Issues report of OpenMRS

New issues

555

Resolved issues

openmrs-api - src/main/java/org/openmrs/Allergen.java

3
New issues

12	import org.apache.commons.lang3.StringUtils;

13	import org.openmrs.Concept;

14	import org.openmrs.util.OpenmrsConstants;

	Remove this unused import 'org.openmrs.util.OpenmrsConstants'. NEW Useless imports should be removed
15	import org.openmrs.api.context.Context;

	Remove this unused import 'org.openmrs.api.context.Context'. NEW Useless imports should be removed
16

17	/**

110	this.nonCodedAllergen = nonCodedAllergen;

111	if (StringUtils.isNotBlank(nonCodedAllergen)) {

112	if (codedAllergen != null && !codedAllergen.getUuid().equals(getOtherNonCodedConceptUuid())) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
113	codedAllergen = null;

114	}

openmrs-api - src/main/java/org/openmrs/BaseCustomizableData.java

3
New issues

84	setAttributes(new LinkedHashSet<A>());

85	}

86	// TODO validate

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
87	getAttributes().add(attribute);

88	attribute.setOwner(this);

91	/**

92	* Convenience method that voids all existing attributes of the given type, and sets this new one.

93	* TODO fail if minOccurs > 1

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
94	* TODO decide whether this should require maxOccurs=1

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
95	* @should void the attribute if an attribute with same attribute type already exists and the maxOccurs is set to 1

96	*

openmrs-api - src/main/java/org/openmrs/BaseCustomizableMetadata.java

3
New issues

84	setAttributes(new LinkedHashSet<A>());

85	}

86	// TODO validate

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
87	getAttributes().add(attribute);

88	attribute.setOwner(this);

91	/**

92	* Convenience method that voids all existing attributes of the given type, and sets this new one.

93	* TODO fail if minOccurs > 1

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
94	* TODO decide whether this should require maxOccurs=1

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
95	* @should void the attribute if an attribute with same attribute type already exists and the maxOccurs is set to 1

96	* @should work for attributes with datatypes whose values are stored in other tables

openmrs-api - src/main/java/org/openmrs/Cohort.java

2
New issues

28	public static final long serialVersionUID = 0L;

29

30	private static final Log log = LogFactory.getLog(Cohort.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Remove this unused "log" private field. NEW Unused private fields should be removed
31

32	private Integer cohortId;

openmrs-api - src/main/java/org/openmrs/Concept.java

22
New issues

3 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

179	if (answers != null) {

180	for (ConceptAnswer ca : answers) {

181	if (!ca.getAnswerConcept().isRetired()) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
182	newAnswers.add(ca);

183	}

445	*/

446	public ConceptName getName() {

447	if (getNames().size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
448	if (log.isDebugEnabled()) {

449	log.debug("there are no names defined for: " + conceptId);

484	}

485

486	if (getSynonyms().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
487	return getSynonyms().iterator().next();

488	}

589

590	// fail early if this concept has no names defined

591	if (getNames().size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
592	if (log.isDebugEnabled()) {

593	log.debug("there are no names defined for: " + conceptId);

629	if (fullySpecifiedName != null) {

630	return fullySpecifiedName;

631	} else if (getSynonyms(locale).size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
632	return getSynonyms(locale).iterator().next();

633	}

650	}

651	// fail early if this concept has no names defined

652	if (getNames(forLocale).size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
653	if (log.isDebugEnabled()) {

654	log.debug("there are no names defined for concept with id: " + conceptId + " in the locale: " + forLocale);

696	*/

697	public ConceptName getFullySpecifiedName(Locale locale) {

698	if (locale != null && getNames(locale).size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
699	//get the first fully specified name, since every concept must have a fully specified name,

700	//then, this loop will have to return a name

731	*/

732	public Collection<ConceptName> getNames(Locale locale) {

733	Collection<ConceptName> localeNames = new Vector<ConceptName>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
734	for (ConceptName possibleName : getNames()) {

735	if (possibleName.getLocale().equals(locale)) {

748	*/

749	private Collection<ConceptName> getPartiallyCompatibleNames(Locale locale) {

750	Collection<ConceptName> localeNames = new Vector<ConceptName>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
751	String language = locale.getLanguage();

752	String country = locale.getCountry();

858	public ConceptName getShortNameInLocale(Locale locale) {

859	ConceptName bestMatch = null;

860	if (locale != null && getShortNames().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
861	for (ConceptName shortName : getShortNames()) {

862	Locale nameLocale = shortName.getLocale();

883	public Collection<ConceptName> getShortNames() {

884	Vector<ConceptName> shortNames = new Vector<ConceptName>();

885	if (getNames().size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
886	if (log.isDebugEnabled()) {

887	log.debug("The Concept with id: " + conceptId + " has no names");

967	*/

968	public Collection<ConceptName> getIndexTerms() {

969	Collection<ConceptName> indexTerms = new Vector<ConceptName>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
970	for (ConceptName name : getNames()) {

971	if (name.isIndexTerm()) {

985	public Collection<ConceptName> getIndexTermsForLocale(Locale locale) {

986

987	Vector<ConceptName> indexTermsForLocale = new Vector<ConceptName>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
988	if (getIndexTerms().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
989	for (ConceptName name : getIndexTerms()) {

990	if (name.getLocale().equals(locale)) {

1019	if (names != null) {

1020	for (ConceptName cn : names) {

1021	if (!cn.isVoided()) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
1022	ret.add(cn);

1023	}

1051	}

1052	if (!names.contains(conceptName)) {

1053	if (getNames().size() == 0

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1054	&& !OpenmrsUtil.nullSafeEquals(conceptName.getConceptNameType(), ConceptNameType.FULLY_SPECIFIED)) {

1055	conceptName.setConceptNameType(ConceptNameType.FULLY_SPECIFIED);

1240	public void addDescription(ConceptDescription description) {

1241	if (description != null && StringUtils.isNotBlank(description.getDescription())) {

1242	if (getDescriptions() == null) {

	Redundant nullcheck of org.openmrs.Concept.getDescriptions(), which is known to be non-null in org.openmrs.Concept.addDescription(ConceptDescription) NEW Dodgy - Redundant nullcheck of value known to be non-null
1243	descriptions = new HashSet<ConceptDescription>();

1244	description.setConcept(this);

1258	*/

1259	public boolean removeDescription(ConceptDescription description) {

1260	if (getDescriptions() != null) {

	Redundant nullcheck of org.openmrs.Concept.getDescriptions(), which is known to be non-null in org.openmrs.Concept.removeDescription(ConceptDescription) NEW Dodgy - Redundant nullcheck of value known to be non-null
1261	return descriptions.remove(description);

1262	} else {

1331	*/

1332	public Collection<ConceptName> getSynonyms() {

1333	Collection<ConceptName> synonyms = new Vector<ConceptName>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
1334	for (ConceptName possibleSynonym : getNames()) {

1335	if (possibleSynonym.isSynonym()) {

1525	*/

1526	public Set<Locale> getAllConceptNameLocales() {

1527	if (getNames().size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1528	if (log.isDebugEnabled()) {

1529	log.debug("The Concept with id: " + conceptId + " has no names");

1714	setAttributes(new LinkedHashSet<>());

1715	}

1716	// TODO validate

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
1717	getAttributes().add(attribute);

1718	attribute.setOwner(this);

openmrs-api - src/main/java/org/openmrs/ConceptComplex.java

1
New issues

88	}

89

90	return getDatatype().getHl7Abbreviation().equals("ED");

	Move the "ED" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
91	}

92

openmrs-api - src/main/java/org/openmrs/ConceptDatatype.java

1
New issues

11

12	import org.hibernate.search.annotations.DocumentId;

13	import org.hibernate.search.annotations.Indexed;

	Remove this unused import 'org.hibernate.search.annotations.Indexed'. NEW Useless imports should be removed
14

15	/**

openmrs-api - src/main/java/org/openmrs/ConceptName.java

2
New issues

587	* @see org.openmrs.Auditable#setChangedBy(org.openmrs.User)

588	*/

589	public void setChangedBy(User changedBy) {

	Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation. NEW Methods should not be empty
590	}

591

595	* @see org.openmrs.Auditable#setDateChanged(java.util.Date)

596	*/

597	public void setDateChanged(Date dateChanged) {

	Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation. NEW Methods should not be empty
598	}

599	}

openmrs-api - src/main/java/org/openmrs/ConceptNameTag.java

2
New issues

267	* @see org.openmrs.Auditable#setChangedBy(org.openmrs.User)

268	*/

269	public void setChangedBy(User changedBy) {

	Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation. NEW Methods should not be empty
270

271	}

276	* @see org.openmrs.Auditable#setDateChanged(java.util.Date)

277	*/

278	public void setDateChanged(Date dateChanged) {

	Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation. NEW Methods should not be empty
279

280	}

openmrs-api - src/main/java/org/openmrs/ConceptNumeric.java

1
New issues

194	@Override

195	public boolean isNumeric() {

196	return getDatatype().getName().equals("Numeric");

	Move the "Numeric" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
197	}

198

openmrs-api - src/main/java/org/openmrs/ConceptProposal.java

1
New issues

1 duplicated blocks of code must be removed.

NEW

Source files should not have any duplicated blocks

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/Encounter.java

5
New issues

15	import java.util.Deque;

16	import java.util.HashMap;

17	import java.util.HashSet;

	Remove this unused import 'java.util.HashSet'. NEW Useless imports should be removed
18	import java.util.Iterator;

19	import java.util.LinkedHashSet;

48	private Patient patient;

49

50	private Integer patientId;

	Remove this unused "patientId" private field. NEW Unused private fields should be removed
51

52	private Location location;

158	}

159	// this should be all thats needed unless the encounter has been built by hand

160	//if (o.isVoided() == false && o.isObsGrouping() == false)

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
161	// ret.add(o);

162	}

440	Set<EncounterProvider> activeEncounterProviders = new LinkedHashSet<EncounterProvider>();

441	Set<EncounterProvider> providers = getEncounterProviders();

442	if (providers != null && providers.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
443	for (EncounterProvider provider : providers) {

444	if (provider.isVoided() == false) {

	Remove the literal "false" boolean value. NEW Literal boolean values should not be used in condition expressions
445	activeEncounterProviders.add(provider);

446	}

openmrs-api - src/main/java/org/openmrs/Field.java

1
New issues

122	*/

123	public void setAttributeName(String attributeName) {

124	// this.dirty = true;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
125	this.attributeName = attributeName;

126	}

openmrs-api - src/main/java/org/openmrs/Obs.java

2
New issues

10	package org.openmrs;

11

12	import org.apache.commons.collections.CollectionUtils;

	Remove this unused import 'org.apache.commons.collections.CollectionUtils'. NEW Useless imports should be removed
13	import org.apache.commons.lang.StringUtils;

14	import org.apache.commons.logging.Log;

830	*/

831	public boolean isComplex() {

832	// if (getValueComplex() != null) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
833	// return true;

834	// }

openmrs-api - src/main/java/org/openmrs/OpenmrsMetadata.java

1
New issues

14	* system and descriptive data such as data types — a relationship type or encounter type.

15	* Metadata are generally referenced by clinical data but don't represent patient-specific data

16	* themselves. OpenMRS objects that represent metadata should implement this interface. TODO:

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
17	* Support localized names and descriptions

18	*

openmrs-api - src/main/java/org/openmrs/Order.java

6
New issues

57	}

58

59	private static final Log log = LogFactory.getLog(Order.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Remove this unused "log" private field. NEW Unused private fields should be removed
60

61	private Integer orderId;

426	}

427	if (checkDate == null) {

428	checkDate = new Date();

	Introduce a new variable instead of reusing the parameter "checkDate". NEW Method parameters, caught exceptions and foreach variables should not be reassigned
429	}

430

464	}

465	if (checkDate == null) {

466	checkDate = new Date();

	Introduce a new variable instead of reusing the parameter "checkDate". NEW Method parameters, caught exceptions and foreach variables should not be reassigned
467	}

468	if (getEffectiveStartDate() == null) {

497	}

498	if (checkDate == null) {

499	checkDate = new Date();

	Introduce a new variable instead of reusing the parameter "checkDate". NEW Method parameters, caught exceptions and foreach variables should not be reassigned
500	}

501	if (!isActivated(checkDate) \|\| dateStopped == null) {

539	}

540	if (checkDate == null) {

541	checkDate = new Date();

	Introduce a new variable instead of reusing the parameter "checkDate". NEW Method parameters, caught exceptions and foreach variables should not be reassigned
542	}

543	if (!isActivated(checkDate)) {

openmrs-api - src/main/java/org/openmrs/Patient.java

8
New issues

17	import java.util.Vector;

18

19	import org.openmrs.api.APIException;

	Remove this unused import 'org.openmrs.api.APIException'. NEW Useless imports should be removed
20

21	/**

48	* as pointers, each individual element is not copied. <br>

49	* <br>

50	* TODO Should the patient specific attributes be copied? (like identifiers)

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
51	*

52	* @param person the person object to copy onto a new Patient

215	* @return Returns the "preferred" patient identifier.

216	*/

217	public PatientIdentifier getPatientIdentifier() {

	The Cyclomatic Complexity of this method "getPatientIdentifier" is 11 which is greater than 10 authorized. NEW Methods should not be too complex
218	// normally the DAO layer returns these in the correct order, i.e. preferred and non-voided first, but it's possible that someone

219	// has fetched a Patient, changed their identifiers around, and then calls this method, so we have to be careful.

