[BI-3082] BrAPI support for sorting/filter/pagination on Germplasm Lists

brapi-java-client/src/main/java/org/brapi/client/v2/BrAPIClient.java

@@ -12,6 +12,7 @@
 
 package org.brapi.client.v2;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import com.google.gson.*;
 import com.google.gson.reflect.TypeToken;
 import okhttp3.*;
@@ -674,6 +675,8 @@ public RequestBody serialize(Object obj, String contentType) throws ApiException
 		} else if (obj instanceof File) {
 			// File body parameter support.
 			return RequestBody.create(MediaType.parse(contentType), (File) obj);
+		} else if (obj instanceof JsonNode) {
+			return RequestBody.create(MediaType.parse(contentType), obj.toString());
 		} else if (isJsonMime(contentType)) {
 			String content;
 			if (obj != null) {
@@ -759,7 +762,8 @@ public File prepareDownloadFile(Response response) throws IOException {
 	 * @return ApiResponse<T>
 	 */
 	public <T> ApiResponse<T> execute(Call call) throws ApiException {
-		return execute(call, null);
+		Type returnType = null;
+		return execute(call, returnType);
 	}
 
 	/**
@@ -784,6 +788,29 @@ public <T> ApiResponse<T> execute(Call call, Type returnType) throws ApiExceptio
 		}
 	}
 
+	/**
+	 * Execute HTTP call and deserialize the HTTP response body into a return type based off of the submitted ResponseDeserializer<T>.
+	 *
+	 * @param call       Call
+	 * @param responseDeserializer A function passed through which will be applied to the final response.
+	 *                             In particular, this function needs to set the <T> return datatype.
+	 *                             See ListsApi.deserializeListItemsResponse() for usage examples.
+	 * @param <T>        The return type corresponding to (same with) returnType
+	 * @return ApiResponse object containing response status, headers and data,
+	 *         which is a Java object deserialized from response body and would be
+	 *         null when returnType is null.
+	 * @throws ApiException If fail to execute the call
+	 */
+	public <T> ApiResponse<T> execute(Call call, ResponseDeserializer<T> responseDeserializer) throws ApiException {
+		try {
+			Response response = call.execute();
+			T data = handleResponse(response, responseDeserializer);
+			return new ApiResponse<T>(response.code(), response.headers().toMultimap(), data);
+		} catch (IOException e) {
+			throw new ApiException(e);
+		}
+	}
+
 	/**
 	 * Execute HTTP call and deserialize the HTTP response body into the given
 	 * return type.
@@ -908,6 +935,42 @@ public <T> T handleResponse(Response response, Type returnType) throws ApiExcept
 		}
 	}
 
+	/**
+	 * Handle the given response, return the deserialized object when the response
+	 * is successful, and apply the additional passed ResponseDeserializer logic.
+	 *
+	 * @param response   Response
+	 * @param deserializer A function passed through which will be applied to the final response.
+	 *                     In particular, this function needs to set the <T> return datatype.
+	 *                     See ListsApi.deserializeListItemsResponse() for usage examples.	 * @throws ApiException If the response has a unsuccessful status code or fail
+	 *                      to deserialize the response body
+	 * @return Type
+	 */
+	public <T> T handleResponse(Response response, ResponseDeserializer<T> deserializer) throws ApiException, IOException {
+		if (response.isSuccessful()) {
+			if (response.code() == 204) {
+				// returning null if the returnType is not defined,
+				// or the status code is 204 (No Content)
+				if (response.body() != null) {
+					response.body().close();
+				}
+				return null;
+			} else {
+				return deserializer.deserialize(response);
+			}
+		} else {
+			String respBody = null;
+			if (response.body() != null) {
+				try {
+					respBody = response.body().string();
+				} catch (IOException e) {
+					throw new ApiException(response.message(), e, response.code(), response.headers().toMultimap());
+				}
+			}
+			throw new ApiException(response.message(), response.code(), response.headers().toMultimap(), respBody);
+		}
+	}
+
 	/**
 	 * Build HTTP call with the given options.
 	 *

