = Configuration.getDefaultApiClient();
+    defaultClient.setBasePath("http://beta.curation.oncokb.dev.aws.mskcc.org");
+
+    AccountResourceApi apiInstance = new AccountResourceApi(defaultClient);
+    try {
+      UserDTO result = apiInstance.getAccount();
+      System.out.println(result);
+    } catch (ApiException e) {
+      System.err.println("Exception when calling AccountResourceApi#getAccount");
+      System.err.println("Status code: " + e.getCode());
+      System.err.println("Reason: " + e.getResponseBody());
+      System.err.println("Response headers: " + e.getResponseHeaders());
+      e.printStackTrace();
+    }
+  }
+}
+```
+
+### Parameters
+This endpoint does not need any parameter.
+
+### Return type
+
+[**UserDTO**](UserDTO.md)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: */*
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+
+<a name="getFirebaseToken"></a>
+# **getFirebaseToken**
+> String getFirebaseToken()
+
+
+
+### Example
+```java
+// Import classes:
+import org.oncokb.oncokb_curation.ApiClient;
+import org.oncokb.oncokb_curation.ApiException;
+import org.oncokb.oncokb_curation.Configuration;
+import org.oncokb.oncokb_curation.models.*;
+import org.oncokb.oncokb_curation.client.AccountResourceApi;
+
+public class Example {
+  public static void main(String[] args) {
+    ApiClient defaultClient = Configuration.getDefaultApiClient();
+    defaultClient.setBasePath("http://beta.curation.oncokb.dev.aws.mskcc.org");
+
+    AccountResourceApi apiInstance = new AccountResourceApi(defaultClient);
+    try {
+      String result = apiInstance.getFirebaseToken();
+      System.out.println(result);
+    } catch (ApiException e) {
+      System.err.println("Exception when calling AccountResourceApi#getFirebaseToken");
+      System.err.println("Status code: " + e.getCode());
+      System.err.println("Reason: " + e.getResponseBody());
+      System.err.println("Response headers: " + e.getResponseHeaders());
+      e.printStackTrace();
+    }
+  }
+}
+```
+
+### Parameters
+This endpoint does not need any parameter.
+
+### Return type
+
+**String**
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: */*
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+
+<a name="isAuthenticated"></a>
+# **isAuthenticated**
+> String isAuthenticated()
+
+
+
+### Example
+```java
+// Import classes:
+import org.oncokb.oncokb_curation.ApiClient;
+import org.oncokb.oncokb_curation.ApiException;
+import org.oncokb.oncokb_curation.Configuration;
+import org.oncokb.oncokb_curation.models.*;
+import org.oncokb.oncokb_curation.client.AccountResourceApi;
+
+public class Example {
+  public static void main(String[] args) {
+    ApiClient defaultClient = Configuration.getDefaultApiClient();
+    defaultClient.setBasePath("http://beta.curation.oncokb.dev.aws.mskcc.org");
+
+    AccountResourceApi apiInstance = new AccountResourceApi(defaultClient);
+    try {
+      String result = apiInstance.isAuthenticated();
+      System.out.println(result);
+    } catch (ApiException e) {
+      System.err.println("Exception when calling AccountResourceApi#isAuthenticated");
+      System.err.println("Status code: " + e.getCode());
+      System.err.println("Reason: " + e.getResponseBody());
+      System.err.println("Response headers: " + e.getResponseHeaders());
+      e.printStackTrace();
+    }
+  }
+}
+```
+
+### Parameters
+This endpoint does not need any parameter.
+
+### Return type
+
+**String**
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: */*
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+

oncokbTranscriptApiClient/docs/AddEnsemblGeneBody.md → oncokbCurationApiClient/docs/AddEnsemblGeneBody.md

@@ -7,10 +7,10 @@
 
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
-**canonical** | **Boolean** |  |  [optional]
-**ensemblGeneId** | **String** |  | 
-**entrezGeneId** | **Integer** |  | 
 **referenceGenome** | **String** |  | 
+**entrezGeneId** | **Integer** |  | 
+**ensemblGeneId** | **String** |  | 
+**canonical** | **Boolean** |  |  [optional]
 
 
 ## Implemented Interfaces

oncokbTranscriptApiClient/docs/AddTranscriptBody.md → oncokbCurationApiClient/docs/AddTranscriptBody.md

@@ -7,10 +7,10 @@
 
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
-**canonical** | **Boolean** |  |  [optional]
-**ensemblTranscriptId** | **String** |  | 
 **entrezGeneId** | **Integer** |  | 
 **referenceGenome** | **String** |  | 
+**ensemblTranscriptId** | **String** |  | 
+**canonical** | **Boolean** |  |  [optional]
 
