Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RestJob	40	88	53	0.4545%	Show methods

Class RestJob

Class RestJob	Line # 40	Total Statements 88	Complexity 53	TOTAL Coverage 0.4545%
RestJob(int,RestJobThread,AlignmentI,int[])   RestJob(int,RestJobThread,AlignmentI,int[])	8080	26.026	10.010	0.775 0.77577.5%
hasResults() : boolean   hasResults() : boolean	159159	1.01	2.02	0.0 0.00%
hasValidInput() : boolean   hasValidInput() : boolean	165165	1.01	1.01	1.0 1.0100%
isRunning() : boolean   isRunning() : boolean	171171	1.01	1.01	1.0 1.0100%
isQueued() : boolean   isQueued() : boolean	178178	1.01	1.01	1.0 1.0100%
isFinished() : boolean   isFinished() : boolean	184184	1.01	1.01	1.0 1.0100%
isFailed() : boolean   isFailed() : boolean	190190	1.01	1.01	1.0 1.0100%
isBroken() : boolean   isBroken() : boolean	197197	1.01	1.01	1.0 1.0100%
isServerError() : boolean   isServerError() : boolean	204204	1.01	1.01	1.0 1.0100%
hasStatus() : boolean   hasStatus() : boolean	211211	1.01	1.01	1.0 1.0100%
getStatus() : String   getStatus() : String	221221	1.01	1.01	1.0 1.0100%
hasResponse() : boolean   hasResponse() : boolean	227227	1.01	1.01	0.0 0.00%
clearResponse() : void   clearResponse() : void	233233	0.00	1.01	-1.0 -1.0 -
getState() : String   getState() : String	245245	1.01	1.01	0.0 0.00%
getPostUrl() : String   getPostUrl() : String	253253	1.01	1.01	1.0 1.0100%
getInputParams() : Set<Map.Entry<String, InputType>>   getInputParams() : Set<Map.Entry<String, InputType>>	260260	1.01	1.01	1.0 1.0100%
getPollUrl() : String   getPollUrl() : String	266266	1.01	1.01	0.0 0.00%
newJalviewDataset() : JalviewDataset   newJalviewDataset() : JalviewDataset	275275	10.010	5.05	0.0 0.00%
getSequencesForInput(String,InputType.molType) : SequenceI[]   getSequencesForInput(String,InputType.molType) : SequenceI[]	315315	13.013	7.07	0.0 0.00%
setAlignmentForInputs(Collection<InputType>,AlignmentI) : void   setAlignmentForInputs(Collection<InputType>,AlignmentI) : void	367367	6.06	3.03	0.8 0.880%
getAlignmentForInput(String,InputType.molType) : AlignmentI   getAlignmentForInput(String,InputType.molType) : AlignmentI	394394	4.04	3.03	0.6666667 0.666666766.7%
hasDataOfType(Class) : boolean   hasDataOfType(Class) : boolean	414414	3.03	2.02	0.6 0.660%
parseResultSet() : void   parseResultSet() : void	441441	4.04	2.02	0.0 0.00%
isInputContextModified() : boolean   isInputContextModified() : boolean	456456	1.01	1.01	0.0 0.00%
isInputUniquified() : boolean   isInputUniquified() : boolean	467467	1.01	1.01	0.0 0.00%
getOrderMap() : int[]   getOrderMap() : int[]	479479	5.05	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.06875	jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq	1PASS

 

Source view

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		package jalview.ws.rest;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.AlignmentOrder;
26		import jalview.datamodel.SequenceGroup;
27		import jalview.datamodel.SequenceI;
28		import jalview.io.packed.JalviewDataset;
29		import jalview.ws.AWsJob;
30		import jalview.ws.rest.params.Alignment;
31		import jalview.ws.rest.params.SeqGroupIndexVector;
32
33		import java.util.ArrayList;
34		import java.util.Collection;
35		import java.util.Hashtable;
36		import java.util.Map;
37		import java.util.Set;
38		import java.util.Vector;
39
		45% Uncovered Elements: 88 (160) Complexity: 53 Complexity Density: 0.6
40		public class RestJob extends AWsJob
41		{
42
43		// TODO: input alignmentview and other data for this job
44		RestServiceDescription rsd;
45
46		// boolean submitted;
47		boolean gotresponse;
48
49		boolean error;
50
51		boolean waiting;
52
53		boolean gotresult;
54
55		Hashtable squniq;
56
57		/**
58		* dataset associated with this input data.
