JAL-2418 source formatting

[jalview.git] / src / jalview / fts / service / pdb / PDBFTSRestClient.java

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index 8e63463..a483f44 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -82,10 +82,12 @@ public class PDBFTSRestClient extends FTSRestClient
       ClientConfig clientConfig = new DefaultClientConfig();
       Client client = Client.create(clientConfig);
 
-      String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest
-              .getWantedFields());
-      int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+      String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+              pdbRestRequest.getWantedFields());
+      int responseSize = (pdbRestRequest.getResponseSize() == 0)
+              ? getDefaultResponsePageSize()
               : pdbRestRequest.getResponseSize();
+      int offSet = pdbRestRequest.getOffSet();
       String sortParam = null;
       if (pdbRestRequest.getFieldToSortBy() == null
               || pdbRestRequest.getFieldToSortBy().trim().isEmpty())
@@ -107,11 +109,11 @@ public class PDBFTSRestClient extends FTSRestClient
         }
       }
 
-      String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
-              .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
-              .getFacetPivot();
-      String facetPivotMinCount = String.valueOf(pdbRestRequest
-              .getFacetPivotMinCount());
+      String facetPivot = (pdbRestRequest.getFacetPivot() == null
+              || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
+                      : pdbRestRequest.getFacetPivot();
+      String facetPivotMinCount = String
+              .valueOf(pdbRestRequest.getFacetPivotMinCount());
 
       String query = pdbRestRequest.getFieldToSearchBy()
               + pdbRestRequest.getSearchTerm()
@@ -128,6 +130,7 @@ public class PDBFTSRestClient extends FTSRestClient
                 .queryParam("wt", "json").queryParam("fl", wantedFields)
                 .queryParam("rows", String.valueOf(responseSize))
                 .queryParam("q", query)
+                .queryParam("start", String.valueOf(offSet))
                 .queryParam("sort", sortParam).queryParam("facet", "true")
                 .queryParam("facet.pivot", facetPivot)
                 .queryParam("facet.pivot.mincount", facetPivotMinCount);
@@ -137,12 +140,12 @@ public class PDBFTSRestClient extends FTSRestClient
         webResource = client.resource(PDB_SEARCH_ENDPOINT)
                 .queryParam("wt", "json").queryParam("fl", wantedFields)
                 .queryParam("rows", String.valueOf(responseSize))
-                .queryParam("q", query)
-                .queryParam("sort", sortParam);
+                .queryParam("start", String.valueOf(offSet))
+                .queryParam("q", query).queryParam("sort", sortParam);
       }
       // Execute the REST request
-      ClientResponse clientResponse = webResource.accept(
-              MediaType.APPLICATION_JSON).get(ClientResponse.class);
+      ClientResponse clientResponse = webResource
+              .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
 
       // Get the JSON string from the response object
       String responseString = clientResponse.getEntity(String.class);
@@ -159,8 +162,8 @@ public class PDBFTSRestClient extends FTSRestClient
         }
         else
         {
-          errorMessage = getMessageByHTTPStatusCode(clientResponse
-                  .getStatus());
+          errorMessage = getMessageByHTTPStatusCode(
+                  clientResponse.getStatus(), "PDB");
           throw new Exception(errorMessage);
         }
       }
@@ -178,16 +181,14 @@ public class PDBFTSRestClient extends FTSRestClient
       if (exceptionMsg.contains("SocketException"))
       {
         // No internet connection
-        throw new Exception(
-                MessageManager
-                        .getString("exception.unable_to_detect_internet_connection"));
+        throw new Exception(MessageManager.getString(
+                "exception.unable_to_detect_internet_connection"));
       }
       else if (exceptionMsg.contains("UnknownHostException"))
       {
         // The server 'www.ebi.ac.uk' is unreachable
-        throw new Exception(
-                MessageManager
-                        .getString("exception.pdb_server_unreachable"));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.fts_server_unreachable", "PDB Solr"));
       }
       else
       {
@@ -196,36 +197,6 @@ public class PDBFTSRestClient extends FTSRestClient
     }
   }
 