 
 ## Implemented Interfaces

oncokbCurationApiClient/docs/Alteration.md

@@ -0,0 +1,27 @@
+
+
+# Alteration
+
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**id** | **Long** |  |  [optional]
+**name** | **String** |  | 
+**alteration** | **String** |  | 
+**proteinStart** | **Integer** |  |  [optional]
+**proteinEnd** | **Integer** |  |  [optional]
+**refResidues** | **String** |  |  [optional]
+**variantResidues** | **String** |  |  [optional]
+**referenceGenomes** | [**Set<AlterationReferenceGenome>**](AlterationReferenceGenome.md) |  |  [optional]
+**genes** | [**Set<Gene>**](Gene.md) |  |  [optional]
+**consequence** | [**Consequence**](Consequence.md) |  |  [optional]
+**biomarkerAssociations** | [**Set<BiomarkerAssociation>**](BiomarkerAssociation.md) |  |  [optional]
+
+
+## Implemented Interfaces
+
+* Serializable
+
+

oncokbCurationApiClient/docs/AlterationControllerApi.md

@@ -0,0 +1,69 @@
+# AlterationControllerApi
+
+All URIs are relative to *http://beta.curation.oncokb.dev.aws.mskcc.org*
+
+Method | HTTP request | Description
+------------- | ------------- | -------------
+[**annotateAlteration**](AlterationControllerApi.md#annotateAlteration) | **POST** /api/annotate-alteration | 
+
+
+<a name="annotateAlteration"></a>
+# **annotateAlteration**
+> Alteration annotateAlteration(alteration)
+
+
+
+### Example
+```java
+// Import classes:
+import org.oncokb.oncokb_curation.ApiClient;
+import org.oncokb.oncokb_curation.ApiException;
+import org.oncokb.oncokb_curation.Configuration;
+import org.oncokb.oncokb_curation.models.*;
+import org.oncokb.oncokb_curation.client.AlterationControllerApi;
+
+public class Example {
+  public static void main(String[] args) {
+    ApiClient defaultClient = Configuration.getDefaultApiClient();
+    defaultClient.setBasePath("http://beta.curation.oncokb.dev.aws.mskcc.org");
+
+    AlterationControllerApi apiInstance = new AlterationControllerApi(defaultClient);
+    Alteration alteration = new Alteration(); // Alteration | 
+    try {
+      Alteration result = apiInstance.annotateAlteration(alteration);
+      System.out.println(result);
+    } catch (ApiException e) {
+      System.err.println("Exception when calling AlterationControllerApi#annotateAlteration");
+      System.err.println("Status code: " + e.getCode());
+      System.err.println("Reason: " + e.getResponseBody());
+      System.err.println("Response headers: " + e.getResponseHeaders());
+      e.printStackTrace();
+    }
+  }
+}
+```
+
+### Parameters
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **alteration** | [**Alteration**](Alteration.md)|  |
+
+### Return type
+
+[**Alteration**](Alteration.md)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: application/json
+ - **Accept**: */*
+
+### HTTP response details
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | OK |  -  |
+

oncokbCurationApiClient/docs/AlterationCriteria.md

@@ -0,0 +1,28 @@
+
+
+# AlterationCriteria
+
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**id** | [**LongFilter**](LongFilter.md) |  |  [optional]
+**name** | [**StringFilter**](StringFilter.md) |  |  [optional]
+**alteration** | [**StringFilter**](StringFilter.md) |  |  [optional]
+**proteinStart** | [**IntegerFilter**](IntegerFilter.md) |  |  [optional]
+**proteinEnd** | [**IntegerFilter**](IntegerFilter.md) |  |  [optional]
+**refResidues** | [**StringFilter**](StringFilter.md) |  |  [optional]
+**variantResidues** | [**StringFilter**](StringFilter.md) |  |  [optional]
+**biomarkerAssociationId** | [**LongFilter**](LongFilter.md) |  |  [optional]
+**referenceGenomesId** | [**LongFilter**](LongFilter.md) |  |  [optional]
+**geneId** | [**LongFilter**](LongFilter.md) |  |  [optional]
+**consequenceId** | [**LongFilter**](LongFilter.md) |  |  [optional]
+**distinct** | **Boolean** |  |  [optional]
+
+
+## Implemented Interfaces
+
+* Serializable
+
+

oncokbCurationApiClient/docs/AlterationReferenceGenome.md

@@ -0,0 +1,28 @@
+
+
+# AlterationReferenceGenome
+
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**id** | **Long** |  |  [optional]
+**referenceGenome** | [**ReferenceGenomeEnum**](#ReferenceGenomeEnum) |  |  [optional]
+**alteration** | [**Alteration**](Alteration.md) |  |  [optional]
+
+
+
+## Enum: ReferenceGenomeEnum
+
+Name | Value
+---- | -----
+GRCH37 | "GRCh37"
+GRCH38 | "GRCh38"
+
+
+## Implemented Interfaces
+
+* Serializable
+
+