X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniprotFTSPanel.java;h=0d9767c42fe8913b3718f550db287e43fadd5b79;hp=ace36004f4aa98731b4e1503210bb9de4b0dd0bc;hb=735e346c658597baaa9194dfb160b294a1198eae;hpb=d2bf6a7b7e1bbb4774f13ba2733487ae6b7aae6d diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java index ace3600..0d9767c 100644 --- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java +++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java @@ -21,18 +21,23 @@ 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 { @@ -40,28 +45,44 @@ public class UniprotFTSPanel extends GFTSPanel private static String defaultFTSFrameTitle = MessageManager .getString("label.uniprot_sequence_fetcher"); - - private static Map tempUserPrefs = new HashMap(); + private static Map 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() { @@ -86,26 +107,25 @@ public class UniprotFTSPanel extends GFTSPanel 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); @@ -115,23 +135,23 @@ public class UniprotFTSPanel extends GFTSPanel 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 { @@ -187,12 +207,12 @@ public class UniprotFTSPanel extends GFTSPanel { disableActionButtons(); StringBuilder selectedIds = new StringBuilder(); - HashSet selectedIdsSet = new HashSet(); + HashSet selectedIdsSet = new HashSet<>(); int primaryKeyColIndex = 0; try { - primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex( - wantedFields, false); + primaryKeyColIndex = getFTSRestClient() + .getPrimaryKeyColumIndex(wantedFields, false); } catch (Exception e) { e.printStackTrace(); @@ -200,8 +220,8 @@ public class UniprotFTSPanel extends GFTSPanel 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); @@ -211,8 +231,7 @@ public class UniprotFTSPanel extends GFTSPanel } 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(); @@ -241,4 +260,86 @@ public class UniprotFTSPanel extends GFTSPanel { 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(); + } + } + }