59		*/
60		AlignmentI dsForIO;
61
62		AlignmentOrder inputOrder;
63
64		/**
65		* context of input data with respect to an AlignmentView's visible contigs.
66		*/
67		int[] origviscontig;
68
69		private AlignmentI contextAl = null;
70
71		/**
72		* create a rest job using data bounded by the given start/end column.
73		*
74		* @param addJobPane
75		* @param restJobThread
76		* @param _input
77		* @param viscontigs
78		* visible contigs of an alignment view from which _input was derived
79		*/
		77.5% Uncovered Elements: 9 (40) Complexity: 10 Complexity Density: 0.38
80	3	public RestJob(int jobNum, RestJobThread restJobThread, AlignmentI _input,...
81		int[] viscontigs)
82		{
83	3	rsd = restJobThread.restClient.service;
84	3	jobnum = jobNum;
85	3	if (viscontigs != null)
86		{
87	2	origviscontig = new int[viscontigs.length];
88	2	System.arraycopy(viscontigs, 0, origviscontig, 0, viscontigs.length);
89		}
90		// get sequences for the alignmentI
91		// get groups trimmed to alignment columns
92		// get any annotation trimmed to start/end columns, too.
93	3	squniq = jalview.analysis.SeqsetUtils
94		.uniquify(_input.getSequencesArray(), true);
95		// prepare input
96		// form alignment+groups+annotation,preprocess and then record references
97		// for formatters
98	3	ArrayList<InputType> alinp = new ArrayList<InputType>();
99	3	int paramsWithData = 0;
100		// TODO: JAL-715 - generalise the following validation logic for all
101		// parameter types
102		// we cheat for moment - since we know a-priori what data is available and
103		// what inputs we have implemented so far
104	3	for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
105		{
106	6	if (!prm.getValue().isConstant())
107		{
108	6	if (prm.getValue() instanceof Alignment)
109		{
110	3	alinp.add(prm.getValue());
111		}
112		else
113		{
114	3	if (prm.getValue() instanceof SeqGroupIndexVector
115		&& _input.getGroups() != null
116		&& _input.getGroups().size() >= -1 + prm.getValue().min)
117		{
118		// the test above is not rigorous but fixes JAL-1298, since
119		// submission will fail if the partition set doesn't contain at
120		// least one partition
121	3	alinp.add(prm.getValue());
122		}
123		else
124		{
125	0	statMessage = ("Not enough groups defined on the alignment - need at least "
126		+ prm.getValue().min);
127		}
128		}
129		}
130		else
131		{
132	0	paramsWithData++;
133		}
134		}
135	3	if ((paramsWithData + alinp.size()) == rsd.inputParams.size())
136		{
137	3	inputOrder = new AlignmentOrder(_input);
138	?	if ((dsForIO = _input.getDataset()) == null)
139		{
140	2	_input.setDataset(null);
141		}
142	3	dsForIO = _input.getDataset();
143	3	if (contextAl == null)
144		{
145	3	contextAl = _input;
146		}
147	3	setAlignmentForInputs(alinp, _input);
148	3	validInput = true;
149		}
150		else
151		{
152		// not enough data, so we bail.
153	0	validInput = false;
154		}
155		}
156
157		boolean validInput = false;
158
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
159	0	@Override...
160		public boolean hasResults()
161		{
162	0	return gotresult && (parsedResults ? validJvresults : true);
163		}
164
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
165	2	@Override...
166		public boolean hasValidInput()
167		{
168	2	return validInput;
169		}
170
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
171	1	@Override...
172		public boolean isRunning()
173		{
174	1	return running; // TODO: can we check the response body for status messages
175		// ?
176		}
177
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
178	1	@Override...
179		public boolean isQueued()
180		{
181	1	return waiting;
182		}
183
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
184	1	@Override...
185		public boolean isFinished()
186		{
187	1	return resSet != null;
188		}
189
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
190	1	@Override...
