400. EPMO Open Source Coordination Office Redaction File Detail Report

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400.1 Files compared

#	Location	File	Last Modified
1	IV-eHMP_CIF.zip\IMAG_Source\VISA\Java\VistaImagingDataSourceProvider\main\src\java\gov\va\med\imaging\vistaimagingdatasource	VistaImagingStudyGraphDataSourceService.java	Mon Dec 4 21:34:50 2017 UTC
2	IV-eHMP_CIF.zip\IMAG_Source\VISA\Java\VistaImagingDataSourceProvider\main\src\java\gov\va\med\imaging\vistaimagingdatasource	VistaImagingStudyGraphDataSourceService.java	Mon Dec 4 22:06:53 2017 UTC

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	1	/**
	2	*
	3	Package: MAG - Vis tA Imaging
	4	WARNING: Per VHA D irective 2 004-038, t his routin e should n ot be modi fied.
	5	Date Cre ated: Jan 7, 2008
	6	Site Nam e: Washin gton OI Fi eld Office , Silver S pring, MD
	7	Develope r:
	8	Descript ion:
	9
	10	;; +-------- ---------- ---------- ---------- ---------- ---------- ---------- +
	11	;; Property of the US Government .
	12	;; No permis sion to co py or redi stribute t his softwa re is give n.
	13	;; Use of un released v ersions of this soft ware requi res the us er
	14	;; to execu te a writt en test ag reement wi th the Vis tA Imaging
	15	;; Developm ent Office of the De partment o f Veterans Affairs,
	16	;; telephon e (301) 73 4-0100.
	17	;;
	18	;; The Food and Drug A dministrat ion classi fies this software a s
	19	;; a Class I I medical device. A s such, it may not b e changed
	20	;; in any wa y. Modifi cations to this soft ware may r esult in a n
	21	;; adulterat ed medical device un der 21CFR8 20, the us e of which
	22	;; is consid ered to be a violati on of US F ederal Sta tutes.
	23	;; +-------- ---------- ---------- ---------- ---------- ---------- ---------- +
	24
	25	*/
	26	package go v.va.med.i maging.vis taimagingd atasource;
	27
	28	import gov .va.med.Gl obalArtifa ctIdentifi er;
	29	import gov .va.med.Pa tientIdent ifier;
	30	import gov .va.med.Ro utingToken ;
	31	import gov .va.med.UR NFactory;
	32	import gov .va.med.im aging.Stud yURN;
	33	import gov .va.med.im aging.arti factsource .ResolvedA rtifactSou rce;
	34	import gov .va.med.im aging.core .interface s.exceptio ns.Connect ionExcepti on;
	35	import gov .va.med.im aging.core .interface s.exceptio ns.MethodE xception;
	36	import gov .va.med.im aging.exce ptions.URN FormatExce ption;
	37	import gov .va.med.im aging.exch ange.busin ess.Site;
	38	import gov .va.med.im aging.exch ange.busin ess.Study;
	39	import gov .va.med.im aging.exch ange.busin ess.StudyF ilter;
	40	import gov .va.med.im aging.exch ange.busin ess.StudyS etResult;
	41	import gov .va.med.im aging.exch ange.enums .StudyDele tedImageSt ate;
	42	import gov .va.med.im aging.exch ange.enums .StudyLoad Level;
	43	import gov .va.med.im aging.prot ocol.vista .VistaImag ingTransla tor;
	44	import gov .va.med.im aging.core .interface s.exceptio ns.Patient NotFoundEx ception;
	45	import gov .va.med.im aging.tran sactioncon text.Trans actionCont extFactory ;
	46	import gov .va.med.im aging.url. vista.Stri ngUtils;
	47	import gov .va.med.im aging.url. vista.Vist aQuery;
	48	import gov .va.med.im aging.url. vista.exce ptions.Inv alidVistaC redentials Exception;
	49	import gov .va.med.im aging.url. vista.exce ptions.Vis taMethodEx ception;
	50	import gov .va.med.im aging.vist adatasourc e.common.V istaCommon Utilities;
	51	import gov .va.med.im aging.vist adatasourc e.session. VistaSessi on;
	52	import gov .va.med.im aging.vist aimagingda tasource.c ommon.Vist aImagingCo mmonUtilit ies;
	53	import gov .va.med.im aging.vist aobjects.V istaGroup;
	54
	55	import jav a.io.IOExc eption;
	56	import jav a.util.Has hMap;
	57	import jav a.util.Map ;
	58	import jav a.util.Sor tedSet;
	59	import jav a.util.Tre eSet;
	60
	61	import org .apache.lo gging.log4 j.LogManag er;
	62	import org .apache.lo gging.log4 j.Logger;
	63
	64	/**
	65	* An impl ementation of a Stud yGraphData SourceSpi that talks to VistA.
	66	*
	67	* NOTE:
	68	* 1.) pub lic method s that do Vista acce ss (partic ularly any thing defi ned
	69	* in the StudyGraph DataSource Spi interf ace) must acquire a VistaSessi on instanc e using
	70	* getVist aSession() .
	71	* 2.) pri vate metho ds which a re only ca lled from public met hods that do Vista a ccess
	72	* must in clude a Vi staSession parameter , they sho uld not ac quire thei r own Vist aSession
	73	* 3.) Whe re a metho d is both public and called fr om within this class , there sh ould be a
	74	* public version fo llowing ru le 1, call ing a priv ate versio n followin g rule 2.
	75	*
	76	* @author BECKEC
	77	*
	78	*/
	79	public cla ss VistaIm agingStudy GraphDataS ourceServi ce
	80	extends Ab stractBase VistaImagi ngStudyGra phService
	81	{
	82	pu blic final static St ring SUPPO RTED_PROTO COL = "vis taimaging" ;
	83
	84	/* ========= ========== ========== ========== ========== ========== ==========
	85	* Instance fields and methods
	86	* ========= ========== ========== ========== ========== ========== ========== */
	87	pr ivate Logg er logger = LogManag er.getLogg er(this.ge tClass());
	88	// private in t maximumP atientSens itivityLev el = DEFAU LT_PATIENT _SENSITIVI TY_LEVEL;
	89
	90	// The requi red versio n of VistA Imaging n eeded to e xecute the RPC calls for this operation
	91	pu blic final static St ring MAG_R EQUIRED_VE RSION = "3 .0P83";
	92
	93	/**
	94	* @param re solvedArti factSource
	95	* @param pr otocol
	96	* /
	97	pu blic Vista ImagingStu dyGraphDat aSourceSer vice(Resol vedArtifac tSource re solvedArti factSource , String p rotocol)
	98	{
	99	supe r(resolved ArtifactSo urce, prot ocol);
	100	}
	101
	102	/* (non-Java doc)
	103	* @see gov. va.med.ima ging.vista datasource .AbstractB aseVistaSt udyGraphSe rvice#getR equiredVis taImagingV ersion()
	104	* /
	105	@O verride
	106	pr otected St ring getRe quiredVist aImagingVe rsion()
	107	{
	108	retu rn VistaIm agingCommo nUtilities .getVistaD ataSourceI magingVers ion(
	109	VistaI magingData SourceProv ider.getVi staConfigu ration(),
	110	this.g etClass(),
	111	MAG_RE QUIRED_VER SION);
	112	}
	113
	114	/* *
	115	* Return th e maximum permissibl e patient sensitivit y level
	116	* that will be includ ed in resu lts. Sens itivity le vels
	117	* range fro m:
	118	* 0 - least sensitive
	119	* - to -
	120	* 3 - most sensitive
	121	*
	122	* @return
	123	* /
	124	pu blic int g etMaximumP atientSens itivityLev el(StudyFi lter filte r)
	125	{
	126	retu rn filter. getMaximum AllowedLev el().getCo de();
	127	}
	128
	129	/**
	130	* Get ting Studi es from Vi sta is a t wo step-pr ocess beca use:
	131	* a.) the Vista data stru cture is n ot organiz ed around a study-se ries-insta nce hierar chy but
	132	* aro und a stud y-group-in stance, wh ere group and study are not sy nonymous. A Study h as
	133	* 1.. n Groups a nd a Group can have 1..n Serie s.
	134	* b.) the filte ring provi ded by Vis ta does no t implemen t all of t he filteri ng that ou r
	135	* Fil ter object requires
	136	*
	137	* @pa ram patien tIcn
	138	* @pa ram filter
	139	* @re turn
	140	* @th rows
	141	* @se e gov.va.m ed.imaging .datasourc e.StudyGra phDataSour ceSpi#getS tudies(Str ing, Filte r)
	142	*/
	143	@Overr ide
	144	public StudySetR esult getP atientStud ies(Routin gToken glo balRouting Token, Pat ientIdenti fier patie ntIdentifi er,
	145	Stud yFilter fi lter, Stud yLoadLevel studyLoad Level)
	146	throws Unsupport edOperatio nException , MethodEx ception, C onnectionE xception
	147	{
	148	Vi staCommonU tilities.s etDataSour ceMethodAn dVersion(" getPatient Studies", getDataSou rceVersion ());
	149	lo gger.info( "getPatien tStudies(" + patient Identifier +
	150	", " + ( filter == null ? "<n ull>" : fi lter.toStr ing()) +
	151	", Study load leve l " + stud yLoadLevel .toString( ) +
	152	") Trans actionCont ext (" + T ransaction ContextFac tory.get() .getDispla yIdentity( ) + ").");
	153
	154	Vist aSession l ocalVistaS ession = n ull;
	155
	156	try
	157	{
	158	localV istaSessio n = getVis taSession( );
	159
	160	String patientDf n = null;
	161	try
	162	{
	163	patientD fn = getPa tientDfn(l ocalVistaS ession, pa tientIdent ifier);
	164	}
	165	catch( PatientNot FoundExcep tion pnfX)
	166	{
	167	// JMW 3 /12/08 The patient w as not fou nd in the database, return an empty set of studies instead o f
	168	logger .warn("Pat ient [" + patientIde ntifier + "] was not found in the VistA database, returning empty stud y set", pn fX);
	169	return StudySetR esult.crea teFullResu lt(new Tre eSet<Study >());
	170	}
	171
	172	// if we are get ting a sin gle study
	173	if((fi lter != nu ll) && (fi lter.isStu dyIenSpeci fied()))
	174	{
	175	// we ar e getting a single s tudy
	176	logger.i nfo("Getti ng study ' " + filter .getStudyI d() + "' f or patient '" + pati entIdentif ier + "'") ;
	177	Study si ngleStudy = null;
	178	if(filte r.isInclud eAllObject s()){
	179	logger.deb ug("Gettin g single s tudy metad ata from b oth old an d new data structure s.");
	180	singleStud y = getSin gleStudyFr omBothData Structures MatchingFi lter(local VistaSessi on, patien tIdentifie r,
	181	patientD fn, filter , studyLoa dLevel);
	182	}
	183	else{
	184	logger.deb ug("Gettin g single s tudy metad ata from o ld data st ructure on ly.");
	185	singleStud y = getSin gleStudyMa tchingFilt er(localVi staSession , patientI dentifier,
	186	pa tientDfn, filter, st udyLoadLev el);
	187	}
	188	SortedSe t<Study> s tudies = n ew TreeSet <Study>();
	189	studies. add(single Study);
	190	return S tudySetRes ult.create FullResult (studies);
	191	}
	192	// we are gettin g multiple studies
	193	else
	194	{
	195	// we ar e getting all the st udies for a patient (that matc h the filt er)
	196	logger.i nfo("Getti ng all stu dies that match filt er for pat ient '" + patientIde ntifier + "'");
	197
	198	// che ck the pat ient sensi tivity fir st, if it fails an e xception w ill be thr own
	199	checkP atientSens itive(loca lVistaSess ion, patie ntDfn, pat ientIdenti fier, filt er);
	200	if(fil ter.isIncl udeAllObje cts()){
	201	logger.deb ug("Gettin g all stud ies metada ta from bo th old and new data structures .");
	202	return S tudySetRes ult.create FullResult (getAllStu diesFromBo thDataStru cturesMatc hingFilter (localVist aSession, patientIde ntifier, p atientDfn, filter, s tudyLoadLe vel));
	203	}
	204	else{
	205	logger.deb ug("Gettin g all stud ies metada ta from ol d data str ucture onl y.");
	206	return S tudySetRes ult.create FullResult (getAllStu diesMatchi ngFilter(l ocalVistaS ession, pa tientIdent ifier, pat ientDfn, f ilter, stu dyLoadLeve l));
	207	}
	208	}
	209	}
	210	catc h (IOExcep tion e)
	211	{
	212	throw new Connec tionExcept ion(e);
	213	}
	214	fina lly
	215	{
	216	try{lo calVistaSe ssion.clos e();}
	217	catch( Throwable t){}
	218	}
	219	}
	220
	221	/**
	222	* Thi s method i s implemen ted here f or complet eness.
	223	* As of this da te it is n ot used in productio n deployme nt.
	224	*/
	225	@Overr ide
	226	pu blic Study getStudy( PatientIde ntifier pa tientIdent ifier, Glo balArtifac tIdentifie r studyId)
	227	throws MethodExc eption, Co nnectionEx ception
	228	{
	229	Vi staCommonU tilities.s etDataSour ceMethodAn dVersion(" getStudy", getDataSo urceVersio n());
	230	if ( !(studyI d instance of StudyUR N) )
	231	thro w new Conn ectionExce ption(this .getClass( ).getSimpl eName() + " does not recognize GAI of ty pe " + stu dyId.getCl ass().getN ame() + ". ");
	232
	233	St udyFilter filter = n ew StudyFi lter(study Id);
	234	Stud yLoadLevel studyLoad Level = St udyLoadLev el.FULL;
	235	Stud ySetResult result = getPatient Studies(st udyId, pat ientIdenti fier, filt er, studyL oadLevel);
	236	if(r esult == n ull)
	237	{
	238	logger .error("Go t null Stu dySetResul t - this s hould NEVE R happen!" );
	239	return null;
	240	}
	241	Sort edSet<Stud y> studies = result. getArtifac ts();
	242	if(s tudies != null && st udies.size () > 0)
	243	return studies.f irst();
	244
	245	retu rn null;
	246	}
	247
	248	/**
	249	* Thi s method i s implemen ted here f or complet eness.
	250	* As of this da te it is n ot used in productio n deployme nt.
	251	*/
	252	@O verride
	253	pu blic Strin g getStudy Report(Pat ientIdenti fier patie ntIdentifi er, Global ArtifactId entifier s tudyId)
	254	th rows Metho dException , Connecti onExceptio n
	255	{
	256	Vist aCommonUti lities.set DataSource MethodAndV ersion("ge tStudyRepo rt", getDa taSourceVe rsion());
	257	Stud y study = getStudy(p atientIden tifier, st udyId);
	258	retu rn study.g etRadiolog yReport();
	259	}
	260
	261	/* *
	262	*
	263	* @pa ram localV istaSessio n
	264	* @pa ram patien tIcn
	265	* @pa ram patien tDfn
	266	* @pa ram filter
	267	* @pa ram studyL oadLevel
	268	* @re turn
	269	* @th rows Conne ctionExcep tion
	270	* @th rows Metho dException
	271	* @th rows IOExc eption
	272	*/
	273	privat e SortedSe t<Study> g etAllStudi esMatching Filter(
	274	Vi staSession localVist aSession,
	275	Pa tientIdent ifier pati entIdentif ier,
	276	St ring patie ntDfn,
	277	St udyFilter filter,
	278	St udyLoadLev el studyLo adLevel)
	279	th rows Conne ctionExcep tion, Meth odExceptio n, IOExcep tion
	280	{
	281	// N ote: a Stu dy has 1.. Groups an d a Group can have 1 .. Series!
	282	Sort edSet<Vist aGroup> gr oups = nul l;
	283	logg er.info("G etting gro ups for pa tient '" + patientId entifier + "'.");
	284	grou ps = getPa tientGroup s(localVis taSession, getSite() , patientD fn, patien tIdentifie r, filter) ; // 23Nov C TB = group s study ie n is null
	285	logg er.info("F ound '" + groups.siz e() + "' g roups for patient '" + patient Identifier + "'");
	286	// n o groups i s not an e xception s cenario bu t it does mean we do n't need t o bother g etting mor e
	287	// i nformation about eac h study
	288	if(g roups.size () == 0)
	289	return new TreeS et<Study>( ); // ret urn a zero -length se t
	290
	291	// W arning: if this filt er (and st udyIen) is not null, reducedGr oup might truncate m ultiple gr oup studie s!!!
	292	Map< String, St ring> stud yMap = new HashMap<S tring, Str ing>();
	293
	294	// J MW 12/17/2 008, call the filter to remove studies f rom the gr oups, this way
	295	// t he datasou rce doesn' t need to have knowl edge of th e filter d etails
	296	if(f ilter != n ull)
	297	filter .preFilter (groups);
	298
	299	// i f we filte red everyt hing out r eturn now, and don't bother ma king the c all
	300	// t o populate the entir e Studies tree
	301	if(g roups.size () == 0)
	302	return new TreeS et<Study>( ); // ret urn a zero -length se t
	303
	304	logg er.info("L oading stu dy graph d ata for fi ltered gro ups");
	305
	306	// B uild a lis t of Study IEN
	307	// T he use of a Map is a n artifact of VistA, which nee ds an inde x of the l ist elemen ts.
	308	// T he Map end s up as so mething li ke {"0", " 662576753" },{"1", "7 61576512"} ...
	309	Stri ngBuilder groupMessa ge = new S tringBuild er();
	310	grou pMessage.a ppend('{') ;
	311	for( VistaGroup group : g roups)
	312	{
	313	// CTB 29Nov2009
	314	//stud yMap.put(" " + studyM ap.size(), Base32Con versionUti lity.base3 2Decode(gr oup.getIen ()));
	315	studyM ap.put( In teger.toSt ring(study Map.size() ), group.g etIen() );
	316	if(gro upMessage. length() > 1)
	317	groupMes sage.appen d(',');
	318	groupM essage.app end(group. getIen());
	319	}
	320	grou pMessage.a ppend('}') ;
	321
	322	//
	323	bool ean includ esDeletedI mages = (f ilter == n ull ? fals e : filter .isInclude Deleted()) ;
	324	bool ean canInc ludeDelete dImages = canRetriev eDeletedIm ages(); // if this d ata source cannot su pport gett ing delete d images, then it is not an op tion
	325	Stud yDeletedIm ageState s tudyDelete dImageStat e = StudyD eletedImag eState.can notInclude DeletedIma ges;
	326	if(c anIncludeD eletedImag es) // if the DS sup ports gett ing delete d images, set approp riately ba sed on use r request
	327	studyD eletedImag eState = ( includesDe letedImage s ? StudyD eletedImag eState.inc ludesDelet edImages : StudyDele tedImageSt ate.doesNo tIncludeDe letedImage s);
	328	Sort edSet<Stud y> studies = getPati entStudyGr aph(localV istaSessio n, studyMa p, patient Dfn,
	329	studyLoa dLevel, st udyDeleted ImageState );
	330	logg er.info("g etPatientS tudyGraph for studie s " + grou pMessage.t oString() + " return ed " + stu dies.size( ) + " stud ies.");
	331	Sort edSet<Stud y> result =
	332	VistaI magingComm onUtilitie s.mergeStu dyLists(lo calVistaSe ssion, stu dies, grou ps, studyL oadLevel);
	333	logg er.info("M erging stu dies and g roups resu lts in " + result.si ze() + " s tudies.");
	334
	335	// J MW 12/17/2 008, call the filter to remove studies f rom the gr oups, this way
	336	// t he datasou rce doesn' t need to have knowl edge of th e filter d etails
	337	if(f ilter != n ull)
	338	{
	339	filter .postFilte r(result);
	340	}
	341	logg er.info("C ompleted g etPatientS tudies(), returning '" + resul t.size() + "' studie s.");
	342	retu rn result;
	343	}
	344
	345	/* *
	346	*
	347	* @pa ram localV istaSessio n
	348	* @pa ram patien tIcn
	349	* @pa ram patien tDfn
	350	* @pa ram filter
	351	* @pa ram studyL oadLevel
	352	* @re turn
	353	* @th rows Conne ctionExcep tion
	354	* @th rows Metho dException
	355	* @th rows IOExc eption
	356	*/
	357	privat e SortedSe t<Study> g etAllStudi esFromBoth DataStruct uresMatchi ngFilter(
	358	Vi staSession localVist aSession,
	359	Pa tientIdent ifier pati entIdentif ier,
	360	St ring patie ntDfn,
	361	St udyFilter filter,
	362	St udyLoadLev el studyLo adLevel)
	363	th rows Conne ctionExcep tion, Meth odExceptio n, IOExcep tion
	364	{
	365	// N ote: a Stu dy has 1.. Groups an d a Group can have 1 .. Series!
	366	//So rtedSet<Vi staGroup> groups = n ull;
	367	//lo gger.info( "Getting g roups for patient '" + patient Identifier + "'.");
	368	//gr oups = get PatientGro ups(localV istaSessio n, getSite (), patien tDfn, pati entIdentif ier, filte r); // 23Nov CTB = groups study ien is null
	369	//lo gger.info( "Found '" + groups.s ize() + "' groups fo r patient '" + patie ntIdentifi er + "'");
	370	// n o groups i s not an e xception s cenario bu t it does mean we do n't need t o bother g etting mor e
	371	// i nformation about eac h study
	372	//if (groups.si ze() == 0)
	373	//re turn new T reeSet<Stu dy>(); // r eturn a ze ro-length set
	374
	375	// W arning: if this filt er (and st udyIen) is not null, reducedGr oup might truncate m ultiple gr oup studie s!!!
	376	Map< String, St ring> stud yMap = new HashMap<S tring, Str ing>();
	377
	378	// J MW 12/17/2 008, call the filter to remove studies f rom the gr oups, this way
	379	// t he datasou rce doesn' t need to have knowl edge of th e filter d etails
	380	//if (filter != null)
	381	// filter .preFilter (groups);
	382
	383	// i f we filte red everyt hing out r eturn now, and don't bother ma king the c all
	384	// t o populate the entir e Studies tree
	385	//if (groups.si ze() == 0)
	386	// return new TreeS et<Study>( ); // ret urn a zero -length se t
	387
	388	//lo gger.info( "Loading s tudy graph data for filtered g roups");
	389
	390	// B uild a lis t of Study IEN
	391	// T he use of a Map is a n artifact of VistA, which nee ds an inde x of the l ist elemen ts.
	392	// T he Map end s up as so mething li ke {"0", " 662576753" },{"1", "7 61576512"} ...
	393	//St ringBuilde r groupMes sage = new StringBui lder();
	394	//gr oupMessage .append('{ ');
	395	//fo r(VistaGro up group : groups)
	396	//{
	397	// CTB 29Nov2009
	398	//stud yMap.put(" " + studyM ap.size(), Base32Con versionUti lity.base3 2Decode(gr oup.getIen ()));
	399	// studyM ap.put( In teger.toSt ring(study Map.size() ), group.g etIen() );
	400	// if(gro upMessage. length() > 1)
	401	// groupMes sage.appen d(',');
	402	// groupM essage.app end(group. getIen());
	403	//}
	404	//gr oupMessage .append('} ');
	405
	406	//
	407	bool ean includ esDeletedI mages = (f ilter == n ull ? fals e : filter .isInclude Deleted()) ;
	408	bool ean canInc ludeDelete dImages = canRetriev eDeletedIm ages(); // if this d ata source cannot su pport gett ing delete d images, then it is not an op tion
	409	Stud yDeletedIm ageState s tudyDelete dImageStat e = StudyD eletedImag eState.can notInclude DeletedIma ges;
	410	if(c anIncludeD eletedImag es) // if the DS sup ports gett ing delete d images, set approp riately ba sed on use r request
	411	studyD eletedImag eState = ( includesDe letedImage s ? StudyD eletedImag eState.inc ludesDelet edImages : StudyDele tedImageSt ate.doesNo tIncludeDe letedImage s);
	412	Sort edSet<Stud y> studies = getPati entStudyGr aphFromBot hDataStruc tures(loca lVistaSess ion, study Map, patie ntDfn, fil ter,
	413	studyLoa dLevel, st udyDeleted ImageState );
	414	//lo gger.info( "getPatien tStudyGrap h for stud ies " + gr oupMessage .toString( ) + " retu rned " + s tudies.siz e() + " st udies.");
	415	//So rtedSet<St udy> resul t =
	416	// VistaI magingComm onUtilitie s.mergeStu dyLists(lo calVistaSe ssion, stu dies, grou ps, studyL oadLevel);
	417	//lo gger.info( "Merging s tudies and groups re sults in " + result. size() + " studies." );
	418
	419	// J MW 12/17/2 008, call the filter to remove studies f rom the gr oups, this way
	420	// t he datasou rce doesn' t need to have knowl edge of th e filter d etails
	421	//if (filter != null)
	422	//{
	423	// filter .postFilte r(result);
	424	//}
	425	//lo gger.info( "Completed getPatien tStudies() , returnin g '" + res ult.size() + "' stud ies.");
	426	//re turn resul t;
	427	//re turn null;
	428	logg er.debug(" Number of studies: " + studies .size());
	429	logg er.debug(s tudies.toS tring());
	430	retu rn studies ;
	431	}
	432
	433	/* *
	434	*
	435	* @pa ram localV istaSessio n
	436	* @pa ram patien tIcn
	437	* @pa ram patien tDfn
	438	* @pa ram filter
	439	* @pa ram studyL oadLevel
	440	* @re turn
	441	* @th rows Conne ctionExcep tion
	442	* @th rows Metho dException
	443	* @th rows IOExc eption
	444	*/
	445	privat e Study ge tSingleStu dyMatching Filter(Vis taSession localVista Session,
	446	Pati entIdentif ier patien tIdentifie r, String patientDfn , StudyFil ter filter , StudyLoa dLevel stu dyLoadLeve l)
	447	th rows Conne ctionExcep tion, Meth odExceptio n, IOExcep tion
	448	{
	449	St udyURN stu dyUrn = nu ll;
	450	if (filter.ge tStudyId() instanceo f StudyURN )
	451	{
	452	try
	453	{
	454	studyU rn = URNFa ctory.crea te(filter. getStudyId ().toStrin g());
	455	}
	456	catc h(URNForma tException urnfX)
	457	{
	458	throw new Method Exception( "Error con verting fi lter study Id to Stu dyURN", ur nfX);
	459	}
	460	}
	461	el se
	462	{
	463	thro w new Meth odExceptio n("Cannot cast filte r study Id '" + filt er.getStud yId() + "' to StudyU RN, must b e study UR N to get s tudy type. ");
	464	}
	465
	466	St ring study Ien = stud yUrn.getSt udyId();
	467	Ma p<String, String> st udyMap = n ew HashMap <String, S tring>();
	468	// C TB 29Nov20 09
	469	// studyMap.p ut("" + st udyMap.siz e(), Base3 2Conversio nUtility.b ase32Decod e(studyIen ));
	470	st udyMap.put ("" + stud yMap.size( ), studyIe n);
	471
	472	bo olean incl udesDelete dImages = (filter == null ? fa lse : filt er.isInclu deDeleted( ));
	473	bo olean canI ncludeDele tedImages = canRetri eveDeleted Images(); // if this data sour ce cannot support ge tting dele ted images , then it is not an option
	474	Stud yDeletedIm ageState s tudyDelete dImageStat e = StudyD eletedImag eState.can notInclude DeletedIma ges;
	475	if(c anIncludeD eletedImag es) // if the DS sup ports gett ing delete d images, set approp riately ba sed on use r request
	476	studyD eletedImag eState = ( includesDe letedImage s ? StudyD eletedImag eState.inc ludesDelet edImages : StudyDele tedImageSt ate.doesNo tIncludeDe letedImage s);
	477
	478	So rtedSet<St udy> studi es = getPa tientStudy Graph(loca lVistaSess ion, study Map, patie ntDfn,
	479	studyL oadLevel, studyDelet edImageSta te);
	480	if ((studies == null) \| \| (studies .size() <= 0))
	481	{
	482	thro w new Meth odExceptio n("Study [ " + studyI en + "] no t found");
	483	}
	484	if (studies.s ize() > 1)
	485	{
	486	thro w new Meth odExceptio n("Found ' " + studie s.size() + "' matchi ng studies , this sho uld never happen!");
	487	}
	488	St udy study = studies. first();
	489	logg er.info("G etting gro ups for pa tient '" + patientId entifier + "'.");
	490	Sort edSet<Vist aGroup> gr oups = get PatientGro ups(localV istaSessio n, getSite (), patien tDfn, pati entIdentif ier, filte r);
	491	if(( groups == null) \|\| ( groups.siz e() <= 0))
	492	{
	493	thro w new Meth odExceptio n("Study [ " + studyI en + "] no t found");
	494	}
	495	logg er.info("F ound '" + groups.siz e() + "' g roups for patient '" + patient Identifier + "'");
	496	Stud y result = VistaImag ingCommonU tilities.m ergeStudyW ithMatchin gGroup(loc alVistaSes sion, stud y, groups, studyLoad Level);
	497	if(r esult == n ull)
	498	{
	499	throw new Method Exception( "Cannot fi nd study ' " + studyI en + "', c ould not m atch group to study. ");
	500	}
	501	retu rn result;
	502	}
	503
	504	/* *
	505	*
	506	* @pa ram localV istaSessio n
	507	* @pa ram patien tIcn
	508	* @pa ram patien tDfn
	509	* @pa ram filter
	510	* @pa ram studyL oadLevel
	511	* @re turn
	512	* @th rows Conne ctionExcep tion
	513	* @th rows Metho dException
	514	* @th rows IOExc eption
	515	*/
	516	privat e Study ge tSingleStu dyFromBoth DataStruct uresMatchi ngFilter(V istaSessio n localVis taSession,
	517	Pati entIdentif ier patien tIdentifie r, String patientDfn , StudyFil ter filter , StudyLoa dLevel stu dyLoadLeve l)
	518	th rows Conne ctionExcep tion, Meth odExceptio n, IOExcep tion
	519	{
	520	St udyURN stu dyUrn = nu ll;
	521	if (filter.ge tStudyId() instanceo f StudyURN )
	522	{
	523	try
	524	{
	525	studyU rn = URNFa ctory.crea te(filter. getStudyId ().toStrin g());
	526	}
	527	catc h(URNForma tException urnfX)
	528	{
	529	throw new Method Exception( "Error con verting fi lter study Id to Stu dyURN", ur nfX);
	530	}
	531	}
	532	el se
	533	{
	534	thro w new Meth odExceptio n("Cannot cast filte r study Id '" + filt er.getStud yId() + "' to StudyU RN, must b e study UR N to get s tudy type. ");
	535	}
	536
	537	St ring study Ien = stud yUrn.getSt udyId();
	538	Ma p<String, String> st udyMap = n ew HashMap <String, S tring>();
	539	st udyMap.put ("" + stud yMap.size( ), studyIe n);
	540
	541	bo olean incl udesDelete dImages = (filter == null ? fa lse : filt er.isInclu deDeleted( ));
	542	bo olean canI ncludeDele tedImages = canRetri eveDeleted Images(); // if this data sour ce cannot support ge tting dele ted images , then it is not an option
	543	Stud yDeletedIm ageState s tudyDelete dImageStat e = StudyD eletedImag eState.can notInclude DeletedIma ges;
	544	if(c anIncludeD eletedImag es) // if the DS sup ports gett ing delete d images, set approp riately ba sed on use r request
	545	studyD eletedImag eState = ( includesDe letedImage s ? StudyD eletedImag eState.inc ludesDelet edImages : StudyDele tedImageSt ate.doesNo tIncludeDe letedImage s);
	546
	547	So rtedSet<St udy> studi es = getSi ngleStudyG raphFromBo thDataStru ctures(loc alVistaSes sion, stud yMap, pati entDfn, fi lter,
	548	studyL oadLevel, studyDelet edImageSta te);
	549	if ((studies == null) \| \| (studies .size() <= 0))
	550	{
	551	thro w new Meth odExceptio n("Study [ " + studyI en + "] no t found");
	552	}
	553	if (studies.s ize() > 1)
	554	{
	555	thro w new Meth odExceptio n("Found ' " + studie s.size() + "' matchi ng studies , this sho uld never happen!");
	556	}
	557	St udy study = studies. first();
	558	//lo gger.info( "Getting g roups for patient '" + patient Identifier + "'.");
	559	//So rtedSet<Vi staGroup> groups = g etPatientG roups(loca lVistaSess ion, getSi te(), pati entDfn, pa tientIdent ifier, fil ter);
	560	//if ((groups = = null) \|\| (groups.s ize() <= 0 ))
	561	// {
	562	// thro w new Meth odExceptio n("Study [ " + studyI en + "] no t found");
	563	// }
	564	//lo gger.info( "Found '" + groups.s ize() + "' groups fo r patient '" + patie ntIdentifi er + "'");
	565	//St udy result = VistaIm agingCommo nUtilities .mergeStud yWithMatch ingGroup(l ocalVistaS ession, st udy, group s, studyLo adLevel);
	566	//if (result == null)
	567	//{
	568	// throw new Method Exception( "Cannot fi nd study ' " + studyI en + "', c ould not m atch group to study. ");
	569	//}
	570	retu rn study;
	571	// return nul l;
	572	}
	573
	574	/**
	575	*
	576	* @pa ram localV istaSessio n
	577	* @pa ram studyM ap
	578	* @pa ram patien tDfn
	579	* @pa ram studyL oadLevel
	580	* @re turn
	581	* @th rows Metho dException
	582	* @th rows Conne ctionExcep tion
	583	*/
	584	privat e SortedSe t<Study> g etPatientS tudyGraph(
	585	Vi staSession localVist aSession,
	586	Ma p<String, String> st udyMap,
	587	St ring patie ntDfn,
	588	St udyLoadLev el studyLo adLevel,
	589	St udyDeleted ImageState studyDele tedImageSt ate)
	590	th rows Metho dException , Connecti onExceptio n
	591	{
	592	tr y
	593	{
	594	Vist aQuery que ry = getPa tientStudy GraphVista Query(stud yMap, pati entDfn, st udyLoadLev el,
	595	studyDel etedImageS tate);
	596	logger .info("Ret rieving st udy graph for patien t containi ng '" + st udyMap.siz e() + "' g roups");
	597	String vistaResp onse = loc alVistaSes sion.call( query);
	598	logger .info(quer y.getRpcNa me()+" RPC Results:" +StringUti ls.display EncodedCha rs(vistaRe sponse));
	599	logger .info("Com pleted stu dy graph R PC call, p arsing res ponse...") ;
	600
	601	Sorted Set<Study> studies = VistaImag ingTransla tor.create StudiesFro mGraph(get Site(),
	602	vistaRespo nse, study LoadLevel, studyDele tedImageSt ate);
	603	logger .info("Con verted res ponse into '" + ((st udies == n ull) ? 0 : studies.s ize()) + " ' studies" );
	604	return studies;
	605	}
	606	catc h (Excepti on ex)
	607	{
	608	logger .error(ex) ;
	609	ex.pri ntStackTra ce();
	610	throw new Method Exception( ex);
	611	}
	612	}
	613
	614	/**
	615	*
	616	* @pa ram localV istaSessio n
	617	* @pa ram studyM ap
	618	* @pa ram patien tDfn
	619	* @pa ram studyL oadLevel
	620	* @re turn
	621	* @th rows Metho dException
	622	* @th rows Conne ctionExcep tion
	623	*/
	624	privat e SortedSe t<Study> g etPatientS tudyGraphF romBothDat aStructure s(
	625	Vi staSession localVist aSession,
	626	Ma p<String, String> st udyMap,
	627	St ring patie ntDfn,
	628	St udyFilter filter,
	629	St udyLoadLev el studyLo adLevel,
	630	St udyDeleted ImageState studyDele tedImageSt ate)
	631	th rows Metho dException , Connecti onExceptio n
	632	{
	633	tr y
	634	{
	635	Vist aQuery que ry = getPa tientStudy GraphFromB othDataStr ucturesVis taQuery(st udyMap, pa tientDfn, filter, st udyLoadLev el,
	636	studyDe letedImage State);
	637	logger .info("Ret rieving st udy graph for patien t containi ng '" + st udyMap.siz e() + "' g roups");
	638	String vistaResp onse = loc alVistaSes sion.call( query);
	639	logger .info(quer y.getRpcNa me()+" RPC Results:" +StringUti ls.display EncodedCha rs(vistaRe sponse));
	640	logger .info("Com pleted stu dy graph R PC call, p arsing res ponse...") ;
	641
	642	Sorted Set<Study> studies = VistaImag ingTransla tor.create StudiesFro mGraph(get Site(),
	643	vistaRespo nse, study LoadLevel, studyDele tedImageSt ate);
	644	logger .info("Con verted res ponse into '" + ((st udies == n ull) ? 0 : studies.s ize()) + " ' studies" );
	645
	646	return studies;
	647	}
	648	catc h (Excepti on ex)
	649	{
	650	logger .error(ex) ;
	651	ex.pri ntStackTra ce();
	652	throw new Method Exception( ex);
	653	}
	654	}
	655
	656
	657	/**
	658	*
	659	* @pa ram localV istaSessio n
	660	* @pa ram studyM ap
	661	* @pa ram patien tDfn
	662	* @pa ram studyL oadLevel
	663	* @re turn
	664	* @th rows Metho dException
	665	* @th rows Conne ctionExcep tion
	666	*/
	667	privat e SortedSe t<Study> g etSingleSt udyGraphFr omBothData Structures (
	668	Vi staSession localVist aSession,
	669	Ma p<String, String> st udyMap,
	670	St ring patie ntDfn,
	671	St udyFilter filter,
	672	St udyLoadLev el studyLo adLevel,
	673	St udyDeleted ImageState studyDele tedImageSt ate)
	674	th rows Metho dException , Connecti onExceptio n
	675	{
	676	tr y
	677	{
	678	Vist aQuery que ry = getSi ngleStudyG raphFromBo thDataStru cturesVist aQuery(stu dyMap, pat ientDfn, f ilter, stu dyLoadLeve l,
	679	studyDel etedImageS tate);
	680	String vistaResp onse = loc alVistaSes sion.call( query);
	681	logger .info(quer y.getRpcNa me()+" RPC Results:" +StringUti ls.display EncodedCha rs(vistaRe sponse));
	682	logger .info("Com pleted stu dy graph R PC call, p arsing res ponse...") ;
	683
	684	Sorted Set<Study> studies = VistaImag ingTransla tor.create StudiesFro mGraph(get Site(),
	685	vistaRespo nse, study LoadLevel, studyDele tedImageSt ate);
	686	logger .info("Con verted res ponse into '" + ((st udies == n ull) ? 0 : studies.s ize()) + " ' studies" );
	687	return studies;
	688	//retu rn null;
	689	}
	690	catc h (Excepti on ex)
	691	{
	692	logger .error(ex) ;
	693	ex.pri ntStackTra ce();
	694	throw new Method Exception( ex);
	695	}
	696	}
	697
	698
	699	protec ted VistaQ uery getPa tientGroup sVistaQuer y(String p atientDfn, StudyFilt er studyFi lter)
	700	{
	701	re turn Vista ImagingQue ryFactory. createGetG roupsVista Query(pati entDfn, st udyFilter) ;
	702	}
	703
	704	/**
	705	* Met hod to get the Vista Query to c all to get the study graph
	706	* @pa ram studyM ap
	707	* @pa ram patien tDfn
	708	* @pa ram studyL oadLevel
	709	* @pa ram studyD eletedImag eState
	710	* @re turn
	711	*/
	712	protec ted VistaQ uery getPa tientStudy GraphVista Query(Map< String, St ring> stud yMap,
	713	Stri ng patient Dfn,
	714	Stud yLoadLevel studyLoad Level,
	715	Stud yDeletedIm ageState s tudyDelete dImageStat e)
	716	{
	717	// this vers ion does n ot use the studyDele tedImageSt ate
	718	re turn Vista ImagingQue ryFactory. createGetS tudiesByIe nVistaQuer y(studyMap ,
	719	patien tDfn, stud yLoadLevel );
	720	}
	721
	722	/**
	723	* Met hod to get the Vista Query to c all to get the study graph
	724	* @pa ram studyM ap
	725	* @pa ram patien tDfn
	726	* @pa ram studyL oadLevel
	727	* @pa ram studyD eletedImag eState
	728	* @re turn
	729	*/
	730	protec ted VistaQ uery getPa tientStudy GraphFromB othDataStr ucturesVis taQuery(Ma p<String, String> st udyMap,
	731	Stri ng patient Dfn,
	732	Stud yFilter fi lter,
	733	Stud yLoadLevel studyLoad Level,
	734	Stud yDeletedIm ageState s tudyDelete dImageStat e)
	735	{
