import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JOptionPane;
import javax.swing.table.DefaultTableModel;
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
PDBRestRequest pdbRequest = new PDBRestRequest();
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
+ }
lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
}
int noOfStructuresFound = 0;
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ + " Found (" + totalTime + ")");
+ }
+ else
+ {
+ mainFrame
+.setTitle("Structure Chooser - Manual association");
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder(
+ "Operation was unsucessful due to the following: \n");
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ }
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
- + " Found (" + totalTime + ")");
}
public void loadLocalCachedPDBEntries()
public void run()
{
long startTime = System.currentTimeMillis();
- try
+ lbl_loading.setVisible(true);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
+ for (SequenceI seq : selectedSequences)
{
- lbl_loading.setVisible(true);
-
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint
- .executeRequest(pdbRequest);
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
}
-
- if (!filteredResponse.isEmpty())
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
{
- final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
- reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
- // Update table selection model here
- tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
- }
+ // Update table selection model here
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
- lbl_loading.setVisible(false);
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
mainFrame.setTitle("Structure Chooser - Filter time ("
+ totalTime + ")");
-
- validateSelections();
- } catch (Exception e)
+ }
+ else
{
- e.printStackTrace();
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder(
+ "Operation unsucessful due to the following: \n");
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JOptionPane.showMessageDialog(null, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ }
}
+
+ lbl_loading.setVisible(false);
+
+ validateSelections();
}
});
filterThread.start();
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
+ mainFrame.setTitle(filterTitle);
idInputAssSeqPanel.loadCmbAssSeq();
fileChooserAssSeqPanel.loadCmbAssSeq();
}
pdbRequest.setSearchTerm(txt_search.getText() + ")");
pdbRequest.setAssociatedSequence(selectedSequence.getName());
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ JOptionPane.showMessageDialog(this, e.getMessage(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ } finally
+ {
+ System.out.println(">>>>> executing finally block");
+ validateSelections();
+ }
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
* @param pdbRestRequest
* the PDBRestRequest instance to be processed
* @return the pdbResponse object for the given request
+ * @throws Exception
*/
public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
+ throws Exception
{
- ClientConfig clientConfig = new DefaultClientConfig();
- clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
- Boolean.TRUE);
- Client client = Client.create(clientConfig);
-
- String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
- .getWantedFields());
- int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
- : pdbRestRequest.getResponseSize();
- String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
- .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
- .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
- : " desc"));
-
- // Build request parameters for the REST Request
- WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", String.valueOf(responseSize))
- .queryParam("q", pdbRestRequest.getQuery())
- .queryParam("sort", sortParam);
-
- // Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
-
- // Get the JSON string from the response object
- String responseString = clientResponse.getEntity(String.class);
-
- // Check the response status and report exception if one occurs
- if (clientResponse.getStatus() != 200)
+ try
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ clientConfig.getFeatures().put(
+ JSONConfiguration.FEATURE_POJO_MAPPING, Boolean.TRUE);
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
+ .getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : pdbRestRequest.getResponseSize();
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
+ .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
+
+ // Build request parameters for the REST Request
+ WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", pdbRestRequest.getQuery())
+ .queryParam("sort", sortParam);
+
+ // Execute the REST request
+ ClientResponse clientResponse = webResource.accept(
+ MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+ // Get the JSON string from the response object
+ String responseString = clientResponse.getEntity(String.class);
+
+ // Check the response status and report exception if one occurs
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = "";
+ if (clientResponse.getStatus() == 400)
+ {
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new Exception(errorMessage);
+ }
+ else
+ {
+ errorMessage = getMessageByHTTPStatusCode(clientResponse
+ .getStatus());
+ throw new Exception(errorMessage);
+ }
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+
+ // Process the response and return the result to the caller.
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
+ } catch (Exception e)
{
- String errorMessage = "";
- if (clientResponse.getStatus() == 400)
+ String exceptionMsg = e.getMessage();
+ if (exceptionMsg.contains("SocketException"))
+ {
+ throw new Exception(
+ "Jalview is unable to detect an internet connection");
+ // No internet connection
+ }
+ else if (exceptionMsg.contains("UnknownHostException"))
{
- errorMessage = parseJsonExceptionString(responseString);
- throw new RuntimeException(errorMessage);
+ throw new Exception(
+ "Jalview couldn't reach the host server @ www.ebi.ac.uk"
+ + "\nPlease ensure that you are connected to the internet.");
+ // The server 'www.ebi.ac.uk' is unreachable
}
else
{
- errorMessage = "Failed : HTTP error code : "
- + clientResponse.getStatus();
- throw new RuntimeException(errorMessage);
+ throw e;
}
}
+ }
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
-
- // Process the response and return the result to the caller.
- return parsePDBJsonResponse(responseString, pdbRestRequest);
+ public String getMessageByHTTPStatusCode(int code)
+ {
+ String message = "";
+ switch (code)
+ {
+ case 410:
+ message = "PDB Rest Service no longer exists!";
+ break;
+ case 403:
+ case 404:
+ message = "The requested resource could not be found";
+ break;
+ case 408:
+ case 409:
+ case 500:
+ case 501:
+ case 502:
+ case 503:
+ case 504:
+ case 505:
+ message = "There seems to be an error from the PDB Rest API server.";
+ break;
+
+ default:
+ break;
+ }
+ return message;
}
/**
return pdbFeildIndexCounter;
}
-
/**
* This enum represents the fields available in the PDB JSON response
*
git://source.jalview.org / jalview.git / commitdiff