Updated client to not include pharmacophore align endpoint + removed …

…align node + updated swagger codegenerator

Refs #4

README.md

@@ -98,12 +98,12 @@ kripodb serve data/similarities.frozen.h5 data/fragments.sqlite data/pharmacopho
 
 2. Download swagger code generator
 ```
-wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.2.2/swagger-codegen-cli-2.2.2.jar
+wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.2.3/swagger-codegen-cli-2.2.3.jar
 ```
 
 3. Generate a client for KripoDB web service
 ```
-java -jar swagger-codegen-cli-2.2.2.jar generate \
+java -jar swagger-codegen-cli-2.2.3.jar generate \
 --input-spec http://localhost:8084/kripo/swagger.json \
 --output client \
 --lang java \

plugin/META-INF/MANIFEST.MF

@@ -15,11 +15,11 @@ Require-Bundle: org.knime.core;bundle-version="[3.3.0,4.0.0)",
  nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy
-Bundle-ClassPath: lib/gson-2.6.2.jar,
+Bundle-ClassPath: lib/gson-2.8.1.jar,
  lib/logging-interceptor-2.7.5.jar,
  lib/okhttp-2.7.5.jar,
  lib/okio-1.6.0.jar,
- lib/swagger-annotations-1.5.12.jar,
+ lib/swagger-annotations-1.5.15.jar,
  .
 Export-Package: nl.esciencecenter.e3dchem.kripodb,
  nl.esciencecenter.e3dchem.kripodb.fragments,

plugin/build.properties

@@ -3,8 +3,8 @@ output.. = target/classes/
 bin.includes = META-INF/,\
                .,\
                plugin.xml,\
-               lib/gson-2.6.2.jar,\
+               lib/gson-2.8.1.jar,\
                lib/logging-interceptor-2.7.5.jar,\
                lib/okhttp-2.7.5.jar,\
                lib/okio-1.6.0.jar,\
-               lib/swagger-annotations-1.5.12.jar
+               lib/swagger-annotations-1.5.15.jar

plugin/plugin.xml

@@ -34,10 +34,6 @@
                deprecated="false"
                factory-class="nl.esciencecenter.e3dchem.kripodb.ws.pharmacophores.PharmacophoresFactory">
         </node>
-        <node
-               category-path="/community/3d-e-chem/kripodb"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.ws.pharmacophores.align.AlignFactory"
-         />
         <node
                category-path="/community/3d-e-chem/kripodb/local"
                deprecated="false"

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/ApiCallback.java

@@ -2,7 +2,7 @@
  * Kripo API
  * API to interact with Kripo fragment, fingerprint and similarity data files.
  *
- * OpenAPI spec version: 2.4.0
+ * OpenAPI spec version: 2.3.1
  * 
  *
  * NOTE: This class is auto generated by the swagger code generator program.

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/ApiClient.java

@@ -2,7 +2,7 @@
  * Kripo API
  * API to interact with Kripo fragment, fingerprint and similarity data files.
  *
- * OpenAPI spec version: 2.4.0
+ * OpenAPI spec version: 2.3.1
  * 
  *
  * NOTE: This class is auto generated by the swagger code generator program.
@@ -127,6 +127,7 @@ public class ApiClient {
 
     private InputStream sslCaCert;
     private boolean verifyingSsl;
+    private KeyManager[] keyManagers;
 
     private OkHttpClient httpClient;
     private JSON json;
@@ -139,6 +140,7 @@ public class ApiClient {
     public ApiClient() {
         httpClient = new OkHttpClient();
 
+
         verifyingSsl = true;
 
         json = new JSON(this);
@@ -270,6 +272,23 @@ public ApiClient setSslCaCert(InputStream sslCaCert) {
         return this;
     }
 
+    public KeyManager[] getKeyManagers() {
+        return keyManagers;
+    }
+
+    /**
+     * Configure client keys to use for authorization in an SSL session.
+     * Use null to reset to default.
+     *
+     * @param managers The KeyManagers to use
+     * @return ApiClient
+     */
+    public ApiClient setKeyManagers(KeyManager[] managers) {
+        this.keyManagers = managers;
+        applySslSettings();
+        return this;
+    }
+
     public DateFormat getDateFormat() {
         return dateFormat;
     }
@@ -723,12 +742,13 @@ public String sanitizeFilename(String filename) {
      *   application/json
      *   application/json; charset=UTF8
      *   APPLICATION/JSON
-     *
+     *   application/vnd.company+json
      * @param mime MIME (Multipurpose Internet Mail Extensions)
      * @return True if the given MIME is JSON, false otherwise.
      */
     public boolean isJsonMime(String mime) {