220	if (getIdentifiers() != null && getIdentifiers().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
221	for (PatientIdentifier id : getIdentifiers()) {

222	if (id.isPreferred() && !id.isVoided()) {

243	*/

244	public PatientIdentifier getPatientIdentifier(PatientIdentifierType pit) {

245	if (getIdentifiers() != null && getIdentifiers().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
246	for (PatientIdentifier id : getIdentifiers()) {

247	if (id.isPreferred() && !id.isVoided() && pit.equals(id.getIdentifierType())) {

266	*/

267	public PatientIdentifier getPatientIdentifier(Integer identifierTypeId) {

268	if (getIdentifiers() != null && getIdentifiers().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
269	for (PatientIdentifier id : getIdentifiers()) {

270	if (id.isPreferred() && !id.isVoided()

291	*/

292	public PatientIdentifier getPatientIdentifier(String identifierTypeName) {

293	if (getIdentifiers() != null && getIdentifiers().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
294	for (PatientIdentifier id : getIdentifiers()) {

295	if (id.isPreferred() && !id.isVoided() && identifierTypeName.equals(id.getIdentifierType().getName())) {

321	for (PatientIdentifier pi : getIdentifiers()) {

322	if (!pi.isVoided()) {

323	if (pi.isPreferred()) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
324	ids.add(pi);

325	} else {

openmrs-api - src/main/java/org/openmrs/PatientIdentifier.java

1
New issues

206	*/

207	@SuppressWarnings("squid:S1210")

208	public int compareTo(PatientIdentifier other) {

	Add the missing @Deprecated annotation. NEW Deprecated elements should have both the annotation and the Javadoc tag
209	DefaultComparator piDefaultComparator = new DefaultComparator();

210	return piDefaultComparator.compare(this, other);

openmrs-api - src/main/java/org/openmrs/PatientIdentifierType.java

2
New issues

67	private String formatDescription;

68

69	private Boolean checkDigit = Boolean.FALSE;

	Remove this unused "checkDigit" private field. NEW Unused private fields should be removed
70

71	private String validator;

188

189	/**

190	* TODO: make this return a more debug-worth string instead of just the name. Check the webapp

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
191	* to make sure it is not depending on this

192	*

openmrs-api - src/main/java/org/openmrs/PatientProgram.java

1
New issues

211	PatientState last = null;

212	PatientState nextToLast = null;

213	if (states.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
214	last = states.get(states.size() - 1);

215	}

openmrs-api - src/main/java/org/openmrs/Person.java

6
New issues

13 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

203	@JsonIgnore

204	public Boolean isBirthdateEstimated() {

205	// if (this.birthdateEstimated == null) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
206	// return new Boolean(false);

207	// }

460	public void removeAttribute(PersonAttribute attribute) {

461	if (attributes != null) {

462	if (attributes.remove(attribute)) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
463	attributeMap = null;

464	allAttributeMap = null;

734	// normally the DAO layer returns these in the correct order, i.e. preferred and non-voided first, but it's possible that someone

735	// has fetched a Person, changed their names around, and then calls this method, so we have to be careful.

736	if (getNames() != null && getNames().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
737	for (PersonName name : getNames()) {

738	if (name.isPreferred() && !name.isVoided()) {

816	// normally the DAO layer returns these in the correct order, i.e. preferred and non-voided first, but it's possible that someone

817	// has fetched a Person, changed their addresses around, and then calls this method, so we have to be careful.

818	if (getAddresses() != null && getAddresses().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
819	for (PersonAddress addr : getAddresses()) {

820	if (addr.isPreferred() && !addr.isVoided()) {

1019	*/

1020	@SuppressWarnings("unused")

1021	private void setPatient(boolean isPatient) {

	Private method 'setPatient' is never used. NEW Unused private method should be removed
1022	this.isPatient = isPatient;

1023	}

openmrs-api - src/main/java/org/openmrs/Role.java

2
New issues

183	*/

184	public boolean inheritsRoles() {

185	return getInheritedRoles() != null && getInheritedRoles().size() > 0;

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
186	}

187

275	*/

276	public boolean hasChildRoles() {

277	return getChildRoles() != null && getChildRoles().size() > 0;

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
278	}

279

openmrs-api - src/main/java/org/openmrs/User.java

1
New issues

138	public boolean hasRole(String r, boolean ignoreSuperUser) {

139	if (!ignoreSuperUser) {

140	if (isSuperUser()) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
141	return true;

142	}

openmrs-api - src/main/java/org/openmrs/Visit.java

1
New issues

4 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/annotation/OpenmrsProfileExcludeFilter.java

1
New issues

45	return !matchOpenmrsProfileAttributes(openmrsProfileAttributes);

46	} else {

47	return false; //do not exclude

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
48	}

49	}

openmrs-api - src/main/java/org/openmrs/aop/LoggingAdvice.java

1
New issues

133	}

134	}

135	log.debug(String.format(

	Format string should use %n rather than \n in org.openmrs.aop.LoggingAdvice.invoke(MethodInvocation) NEW Format string should use %n rather than \n
136	"An error occurred while executing this method.\nCurrent user: %s\nError message: %s", username, e

137	.getMessage()), e);

openmrs-api - src/main/java/org/openmrs/api/AdministrationService.java

1
New issues

292	* AdministrationService).

293	*

294	* @return list of allowed presentation locales TODO change this return type to list?

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
295	* @should return at least one locale if no locales defined in database yet

296	* @should not return more locales than message source service locales

openmrs-api - src/main/java/org/openmrs/api/DatatypeService.java

1
New issues

44	/**

45	* Gets the default handler for a {@link CustomDatatype}, and sets its configuration

46	* TODO probably remove the config argument since it doesn't make sense to let people provide handlerConfig to the default handler. If we remove this argument, we also need to change BaseAttributeTypeValidator

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
47	*

48	* @param datatype

openmrs-api - src/main/java/org/openmrs/api/EventListeners.java

1
New issues

39	public void setGlobalPropertyListeners(List<GlobalPropertyListener> globalPropertyListeners) {

40	if (log.isDebugEnabled()) {

41	StringBuffer sb = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
42	for (GlobalPropertyListener gpl : globalPropertyListeners) {

43	if (sb.length() > 0) {

openmrs-api - src/main/java/org/openmrs/api/GlobalPropertyListener.java

1
New issues

14	/**

15	* This interface allows code to be run when global properties are created, edited, or deleted. <br>

16	* TODO: Make sure listeners are notified if a global property's name is changed.

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
17	*

18	* @see AdministrationService#addGlobalPropertyListener(GlobalPropertyListener)

openmrs-api - src/main/java/org/openmrs/api/ObsService.java

1
New issues

368	/**

369	* Get a complex observation. If obs.isComplex() is true, then returns an Obs with its

370	* ComplexData. Otherwise returns a simple Obs. TODO: Possibly remove this method. It is

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
371	* confusing because you may have a complexObs, but not want the complexData attached at the

372	* time. Nevertheless, you may think that this method is necessary to use, when you could just

openmrs-api - src/main/java/org/openmrs/api/OrderService.java

2
New issues

487	@Authorized({ PrivilegeConstants.ADD_ORDERS, PrivilegeConstants.EDIT_ORDERS })

488	public Order discontinueOrder(Order orderToDiscontinue, Concept reasonCoded, Date discontinueDate, Provider orderer,

489	Encounter encounter) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
490

491	/**

510	@Authorized({ PrivilegeConstants.ADD_ORDERS, PrivilegeConstants.EDIT_ORDERS })

511	public Order discontinueOrder(Order orderToDiscontinue, String reasonNonCoded, Date discontinueDate, Provider orderer,

512	Encounter encounter) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
513

514	/**

openmrs-api - src/main/java/org/openmrs/api/PatientService.java

2
New issues

564	* Convenience method to establish that a patient has died. In addition to exiting the patient

565	* from care (see above), this method will also set the appropriate patient characteristics to

566	* indicate that they have died, when they died, etc. TODO Keep this in the PatientService? Or

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
567	* move to appropriate service

568	*

580	/**

581	* Convenience method that saves the Obs that indicates when and why the patient died (including

582	* any "other" reason there might be) TODO keep this in the PatientService?

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
583	*

584	* @param patient - the patient who has died

openmrs-api - src/main/java/org/openmrs/api/ProgramWorkflowService.java

1
New issues

457

458	/**

459	* TODO: refactor?

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
460	*

461	* @param cohort

openmrs-api - src/main/java/org/openmrs/api/context/Context.java

1
New issues

748	public static void closeSessionWithCurrentUser() {

749	getContextDAO().closeSession();

750	;

	Remove this empty statement. NEW Empty statements should be removed
751	}

752

openmrs-api - src/main/java/org/openmrs/api/context/Daemon.java

1
New issues

118

119	// quick check to make sure we're only being called by ourselves

120	//Class<?> callerClass = Reflection.getCallerClass(0);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
121	Class<?> callerClass = new OpenmrsSecurityManager().getCallerClass(0);

122	if (!TimerSchedulerTask.class.isAssignableFrom(callerClass)) {

openmrs-api - src/main/java/org/openmrs/api/db/CohortDAO.java

1
New issues

56	* @throws DAOException

57	*/

58	public List<Cohort> getCohortsContainingPatientId(Integer patientId) throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
59

60	/**

openmrs-api - src/main/java/org/openmrs/api/db/NoteDAO.java

7
New issues

28	* @throws DAOException

29	*/

30	public List<Note> getNotes() throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
31

32	/**

36	* @throws DAOException

37	*/

38	public void createNote(Note note) throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
39

40	/**

45	* @throws DAOException

46	*/

47	public Note getNote(Integer noteId) throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
48

49	/**

53	* @throws DAOException

54	*/

55	public void updateNote(Note note) throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
56

57	/**

58	* TODO: Couldn't find a voidNote method Delete note from database. This <b>should not be

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
59	* called</b> except for testing and administration purposes. Use the void method instead.

60	*

62	* @throws DAOException

63	*/

64	public void deleteNote(Note note) throws DAOException;

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
65

66	/**

69	* @throws APIException

70	*/

71	public Note voidNote(Note note, String reason) throws APIException;

	Remove the declaration of thrown exception 'org.openmrs.api.APIException' which is a runtime exception. NEW Throws declarations should not be redundant
72	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/AuditableInterceptor.java

1
New issues

119

120	for (String property : propertyValues.keySet()) {

121	if (changePropertyValue(currentState, propertyNames, property, propertyValues.get(property), setNullOnly)) {

	org.openmrs.api.db.hibernate.AuditableInterceptor.changeProperties(Object[], String[], boolean, Map, Boolean) makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
122	objectWasChanged = true;

123	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/ChainingInterceptor.java

1
New issues

116

117	public Boolean isTransient(Object entity) {

118	Boolean returnValue = null; // by default let hibernate figure it out

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
119

120	for (Interceptor i : interceptors) {

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateAdministrationDAO.java

1
New issues

35	import org.springframework.context.ApplicationContext;

36	import org.springframework.context.ApplicationContextAware;

37	import org.springframework.orm.hibernate3.LocalSessionFactoryBean;

	Remove this unused import 'org.springframework.orm.hibernate3.LocalSessionFactoryBean'. NEW Useless imports should be removed
38	import org.springframework.validation.Errors;

39	import org.springframework.validation.Validator;

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateConceptDAO.java

9
New issues

105	// and re-fetch it as a ConceptComplex

106	if (obj != null && !obj.getClass().equals(ConceptComplex.class)) {

107	sessionFactory.getCurrentSession().evict(obj); // remove from cache

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
108	// session.get() did not work here, we need to perform a query to get a ConceptComplex

109	Query query = sessionFactory.getCurrentSession().createQuery("from ConceptComplex where conceptId = :conceptId")

506	// and re-fetch it as a ConceptNumeric

507	if (obj != null && !obj.getClass().equals(ConceptNumeric.class)) {

508	sessionFactory.getCurrentSession().evict(obj); // remove from cache

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
509	// session.get() did not work here, we need to perform a query to get a ConceptNumeric

510	Query query = sessionFactory.getCurrentSession().createQuery("from ConceptNumeric where conceptId = :conceptId")

665	Restrictions.lt("conceptId", i)).addOrder(Order.desc("conceptId")).setFetchSize(1).list();

666

667	if (concepts.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
668	return null;

669	}

681	Restrictions.gt("conceptId", i)).addOrder(Order.asc("conceptId")).setMaxResults(1).list();

682

683	if (concepts.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
684	return null;

685	}

841	Restrictions.eq("tag", name));

842

843	if (crit.list().size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
844	return null;

845	}

947	*/

948	public boolean hasNext() {

949	return (nextConcept != null);

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
950	}

951

1512	criteria.add(Restrictions.eq("conceptSource", conceptSource));

1513	List terms = criteria.list();

1514	if (terms.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1515	return null;

1516	} else if (terms.size() > 1) {

1532	criteria.add(Restrictions.eq("conceptSource", conceptSource));

1533	List terms = criteria.list();

1534	if (terms.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1535	return null;

1536	} else if (terms.size() > 1) {

1847

1848	// match with any of the supplied collection or order of preference of conceptMapTypes

1849	if (withAnyOfTheseTypesOrOrderOfPreference.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1850	for (ConceptMapType conceptMapType : withAnyOfTheseTypesOrOrderOfPreference) {

1851	criteria.add(Restrictions.eq("map.conceptMapType", conceptMapType));

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateContextDAO.java

4
New issues

116	String lockoutTimeString = candidateUser.getUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP, null);

117	Long lockoutTime = null;

118	if (lockoutTimeString != null && !lockoutTimeString.equals("0")) {

	Move the "0" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
119	try {

120	// putting this in a try/catch in case the admin decided to put junk into the property

442	while (results.next()) {

443	index++;

444	session.index(results.get(0)); //index each element

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
445	if (index % 1000 == 0) {

446	session.flushToIndexes(); //apply changes to indexes

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
447	session.clear(); //free memory since the queue is processed

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
448	}

449	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateEncounterDAO.java

5
New issues

136	);

137	}

138	if (searchCriteria.getEnteredViaForms() != null && searchCriteria.getEnteredViaForms().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
139	crit.add(Restrictions.in("form", searchCriteria.getEnteredViaForms()));

140	}

141	if (searchCriteria.getEncounterTypes() != null && searchCriteria.getEncounterTypes().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
142	crit.add(Restrictions.in("encounterType", searchCriteria.getEncounterTypes()));

143	}

144	if (searchCriteria.getProviders() != null && searchCriteria.getProviders().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
145	crit.createAlias("encounterProviders", "ep");

146	crit.add(Restrictions.in("ep.provider", searchCriteria.getProviders()));

147	}

148	if (searchCriteria.getVisitTypes() != null && searchCriteria.getVisitTypes().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
149	crit.createAlias("visit", "v");

150	crit.add(Restrictions.in("v.visitType", searchCriteria.getVisitTypes()));

151	}

152	if (searchCriteria.getVisits() != null && searchCriteria.getVisits().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
153	crit.add(Restrictions.in("visit", searchCriteria.getVisits()));

154	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateFormDAO.java

3
New issues

202	String err = "FormField warning. No FormField matching concept '" + concept + "' for form '" + form + "'";

203

204	if (formFields.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
205	log.debug(err);

206	return null;

215	// if we ended up removing all of the formfields, check to see if we're

216	// in a "force" situation

217	if (formFields.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
218	if (!force) {

219	return backupPlan;

222	return null;

223	}

224	} else { // if formFields.size() is still greater than 0

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
225	FormField ff = (FormField) formFields.get(0);

226	return ff;

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateNoteDAO.java

5
New issues

10	package org.openmrs.api.db.hibernate;

11

12	import java.util.ArrayList;

	Remove this unused import 'java.util.ArrayList'. NEW Useless imports should be removed
13	import java.util.List;

14

23	public class HibernateNoteDAO implements NoteDAO {

24

25	protected final static Log log = LogFactory.getLog(HibernateNoteDAO.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
26

27	/**

69	}

70

71	public void deleteNote(Note note) throws DAOException {

	Remove the declaration of thrown exception 'org.openmrs.api.db.DAOException' which is a runtime exception. NEW Throws declarations should not be redundant
72	log.debug("Deleting existing note");

73	sessionFactory.getCurrentSession().delete(note);

77	* @see org.openmrs.api.db.NoteDAO#voidNote(org.openmrs.notification.Note, java.lang.String)

78	*/

79	public Note voidNote(Note note, String reason) throws APIException {

	Remove the declaration of thrown exception 'org.openmrs.api.APIException' which is a runtime exception. NEW Throws declarations should not be redundant
80	log.debug("voiding note because " + reason);

81	sessionFactory.getCurrentSession().save(note);

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateObsDAO.java

1
New issues

242	if (personTypes.contains(PERSON_TYPE.PERSON)) {

243	// all observations are already on person's. Limit to non-patient and non-users here?