	736	// this vers ion does n ot use the studyDele tedImageSt ate
	737	re turn Vista ImagingQue ryFactory. createGetS tudiesFrom BothDataSt ructuresBy PatientVis taQuery(st udyMap,
	738	patien tDfn, filt er, studyL oadLevel);
	739	}
	740
	741	/**
	742	* Met hod to get the Vista Query to c all to get the study graph
	743	* @pa ram studyM ap
	744	* @pa ram patien tDfn
	745	* @pa ram studyL oadLevel
	746	* @pa ram studyD eletedImag eState
	747	* @re turn
	748	*/
	749	protec ted VistaQ uery getSi ngleStudyG raphFromBo thDataStru cturesVist aQuery(Map <String, S tring> stu dyMap,
	750	Stri ng patient Dfn,
	751	Stud yFilter fi lter,
	752	Stud yLoadLevel studyLoad Level,
	753	Stud yDeletedIm ageState s tudyDelete dImageStat e)
	754	{
	755	// this vers ion does n ot use the studyDele tedImageSt ate
	756	re turn Vista ImagingQue ryFactory. createGetS ingleStudy FromBothDa taStructur esByCprsId entifierVi staQuery(s tudyMap,
	757	patien tDfn, filt er, studyL oadLevel);
	758	}
	759
	760	/* *
	761	* @throws I OException
	762	* @throws M ethodExcep tion
	763	* @throws C onnectionE xception
	764	* @throws I nvalidVist aCredentia lsExceptio n
	765	*
	766	* /
	767	pr ivate Sort edSet<Vist aGroup> ge tPatientGr oups(
	768	Vist aSession s ession,
	769	Site site,
	770	Stri ng patient Dfn,
	771	Pati entIdentif ier patien tIdentifie r,
	772	Stud yFilter fi lter)
	773	th rows Metho dException , IOExcept ion, Conne ctionExcep tion
	774	{
	775	logg er.info("g etPatientG roups(" + patientIde ntifier + ") Transac tionContex t (" + Tra nsactionCo ntextFacto ry.get().g etDisplayI dentity() + ").");
	776
	777	// c reates cal l to RPC M AG4_PAT_GE T_IMAGES
	778	Vist aQuery vm = getPatie ntGroupsVi staQuery(p atientDfn, filter);
	779	logg er.info("g etPatientG roups with RPC '" + vm.getRpcN ame() + "' .");
	780
	781	Stri ng rtn = n ull;
	782	try
	783	{
	784	logger .info("Mak ing call t o get grou ps for pat ient '" + patientIde ntifier + "'");
	785	rtn = session.ca ll(vm);
	786	logger .info(vm.g etRpcName( )+" RPC Re sults:"+St ringUtils. displayEnc odedChars( rtn));
	787
	788	// che ck to be s ure first character is a 1 (me ans result is ok)
	789
	790	// if no images for patien t, respons e is [0^No images fo r filter: All Images ]
	791
	792	if(rtn .charAt(0) == '1')
	793	{
	794	boolean includesDe letedImage s = (filte r == null ? false : filter.isI ncludeDele ted());
	795	boolean canInclude DeletedIma ges = canR etrieveDel etedImages (); // if this data source can not suppor t getting deleted im ages, then it is not an option
	796	StudyDel etedImageS tate study DeletedIma geState = StudyDelet edImageSta te.cannotI ncludeDele tedImages;
	797	if(canIn cludeDelet edImages) // if the DS support s getting deleted im ages, set appropriat ely based on user re quest
	798	studyDelet edImageSta te = (incl udesDelete dImages ? StudyDelet edImageSta te.include sDeletedIm ages : Stu dyDeletedI mageState. doesNotInc ludeDelete dImages);
	799	return V istaImagin gTranslato r.createGr oupsFromGr oupLines(s ite, rtn, patientIde ntifier,
	800	st udyDeleted ImageState );
	801	}
	802	else i f(rtn.star tsWith("0^ No images for filter "))
	803	{
	804	logger.i nfo("0 res ponse from getPatien tGroupsVis taQuery() rpc, no im ages found , [" + rtn + "]");
	805	return n ew TreeSet <VistaGrou p>();
	806	}
	807	else i f(rtn.star tsWith("0^ No Such Pa tient:"))
	808	{
	809	logger.i nfo("0 res ponse from getPatien tGroupsVis taQuery() rpc, [" + rtn + "]") ;
	810	throw ne w VistaMet hodExcepti on("No pat ient [ "+ patientIde ntifier + "] found i n database ");
	811	}
	812	else
	813	{
	814	logger.i nfo("0 res ponse from getPatien tGroupsVis taQuery() rpc, [" + rtn + "]") ;
	815	throw ne w VistaMet hodExcepti on(rtn);
	816	}
	817	}
	818	catc h (Excepti on ex)
	819	{
	820	logger .error(ex) ;
	821	throw new Method Exception( ex);
	822	}
	823	}
	824
	825	/* *
	826	*
	827	* @param pr ocedure
	828	* @param fi lter
	829	* @return
	830	* /
	831	/*
	832	pr ivate bool ean proced ureUsed(St ring proce dure, Stud yFilter fi lter)
	833	{
	834	if(p rocedure = = null)
	835	return false;
	836
	837	if( filter.get AllowableS tudyTypes( ) == null \|\| filter. getAllowab leStudyTyp es().size( ) == 0 )
	838	return true;
	839
	840	for( int i = 0 ; i < filt er.getAllo wableStudy Types().si ze(); i++ )
	841	if( pr ocedure.eq ualsIgnore Case(filte r.getAllow ableStudyT ypes().get (i)) )
	842	return t rue;
	843
	844	retu rn false;
	845	}
	846	*/
	847
	848	/**
	849	*
	850	* @re turn
	851	* @th rows IOExc eption
	852	* @th rows Vista Exception
	853	*/
	854	pu blic boole an disconn ect()
	855	th rows IOExc eption
	856	{
	857	// d on;t do an ything, le t the conn ection tim eout
	858	retu rn true;
	859	}
	860
	861	/* *
	862	* Determine s if this data sourc e can hand le retriev ing delete d images i f the user requests them
	863	* @return
	864	* /
	865	pr otected bo olean canR etrieveDel etedImages ()
	866	{
	867	retu rn false;
	868	}
	869
	870	@O verride
	871	pr otected St ring getDa taSourceVe rsion()
	872	{
	873	retu rn "1";
	874	}
	875	}