brapi-java-client/src/main/java/org/brapi/client/v2/ResponseDeserializer.java

@@ -0,0 +1,15 @@
+package org.brapi.client.v2;
+
+import okhttp3.Response;
+import org.brapi.client.v2.model.exceptions.ApiException;
+
+import java.io.IOException;
+
+/**
+ * Generic interface to apply extra deserialization logic to handle responses in the BrAPIClient.
+ * @param <T> The response type this response deserializer should apply to.
+ */
+@FunctionalInterface
+public interface ResponseDeserializer<T> {
+    T deserialize(Response response) throws ApiException, IOException;
+}

brapi-java-client/src/main/java/org/brapi/client/v2/modules/core/ListsApi.java

@@ -12,15 +12,23 @@
 
 package org.brapi.client.v2.modules.core;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+import com.google.gson.JsonPrimitive;
 import com.google.gson.reflect.TypeToken;
 
 import okhttp3.Call;
+
+import java.io.IOException;
 import java.lang.reflect.Type;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 
+import okhttp3.Response;
 import org.apache.commons.lang3.tuple.Pair;
 import org.brapi.client.v2.ApiCallback;
 import org.brapi.client.v2.BrAPIClient;
@@ -29,11 +37,14 @@
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.client.v2.model.queryParams.core.ListQueryParams;
 import org.brapi.v2.model.BrAPIAcceptedSearchResponse;
+import org.brapi.v2.model.core.BrAPIListTypes;
 import org.brapi.v2.model.core.request.BrAPIListNewRequest;
+import org.brapi.v2.model.core.response.BrAPIListItemsListResponse;
 import org.brapi.v2.model.core.response.BrAPIListResponse;
 import org.brapi.v2.model.core.request.BrAPIListSearchRequest;
 import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
+import org.brapi.v2.model.germ.BrAPIGermplasm;
 
 public class ListsApi {
     private BrAPIClient apiClient;
@@ -54,6 +65,12 @@ public void setApiClient(BrAPIClient apiClient) {
         this.apiClient = apiClient;
     }
 
+    private static final Map<BrAPIListTypes, Class<?>> supportedItemClassByBrAPIListTypes = new HashMap<>();
+
+    static {
+        supportedItemClassByBrAPIListTypes.put(BrAPIListTypes.GERMPLASM, BrAPIGermplasm.class);
+    }
+
     /**
      * Build call for listsGet
      * @param queryParams
@@ -537,6 +554,45 @@ private Call searchListsPostCall(BrAPIListSearchRequest body) throws ApiExceptio
         return apiClient.buildCall(localVarPath, "POST", localVarQueryParams, localVarCollectionQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames);
     }
 