244	//criteria.createAlias("Person", "person");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
245	//criteria.add(Restrictions.eqProperty("obs.person.personId", "person.personId"));

246	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateOrderDAO.java

9
New issues

123	}

124

125	if (patients.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
126	crit.add(Restrictions.in("patient", patients));

127	}

128

129	if (concepts.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
130	crit.add(Restrictions.in("concept", concepts));

131	}

134	// algorithm dependent

135

136	if (orderers.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
137	crit.add(Restrictions.in("orderer", orderers));

138	}

139

140	if (encounters.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
141	crit.add(Restrictions.in("encounter", encounters));

142	}

327	criteria.add(Restrictions.eq("careSetting", careSetting));

328	}

329	if (orderTypes != null && orderTypes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
330	criteria.add(Restrictions.in("orderType", orderTypes));

331	}

476	Class<?> entityClass = classMetadata.getMappedClass();

477	if (Order.class.equals(entityClass)) {

478	continue; //ignore the org.openmrs.Order class itself

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
479	}

480

481	if (!Order.class.isAssignableFrom(entityClass)) {

482	continue; //not a sub class of Order

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
483	}

484

489	criteria.add(Restrictions.eq(name, orderFrequency));

490	criteria.setMaxResults(1);

491	if (criteria.list().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
492	return true;

493	}

580	Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Order.class);

581	criteria.add(Restrictions.eq("orderType", orderType));

582	return criteria.list().size() > 0;

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
583	}

584	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateOrderSetDAO.java

1
New issues

16	import org.hibernate.SessionFactory;

17	import org.hibernate.criterion.Restrictions;

18	import org.openmrs.ConceptDescription;

	Remove this unused import 'org.openmrs.ConceptDescription'. NEW Useless imports should be removed
19	import org.openmrs.OrderSet;

20	import org.openmrs.OrderSetMember;

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernatePatientDAO.java

23
New issues

27	import org.apache.commons.logging.LogFactory;

28	import org.hibernate.Criteria;

29	import org.hibernate.HibernateException;

	Remove this unused import 'org.hibernate.HibernateException'. NEW Useless imports should be removed
30	import org.hibernate.Query;

31	import org.hibernate.SQLQuery;

104	// and Persons are the same objects. So it sees a Person object in the

105	// cache and claims it is a duplicate of this Patient object.

106	//patient = (Patient) sessionFactory.getCurrentSession().merge(patient);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
107	sessionFactory.getCurrentSession().saveOrUpdate(patient);

108

131

132	if (stubInsertNeeded) {

133	if (patient.getCreator() == null) { //If not yet persisted

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
134	patient.setCreator(Context.getAuthenticatedUser());

135	}

136	if (patient.getDateCreated() == null) { //If not yet persisted

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
137	patient.setDateCreated(new Date());

138	}

161	*/

162	@Override

163	public List<Patient> getPatients(String query, boolean includeVoided, Integer start, Integer length) throws DAOException {

	The Cyclomatic Complexity of this method "getPatients" is 13 which is greater than 10 authorized. NEW Methods should not be too complex
164	if (StringUtils.isBlank(query) \|\| (length != null && length < 1)) {

165	return Collections.emptyList();

305	}

306

307	// TODO add junit test for getting by identifier type

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
308	if (patientIdentifierTypes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
309	criteria.add(Restrictions.in("identifierType", patientIdentifierTypes));

310	}

311

312	if (locations.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
313	criteria.add(Restrictions.in("location", locations));

314	}

315

316	// TODO add junit test for getting by patients

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
317	if (patients.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
318	criteria.add(Restrictions.in("patient", patients));

319	}

364	criteria.add(Restrictions.eq("retired", false));

365	} else {

366	criteria.addOrder(Order.asc("retired")); //retired last

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
367	}

368

369	criteria.addOrder(Order.desc("required")); //required first

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
370	criteria.addOrder(Order.asc("name"));

371	criteria.addOrder(Order.asc("patientIdentifierTypeId"));

414	criteria.add(Restrictions.eq("retired", false));

415

416	criteria.addOrder(Order.desc("required")); //required first

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
417	criteria.addOrder(Order.asc("name"));

418	criteria.addOrder(Order.asc("patientIdentifierTypeId"));

429	List<Integer> patientIds = new Vector<Integer>();

430

431	if (attributes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
432

433	String sqlString = getDuplicatePatientsSQLString(attributes);

436	SQLQuery sqlquery = sessionFactory.getCurrentSession().createSQLQuery(sqlString);

437	patientIds = sqlquery.list();

438	if (patientIds.size() >= 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
439	Query query = sessionFactory.getCurrentSession().createQuery(

440	"from Patient p1 where p1.patientId in (:ids)");

493	if (patientFieldNames.contains(attribute)) {

494

495	AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory.getClassMetadata(Patient.class));

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
496	String[] properties = aep.getPropertyColumnNames(attribute);

497	if (properties.length >= 1) {

498	attribute = properties[0];

499	}

500	whereConditions.add(" t1." + attribute + " = t5." + attribute);

	Define a constant instead of duplicating this literal " = t5." 4 times. NEW String literals should not be duplicated
501	innerFields.add("p1." + attribute);

502	} else if (personFieldNames.contains(attribute)) {

506	}

507

508	AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory.getClassMetadata(Person.class));

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
509	if (aep != null) {

510	String[] properties = aep.getPropertyColumnNames(attribute);

523

524	//Since we are firing a native query get the actual table column name from the field name of the entity

525	AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
526	.getClassMetadata(PersonName.class));

527	if (aep != null) {

541	}

542

543	AbstractEntityPersister aep = ((AbstractEntityPersister) sessionFactory

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
544	.getClassMetadata(PatientIdentifier.class));

545	if (aep != null) {

557	}

558	}

559	if(innerFields.size() > 0 \|\| whereConditions.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
560	String innerFieldsJoined = StringUtils.join(innerFields, ", ");

561	String whereFieldsJoined = StringUtils.join(whereConditions, " and ");

659	query.setInteger("locationId", patientIdentifier.getLocation().getLocationId());

660	}

661	return !query.uniqueResult().toString().equals("0");

	Move the "0" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
662	}

663

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernatePersonDAO.java

4
New issues

158	q.append(" when soundex(pname.familyName2) = soundex(:n").append(i + 1).append(") then 1");

159	}

160	q.append(" else 0").append(" end").append(") >= ").append((int) (names.length * .75)); // if most of the names have at least a hit somewhere

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
161	}

162

240	PersonSearchCriteria personSearchCriteria = new PersonSearchCriteria();

241

242	searchString = searchString.replace(", ", " ");

	Introduce a new variable instead of reusing the parameter "searchString". NEW Method parameters, caught exceptions and foreach variables should not be reassigned
243	String[] values = searchString.split(" ");

244

247	personSearchCriteria.addAliasForName(criteria);

248	personSearchCriteria.addAliasForAttribute(criteria);

249	if (voided == null \|\| voided == false) {

	Remove the literal "false" boolean value. NEW Literal boolean values should not be used in condition expressions
250	criteria.add(Restrictions.eq("personVoided", false));

251	}

269	criteria.setMaxResults(getMaximumSearchResults());

270

271	// TODO - remove

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
272	log.debug(criteria.toString());

273

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateSerializedObjectDAO.java

1
New issues

227	serializedObject.setName(metaObj.getName());

228	serializedObject.setDescription(metaObj.getDescription());

229	serializedObject.setRetired(metaObj.isRetired() == Boolean.TRUE);

	Suspicious comparison of Boolean references in org.openmrs.api.db.hibernate.HibernateSerializedObjectDAO.saveObject(OpenmrsObject, OpenmrsSerializer) NEW Correctness - Suspicious reference comparison of Boolean values
230	serializedObject.setRetiredBy(metaObj.getRetiredBy());

231	serializedObject.setDateRetired(metaObj.getDateRetired());

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/HibernateUserDAO.java

3
New issues

99	List<User> users = query.list();

100

101	if (users == null \|\| users.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
102	log.warn("request for username '" + username + "' not found");

103	return null;

573	}

574

575	if (criteria.size() > 0 \|\| searchOnRoles) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
576	hql.append("where ");

577	}

585	//Match against the specified roles

586	if (searchOnRoles) {

587	if (criteria.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
588	hql.append(" and ");

589	}

openmrs-api - src/main/java/org/openmrs/api/db/hibernate/PatientSearchCriteria.java

1
New issues

309	}

310

311	// TODO add a junit test for patientIdentifierType restrictions

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
312

313	// do the type restriction

openmrs-api - src/main/java/org/openmrs/api/handler/PersonSaveHandler.java

3
New issues

41

42	// address collection

43	if (person.getAddresses() != null && person.getAddresses().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
44	for (PersonAddress pAddress : person.getAddresses()) {

45	pAddress.setPerson(person);

48

49	// name collection

50	if (person.getNames() != null && person.getNames().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
51	for (PersonName pName : person.getNames()) {

52	pName.setPerson(person);

55

56	// attribute collection

57	if (person.getAttributes() != null && person.getAttributes().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
58	for (PersonAttribute pAttr : person.getAttributes()) {

59	pAttr.setPerson(person);

openmrs-api - src/main/java/org/openmrs/api/impl/AdministrationServiceImpl.java

2
New issues

267	}

268	} else if (gp.getProperty().equals(OpenmrsConstants.GLOBAL_PROPERTY_DEFAULT_LOCALE)) {

269	if (gp.getPropertyValue() != null) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
270	List<Locale> localeList = getAllowedLocales();

271

272	if (!localeList.contains(LocaleUtility.fromSpecification(gp.getPropertyValue().trim()))) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
273	String value = gp.getPropertyValue();

274	gp.setPropertyValue(LocaleUtility.getDefaultLocale().toString());

openmrs-api - src/main/java/org/openmrs/api/impl/ConceptServiceImpl.java

5
New issues

148	}

149	catch (IllegalAccessException e) {

150	log.error("Error generated", e);

	Define a constant instead of duplicating this literal "Error generated" 6 times. NEW String literals should not be duplicated
151	}

152	catch (InvocationTargetException e) {

225

226	// force isSet when concept has members

227	if (!concept.isSet() && (concept.getSetMembers().size() > 0)) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
228	concept.setSet(true);

229	}

230

231	Concept conceptToReturn = dao.saveConcept(concept);

	Immediately return this expression instead of assigning it to the temporary variable "conceptToReturn". NEW Local Variables should not be declared and then immediately returned or thrown
232

233	return conceptToReturn;

455	log.warn("more than one drug name returned with name:" + drugNameOrId);

456	}

457	if (drugs.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
458	return null;

459	}

1049	List<Concept> concepts = Context.getConceptService().getConceptsByMapping(code, sourceName, includeRetired);

1050

1051	if (concepts.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1052	return null;

1053	}

openmrs-api - src/main/java/org/openmrs/api/impl/DatatypeServiceImpl.java

1
New issues

191	for (Class dt : getAllDatatypeClasses()) {

192	List<Class<? extends CustomDatatypeHandler>> handlerClasses = getHandlerClasses(dt);

193	if (handlerClasses == null \|\| handlerClasses.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
194	prioritizedHandlerClasses.put(dt, null);

195	} else {

openmrs-api - src/main/java/org/openmrs/api/impl/EncounterServiceImpl.java

3
New issues

64	public class EncounterServiceImpl extends BaseOpenmrsService implements EncounterService {

65

66	// private Log log = LogFactory.getLog(this.getClass());

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
67

68	private EncounterDAO dao;

882	String locked = Context.getAdministrationService().getGlobalProperty(

883	OpenmrsConstants.GLOBAL_PROPERTY_ENCOUNTER_TYPES_LOCKED, "false");

884	if (locked.toLowerCase().equals("true")) {

	Replace these toUpperCase()/toLowerCase() and equals() calls with a single equalsIgnoreCase() call. NEW Case insensitive string comparisons should be made without intermediate upper or lower casing Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
885	throw new EncounterTypeLockedException();

886	}

openmrs-api - src/main/java/org/openmrs/api/impl/FormServiceImpl.java

6
New issues

102	public Form duplicateForm(Form form) throws APIException {

103	// Map of /Old FormFieldId/ to /New FormField Object/

104	//TreeMap<Integer, FormField> formFieldMap = new TreeMap<Integer, FormField>();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
105	//formFieldMap.put(null, null); //for parentless formFields

106	checkIfFormsAreLocked();

109

110	for (FormField formField : form.getFormFields()) {

111	//formFieldMap.put(formField.getFormFieldId(), formField);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
112	formField.setUuid(null);

113	formField.setFormFieldId(null);

114	//formField.setParent(formFieldMap.get(formField.getParent().getFormFieldId()));

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
115	}

116	// this is required because Hibernate would recognize the original collection

343	public Form getForm(String name) throws APIException {

344	List<Form> forms = dao.getFormsByName(name);

345	if (forms == null \|\| forms.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
346	return null;

347	} else {

785	String locked = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_FORMS_LOCKED,

786	"false");

787	if (locked.toLowerCase().equals("true")) {

	Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Replace these toUpperCase()/toLowerCase() and equals() calls with a single equalsIgnoreCase() call. NEW Case insensitive string comparisons should be made without intermediate upper or lower casing
788	throw new FormsLockedException();

789	}

openmrs-api - src/main/java/org/openmrs/api/impl/LocationServiceImpl.java

2
New issues

131	}

132

133	// TODO Figure out if we should/could throw an exception if there's

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
134	// no location to fall back on.