-        return mime != null && mime.matches("(?i)application\\/json(;.*)?");
+      String jsonMime = "(?i)^(application/json|[^;/ \t]+/[^;/ \t]+[+]json)[ \t]*(;.*)?$";
+      return mime != null && (mime.matches(jsonMime) || mime.equalsIgnoreCase("application/json-patch+json"));
     }
 
     /**
@@ -1030,6 +1050,13 @@ public <T> T handleResponse(Response response, Type returnType) throws ApiExcept
             if (returnType == null || response.code() == 204) {
                 // returning null if the returnType is not defined,
                 // or the status code is 204 (No Content)
+                if (response.body() != null) {
+                    try {
+                        response.body().close();
+                    } catch (IOException e) {
+                        throw new ApiException(response.message(), e, response.code(), response.headers().toMultimap());
+                    }
+                }
                 return null;
             } else {
                 return deserialize(response, returnType);
@@ -1062,6 +1089,26 @@ public <T> T handleResponse(Response response, Type returnType) throws ApiExcept
      * @throws ApiException If fail to serialize the request body object
      */
     public Call buildCall(String path, String method, List<Pair> queryParams, Object body, Map<String, String> headerParams, Map<String, Object> formParams, String[] authNames, ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException {
+        Request request = buildRequest(path, method, queryParams, body, headerParams, formParams, authNames, progressRequestListener);
+
+        return httpClient.newCall(request);
+    }
+
+    /**
+     * Build an HTTP request with the given options.
+     *
+     * @param path The sub-path of the HTTP URL
+     * @param method The request method, one of "GET", "HEAD", "OPTIONS", "POST", "PUT", "PATCH" and "DELETE"
+     * @param queryParams The query parameters
+     * @param body The request body object
+     * @param headerParams The header parameters
+     * @param formParams The form parameters
+     * @param authNames The authentications to apply
+     * @param progressRequestListener Progress request listener
+     * @return The HTTP request 
+     * @throws ApiException If fail to serialize the request body object
+     */
+    public Request buildRequest(String path, String method, List<Pair> queryParams, Object body, Map<String, String> headerParams, Map<String, Object> formParams, String[] authNames, ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException {
         updateParamsForAuth(authNames, queryParams, headerParams);
 
         final String url = buildUrl(path, queryParams);
@@ -1102,7 +1149,7 @@ public Call buildCall(String path, String method, List<Pair> queryParams, Object
             request = reqBuilder.method(method, reqBody).build();
         }
 
-        return httpClient.newCall(request);
+        return request;
     }
 
     /**
@@ -1251,7 +1298,6 @@ private void initDatetimeFormat() {
      */
     private void applySslSettings() {
         try {
-            KeyManager[] keyManagers = null;
             TrustManager[] trustManagers = null;
             HostnameVerifier hostnameVerifier = null;
             if (!verifyingSsl) {

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/ApiException.java

@@ -2,7 +2,7 @@
  * Kripo API
  * API to interact with Kripo fragment, fingerprint and similarity data files.
  *
- * OpenAPI spec version: 2.4.0
+ * OpenAPI spec version: 2.3.1
  * 
  *
  * NOTE: This class is auto generated by the swagger code generator program.

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/ApiResponse.java

@@ -2,7 +2,7 @@
  * Kripo API
  * API to interact with Kripo fragment, fingerprint and similarity data files.
  *
- * OpenAPI spec version: 2.4.0
+ * OpenAPI spec version: 2.3.1
  * 
  *
  * NOTE: This class is auto generated by the swagger code generator program.

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/Configuration.java

@@ -2,7 +2,7 @@
  * Kripo API
  * API to interact with Kripo fragment, fingerprint and similarity data files.
  *
- * OpenAPI spec version: 2.4.0
+ * OpenAPI spec version: 2.3.1
  * 
  *
  * NOTE: This class is auto generated by the swagger code generator program.