191		public boolean isFailed()
192		{
193		// TODO logic for error
194	1	return error;
195		}
196
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
197	1	@Override...
198		public boolean isBroken()
199		{
200		// TODO logic for error
201	1	return error;
202		}
203
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
204	1	@Override...
205		public boolean isServerError()
206		{
207		// TODO logic for error
208	1	return error;
209		}
210
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
211	1	@Override...
212		public boolean hasStatus()
213		{
214	1	return statMessage != null;
215		}
216
217		protected String statMessage = null;
218
219		public HttpResultSet resSet;
220
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
221	1	@Override...
222		public String getStatus()
223		{
224	1	return statMessage;
225		}
226
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
227	0	@Override...
228		public boolean hasResponse()
229		{
230	0	return statMessage != null || resSet != null;
231		}
232
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
233	0	@Override...
234		public void clearResponse()
235		{
236		// only clear the transient server response
237		// statMessage=null;
238		}
239
240		/*
241		* (non-Javadoc)
242		*
243		* @see jalview.ws.AWsJob#getState()
244		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
245	0	@Override...
246		public String getState()
247		{
248		// TODO generate state string - prolly should have a default abstract method
249		// for this
250	0	return "Job is clueless";
251		}
252
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
253	1	public String getPostUrl()...
254		{
255
256		// TODO Auto-generated method stub
257	1	return rsd.postUrl;
258		}
259
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
260	1	public Set<Map.Entry<String, InputType>> getInputParams()...
261		{
262	1	return rsd.inputParams.entrySet();
263		}
264
265		// return the URL that should be polled for this job
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
266	0	public String getPollUrl()...
267		{
268	0	return rsd.getDecoratedResultUrl(jobId);
269		}
270
271		/**
272		*
273		* @return the context for parsing results from service
274		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.5
275	0	public JalviewDataset newJalviewDataset()...
276		{
277	0	if (context == null)
278		{
279	0	context = new JalviewDataset(dsForIO, null, squniq, null);
280	0	if (contextAl != null)
281		{
282		// TODO devise way of merging new annotation onto (identical) existing
283		// annotation that was used as input
284		// delete all input annotation
285	0	if (contextAl.getAlignmentAnnotation() != null)
286		{
287	0	for (AlignmentAnnotation alan : contextAl
288		.getAlignmentAnnotation())
289		{
290	0	contextAl.deleteAnnotation(alan);
291		}
292		}
293		// TODO devise way of merging new groups onto (identical) existing
294		// groups when they were used as input to service
295		// delete all existing groups
296	0	if (contextAl.getGroups() != null)
297		{
298	0	contextAl.deleteAllGroups();
299		}
300	0	context.addAlignment(contextAl);
301		}
302
303		}
304	0	return context;
305		}
306
307		/**
308		* Extract list of sequence IDs for input parameter 'token' with given
309		* molecule type
310		*
311		* @param token
312		* @param type
313		* @return
314		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.54
315	0	public SequenceI[] getSequencesForInput(String token,...
316		InputType.molType type) throws NoValidInputDataException
317		{
318	0	Object sgdat = inputData.get(token);
319		// can we form an alignment from this data ?
320	0	if (sgdat == null)
321		{
322	0	throw new NoValidInputDataException(
323		"No Sequence vector data bound to input '" + token
324		+ "' for service at " + rsd.postUrl);
325		}
326	0	if (sgdat instanceof AlignmentI)
327		{
328	0	return ((AlignmentI) sgdat).getSequencesArray();
329		}
330	0	if (sgdat instanceof SequenceGroup)
331		{
332	0	return ((SequenceGroup) sgdat).getSequencesAsArray(null);
333		}
334	0	if (sgdat instanceof Vector)
335		{
336	0	if (((Vector) sgdat).size() > 0
337		&& ((Vector) sgdat).get(0) instanceof SequenceI)
338		{
339	0	SequenceI[] sq = new SequenceI[((Vector) sgdat).size()];
340	0	((Vector) sgdat).copyInto(sq);
341	0	return sq;
342		}
343		}
344	0	throw new NoValidInputDataException(
345		"No Sequence vector data bound to input '" + token
346		+ "' for service at " + rsd.postUrl);
347		}
348
349		/**
350		* binding between input data (AlignmentI, SequenceGroup, NJTree) and input
351		* param names.