135	//if (location == null) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
136	// throw new APIException("Default location does not exist");

137	//}

openmrs-api - src/main/java/org/openmrs/api/impl/ObsServiceImpl.java

2
New issues

411	List<Obs> returnList = new Vector<Obs>();

412

413	if (encounters.size() > 0 \|\| persons.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
414	returnList = Context.getObsService().getObservations(persons, encounters, null, null, null, null, null, null,

415	null, null, null, false);

openmrs-api - src/main/java/org/openmrs/api/impl/OrderServiceImpl.java

4
New issues

279	int minutes = cal.get(Calendar.MINUTE);

280	int seconds = cal.get(Calendar.SECOND);

281	int milliseconds = cal.get(Calendar.MILLISECOND);

	Remove this unused "milliseconds" local variable. NEW Unused local variables should be removed Dead store to milliseconds in org.openmrs.api.impl.OrderServiceImpl.saveOrderInternal(Order, OrderContext) NEW Dodgy - Dead store to local variable
282	//roll autoExpireDate to end of day (23:59:59) if no time portion is specified

283	if (hours == 0 && minutes == 0 && seconds == 0) {

285	cal.set(Calendar.MINUTE, 59);

286	cal.set(Calendar.SECOND, 59);

287	cal.set(Calendar.MILLISECOND, 0); // the OpenMRS database is only precise to the second

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
288	order.setAutoExpireDate(cal.getTime());

289	}

762	public OrderFrequency saveOrderFrequency(OrderFrequency orderFrequency) throws APIException {

763	if (orderFrequency.getOrderFrequencyId() != null) {

764	if (dao.isOrderFrequencyInUse(orderFrequency)) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
765	throw new APIException("Order.frequency.cannot.edit");

766	}

openmrs-api - src/main/java/org/openmrs/api/impl/OrderSetServiceImpl.java

3
New issues

11

12	import org.apache.commons.collections.CollectionUtils;

13	import org.openmrs.ConceptDescription;

	Remove this unused import 'org.openmrs.ConceptDescription'. NEW Useless imports should be removed
14	import org.openmrs.OrderSet;

15	import org.openmrs.OrderSetMember;

16	import org.openmrs.annotation.Authorized;

	Remove this unused import 'org.openmrs.annotation.Authorized'. NEW Useless imports should be removed
17	import org.openmrs.api.APIException;

18	import org.openmrs.api.OrderSetService;

19	import org.openmrs.api.context.Context;

20	import org.openmrs.api.db.OrderSetDAO;

21	import org.openmrs.util.PrivilegeConstants;

	Remove this unused import 'org.openmrs.util.PrivilegeConstants'. NEW Useless imports should be removed
22	import org.springframework.transaction.annotation.Transactional;

23	import org.springframework.util.StringUtils;

openmrs-api - src/main/java/org/openmrs/api/impl/PatientServiceImpl.java

17
New issues

116	* @see org.openmrs.api.PatientService#savePatient(org.openmrs.Patient)

117	*/

118	public Patient savePatient(Patient patient) throws APIException {

	The Cyclomatic Complexity of this method "savePatient" is 27 which is greater than 10 authorized. NEW Methods should not be too complex
119	if (patient.getPatientId() == null) {

120	Context.requirePrivilege(PrivilegeConstants.ADD_PATIENTS);

256	*/

257	@Transactional(readOnly = true)

258	public void checkPatientIdentifiers(Patient patient) throws PatientIdentifierException {

	The Cyclomatic Complexity of this method "checkPatientIdentifiers" is 17 which is greater than 10 authorized. NEW Methods should not be too complex
259	// check patient has at least one identifier

260	if (!patient.isVoided() && patient.getActiveIdentifiers().size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
261	throw new InsufficientIdentifiersException("At least one nonvoided Patient Identifier is required");

262	}

263

264	List<PatientIdentifier> identifiers = new Vector<PatientIdentifier>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
265	identifiers.addAll(patient.getIdentifiers());

266	List<String> identifiersUsed = new Vector<String>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
267	List<PatientIdentifierType> requiredTypes = Context.getPatientService().getPatientIdentifierTypes(null, null, true,

268	null);

294	}

295

296	// TODO: check patient has at least one "sufficient" identifier

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
297	// TODO: what makes a patient identifier unique ... can you have the

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
298	// same identifier number at different locations? if so, then this

299	// check duplicate algorithm does not handle this case

310	}

311

312	if (requiredTypes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
313	String missingNames = "";

314	for (PatientIdentifierType pit : requiredTypes) {

383

384	/**

385	* TODO: Add changedBy and DateChanged columns to table patient_identifier_type

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
386	*

387	* @see org.openmrs.api.PatientService#savePatientIdentifierType(org.openmrs.PatientIdentifierType)

433	List<PatientIdentifierType> types = getPatientIdentifierTypes(name, null, null, null);

434

435	if (types.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
436	return types.get(0);

437	}

511	public List<Patient> getDuplicatePatientsByAttributes(List<String> attributes) throws APIException {

512

513	if (attributes == null \|\| attributes.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
514	throw new APIException("Patient.no.attribute", (Object[]) null);

515	}

869	}

870	/*

871	* if (preferred.getRace() == null \|\| preferred.getRace().equals(""))

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
872	* preferred.setRace(notPreferred.getRace());

873	*/

1057	*/

1058	public void processDeath(Patient patient, Date dateDied, Concept causeOfDeath, String otherReason) throws APIException {

1059	//SQLStateConverter s = null;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
1060

1061	if (patient != null && dateDied != null && causeOfDeath != null) {

1294

1295	try {

1296	return getIdentifierValidator(((Class<IdentifierValidator>) Context.loadClass(pivClassName)));

	Remove those useless parentheses. NEW Useless parentheses around expressions should be removed to prevent any misunderstanding
1297	}

1298	catch (ClassNotFoundException e) {

1390	Allergies allergies = new Allergies();

1391	List<Allergy> allergyList = dao.getAllergies(patient);

1392	if (allergyList.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1393	allergies.addAll(allergyList);

1394	} else {

1596	String locked = Context.getAdministrationService().getGlobalProperty(

1597	OpenmrsConstants.GLOBAL_PROPERTY_PATIENT_IDENTIFIER_TYPES_LOCKED, "false");

1598	if (locked.toLowerCase().equals("true")) {

	Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Replace these toUpperCase()/toLowerCase() and equals() calls with a single equalsIgnoreCase() call. NEW Case insensitive string comparisons should be made without intermediate upper or lower casing
1599	throw new PatientIdentifierTypeLockedException();

1600	}

openmrs-api - src/main/java/org/openmrs/api/impl/PersonServiceImpl.java

13
New issues

27 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

113	List<PersonAttributeType> types = Context.getPersonService().getPersonAttributeTypes(typeName, null, null, null);

114

115	if (types.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
116	return null;

117	} else {

135	if (type.getSortWeight() == null) {

136	List<PersonAttributeType> allTypes = Context.getPersonService().getAllPersonAttributeTypes();

137	if (allTypes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
138	type.setSortWeight(allTypes.get(allTypes.size() - 1).getSortWeight() + 1);

139	} else {

246	List<RelationshipType> types = dao.getRelationshipTypes(relationshipTypeName, null);

247

248	if (types.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
249	return null;

250	} else {

514	*/

515	@Transactional(readOnly = true)

516	public List<PersonAttributeType> getPersonAttributeTypes(PERSON_TYPE personType, ATTR_VIEW_TYPE viewType)

	The Cyclomatic Complexity of this method "getPersonAttributeTypes" is 25 which is greater than 10 authorized. NEW Methods should not be too complex
517	throws APIException {

518	AdministrationService as = Context.getAdministrationService();

520	String attrString = "";

521

522	// TODO cache the global properties to speed this up??

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
523	// Is hibernate taking care of caching and not hitting the db every time? (hopefully it is)

524	if (viewType == null) {

546	attrString = userViewing;

547	} else {

548	log.fatal("Should not be here");

	Define a constant instead of duplicating this literal "Should not be here" 3 times. NEW String literals should not be duplicated
549	}

550	} else if (viewType == ATTR_VIEW_TYPE.HEADER) {

566

567	// the java list object to hold the values from the global properties

568	List<String> attrNames = new Vector<String>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
569

570	// split the comma delimited string into a java list object

573	if (s != null) {

574	s = s.trim();

575	if (s.length() > 0) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
576	attrNames.add(s);

577	}

581

582	// the actual list we'll be returning

583	List<PersonAttributeType> attrObjects = new Vector<PersonAttributeType>();

	Replace the synchronized class "Vector" by an unsynchronized one such as "ArrayList" or "LinkedList". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
584

585	// get the PersonAttribute objects for each name/id

586	if (attrNames.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
587	for (String nameOrId : attrNames) {

588	if (nameOrId.matches("\\d")) {

933	String locked = Context.getAdministrationService().getGlobalProperty(

934	OpenmrsConstants.GLOBAL_PROPERTY_PERSON_ATRIBUTE_TYPES_LOCKED, "false");

935	if (locked.toLowerCase().equals("true")) {

	Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Replace these toUpperCase()/toLowerCase() and equals() calls with a single equalsIgnoreCase() call. NEW Case insensitive string comparisons should be made without intermediate upper or lower casing
936	throw new PersonAttributeTypeLockedException();

937	}

openmrs-api - src/main/java/org/openmrs/api/impl/ProgramWorkflowServiceImpl.java

1
New issues

272	@Transactional(readOnly = true)

273	public List<PatientProgram> getPatientPrograms(Cohort cohort, Collection<Program> programs) {

274	if (cohort.getMemberIds().size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
275	return dao.getPatientPrograms(null, programs);

276	} else {

openmrs-api - src/main/java/org/openmrs/api/impl/VisitServiceImpl.java

3
New issues

210	return;

211	}

212	if (Context.getEncounterService().getEncountersByVisit(visit, true).size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
213	throw new APIException("Visit.purge.inUse", (Object[]) null);

214	}

367	}

368

369	if (visitTypesToStop.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
370	int counter = 0;

371	Date stopDate = new Date();

374	nextVisit.setStopDatetime(stopDate);

375	dao.saveVisit(nextVisit);

376	if (counter++ > 50) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
377	//ensure changes are persisted to DB before reclaiming memory

378	Context.flushSession();

openmrs-api - src/main/java/org/openmrs/customdatatype/datatype/LongFreeTextDatatype.java

1
New issues

73	* Use this code snippet instead if we think that fetching the clob is fast enough

74	*

75	ClobDatatypeStorage storage = Context.getDatatypeService().getClobDatatypeStorageByUuid(referenceString);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
76	if (storage == null)

77	return Context.getMessageSourceService().getMessage("CustomDatatype.error.missingValue");

openmrs-api - src/main/java/org/openmrs/hl7/HL7Util.java

3
New issues

79	}

80

81	StringBuffer dateString = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
82	dateString.append(s.substring(0, 4)); // year

83	if (s.length() >= 6) {

226	s = s.replace(timeZoneOffset, ""); // remove the timezone from the string

227

228	StringBuffer timeString = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
229

230	if (s.length() < 2 \|\| s.length() > 16) {

296	}

297

298	//TODO Should take care of the case where the user is using removable media, this might explode

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
299	return OpenmrsUtil.getDirectoryInApplicationDataDirectory(archiveDir);

300	}

openmrs-api - src/main/java/org/openmrs/hl7/handler/ADTA28Handler.java

2
New issues

168

169	} else {

170	// TODO: Add a global property that enables different behavior here.

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
171	log.info("Ignoring ADT_A28 message because patient (" + patientId + ") already exists.");

172	}

256	}

257	}

258	if (goodIdentifiers.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
259	throw new HL7Exception("PID segment has no recognizable patient identifiers.");

260	}

openmrs-api - src/main/java/org/openmrs/hl7/handler/ORUR01Handler.java

6
New issues

184	// TODO: ideally, we would branch or alter our behavior based on the

185	// sending application.

186	// String sendingApplication = getSendingApplication(oru);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
187

188	// validate message

204	}

205

206	HL7Service hl7Service = Context.getHL7Service();

	Remove this unused "hl7Service" local variable. NEW Unused local variables should be removed Dead store to hl7Service in org.openmrs.hl7.handler.ORUR01Handler.processORU_R01(ORU_R01) NEW Dodgy - Dead store to local variable
207

208	// create the encounter

674	obs.setConcept(concept);

675	if (concept.getDatatype().isBoolean()) {

676	obs.setValueBoolean(value.equals("1"));

	Move the "1" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
677	} else if (concept.getDatatype().isNumeric()) {

678	try {

689	boolean isValidAnswer = false;

690	Collection<ConceptAnswer> conceptAnswers = concept.getAnswers();

691	if (conceptAnswers != null && conceptAnswers.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
692	for (ConceptAnswer conceptAnswer : conceptAnswers) {

693	if (conceptAnswer.getAnswerConcept().getId().equals(answer.getId())) {

1197	Calendar cal = Calendar.getInstance();

1198	cal.set(year, month, day, hour, min, sec);

1199	// if (cal.getTimeZone().getRawOffset() != timeZoneOffsetMillis) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
1200	// TimeZone tz = (TimeZone)TimeZone.getDefault().clone();

1201	// tz.setRawOffset(timeZoneOffsetMillis);

openmrs-api - src/main/java/org/openmrs/hl7/impl/HL7ServiceImpl.java

11
New issues

402	@Transactional(readOnly = true)

403	public Integer resolveUserId(XCN xcn) throws HL7Exception {

404	// TODO: properly handle family and given names. For now I'm treating

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
405	// givenName+familyName as a username.