-  public String getMessageByHTTPStatusCode(int code)
-  {
-    String message = "";
-    switch (code)
-    {
-    case 410:
-      message = MessageManager
-              .getString("exception.pdb_rest_service_no_longer_available");
-      break;
-    case 403:
-    case 404:
-      message = MessageManager.getString("exception.resource_not_be_found");
-      break;
-    case 408:
-    case 409:
-    case 500:
-    case 501:
-    case 502:
-    case 503:
-    case 504:
-    case 505:
-      message = MessageManager.getString("exception.pdb_server_error");
-      break;
-
-    default:
-      break;
-    }
-    return message;
-  }
-
   /**
    * Process error response from PDB server if/when one occurs.
    * 
@@ -289,8 +260,8 @@ public class PDBFTSRestClient extends FTSRestClient
               .parse(pdbJsonResponseString);
 
       JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
-      String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
-              "QTime").toString();
+      String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
+              .get("QTime").toString();
       int numFound = Integer
               .valueOf(pdbResponse.get("numFound").toString());
       if (numFound > 0)
@@ -327,8 +298,9 @@ public class PDBFTSRestClient extends FTSRestClient
     Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
     SequenceI associatedSeq = request.getAssociatedSequence();
     int colCounter = 0;
-    summaryRowData = new Object[(associatedSeq != null) ? diplayFields
-            .size() + 1 : diplayFields.size()];
+    summaryRowData = new Object[(associatedSeq != null)
+            ? diplayFields.size() + 1
+            : diplayFields.size()];
     if (associatedSeq != null)
     {
       associatedSequence = associatedSeq;
@@ -353,15 +325,17 @@ public class PDBFTSRestClient extends FTSRestClient
       {
         try
         {
-          summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
-                  .valueOf(fieldData)
-                  : (field.getDataColumnClass() == Double.class) ? Double
-                          .valueOf(fieldData)
-                          : fieldData;
+          summaryRowData[colCounter++] = (field.getDataType()
+                  .getDataTypeClass() == Integer.class)
+                          ? Integer.valueOf(fieldData)
+                          : (field.getDataType()
+                                  .getDataTypeClass() == Double.class)
+                                          ? Double.valueOf(fieldData)
+                                          : sanitiseData(fieldData);
         } catch (Exception e)
         {
           e.printStackTrace();
-            System.out.println("offending value:" + fieldData);
+          System.out.println("offending value:" + fieldData);
         }
       }
     }
@@ -407,16 +381,29 @@ public class PDBFTSRestClient extends FTSRestClient
       {
         return Objects.hash(primaryKey1, this.toString());
       }
+
+      @Override
+      public boolean equals(Object that)
+      {
+        return this.toString().equals(that.toString());
+      }
     };
   }
 
+  private static String sanitiseData(String data)
+  {
+    String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
+            .replaceAll("\\[", "").replaceAll("\\]", "")
+            .replaceAll("\",\"", ", ").replaceAll("\"", "");
+    return cleanData;
+  }
+
   @Override
   public String getColumnDataConfigFileName()
   {
-    return getResourceFile("/fts/pdb_data_columns.conf");
+    return "/fts/pdb_data_columns.txt";
   }
 
-
   public static FTSRestClientI getInstance()
   {
     if (instance == null)
@@ -425,4 +412,18 @@ public class PDBFTSRestClient extends FTSRestClient
     }
     return instance;
   }
+
+  private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+
+  public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
+  {
+    if (allDefaultDisplayedStructureDataColumns == null
+            || allDefaultDisplayedStructureDataColumns.isEmpty())
+    {
+      allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+      allDefaultDisplayedStructureDataColumns
+              .addAll(super.getAllDefaultDisplayedFTSDataColumns());
+    }
+    return allDefaultDisplayedStructureDataColumns;
+  }
 }