package jalview.fts.service.uniprot;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.help.HelpSetException;
+
+import jalview.bin.Console;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.uniprot_sequence_fetcher");
-
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
- public UniprotFTSPanel(SequenceFetcher seqFetcher)
+ private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
+
+ /**
+ * Constructor given an (optional) sequence fetcher panel to revert to on
+ * clicking the 'Back' button
+ *
+ * @param fetcher
+ */
+ public UniprotFTSPanel(SequenceFetcher fetcher)
{
- super();
+ super(fetcher);
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
- this.seqFetcher = seqFetcher;
- this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
+ this.seqFetcher = fetcher;
+ this.progressIndicator = (fetcher == null) ? null
+ : fetcher.getProgressIndicator();
}
@Override
public void searchAction(boolean isFreshSearch)
{
+ searchAction(null, isFreshSearch);
+ }
+
+ public void searchAction(String cursor, boolean isFreshSearch)
+ {
mainFrame.requestFocusInWindow();
if (isFreshSearch)
{
offSet = 0;
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ c.clearCursors();
+ c.setCursorPage(0);
+ c.setCursor(0, "");
}
new Thread()
{
request.setSearchTerm(searchTerm);
request.setOffSet(offSet);
request.setWantedFields(wantedFields);
- FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
+ UniProtFTSRestClient uniProtRestClient = UniProtFTSRestClient
.getInstance();
FTSRestResponse resultList;
try
{
- resultList = uniProtRestCleint.executeRequest(request);
+ resultList = uniProtRestClient.executeRequest(request, cursor);
} catch (Exception e)
{
- e.printStackTrace();
setErrorMessage(e.getMessage());
checkForErrors();
+ setSearchInProgress(false);
return;
}
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
- getResultTable().setModel(
- FTSRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
+ getResultTable().setModel(FTSRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().setVisible(true);
totalResultSetCount = resultList.getNumberOfItemsFound();
resultSetCount = resultList.getSearchSummary() == null ? 0
: resultList.getSearchSummary().size();
- String result = (resultSetCount > 0) ? MessageManager
- .getString("label.results") : MessageManager
- .getString("label.result");
+ String result = (resultSetCount > 0)
+ ? MessageManager.getString("label.results")
+ : MessageManager.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
- updateSearchFrameTitle(defaultFTSFrameTitle
- + " - "
- + result
- + " "
- + totalNumberformatter.format((Number) (offSet + 1))
- + " to "
- + totalNumberformatter
- .format((Number) (offSet + resultSetCount))
- + " of "
- + totalNumberformatter
- .format((Number) totalResultSetCount) + " "
- + " (" + (endTime - startTime) + " milli secs)");
+ updateSearchFrameTitle(
+ defaultFTSFrameTitle + " - " + result + " "
+ + totalNumberformatter
+ .format(Integer.valueOf(offSet + 1))
+ + " to "
+ + totalNumberformatter.format(Integer
+ .valueOf(offSet + resultSetCount))
+ + " of "
+ + totalNumberformatter.format(
+ Integer.valueOf(totalResultSetCount))
+ + " " + " (" + (endTime - startTime)
+ + " milli secs)");
}
else
{
{
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
- primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
- wantedFields, false);
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
int[] selectedRows = getResultTable().getSelectedRows();
for (int summaryRow : selectedRows)
{
- String idStr = getResultTable().getValueAt(summaryRow,
- primaryKeyColIndex).toString();
+ String idStr = getResultTable()
+ .getValueAt(summaryRow, primaryKeyColIndex).toString();
selectedIdsSet.add(idStr);
}
selectedIdsSet.addAll(paginatorCart);
}
String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.getTextArea().setText(ids);
+ seqFetcher.setQuery(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
delayAndEnableActionButtons();
{
return UNIPROT_FTS_CACHE_KEY;
}
+
+ @Override
+ public String getAutosearchPreference()
+ {
+ return UNIPROT_AUTOSEARCH;
+ }
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.UniprotFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+
+ /*
+ * 2022-07-20 bsoares
+ * The new Uniprot API has a strange pagination process described at
+ * https://www.uniprot.org/help/pagination
+ * When a successful request returns results, with more results past the size
+ * limit, the response sends a "Link" header with a URL containing the a "cursor"
+ * parameter with an opaque string that refers to the next page of results.
+ * These are store as nextCursor in the UniProtFTSRestClient along with the currCursor.
+ * When navigation across pages occurs these should be swapped around.
+ */
+ @Override
+ public void refreshPaginatorState()
+ {
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ setNextPageButtonEnabled(c.getNextCursor() != null);
+ setPrevPageButtonEnabled(c.getPrevCursor() != null);
+ }
+
+ @Override
+ public void prevPageAction()
+ {
+ updatePaginatorCart();
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ String prevCursor = c.getPrevCursor();
+ if (prevCursor != null)
+ {
+ if (offSet >= pageLimit)
+ {
+ offSet -= pageLimit;
+ }
+ else
+ {
+ // not sure what's happening if we get here though it wouldn't surprise
+ // me
+ Console.warn(
+ "UniprotFTSPanel: prevCursor exists but offset < pageLimit. This probably shouldn't be happening.");
+ }
+ c.setPrevCursorPage();
+ searchAction(prevCursor, false);
+ }
+ else
+ {
+ refreshPaginatorState();
+ }
+ }
+
+ @Override
+ public void nextPageAction()
+ {
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ String nextCursor = c.getNextCursor();
+ if (nextCursor != null)
+ {
+ offSet += pageLimit;
+ c.setNextCursorPage();
+ searchAction(nextCursor, false);
+ }
+ else
+ {
+ refreshPaginatorState();
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff