Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UniprotFTSPanel	42	112	36	0.00%	Show methods

Class UniprotFTSPanel

Class UniprotFTSPanel	Line # 42	Total Statements 112	Complexity 36	TOTAL Coverage 0.00%
UniprotFTSPanel(SequenceFetcher)   UniprotFTSPanel(SequenceFetcher)	6060	4.04	2.02	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	7070	1.01	1.01	0.0 0.00%
run() : void   run() : void	8989	37.037	9.09	0.0 0.00%
searchAction(String,boolean) : void   searchAction(String,boolean) : void	7676	8.08	2.02	0.0 0.00%
decodeSearchTerm(String,String) : String   decodeSearchTerm(String,String) : String	172172	13.013	5.05	0.0 0.00%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	199199	1.01	1.01	0.0 0.00%
okAction() : void   okAction() : void	205205	19.019	2.02	0.0 0.00%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	240240	1.01	1.01	0.0 0.00%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	246246	1.01	1.01	0.0 0.00%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	252252	1.01	1.01	0.0 0.00%
getCacheKey() : String   getCacheKey() : String	258258	1.01	1.01	0.0 0.00%
getAutosearchPreference() : String   getAutosearchPreference() : String	264264	1.01	1.01	0.0 0.00%
showHelp() : void   showHelp() : void	270270	3.03	2.02	0.0 0.00%
refreshPaginatorState() : void   refreshPaginatorState() : void	292292	3.03	1.01	0.0 0.00%
prevPageAction() : void   prevPageAction() : void	300300	10.010	3.03	0.0 0.00%
nextPageAction() : void   nextPageAction() : void	328328	7.07	2.02	0.0 0.00%
getDbName() : String   getDbName() : String	345345	1.01	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21
22		package jalview.fts.service.uniprot;
23
24		import java.util.HashMap;
25		import java.util.HashSet;
26		import java.util.Map;
27
28		import javax.help.HelpSetException;
29
30		import jalview.bin.Console;
31		import jalview.fts.api.FTSDataColumnI;
32		import jalview.fts.api.FTSRestClientI;
33		import jalview.fts.core.FTSRestRequest;
34		import jalview.fts.core.FTSRestResponse;
35		import jalview.fts.core.GFTSPanel;
36		import jalview.gui.Help;
37		import jalview.gui.Help.HelpId;
38		import jalview.gui.SequenceFetcher;
39		import jalview.util.MessageManager;
40
41		@SuppressWarnings("serial")
		0% Uncovered Elements: 157 (157) Complexity: 36 Complexity Density: 0.32
42		public class UniprotFTSPanel extends GFTSPanel
43		{
44
45		private static String defaultFTSFrameTitle = MessageManager
46		.getString("label.uniprot_sequence_fetcher");
47
48		private static Map<String, Integer> tempUserPrefs = new HashMap<>();
49
50		private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_2022_FTS";
51
52		private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
53
54		/**
55		* Constructor given an (optional) sequence fetcher panel to revert to on
56		* clicking the 'Back' button
57		*
58		* @param fetcher
59		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
60	0	public UniprotFTSPanel(SequenceFetcher fetcher)...
61		{
62	0	super(fetcher);
63	0	pageLimit = UniProtFTSRestClient.getInstance()
64		.getDefaultResponsePageSize();
65	0	this.seqFetcher = fetcher;
66	0	this.progressIndicator = (fetcher == null) ? null
67		: fetcher.getProgressIndicator();
68		}
69
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	@Override...
71		public void searchAction(boolean isFreshSearch)
72		{
73	0	searchAction(null, isFreshSearch);
74		}
75
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
76	0	public void searchAction(String cursor, boolean isFreshSearch)...
77		{
78	0	mainFrame.requestFocusInWindow();
79	0	if (isFreshSearch)
80		{
81	0	offSet = 0;
82	0	UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
83	0	c.clearCursors();
84	0	c.setCursorPage(0);
85	0	c.setCursor(0, "");
86		}
87	0	new Thread()
88		{
		0% Uncovered Elements: 47 (47) Complexity: 9 Complexity Density: 0.24
89	0	@Override...
90		public void run()
91		{
92	0	reset();
93	0	String searchInput = getTypedText();
94	0	if (searchInput.length() > 0)
95		{
96	0	setSearchInProgress(true);
97	0	long startTime = System.currentTimeMillis();
98	0	searchInput = getTypedText();
99	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
100		.getSelectedItem()).getAltCode();
101	0	wantedFields = UniProtFTSRestClient.getInstance()
102		.getAllDefaultDisplayedFTSDataColumns();
103	0	String searchTerm = decodeSearchTerm(searchInput, searchTarget);
104
105	0	FTSRestRequest request = new FTSRestRequest();
106	0	request.setFieldToSearchBy(searchTarget);
107	0	request.setSearchTerm(searchTerm);
108	0	request.setOffSet(offSet);
109	0	request.setWantedFields(wantedFields);
110	0	UniProtFTSRestClient uniProtRestClient = UniProtFTSRestClient
111		.getInstance();
112	0	FTSRestResponse resultList;
113	0	try
114		{
115	0	resultList = uniProtRestClient.executeRequest(request, cursor);
116		} catch (Exception e)
117		{
118	0	setErrorMessage(e.getMessage());
119	0	checkForErrors();
120	0	setSearchInProgress(false);
121	0	return;
122		}
123
124	0	if (resultList.getSearchSummary() != null
125		&& resultList.getSearchSummary().size() > 0)
126		{
127	0	getResultTable().setModel(FTSRestResponse.getTableModel(request,
128		resultList.getSearchSummary()));
129	0	FTSRestResponse.configureTableColumn(getResultTable(),
130		wantedFields, tempUserPrefs);
131	0	getResultTable().setVisible(true);
132		}
133
134	0	long endTime = System.currentTimeMillis();
135	0	totalResultSetCount = resultList.getNumberOfItemsFound();
136	0	resultSetCount = resultList.getSearchSummary() == null ? 0
137		: resultList.getSearchSummary().size();
138	0	String result = (resultSetCount > 0)
139		? MessageManager.getString("label.results")
140		: MessageManager.getString("label.result");
141	0	if (isPaginationEnabled() && resultSetCount > 0)
142		{
143	0	updateSearchFrameTitle(
144		defaultFTSFrameTitle + " - " + result + " "
145		+ totalNumberformatter
146		.format(Integer.valueOf(offSet + 1))
147		+ " to "
148		+ totalNumberformatter.format(Integer
149		.valueOf(offSet + resultSetCount))
150		+ " of "
151		+ totalNumberformatter.format(
152		Integer.valueOf(totalResultSetCount))
153		+ " " + " (" + (endTime - startTime)
154		+ " milli secs)");
155		}
156		else
157		{
158	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
159		+ resultSetCount + " " + result + " ("
160		+ (endTime - startTime) + " milli secs)");
161		}
162	0	setSearchInProgress(false);
163	0	refreshPaginatorState();
164	0	updateSummaryTableSelections();
165		}
166	0	txt_search.updateCache();
167		}
168		}.start();
169
170		}
171
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
172	0	public String decodeSearchTerm(String enteredText, String targetField)...
173		{
174	0	int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
175		: targetField.length() + 1;
176	0	String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
177		: targetField + ":";
178	0	String foundSearchTerms = enteredText;
179	0	StringBuilder foundSearchTermsBuilder = new StringBuilder();
180	0	if (enteredText.contains(";"))
181		{
182	0	String[] searchTerms = enteredText.split(";");
183	0	for (String searchTerm : searchTerms)
184		{
185	0	foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
186		.append(" OR ");
187		}
188	0	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
189	0	foundSearchTerms = foundSearchTermsBuilder.toString();
190	0	if (foundSearchTerms.contains(" OR "))
191		{
192	0	foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
193		endIndex);
194		}
195		}
196	0	return foundSearchTerms;
197		}
198
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
199	0	@Override...
200		public boolean isPaginationEnabled()
201		{
202	0	return true;
203		}
204
		0% Uncovered Elements: 19 (19) Complexity: 2 Complexity Density: 0.11
205	0	@Override...