406	String idNumber = xcn.getIDNumber().getValue();

410	// unused

411	// String assigningAuthority = xcn.getAssigningAuthority()

412	// .getUniversalID().getValue();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
413

414	/*

415	* if ("null".equals(familyName)) familyName = null; if

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
416	* ("null".equals(givenName)) givenName = null; if

417	* ("null".equals(assigningAuthority)) assigningAuthority = null;

418	*/

419	if (idNumber != null && idNumber.length() > 0) {

420	// log.debug("searching for user by id " + idNumber);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
421	try {

422	Integer userId = Integer.valueOf(idNumber);

429	}

430	} else {

431	// log.debug("searching for user by name");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
432	try {

433	StringBuilder username = new StringBuilder();

441	username.append(givenName);

442	}

443	// log.debug("looking for username '" + username + "'");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
444	User user = Context.getUserService().getUserByUsername(username.toString());

445	return user.getUserId();

475	if (persons.size() == 1) {

476	return persons.get(0).getPersonId();

477	} else if (persons.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
478	log.error("Couldn't find a person named " + givenName + " " + familyName);

479	return null;

561	// TODO other potential identifying characteristics in PID we could use

562	// to identify the patient

563	// XPN[] patientName = pid.getPersonName();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
564	// String gender = pid.getAdministrativeSex().getValue();

565	// TS dateOfBirth = pid.getDateTimeOfBirth();

618	List<PatientIdentifier> matchingIds = Context.getPatientService().getPatientIdentifiers(hl7PersonId,

619	Collections.singletonList(pit), null, null, null);

620	if (matchingIds == null \|\| matchingIds.size() < 1) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
621	// no matches

622	log.warn("NO matches found for " + hl7PersonId);

711	OpenmrsConstants.GLOBAL_PROPERTY_IGNORE_MISSING_NONLOCAL_PATIENTS, "false"));

712	if (e.getCause() != null

713	&& e.getCause().getMessage().equals("Could not resolve patient")

	Move the "Could not resolve patient" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
714	&& !"local".equals(hl7InQueue.getHL7Source().getName())

715	&& "true".equals(Context.getAdministrationService().getGlobalProperty(

1023	// while we still we have any archives to be processed, process them

1024	while (Hl7InArchivesMigrateThread.isActive() && Hl7InArchivesMigrateThread.getTransferStatus() == Status.RUNNING

1025	&& hl7InArchives != null && hl7InArchives.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
1026

1027	Iterator<HL7InArchive> iterator = hl7InArchives.iterator();

openmrs-api - src/main/java/org/openmrs/layout/LayoutTemplate.java

7
New issues

45	protected List<String> requiredElements;

46

47	protected int maxTokens = 0; // The largest number of tokens on one given line

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
48

49	protected String startDate;

101	currToken.put("displaySize", this.getSizeMappings().get(realToken));

102	currToken.put("codeName", realToken);

103	//numTokens++;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
104	ret.add(currToken);

105	}

120	currToken.put("displaySize", this.getSizeMappings().get(realToken));

121	currToken.put("codeName", realToken);

122	//numTokens++;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
123	ret.add(currNonToken);

124	ret.add(currToken);

140	currToken.put("displaySize", this.getSizeMappings().get(realToken));

141	currToken.put("codeName", realToken);

142	//numTokens++;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
143	ret.add(currToken);

144	}

163	currToken.put("displaySize", this.getSizeMappings().get(realToken));

164	currToken.put("codeName", realToken);

165	//numTokens++;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
166

167	ret.add(currToken);

324	public int getMaxTokens() {

325	if (maxTokens == -1) {

326	getLines(); // initialize the maxTokens variable

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
327	}

328

369	public List<String> nonUniqueStringsGoLast(List<String> strListArg) {

370	List<String> dup = new ArrayList<String>();

371	List<String> strList = new ArrayList(strListArg); // copy the list so we don't get concurrentmodification exceptions

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
372	for (String s : strList) {

373	for (String sInner : strList) {

openmrs-api - src/main/java/org/openmrs/logic/LogicTransform.java

1
New issues

52

53	public String toString() {

54	StringBuffer result = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
55

56	if (transformOperator != null) {

openmrs-api - src/main/java/org/openmrs/logic/result/Result.java

7
New issues

31	* get to the full-featured objects instead of the simplified values in the date-value pairs.<br>

32	* <br>

33	* TODO: eliminate unnecessary methods (toDatetime(), getDatetime(), and getDate() should all do the

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
34	* same thing)<br>

35	* TODO: better support/handling of NULL_RESULT

112	*/

113	public Result(List<Result> list) {

114	if (!(list == null \|\| list.size() < 1)) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
115	this.addAll(list);

116	}

637	}

638	}

639	StringBuffer s = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
640	for (Result r : this) {

641	if (s.length() > 0) {

761	}

762

763	//TODO rewrite this method

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
764	//

765	// /**

766	// * @see java.lang.Object#hashCode()

767	// */

768	// public int hashCode() {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
769	// int hashCode = 49867; // some random number

770	// hashCode += this.hashCode();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
771	//

772	// return hashCode;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
773	// }

774

openmrs-api - src/main/java/org/openmrs/messagesource/MutableMessageSource.java

1
New issues

15	import org.springframework.context.HierarchicalMessageSource;

16	import org.springframework.context.MessageSource;

17	import org.springframework.transaction.annotation.Transactional;

	Remove this unused import 'org.springframework.transaction.annotation.Transactional'. NEW Useless imports should be removed
18

19	/**

openmrs-api - src/main/java/org/openmrs/messagesource/PresentationMessageMap.java

1
New issues

102	*/

103	public void putAll(Map<? extends String, ? extends PresentationMessage> t) {

104	//Map<String, PresentationMessage> compatibleMap = new HashMap<String, PresentationMessage>();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
105	for (Entry<? extends String, ? extends PresentationMessage> entry : t.entrySet()) {

106	put(entry.getKey(), entry.getValue());

openmrs-api - src/main/java/org/openmrs/messagesource/impl/CachedMessageSource.java

1
New issues

58

59	for (Locale locale : localizedMap.keySet()) {

60	PresentationMessageMap codeMessageMap = localizedMap.get(locale);

	org.openmrs.messagesource.impl.CachedMessageSource.getPresentations() makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
61	allMessages.addAll(codeMessageMap.values());

62	}

openmrs-api - src/main/java/org/openmrs/messagesource/impl/MutableResourceBundleMessageSource.java

2
New issues

94	}

95

96	if (foundLocales.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
97	log.warn("no locales found.");

98	}

144	}

145	}

146	catch (Exception e) {

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
147	// skip over errors in loading a single file

148	log.error("Unable to load properties from file: " + propertiesFile.getFilename());

openmrs-api - src/main/java/org/openmrs/migration/MigrationHelper.java

4
New issues

292	PatientService ps = Context.getPatientService();

293	List<PatientProgram> patientPrograms = new ArrayList<PatientProgram>();

294	//List<PatientState> patientStates = new ArrayList<PatientState>();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
295	Map<String, PatientProgram> knownPatientPrograms = new HashMap<String, PatientProgram>();

296	Map<String, Program> programsByName = new HashMap<String, Program>();

331	String[] temp = s.split(",");

332	/* We're using a cache of 'knownPatientPrograms' instead of the following commented code

333	PatientIdentifierType pit = ps.getPatientIdentifierType(temp[0]);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
334	String identifier = temp[1];

335	List<PatientIdentifier> pis = ps.getPatientIdentifiers(identifier, pit);

342	throw new RuntimeException("Couldn't find program \"" + temp[2] + "\" in " + programsByName);

343	}

344	//ProgramWorkflow wf = pws.getWorkflow(program, temp[3]);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
345	ProgramWorkflow wf = program.getWorkflowByName(temp[3]);

346	if (wf == null) {

348	+ program.getAllWorkflows() + ")");

349	}

350	//ProgramWorkflowState st = pws.getState(wf, temp[4]);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
351	ProgramWorkflowState st = wf.getStateByName(temp[4]);

352	if (st == null) {

openmrs-api - src/main/java/org/openmrs/module/AdvicePoint.java

1
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/module/Module.java

2
New issues

547	}

548	catch (ClassNotFoundException e) {

549	log.warn("Unable to load class for extension: " + point, e);

	Define a constant instead of duplicating this literal "Unable to load class for extension: " 3 times. NEW String literals should not be duplicated
550	}

551	catch (IllegalAccessException e) {

715	}

716

717	StringBuffer sb = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
718

719	// if exceptionMessage is not null, append it

openmrs-api - src/main/java/org/openmrs/module/ModuleClassLoader.java

8
New issues

76	* This is also used to fix: https://tickets.openmrs.org/browse/TRUNK-4053

77	*/

78	private Map<String, Class<?>> loadedClasses = new HashMap<String, Class<?>>();

	Remove this unused "loadedClasses" private field. NEW Unused private fields should be removed
79

80	/**

507

508	if (log.isDebugEnabled()) {

509	StringBuffer buf = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
510	buf.append("New code URL's populated for module " + getModule() + ":\r\n");

511	for (URL u : newUrls) {

742	String libname = System.mapLibraryName(name);

743	String result = null;

744	//TODO

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
745	//PathResolver pathResolver = ModuleFactory.getPathResolver();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
746	// for (Library lib : getModule().getLibraries()) {

747	// if (lib.isCodeLibrary()) {

756	// if (log.isDebugEnabled()) {

757	// log.debug("findLibrary(String): URL " + libUrl

758	// + " resolved as local file " + libFile);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
759	// }

760	// if (libFile.isFile()) {

766	// // we have some kind of non-local URL

767	// // try to copy it to local temporary file

768	// libFile = (File) libraryCache.get(libUrl);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
769	// if (libFile != null) {

770	// if (libFile.isFile()) {

776	// if (libraryCache.containsKey(libUrl)) {

777	// // already tried to cache this library

778	// break;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
779	// }

780	// libFile = cacheLibrary(libUrl, libname);

1004	}

1005	}

1006	// if (resourceLoader != null) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
1007	// for (Enumeration enm = resourceLoader.findResources(name);

1008	// enm.hasMoreElements();) {

openmrs-api - src/main/java/org/openmrs/module/ModuleFactory.java

10
New issues

195	Map<String, Module> loadedModulesMap = getLoadedModulesMapPackage();

196	for (String key : loadedModules.keySet()) {

197	Module m = loadedModules.get(key);

	org.openmrs.module.ModuleFactory.loadModules(List) makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
198	Map<String, String> startBeforeModules = m.getStartBeforeModulesMap();

199	if (startBeforeModules.size() > 0) {

217

218	// loop over and try starting each of the loaded modules

219	if (getLoadedModules().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
220

221	List<Module> modules = getModulesThatShouldStart();

282	// if a 'moduleid.started' property doesn't exist, start the module anyway

283	// as this is probably the first time they are loading it

284	if (startedProp == null \|\| startedProp.equals("true") \|\| "true".equalsIgnoreCase(mandatoryProp)

	Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
285	\|\| mod.isMandatory() \|\| isCoreToOpenmrs) {

286	modules.add(mod);

470	Map<String, Module> map = new WeakHashMap<String, Module>();

471	for (String key : loadedModules.keySet()) {

472	map.put(loadedModules.get(key).getPackageName(), loadedModules.get(key));

	org.openmrs.module.ModuleFactory.getLoadedModulesMapPackage() makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
473	}

474	return map;

658	// into spring yet. All advice for all modules must be reloaded

659	// a spring context refresh anyway, so skip the advice loading here

660	// loadAdvice(module);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
661

662	// map extension point to a list of extensions for this module only

756	// (Unfortunately, placing the call here will duplicate work

757	// done at initial app startup)

758	if (module.getPrivileges().size() > 0 \|\| module.getGlobalProperties().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
759	log.debug("Updating core dataset");

760	Context.checkCoreDataset();

896	catch (ClassNotFoundException e) {

897	log.warn("Could not load advice point: " + advice.getPoint(), e);

898	//throw new ModuleException("Could not load advice point: " + advice.getPoint(), e);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
899	}

900	}

1115	for (Module dependentModule : startedModulesCopy) {

1116	if (dependentModule != null && !dependentModule.equals(mod)) {

1117	if (dependentModule.getRequiredModules() != null && dependentModule.getRequiredModules().contains(modulePackage)) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
1118	dependentModulesStopped.add(dependentModule);

1119	dependentModulesStopped.addAll(stopModule(dependentModule, skipOverStartedProperty, isFailedStartup));

1169	try {

1170	List<Extension> tmpExtensions = getExtensions(extId);

1171	if (tmpExtensions == null) {

	Redundant nullcheck of tmpExtensions, which is known to be non-null in org.openmrs.module.ModuleFactory.stopModule(Module, boolean, boolean) NEW Dodgy - Redundant nullcheck of value known to be non-null
1172	tmpExtensions = new Vector<Extension>();

1173	}

openmrs-api - src/main/java/org/openmrs/module/ModuleUtil.java

4
New issues

131	if (log.isDebugEnabled()) {

132	Collection<Module> modules = ModuleFactory.getStartedModules();

133	if (modules == null \|\| modules.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
134	log.debug("No modules loaded");

135	} else {

920

921	// any module ids left in the list are not started

922	if (mandatoryModuleIds.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
923	throw new MandatoryModuleException(mandatoryModuleIds);

924	}

1106

1107	if (packagesProvided.add(packageName)) {

1108	if (log.isTraceEnabled()) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
1109	log.trace("Adding module's jarentry with package: " + packageName);

1110	}

openmrs-api - src/main/java/org/openmrs/module/UpdateFileParser.java

1
New issues

13 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/notification/AlertService.java

1
New issues

10	package org.openmrs.notification;

11

12	import java.util.Collection;

	Remove this unused import 'java.util.Collection'. NEW Useless imports should be removed
13	import java.util.List;

14

openmrs-api - src/main/java/org/openmrs/notification/Note.java

6
New issues

Class org.openmrs.notification.Note defines non-transient non-serializable instance field noteType

NEW

Non-transient non-serializable instance field in serializable class

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

48	private NoteType noteType;

49

50	//private Observation observation;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
51	//private Encounter encounter;

52	//private User createdBy;

71

72	public Date getDateChanged() {

73	return dateChanged;

	org.openmrs.notification.Note.getDateChanged() may expose internal representation by returning Note.dateChanged NEW Malicious code vulnerability - May expose internal representation by returning reference to mutable object
74	}

75

76	public void setDateChanged(Date dateChanged) {

77	this.dateChanged = dateChanged;

	org.openmrs.notification.Note.setDateChanged(Date) may expose internal representation by storing an externally mutable object into Note.dateChanged NEW Malicious code vulnerability - May expose internal representation by incorporating reference to mutable object
78	}

79

80	public Date getDateCreated() {

81	return dateCreated;

	org.openmrs.notification.Note.getDateCreated() may expose internal representation by returning Note.dateCreated NEW Malicious code vulnerability - May expose internal representation by returning reference to mutable object
82	}

83

84	public void setDateCreated(Date dateCreated) {

85	this.dateCreated = dateCreated;

	org.openmrs.notification.Note.setDateCreated(Date) may expose internal representation by storing an externally mutable object into Note.dateCreated NEW Malicious code vulnerability - May expose internal representation by incorporating reference to mutable object
86	}

87

openmrs-api - src/main/java/org/openmrs/notification/NoteService.java

5
New issues

31	*/

32	@Authorized(PrivilegeConstants.GET_NOTE)

33	public List<Note> getNotes(User user) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
34

35	/**

38	* @param note the Note being created

39	*/

40	public void createNote(Note note) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
41

42	/**

45	* @param noteId the internal primary key identifier for a Note

46	*/

47	public Note getNote(Integer noteId) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
48

49	/**

52	* @param note note being updated

53	*/

54	public void updateNote(Note note) throws Exception;

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
55

56	/**

63	*/

64	@Authorized(PrivilegeConstants.DELETE_NOTE)

65	public Note voidNote(Note note, String reason) throws APIException;

	Remove the declaration of thrown exception 'org.openmrs.api.APIException' which is a runtime exception. NEW Throws declarations should not be redundant
66	}

openmrs-api - src/main/java/org/openmrs/notification/db/hibernate/HibernateAlertDAO.java

1
New issues

101	// getting here means we passed in no user or a blank user.

102	// a null recipient column means get stuff for the anonymous user

103	//crit.add(Expression.isNull("recipient.recipient"));

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
104

105	// returning an empty list for now because the above throws an error.

openmrs-api - src/main/java/org/openmrs/notification/impl/MessageServiceImpl.java

2
New issues

164	User user = Context.getUserService().getUser(recipientId);

165	message.addRecipient(user.getUserProperty(OpenmrsConstants.USER_PROPERTY_NOTIFICATION_ADDRESS));

166	// message.setFormat( user( OpenmrsConstants.USER_PROPERTY_NOTIFICATION_FORMAT ) );

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
167	Context.getMessageService().sendMessage(message);

168	}

180	message.addRecipient(address);

181	}

182	// message.setFormat( user.getProperty( OpenmrsConstants.USER_PROPERTY_NOTIFICATION_FORMAT ) );

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
183	Context.getMessageService().sendMessage(message);

184	}

openmrs-api - src/main/java/org/openmrs/notification/impl/NoteServiceImpl.java

7
New issues

Class org.openmrs.notification.impl.NoteServiceImpl defines non-transient non-serializable instance field log

NEW

Non-transient non-serializable instance field in serializable class

Class org.openmrs.notification.impl.NoteServiceImpl defines non-transient non-serializable instance field dao

NEW

Non-transient non-serializable instance field in serializable class

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

42	* Logger

43	*/

44	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
45

46	/**

56	* @throws Exception

57	*/

58	public Collection<Note> getNotes() throws Exception {

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
59	log.info("Get all notes");

60	return getNoteDAO().getNotes();

102	*/

103	public List<Note> getNotes(User user) throws Exception {

104	// TODO Auto-generated method stub

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
105	return null;

	Return an empty collection instead of null. NEW Empty arrays and collections should be returned instead of null
106	}

107

113	* @throws APIException

114	*/

115	public Note voidNote(Note note, String reason) throws APIException {

	Remove the declaration of thrown exception 'org.openmrs.api.APIException' which is a runtime exception. NEW Throws declarations should not be redundant
116	log.debug("voiding note because " + reason);

117	return dao.voidNote(note, reason);

openmrs-api - src/main/java/org/openmrs/notification/mail/MailMessageSender.java

1
New issues

96	MimeMessage mimeMessage = new MimeMessage(session);

97

98	// TODO Need to test the null case.

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
99	// Transport should use default mail.from value defined in properties.

100	if (message.getSender() != null) {

openmrs-api - src/main/java/org/openmrs/obs/handler/AbstractHandler.java

2
New issues

77	title = title.replace("." + extension, "");

78	outputfile = new File(dir, title + "." + extension);

79	// outputfile = new File(dir, title);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
80	}

81

149	} else if (file.delete()) {

150	obs.setComplexData(null);

151	// obs.setValueComplex(null);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
152	return true;

153	}

openmrs-api - src/main/java/org/openmrs/person/PersonMergeLogData.java

1
New issues

290	}

291

292	//public void setPriorDateOfDeathEstimated(boolean priorDateOfDeathEstimated) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
293	public void setPriorDateOfDeathEstimated(Boolean priorDateOfDeathEstimated) {

294	this.priorDateOfDeathEstimated = priorDateOfDeathEstimated;

openmrs-api - src/main/java/org/openmrs/propertyeditor/CohortEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

28	public class CohortEditor extends PropertyEditorSupport {

29

30	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
31

32	public CohortEditor() {

37	* @should set using uuid

38	*/

39	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
40	if (StringUtils.hasText(text)) {

41	try {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptAnswerEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptAnswerEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptAnswerEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	ConceptService cs = Context.getConceptService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptAnswersEditor.java

1
New issues

63	for (String id : conceptIds) {

64	id = id.trim();

65	if (!id.equals("") && !requestConceptIds.contains(id)) { //remove whitespace, blank lines, and duplicates

	Move the "" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
66	requestConceptIds.add(id);

67	}

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptAttributeTypeEditor.java

2
New issues

6 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

33	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

34	*/

35	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
36	ConceptService conceptService = Context.getConceptService();

37	if (Context.isAuthenticated() && StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptClassEditor.java

4
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptClassEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptClassEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	log.debug("Setting text: " + text);

42	ConceptService cs = Context.getConceptService();

45	setValue(cs.getConceptClass(Integer.valueOf(text)));

46	}

47	catch (Exception ex) {

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
48	ConceptClass conceptClass = cs.getConceptClassByUuid(text);

49	setValue(conceptClass);

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptDatatypeEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptDatatypeEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptDatatypeEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	log.debug("setting text: " + text);

42	ConceptService cs = Context.getConceptService();

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	ConceptService cs = Context.getConceptService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptMapTypeEditor.java

1
New issues

4 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptNameEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptNameEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptNameEditor() {

40	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

41	*/

42	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
43	ConceptService cs = Context.getConceptService();

44	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptNumericEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptNumericEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptNumericEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	ConceptService cs = Context.getConceptService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptReferenceTermEditor.java

1
New issues

4 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptSetsEditor.java

1
New issues

59	for (String id : conceptIds) {

60	id = id.trim();

61	if (!id.equals("") && !requestConceptIds.contains(Integer.valueOf(id))) { //remove whitespace, blank lines, and duplicate entries

	Move the "" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
62	requestConceptIds.add(Integer.valueOf(id));

63	}

openmrs-api - src/main/java/org/openmrs/propertyeditor/ConceptSourceEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ConceptSourceEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ConceptSourceEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	log.debug("Setting text: " + text);

42	ConceptService cs = Context.getConceptService();

openmrs-api - src/main/java/org/openmrs/propertyeditor/DrugEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class DrugEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public DrugEditor() {

44	* @should fail if drug does not exist with non-empty identifier

45	*/

46	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
47	ConceptService es = Context.getConceptService();

48	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/EncounterEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class EncounterEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public EncounterEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	EncounterService es = Context.getEncounterService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/EncounterTypeEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class EncounterTypeEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public EncounterTypeEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	EncounterService ps = Context.getEncounterService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/FormEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class FormEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public FormEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	FormService ps = Context.getFormService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/LocationAttributeTypeEditor.java

2
New issues

6 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

38	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	LocationService ls = Context.getLocationService();

42	if (Context.isAuthenticated() && StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/LocationEditor.java

5
New issues

5 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class LocationEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public LocationEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	LocationService ls = Context.getLocationService();

42	if (StringUtils.hasText(text)) {

60	Location t = (Location) getValue();

61	if (t == null && Context.isAuthenticated()) {

62	return null; //return Context.getAuthenticatedUser().getUserProperty(OpenmrsConstants.USER_PROPERTY_DEFAULT_LOCATION);

	Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
63	} else {

64	if (t != null) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/LocationTagEditor.java

3
New issues

3 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

27	public class LocationTagEditor extends PropertyEditorSupport {

28

29	private static Log log = LogFactory.getLog(LocationTagEditor.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
30

31	public LocationTagEditor() {

38	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	LocationService ls = Context.getLocationService();

42	if (Context.isAuthenticated() && StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/OrderEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class OrderEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	/**

37	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

38	*/

39	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
40	OrderService ps = Context.getOrderService();

41	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/PatientEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class PatientEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	/**

37	* @see java.beans.PropertyEditorSupport#setAsText(java.lang.String)

38	*/

39	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
40	PatientService ps = Context.getPatientService();

41	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/PatientIdentifierTypeEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class PatientIdentifierTypeEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public PatientIdentifierTypeEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	PatientService ps = Context.getPatientService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/PersonAttributeEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class PersonAttributeEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	/**

35	* @should set using uuid

36	*/

37	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
38	PersonService ps = Context.getPersonService();

39	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/PersonAttributeTypeEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class PersonAttributeTypeEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	/**

35	* @should set using uuid

36	*/

37	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
38	PersonService ps = Context.getPersonService();

39	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/PersonEditor.java

1
New issues

4 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/propertyeditor/ProgramWorkflowEditor.java

3
New issues

3 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ProgramWorkflowEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ProgramWorkflowEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	ProgramWorkflowService pws = Context.getProgramWorkflowService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ProgramWorkflowStateEditor.java

3
New issues

3 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class ProgramWorkflowStateEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public ProgramWorkflowStateEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	ProgramWorkflowService pws = Context.getProgramWorkflowService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/ProviderEditor.java

1
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

openmrs-api - src/main/java/org/openmrs/propertyeditor/UserEditor.java

3
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

29	public class UserEditor extends PropertyEditorSupport {

30

31	private Log log = LogFactory.getLog(this.getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
32

33	public UserEditor() {

38	* @should set using uuid

39	*/

40	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
41	UserService ps = Context.getUserService();

42	if (StringUtils.hasText(text)) {

openmrs-api - src/main/java/org/openmrs/propertyeditor/VisitEditor.java

5
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

27	public class VisitEditor extends PropertyEditorSupport {

28

29	private static final Log log = LogFactory.getLog(VisitEditor.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Remove this unused "log" private field. NEW Unused private fields should be removed
30

31	public VisitEditor() {

36	* @should set using uuid

37	*/

38	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
39	VisitService vs = Context.getVisitService();

40	if (StringUtils.hasText(text)) {

42	setValue(vs.getVisit(Integer.valueOf(text)));

43	}

44	catch (Exception ex) {

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
45	Visit v = vs.getVisitByUuid(text);

46	setValue(v);

openmrs-api - src/main/java/org/openmrs/propertyeditor/VisitTypeEditor.java

5
New issues

2 more branches need to be covered by unit tests to reach the minimum threshold of 65.0% branch coverage.

NEW

Branches should have sufficient coverage by unit tests

1	/**

2	* This Source Code Form is subject to the terms of the Mozilla Public License,

27	public class VisitTypeEditor extends PropertyEditorSupport {

28

29	private static final Log log = LogFactory.getLog(VisitTypeEditor.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Remove this unused "log" private field. NEW Unused private fields should be removed
30

31	public VisitTypeEditor() {

36	* @should set using uuid

37	*/

38	public void setAsText(String text) throws IllegalArgumentException {

	Remove the declaration of thrown exception 'java.lang.IllegalArgumentException' which is a runtime exception. NEW Throws declarations should not be redundant
39	VisitService vs = Context.getVisitService();

40	if (StringUtils.hasText(text)) {

42	setValue(vs.getVisitType(Integer.valueOf(text)));

43	}

44	catch (Exception ex) {

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
45	VisitType v = vs.getVisitTypeByUuid(text);

46	setValue(v);

openmrs-api - src/main/java/org/openmrs/propertyeditor/WorkflowCollectionEditor.java

1
New issues

114	public String getAsText() {

115	Collection<ProgramWorkflow> pws = (Collection<ProgramWorkflow>) getValue();

116	if (pws == null \|\| pws.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
117	return ":";

118	} else {

openmrs-api - src/main/java/org/openmrs/scheduler/Schedule.java

4
New issues

77	public static final int DAYS_PER_WEEK = 7;

78

79	//public static DEFAULT_DATE_FORMAT = new SimpleDateFormat("MM-dd-yyyy hh:mm:ss");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
80	public static final int DAILY = MILLISECONDS_PER_SECOND * SECONDS_PER_MINUTE * MINUTES_PER_HOUR;

81

82	public static final int WEEKLY = DAILY * DAYS_PER_WEEK;

83

84	//public static final int MONTHLY;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
85	//public static final int ANNUALLY;

86

201	* @param startTime start time for the task

202	*/

203	/* public void setStartTime(String startTime) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
204	try {

205	this.startTime = this.dateFormatter.parse(startTime);

207	catch (Exception e) {

208	//If there's an error, we'll just set the start time to now.

209	// TODO: This might not be the desired behavior, so I'll have to come back to it.

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
210	this.startTime = new Date();

211	}

openmrs-api - src/main/java/org/openmrs/scheduler/SchedulerUtil.java

2
New issues

10	package org.openmrs.scheduler;

11

12	import java.io.PrintWriter;

	Remove this unused import 'java.io.PrintWriter'. NEW Useless imports should be removed
13	import java.io.StringWriter;

	Remove this unused import 'java.io.StringWriter'. NEW Useless imports should be removed
14	import java.util.Calendar;

15	import java.util.Date;

openmrs-api - src/main/java/org/openmrs/scheduler/TaskDefinition.java

1
New issues

17	import org.apache.commons.logging.LogFactory;

18	import org.openmrs.BaseOpenmrsMetadata;

19	import org.openmrs.User;

	Remove this unused import 'org.openmrs.User'. NEW Useless imports should be removed
20

21	/**

openmrs-api - src/main/java/org/openmrs/scheduler/db/SchedulerDAO.java

4
New issues

78	* @throws DAOException

79	*/

80	//public void createSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
81	/**

82	* Get schedule by internal identifier

103	* @throws DAOException

104	*/

105	//public void updateSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
106	/**

107	* Get all schedules.

110	* @throws DAOException

111	*/

112	//public Set<Schedule> getSchedules() throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
113	/**

114	* Delete schedule from database.

117	* @throws DAOException

118	*/

119	//public void deleteSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
120	}

openmrs-api - src/main/java/org/openmrs/scheduler/db/hibernate/HibernateSchedulerDAO.java

4
New issues

148	* @throws DAOException

149	*/

150	//public void createSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
151	/**

152	* Get schedule by internal identifier

172	* @throws DAOException

173	*/

174	//public void updateSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
175	/**

176	* Get all schedules.

179	* @throws DAOException

180	*/

181	//public Set<Schedule> getAllSchedules() throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
182	/**

183	* Delete schedule from database.

186	* @throws DAOException

187	*/

188	//public void deleteSchedule(Schedule schedule) throws DAOException;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
189	}

openmrs-api - src/main/java/org/openmrs/scheduler/timer/TimerSchedulerServiceImpl.java

1
New issues

207	TimerSchedulerTask schedulerTask = scheduledTasks.get(taskDefinition.getId());

208	if (schedulerTask != null) {

209	//schedulerTask.cancel();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
210	log.info("Shutting down the existing instance of this task to avoid conflicts!!");

211	schedulerTask.shutdown();

openmrs-api - src/main/java/org/openmrs/util/AttributableDate.java

1
New issues

100

101	// returning null causes the field to be blanked out

102	//return null;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
103	}

104	}

openmrs-api - src/main/java/org/openmrs/util/DatabaseUpdater.java

6
New issues

245	* @should always have a valid update to latest file

246	*/

247	public static boolean updatesRequired() throws Exception {

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
248	log.debug("checking for updates");

249	List<OpenMRSChangeSet> changesets = getUnrunDatabaseChanges();

253	// returning true here stops the openmrs startup and shows

254	// the user the maintenance wizard for updates

255	if (isLocked() && changesets.size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
256	// if there is a db lock but there are no db changes we undo the

257	// lock

261	}

262

263	return changesets.size() > 0;

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
264	}

265

275

276	List<OpenMRSChangeSet> changesets = getUnrunDatabaseChanges(changeLogFilenames);

277	return changesets.size() > 0;

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
278	}

279

580	*/

581	@Authorized(PrivilegeConstants.GET_DATABASE_CHANGES)

582	public static List<OpenMRSChangeSet> getUnrunDatabaseChanges() throws Exception {

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
583	return getUnrunDatabaseChanges(CHANGE_LOG_FILE);

584	}

594	*/

595	@Authorized(PrivilegeConstants.GET_DATABASE_CHANGES)

596	public static List<OpenMRSChangeSet> getUnrunDatabaseChanges(String... changeLogFilenames) throws Exception {

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
597	log.debug("Getting unrun changesets");

598

openmrs-api - src/main/java/org/openmrs/util/DoubleRange.java

1
New issues

146	*/

147	public String toString() {

148	StringBuffer ret = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
149	if (low != null && low.doubleValue() != Double.NEGATIVE_INFINITY) {

150	ret.append(">");

openmrs-api - src/main/java/org/openmrs/util/FormUtil.java

1
New issues

222	public static String conceptToString(Concept concept, ConceptName localizedName) {

223	return concept.getConceptId() + "^" + localizedName.getName() + "^" + HL7Constants.HL7_LOCAL_CONCEPT; // + "^"

224	// + localizedName.getConceptNameId() + "^" + localizedName.getName() + "^" + FormConstants.HL7_LOCAL_CONCEPT_NAME;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
225	}

226

openmrs-api - src/main/java/org/openmrs/util/Format.java

2
New issues

10	package org.openmrs.util;

11

12	import java.io.PrintWriter;

	Remove this unused import 'java.io.PrintWriter'. NEW Useless imports should be removed
13	import java.io.StringWriter;

	Remove this unused import 'java.io.StringWriter'. NEW Useless imports should be removed
14	import java.text.DateFormat;

15	import java.text.NumberFormat;

openmrs-api - src/main/java/org/openmrs/util/HttpClient.java

1
New issues

79	String line;

80	while ((line = rd.readLine()) != null) {

81	response = String.format("%s%s\n", response, line);

	Format string should use %n rather than \n in org.openmrs.util.HttpClient.post(Map) NEW Format string should use %n rather than \n
82	}

83

openmrs-api - src/main/java/org/openmrs/util/MemoryLeakUtil.java

1
New issues

16	import org.apache.commons.logging.LogFactory;

17

18	import sun.net.www.http.KeepAliveCache;

	Replace this usage of Sun classes by ones from the Java API. NEW Classes from "sun.*" packages should not be used
19

20	/**

openmrs-api - src/main/java/org/openmrs/util/OpenmrsClassLoader.java

4
New issues

11

12	import java.io.File;

13	import java.io.FilenameFilter;

	Remove this unused import 'java.io.FilenameFilter'. NEW Useless imports should be removed
14	import java.io.IOException;

15	import java.io.InputStream;

361	log.info("this classloader hashcode: " + OpenmrsClassLoaderHolder.INSTANCE.hashCode());

362

363	// List<Thread> threads = listThreads(rootGroup, "");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
364	// for (Thread thread : threads) {

365	// if (thread.getContextClassLoader() != null) {

366	// log.debug("context classloader on thread: " + thread.getName() + " is: "

367	// + thread.getContextClassLoader().getClass().getName() + ":"

368	// + thread.getContextClassLoader().hashCode());

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
369	// if (thread.getContextClassLoader() == OpenmrsClassLoaderHolder.INSTANCE) {

370	// thread.setContextClassLoader(OpenmrsClassLoaderHolder.INSTANCE.getParent());

371	// log.error("Cleared context classloader to save the world from memory leaks. thread: " + thread.getName()

372	// + " ");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
373	// }

374	// }

openmrs-api - src/main/java/org/openmrs/util/OpenmrsUtil.java

11
New issues

120	public class OpenmrsUtil {

121

122	private static Log log = LogFactory.getLog(OpenmrsUtil.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
123

124	private static Map<Locale, SimpleDateFormat> dateFormatCache = new HashMap<Locale, SimpleDateFormat>();

219	*/

220	public static String getFileAsString(File file) throws IOException {

221	StringBuffer fileData = new StringBuffer(1000);

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
222	BufferedReader reader = new BufferedReader(new FileReader(file));

223	char[] buf = new char[1024];

272	* @throws IOException thrown if an error occurs during read/write

273	*/

274	public static void copyFile(InputStream inputStream, OutputStream outputStream) throws IOException {

	The Cyclomatic Complexity of this method "copyFile" is 11 which is greater than 10 authorized. NEW Methods should not be too complex
275	if (inputStream == null \|\| outputStream == null) {

276	if (outputStream != null) {

278	outputStream.close();

279	}

280	catch (Exception e) { /* pass */

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
281	}

282	}

308	outputStream.close();

309	}

310	catch (Exception e) { /* pass */

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
311	}

312	}

1053	if (filepath == null) {

1054	if (OpenmrsConstants.UNIX_BASED_OPERATING_SYSTEM) {

1055	filepath = System.getProperty("user.home") + File.separator + ".OpenMRS";

	Define a constant instead of duplicating this literal "user.home" 3 times. NEW String literals should not be duplicated
1056	if (!canWrite(new File(filepath))) {

1057	log.warn("Unable to write to users home dir, fallback to: "

	Define a constant instead of duplicating this literal "Unable to write to users home dir, fallback to: " 3 times. NEW String literals should not be duplicated
1058	+ OpenmrsConstants.APPLICATION_DATA_DIRECTORY_FALLBACK_UNIX);

1059	filepath = OpenmrsConstants.APPLICATION_DATA_DIRECTORY_FALLBACK_UNIX + File.separator + "OpenMRS";

	Define a constant instead of duplicating this literal "OpenMRS" 4 times. NEW String literals should not be duplicated
1060	}

1061	} else {

1062	if (OpenmrsConstants.UNIX_BASED_OPERATING_SYSTEM) {

1063	filepath = System.getProperty("user.home") + File.separator + ".OpenMRS";

1064	if (!canWrite(new File(filepath))) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
1065	log.warn("Unable to write to users home dir, fallback to: "

1066	+ OpenmrsConstants.APPLICATION_DATA_DIRECTORY_FALLBACK_UNIX);

1070	filepath = System.getProperty("user.home") + File.separator + "Application Data" + File.separator

1071	+ "OpenMRS";

1072	if (!canWrite(new File(filepath))) {

	Refactor this code to not nest more than 3 if/for/while/switch/try statements. NEW Control flow statements "if", "for", "while", "switch" and "try" should not be nested too deeply
1073	log.warn("Unable to write to users home dir, fallback to: "

1074	+ OpenmrsConstants.APPLICATION_DATA_DIRECTORY_FALLBACK_WIN);

1614	public static String generateUid(Integer size) {

1615	Random gen = new Random();

1616	StringBuffer sb = new StringBuffer(size);

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
1617	for (int i = 0; i < size; i++) {

1618	int ch = gen.nextInt() * 62;

openmrs-api - src/main/java/org/openmrs/util/Reflect.java

1
New issues

20	import java.util.List;

21

22	import org.azeckoski.reflectutils.ClassData;

	Remove this unused import 'org.azeckoski.reflectutils.ClassData'. NEW Useless imports should be removed
23	import org.azeckoski.reflectutils.ClassDataCacher;

24	import org.azeckoski.reflectutils.ClassFields;

openmrs-api - src/main/java/org/openmrs/util/Security.java

6
New issues

88	catch (NoSuchAlgorithmException e) {

89	// Yikes! Can't encode password...what to do?

90	log.error("Can't encode password because the given algorithm: " + algorithm + "was not found! (fail)", e);

	Define a constant instead of duplicating this literal "Can't encode password because the given algorithm: " 3 times. NEW String literals should not be duplicated Define a constant instead of duplicating this literal "was not found! (fail)" 3 times. NEW String literals should not be duplicated
91	throw new APIException("system.cannot.find.password.encryption.algorithm", null, e);

92	}

129	*/

130	private static String hexString(byte[] block) {

131	StringBuffer buf = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
132	char[] hexChars = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f' };

133	int len = block.length;

184	return "";

185	}

186	StringBuffer s = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
187	for (int i = 0; i < b.length; i++) {

188	s.append(Integer.toHexString(b[i] & 0xFF));

319	new SecureRandom().nextBytes(initVector);

320

321	// TODO get the following (better) method working

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
322	// Cipher cipher = Cipher.getInstance(CIPHER_CONFIGURATION);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
323	// AlgorithmParameters params = cipher.getParameters();

324	// byte[] initVector = params.getParameterSpec(IvParameterSpec.class).getIV();

openmrs-api - src/main/java/org/openmrs/util/UpgradeUtil.java

1
New issues

40	String conceptId = null;

41	try {

42	FileInputStream fis = new FileInputStream(appDataDir + System.getProperty("file.separator")

	org.openmrs.util.UpgradeUtil.getConceptIdForUnits(String) may fail to close stream NEW Bad practice - Method may fail to close stream
43	+ DatabaseUtil.ORDER_ENTRY_UPGRADE_SETTINGS_FILENAME);

44	props.load(fis);

openmrs-api - src/main/java/org/openmrs/util/databasechange/CheckDrugOrderUnitAndFrequencyTextNotMappedToConcepts.java

2
New issues

38	connection.getUnderlyingConnection());

39	Set<String> unmappedDoseUnits = getUnMappedText(doseUnits, connection);

40	if (unmappedDoseUnits.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
41	throw new CustomPreconditionFailedException(

42	"Upgrade failed because of the following unmapped drug order dose units that were found: ["

50	connection.getUnderlyingConnection());

51	Set<String> unmappedFrequencies = getUnMappedText(frequencies, connection);

52	if (unmappedFrequencies.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
53	throw new CustomPreconditionFailedException(

54	"Upgrade failed because of the following unmapped drug order frequencies that were found: ["

openmrs-api - src/main/java/org/openmrs/util/databasechange/ConceptValidatorChangeSet.java

2
New issues

140

141	//for each name in the locale

142	for (ConceptName nameInLocale : localeConceptNamesMap.get(conceptNameLocale)) {

	org.openmrs.util.databasechange.ConceptValidatorChangeSet.validateAndCleanUpConcepts(JdbcConnection) makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
143	if (StringUtils.isBlank(nameInLocale.getName())) {

144	updateWarnings.add("ConceptName with id " + nameInLocale.getConceptNameId() + " ("

256	+ conceptId + "' in locale '" + conceptNameLocale.getDisplayName() + "'");

257

258	/*ConceptName chosenName = null;

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
259	List<ConceptName> voidedNames = new ArrayList<ConceptName>();

260	for (ConceptName duplicate : entry.getValue()) {

openmrs-api - src/main/java/org/openmrs/util/databasechange/DuplicateEncounterRoleNameChangeSet.java

1
New issues

182	connection.setAutoCommit(initialAutoCommit);

183	}

184	// connection.close();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
185	}

186	catch (DatabaseException e) {

openmrs-api - src/main/java/org/openmrs/util/databasechange/GenerateUuid.java

1
New issues

107	connection.setAutoCommit(false);

108

109	if (database.getTypeName().equals("mysql")) {

	Move the "mysql" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
110	String updateSql = "update %s set " + columnName + " = uuid() where " + columnName + " is null";

111	for (String tablename : tableNamesArray) {

openmrs-api - src/main/java/org/openmrs/util/databasechange/MigrateConceptReferenceTermChangeSet.java

1
New issues

231	comment = comment.substring(9).trim();

232

233	if (comment.equals("SAME-AS FROM RXNORM")) {

	Move the "SAME-AS FROM RXNORM" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
234	comment = "SAME-AS";

235	}

openmrs-api - src/main/java/org/openmrs/util/databasechange/ProgramValidatorChangeSet.java

1
New issues

86	for (List<Object> row : results) {

87	Integer conceptId = Integer.valueOf(row.get(0).toString());

88	boolean isInitial = row.get(1).toString().equals("1");

	Move the "1" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
89	int num = Integer.parseInt(row.get(2).toString());

90	if (isInitial && num > 0) {

openmrs-api - src/main/java/org/openmrs/util/databasechange/SourceMySqldiffFile.java

2
New issues

128

129	// run the command line string

130	StringBuffer output = new StringBuffer();

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
131	Integer exitValue = -1; // default to a non-zero exit value in case of exceptions

132	try {

191	* @return process exit value

192	*/

193	private Integer execCmd(File wd, String[] cmdWithArguments, StringBuffer out) throws Exception {

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
194	log.debug("executing command: " + Arrays.toString(cmdWithArguments));

195

openmrs-api - src/main/java/org/openmrs/validator/ConceptMapTypeValidator.java

2
New issues

29

30	// Log for this class

31	private static final Log log = LogFactory.getLog(ConceptMapTypeValidator.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention Remove this unused "log" private field. NEW Unused private fields should be removed
32

33	/**

openmrs-api - src/main/java/org/openmrs/validator/ConceptValidator.java

2
New issues

97	Concept conceptToValidate = (Concept) obj;

98	//no name to validate, but why is this the case?