+    /**
+     * Build call for searchListsPost
+     * @param body  (optional)
+     * @return Call to execute
+     * @throws ApiException If fail to serialize the request body object
+     */
+    private Call searchListItemsPostCall(String listDbId, JsonNode body) throws ApiException {
+        if(body == null) {
+            throw new IllegalArgumentException("body cannot be null");
+        }
+        Object localVarPostBody = body;
+
+        // create path and map variables
+        String localVarPath = "/search/lists/{listDbId}"
+                .replaceAll("\\{" + "listDbId" + "\\}", apiClient.escapeString(listDbId)) + "/items";
+
+        Map<String, String> localVarQueryParams = new HashMap<>();
+        Map<String, String> localVarCollectionQueryParams = new HashMap<>();
+
+        Map<String, String> localVarHeaderParams = new HashMap<String, String>();
+
+        Map<String, Object> localVarFormParams = new HashMap<String, Object>();
+
+        final String[] localVarAccepts = {
+                "application/json"
+        };
+        final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts);
+        if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept);
+
+        final String[] localVarContentTypes = {
+                "application/json"
+        };
+        final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes);
+        localVarHeaderParams.put("Content-Type", localVarContentType);
+
+        String[] localVarAuthNames = new String[] { "AuthorizationToken" };
+        return apiClient.buildCall(localVarPath, "POST", localVarQueryParams, localVarCollectionQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames);
+    }
+
     /**
      * Submit a search request for Lists
      * Advanced searching for the list resource. See Search Services for additional implementation details.
@@ -642,4 +698,60 @@ public Call searchListsSearchResultsDbIdGetAsync(String searchResultsDbId, Integ
         apiClient.executeAsync(call, localVarReturnType, callback);
         return call;
     }
+
+    /**
+     * Submit a search request for ListItems
+     * Unlike other endpoints, this endpoint is not strongly typed to the search request, and is detected based off of the submitted listDbId.
+     * To accommodate for this, a functional interface is passed to the apiClient to ensure the parameterized<T> is properly initialized to the right BrAPI model object.
+     * Async and searchDbIds are not currently supported for this endpoint.
+     * @param listDbId (required)
+     * @param body  (required)
+     * @return ApiResponse&lt;ListsListResponse&gt;
+     * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body
+     */
+    public <T> ApiResponse<BrAPIListItemsListResponse<T>> searchListItemsByList(String listDbId, JsonNode body) throws ApiException {
+        Call call = searchListItemsPostCall(listDbId, body);
+
+        return apiClient.execute(call, this::deserializeListItemsResponse);
+    }
+
+    private <T> BrAPIListItemsListResponse<T> deserializeListItemsResponse(Response response) throws ApiException, IOException {
+
+        // Ignore NPE check here, this function is used after a response check has already occurred further downstream
+        String json = response.body().string();
+
+        JsonParser parser = new JsonParser();
+
+        JsonObject root = parser.parse(json).getAsJsonObject();
+
+        // The prod server response will return with the data type.
+        JsonPrimitive resultListType = root.getAsJsonPrimitive("resultListType");
+
+        if (resultListType == null) {
+            throw new ApiException(500, "BrAPI server responded without resultListType in the response");
+        }
+
+        BrAPIListTypes listType =  BrAPIListTypes.fromValue(resultListType.getAsString());
+
+        if (listType == null) {
+            throw new ApiException(500, "BrAPI server responded with an invalid BrPIListType in the response");
+        }
+
+        // Get the BrAPI model object that corresponds to the returned data type.
+        Class<?> itemClass = supportedItemClassByBrAPIListTypes.get(listType);
+
+        if (itemClass == null) {
+            throw new ApiException("Unsupported list type: " + listType);
+        }
+
+        // Ensure that BrAPIListItemsListResponse has its parameterized <T> set with the appropriate object, which will
+        // populate all the way down to BrAPIListItemWithFullItem<T>
+        Type responseType = TypeToken.getParameterized(
+                BrAPIListItemsListResponse.class,
+                itemClass
+        ).getType();
+
+        // Apply deserialization of the response
+        return apiClient.getJSON().deserialize(json, responseType);
+    }
 }

brapi-java-model/pom.xml

@@ -40,6 +40,11 @@
             <artifactId>jackson-annotations</artifactId>
             <version>${jackson.annotations.version}</version>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>${jackson.annotations.version}</version>
+        </dependency>
         <dependency>
             <groupId>javax.validation</groupId>
             <artifactId>validation-api</artifactId>

brapi-java-model/src/main/java/org/brapi/v2/model/core/BrAPIListItem.java

@@ -0,0 +1,84 @@
+package org.brapi.v2.model.core;
+
+import java.util.Objects;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+/**
+ * ListItem
+ */
+public class BrAPIListItem  {
+    @JsonProperty("listItemDbId")
+    private String listItemDbId = null;
+
+    @JsonProperty("position")
+    private Integer position = null;
+
+    // This represents the actual value stored in the list_item table
+    @JsonProperty("item")
+    private String item = null;
+
+
+    public String getListItemDbId() {
+        return listItemDbId;
+    }
+
+    public void setListItemDbId(String listItemDbId) {
+        this.listItemDbId = listItemDbId;
+    }
+
+    public Integer getPosition() {
+        return position;
+    }
+
+    public void setPosition(Integer position) {
+        this.position = position;
+    }
+
+    public String getItem() {
+        return item;
+    }
+
+    public void setItem(String item) {
+        this.item = item;
+    }
+
+    @Override
+    public boolean equals(java.lang.Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        BrAPIListItem ListItem = (BrAPIListItem) o;
+        return Objects.equals(this.listItemDbId, ListItem.listItemDbId);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(listItemDbId, super.hashCode());
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        sb.append("class ListItem {\n");
+        sb.append("    ").append(toIndentedString(super.toString())).append("\n");
+        sb.append("    listDbId: ").append(toIndentedString(listItemDbId)).append("\n");
+        sb.append("}");
+        return sb.toString();
+    }
+
+    /**
+     * Convert the given object to string with each line indented by 4 spaces
+     * (except the first line).
+     */
+    private String toIndentedString(java.lang.Object o) {
+        if (o == null) {
+            return "null";
+        }
+        return o.toString().replace("\n", "\n    ");
+    }
+}
+
+