206		public void okAction()
207		{
208	0	disableActionButtons();
209	0	StringBuilder selectedIds = new StringBuilder();
210	0	HashSet<String> selectedIdsSet = new HashSet<>();
211	0	int primaryKeyColIndex = 0;
212	0	try
213		{
214	0	primaryKeyColIndex = getFTSRestClient()
215		.getPrimaryKeyColumIndex(wantedFields, false);
216		} catch (Exception e)
217		{
218	0	e.printStackTrace();
219		}
220	0	int[] selectedRows = getResultTable().getSelectedRows();
221	0	for (int summaryRow : selectedRows)
222		{
223	0	String idStr = getResultTable()
224		.getValueAt(summaryRow, primaryKeyColIndex).toString();
225	0	selectedIdsSet.add(idStr);
226		}
227	0	selectedIdsSet.addAll(paginatorCart);
228	0	for (String selectedId : selectedIdsSet)
229		{
230	0	selectedIds.append(selectedId).append(";");
231		}
232
233	0	String ids = selectedIds.toString();
234	0	seqFetcher.setQuery(ids);
235	0	Thread worker = new Thread(seqFetcher);
236	0	worker.start();
237	0	delayAndEnableActionButtons();
238		}
239
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
240	0	@Override...
241		public FTSRestClientI getFTSRestClient()
242		{
243	0	return UniProtFTSRestClient.getInstance();
244		}
245
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
246	0	@Override...
247		public String getFTSFrameTitle()
248		{
249	0	return defaultFTSFrameTitle;
250		}
251
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
252	0	@Override...
253		public Map<String, Integer> getTempUserPrefs()
254		{
255	0	return tempUserPrefs;
256		}
257
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	@Override...
259		public String getCacheKey()
260		{
261	0	return UNIPROT_FTS_CACHE_KEY;
262		}
263
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
264	0	@Override...
265		public String getAutosearchPreference()
266		{
267	0	return UNIPROT_AUTOSEARCH;
268		}
269
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
270	0	@Override...
271		protected void showHelp()
272		{
273	0	try
274		{
275	0	Help.showHelpWindow(HelpId.UniprotFts);
276		} catch (HelpSetException e1)
277		{
278	0	e1.printStackTrace();
279		}
280		}
281
282		/*
283		* 2022-07-20 bsoares
284		* The new Uniprot API has a strange pagination process described at
285		* https://www.uniprot.org/help/pagination
286		* When a successful request returns results, with more results past the size
287		* limit, the response sends a "Link" header with a URL containing the a "cursor"
288		* parameter with an opaque string that refers to the next page of results.
289		* These are store as nextCursor in the UniProtFTSRestClient along with the currCursor.
290		* When navigation across pages occurs these should be swapped around.
291		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
292	0	@Override...
293		public void refreshPaginatorState()
294		{
295	0	UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
296	0	setNextPageButtonEnabled(c.getNextCursor() != null);
297	0	setPrevPageButtonEnabled(c.getPrevCursor() != null);
298		}
299
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
300	0	@Override...
301		public void prevPageAction()
302		{
303	0	updatePaginatorCart();
304	0	UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
305	0	String prevCursor = c.getPrevCursor();
306	0	if (prevCursor != null)
307		{
308	0	if (offSet >= pageLimit)
309		{
310	0	offSet -= pageLimit;
311		}
312		else
313		{
314		// not sure what's happening if we get here though it wouldn't surprise
315		// me
316	0	Console.warn(
317		"UniprotFTSPanel: prevCursor exists but offset < pageLimit. This probably shouldn't be happening.");
318		}
319	0	c.setPrevCursorPage();
320	0	searchAction(prevCursor, false);
321		}
322		else
323		{
324	0	refreshPaginatorState();
325		}
326		}
327
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
328	0	@Override...
329		public void nextPageAction()
330		{
331	0	UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
332	0	String nextCursor = c.getNextCursor();
333	0	if (nextCursor != null)
334		{
335	0	offSet += pageLimit;
336	0	c.setNextCursorPage();
337	0	searchAction(nextCursor, false);
338		}
339		else
340		{
341	0	refreshPaginatorState();
342		}
343		}
344
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
345	0	public String getDbName()...
346		{
347	0	return "UniProt";
348		}
349		}