352		*/
353		private Hashtable<String, Object> inputData = new Hashtable<String, Object>();
354
355		/**
356		* is the job fully submitted to server and apparently in progress ?
357		*/
358		public boolean running = false;
359
360		/**
361		*
362		* @param itypes
363		* @param al
364		* - reference to object to be stored as input. Note - input data may
365		* be modifed by formatter
366		*/
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.5
367	4	public void setAlignmentForInputs(Collection<InputType> itypes,...
368		AlignmentI al)
369		{
370	4	for (InputType itype : itypes)
371		{
372	8	if (!rsd.inputParams.values().contains(itype))
373		{
374	0	throw new IllegalArgumentException("InputType " + itype.getClass()
375		+ " is not valid for service at " + rsd.postUrl);
376		}
377	8	if (itype instanceof AlignmentProcessor)
378		{
379	4	((AlignmentProcessor) itype).prepareAlignment(al);
380		}
381		// stash a reference for recall when the alignment data is formatted
382	8	inputData.put(itype.token, al);
383		}
384
385		}
386
387		/**
388		*
389		* @param token
390		* @param type
391		* @return alignment object bound to the given token
392		* @throws NoValidInputDataException
393		*/
		66.7% Uncovered Elements: 2 (6) Complexity: 3 Complexity Density: 0.75
394	4	public AlignmentI getAlignmentForInput(String token,...
395		InputType.molType type) throws NoValidInputDataException
396		{
397	4	Object al = inputData.get(token);
398		// can we form an alignment from this data ?
399	4	if (al == null || !(al instanceof AlignmentI))
400		{
401	0	throw new NoValidInputDataException(
402		"No alignment data bound to input '" + token
403		+ "' for service at " + rsd.postUrl);
404		}
405	4	return (AlignmentI) al;
406		}
407
408		/**
409		* test to see if the job has data of type cl that's needed for the job to run
410		*
411		* @param cl
412		* @return true or false
413		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
414	2	public boolean hasDataOfType(Class cl)...
415		{
416	2	if (AlignmentI.class.isAssignableFrom(cl))
417		{
418	2	return true;
419		}
420		// TODO: add more source data types
421
422	0	return false;
423		}
424
425		/**
426		* context used to parse results from service
427		*/
428		JalviewDataset context = null;
429
430		protected boolean parsedResults = false;
431
432		protected boolean validJvresults = false;
433
434		Object[] jvresultobj = null;
435
436		/**
437		* process the results obtained from the server into jalview datamodel objects
438		* ready to be merged/added to the users' view. Use hasResults to test if
439		* results were added to context.
440		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
441	0	public void parseResultSet() throws Exception, Error...
442		{
443	0	if (!parsedResults)
444		{
445	0	parsedResults = true;
446	0	jvresultobj = resSet.parseResultSet();
447	0	validJvresults = true;
448		}
449		}
450
451		/**
452		*
453		* @return true if job has an input alignment and it was annotated when
454		* results were parsed
455		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
456	0	public boolean isInputContextModified()...
457		{
458	0	return contextAl != null && validJvresults
459		&& context.getAl().get(0).isModified();
460		}
461
462		/**
463		*
464		* @return true if the ID/metadata for the input sequences were saved and
465		* sequence IDs renamed.
466		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
467	0	public boolean isInputUniquified()...
468		{
469		// TODO Auto-generated method stub
470	0	return false;
471		}
472
473		/**
474		* Return map between ordering of alignment submitted as input, and ordering
475		* of alignment as provided by user
476		*
477		* @return int[sequence index in submitted data]==sequence index in input.
478		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
479	0	public int[] getOrderMap()...
480		{
481	0	SequenceI[] contseq = contextAl.getSequencesArray();
482	0	int map[] = new int[contseq.length];
483	0	for (int i = 0; i < contseq.length; i++)
484		{
485		// TODO: optimise for large N - build a lookup hash for IDs returning
486		// order, and then lookup each sequ's original order
487	0	map[i] = inputOrder.getOrder().indexOf(contseq[i]);
488		}
489	0	return map;
490		}
491
492		}