99	if (conceptToValidate.getNames().size() == 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
100	errors.reject("Concept.name.atLeastOneRequired");

101	return;

223

224	}

225	/*if (map.getConceptMapType() == null) {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
226	errors.rejectValue("conceptMappings[" + index + "].conceptMapType", "Concept.map.typeRequired",

227	"The concept map type is required for a concept map");

openmrs-api - src/main/java/org/openmrs/validator/OrderValidator.java

1
New issues

133	private void validateSamePatientInOrderAndEncounter(Order order, Errors errors) {

134	if (order.getEncounter() != null && order.getPatient() != null) {

135	if (!order.getEncounter().getPatient().equals(order.getPatient())) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
136	errors.rejectValue("encounter", "Order.error.encounterPatientMismatch");

137	}

openmrs-api - src/main/java/org/openmrs/validator/PatientValidator.java

1
New issues

97	if (!errors.hasErrors()) {

98	// Validate PatientIdentifers

99	if (patient.getIdentifiers() != null) {

	Merge this if statement with the enclosing one. NEW Collapsible "if" statements should be merged
100	for (PatientIdentifier identifier : patient.getIdentifiers()) {

101	errors.pushNestedPath("identifiers[" + index + "]");

openmrs-api - src/main/java/org/openmrs/validator/PersonNameValidator.java

1
New issues

131	if (StringUtils.isBlank(personName.getFamilyName())

132	\|\| StringUtils.isBlank(personName.getFamilyName().replaceAll("\"", ""))) {

133	errors.rejectValue(getFieldKey("familyName", arrayInd, testInd), "Patient.names.required.given.family");

	Define a constant instead of duplicating this literal "familyName" 3 times. NEW String literals should not be duplicated
134	}

135	// Make sure the entered name value is sensible

openmrs-api - src/main/java/org/openmrs/validator/PersonValidator.java

1
New issues

56	*/

57	@Override

58	public void validate(Object target, Errors errors) {

	The Cyclomatic Complexity of this method "validate" is 11 which is greater than 10 authorized. NEW Methods should not be too complex
59	if (log.isDebugEnabled()) {

60	log.debug(this.getClass().getName() + ".validate...");

openmrs-api - src/main/java/org/openmrs/validator/UserValidator.java

1
New issues

26	import org.springframework.beans.factory.annotation.Autowired;

27	import org.springframework.validation.Errors;

28	import org.springframework.validation.ValidationUtils;

	Remove this unused import 'org.springframework.validation.ValidationUtils'. NEW Useless imports should be removed
29	import org.springframework.validation.Validator;

30

openmrs-web - src/main/java/org/openmrs/module/web/WebModuleUtil.java

13
New issues

154	String filepath = name.substring(11);

155

156	StringBuffer absPath = new StringBuffer(realPath + "/WEB-INF");

	Replace the synchronized class "StringBuffer" by an unsynchronized one such as "StringBuilder". NEW Synchronized classes Vector, Hashtable, Stack and StringBuffer should not be used
157

158	// If this is within the tag file directory, copy it into /WEB-INF/tags/module/moduleId/...

186	}

187

188	//if (outFile.getName().endsWith(".jsp") == false)

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
189	// outFile = new File(absPath.replace("/", File.separator) + MODULE_NON_JSP_EXTENSION);

190

194	OpenmrsUtil.copyFile(inStream, outStream);

195	}

196	} else if (name.equals("moduleApplicationContext.xml") \|\| name.equals("webModuleApplicationContext.xml")) {

	Move the "moduleApplicationContext.xml" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Move the "webModuleApplicationContext.xml" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
197	moduleNeedsContextRefresh = true;

198	} else if (name.equals(mod.getModuleId() + "Context.xml")) {

294

295	// additional checks on module needing a context refresh

296	if (moduleNeedsContextRefresh == false && mod.getAdvicePoints() != null && mod.getAdvicePoints().size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness Remove the literal "false" boolean value. NEW Literal boolean values should not be used in condition expressions
297

298	// AOP advice points are only loaded during the context refresh now.

305	// refresh the spring web context to get the just-created xml

306	// files into it (if we copied an xml file)

307	if (moduleNeedsContextRefresh && delayContextRefresh == false) {

	Remove the literal "false" boolean value. NEW Literal boolean values should not be used in condition expressions
308	if (log.isDebugEnabled()) {

309	log.debug("Refreshing context for module" + mod);

355

356	// return true if the module needs a context refresh and we didn't do it here

357	return (moduleNeedsContextRefresh && delayContextRefresh == true);

	Remove the literal "true" boolean value. NEW Literal boolean values should not be used in condition expressions
358

359	}

482	HttpServlet otherServletUsingSameName = moduleServlets.get(name);

483	if (otherServletUsingSameName != null) {

484	//log.debug("A servlet mapping with name " + name + " already exists. " + mod.getModuleId() + "'s servlet is overwriting it");

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
485	String otherServletName = otherServletUsingSameName.getClass().getPackage() + "."

486	+ otherServletUsingSameName.getClass().getName();

595	for (Iterator<String> i = moduleFiltersByName.keySet().iterator(); i.hasNext();) {

596	String filterName = i.next();

597	Filter filterVal = moduleFiltersByName.get(filterName);

	org.openmrs.module.web.WebModuleUtil.unloadFilters(Module) makes inefficient use of keySet iterator instead of entrySet iterator NEW Performance - Inefficient use of keySet iterator instead of entrySet iterator
598	if (filters.contains(filterVal)) {

599	i.remove();

826	}

827

828	if (skipRefresh == false) {

	Remove the literal "false" boolean value. NEW Literal boolean values should not be used in condition expressions
829	//try {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
830	// if (dispatcherServlet != null)

831	// dispatcherServlet.reInitFrameworkServlet();

966

967	// Output to console for testing

968	// StreamResult result = new StreamResult(System.out);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
969

970	transformer.transform(source, result);

openmrs-web - src/main/java/org/openmrs/module/web/filter/ModuleFilterMapping.java

2
New issues

191

192	// Match exact or full wildcard

193	if (patternToCheck.equals("") \|\| patternToCheck.equals("/") \|\| patternToCheck.equals(requestPath)) {

	Move the "" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Move the "/" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
194	return true;

195	}

openmrs-web - src/main/java/org/openmrs/web/DispatcherServlet.java

2
New issues

46	// refresh the application context to look for module xml config files as well

47

48	//XmlWebApplicationContext wac = ((XmlWebApplicationContext)getWebApplicationContext());

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
49	Thread.currentThread().setContextClassLoader(OpenmrsClassLoader.getInstance());

50	//wac.refresh();

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
51

52	log.debug("Framework being initialized");

openmrs-web - src/main/java/org/openmrs/web/Listener.java

13
New issues

72	* modules 2) Copy the custom look/images/messages over into the web layer

73	*/

74	public final class Listener extends ContextLoader implements ServletContextListener { // extends ContextLoaderListener {

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out" Move this trailing comment on the previous empty line. NEW Comments should not be located at the end of lines of code
75

76	protected final Log log = LogFactory.getLog(getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
77

78	private static boolean runtimePropertiesFound = false;

137	@Override

138	public void contextInitialized(ServletContextEvent event) {

139	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
140

141	log.debug("Starting the OpenMRS webapp");

183	copyCustomizationIntoWebapp(servletContext, props);

184

185	//super.contextInitialized(event);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
186	// also see commented out line in contextDestroyed

187

232

233	//Ensure that we are being called from WebDaemon

234	//TODO this did not work because callerClass was org.openmrs.web.WebDaemon$1 instead of org.openmrs.web.WebDaemon

	Complete the task associated to this TODO comment. NEW "TODO" tags should be handled
235	/*Class<?> callerClass = new OpenmrsSecurityManager().getCallerClass(0);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
236	if (!WebDaemon.class.isAssignableFrom(callerClass))

237	throw new APIException("This method can only be called from the WebDaemon class, not " + callerClass.getName());*/

353	*/

354	private void clearDWRFile(ServletContext servletContext) {

355	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
356

357	String realPath = servletContext.getRealPath("");

408	*/

409	private void copyCustomizationIntoWebapp(ServletContext servletContext, Properties props) {

410	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
411

412	String realPath = servletContext.getRealPath("");

472	*/

473	private boolean copyFile(String fromPath, String toPath) {

474	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
475

476	FileInputStream inputStream = null;

514	*/

515	public static void loadBundledModules(ServletContext servletContext) {

516	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
517

518	String path = servletContext.getRealPath("");

582

583	// commented out because we are not init'ing it in the contextInitialization anymore

584	// super.contextDestroyed(event);

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
585

586	try {

640	public static void performWebStartOfModules(Collection<Module> startedModules, ServletContext servletContext)

641	throws ModuleMustStartException, Exception {

642	Log log = LogFactory.getLog(Listener.class);

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
643

644	boolean someModuleNeedsARefresh = false;

openmrs-web - src/main/java/org/openmrs/web/OpenmrsBindingInitializer.java

1
New issues

135

136	// can't really do this because PropertyEditors are not told what type of class they are changing :-(

137	//wdb.registerCustomEditor(OpenmrsObject.class, new OpenmrsObjectByUuidEditor());

	This block of commented-out lines of code should be removed. NEW Sections of code should not be "commented out"
138	}

139

openmrs-web - src/main/java/org/openmrs/web/filter/GZIPFilter.java

2
New issues

131	OpenmrsConstants.GLOBAL_PROPERTY_GZIP_ENABLED, "");

132

133	boolean isEnabled = gzipEnabled.toLowerCase().equals("true");

	Move the "true" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality Replace these toUpperCase()/toLowerCase() and equals() calls with a single equalsIgnoreCase() call. NEW Case insensitive string comparisons should be made without intermediate upper or lower casing
134	cachedGZipEnabledFlag = isEnabled;

135	return cachedGZipEnabledFlag;

openmrs-web - src/main/java/org/openmrs/web/filter/StartupFilter.java

2
New issues

150	} else {

151

152	if (httpRequest.getMethod().equals("GET")) {

	Move the "GET" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
153	doGet(httpRequest, httpResponse);

154	} else if (httpRequest.getMethod().equals("POST")) {

	Move the "POST" string literal on the left side of this string comparison. NEW Strings literals should be placed on the left side when checking for equality
155	// only clear errors before POSTS so that redirects can show errors too.

156	errors.clear();

openmrs-web - src/main/java/org/openmrs/web/filter/initialization/InitializationFilter.java

4
New issues

84	public class InitializationFilter extends StartupFilter {

85

86	private static final Log log = LogFactory.getLog(InitializationFilter.class);

	Rename the "log" logger to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
87

88	private static final String LIQUIBASE_SCHEMA_DATA = "liquibase-schema-only.xml";

1570	+ RELEASE_TESTING_MODULE_PATH + "generateTestDataSet.form",

1571	wizardModel.remoteUsername, wizardModel.remotePassword);

1572	if (inData == null) {

	Redundant nullcheck of inData, which is known to be non-null in org.openmrs.web.filter.initialization.InitializationFilter$InitializationCompletion$1.run() NEW Dodgy - Redundant nullcheck of value known to be non-null
1573	reportError(ErrorMessageConstants.ERROR_DB_IMPORT_TEST_DATA, DEFAULT_PAGE, "");

1574	return;

1590	+ RELEASE_TESTING_MODULE_PATH + "getModules.htm", wizardModel.remoteUsername,

1591	wizardModel.remotePassword);

1592	if (inModules == null) {

	Redundant nullcheck of inModules, which is known to be non-null in org.openmrs.web.filter.initialization.InitializationFilter$InitializationCompletion$1.run() NEW Dodgy - Redundant nullcheck of value known to be non-null
1593	reportError(ErrorMessageConstants.ERROR_DB_UNABLE_TO_FETCH_MODULES, DEFAULT_PAGE, "");

1594	return;

1772	Context.logout();

1773	}

1774	catch (ContextAuthenticationException ex) {

	Either log or rethrow this exception. NEW Exception handlers should preserve the original exception
1775	log.info("No need to change admin password.");

1776	}

openmrs-web - src/main/java/org/openmrs/web/filter/startuperror/StartupErrorFilterModel.java

2
New issues

10	package org.openmrs.web.filter.startuperror;

11

12	import java.io.PrintWriter;

	Remove this unused import 'java.io.PrintWriter'. NEW Useless imports should be removed
13	import java.io.StringWriter;

	Remove this unused import 'java.io.StringWriter'. NEW Useless imports should be removed
14

15	import org.apache.commons.lang.exception.ExceptionUtils;

openmrs-web - src/main/java/org/openmrs/web/filter/update/UpdateFilter.java

16
New issues

66	public class UpdateFilter extends StartupFilter {

67

68	protected final Log log = LogFactory.getLog(getClass());

	Make the "log" logger private static final and rename it to comply with the format "LOG(?:GER)?". NEW Loggers should be "private static final" and should share a naming convention
69

70	/**

169	// allow current super user to review update progress

170	if (isDatabaseUpdateInProgress) {

171	referenceMap.put("updateJobStarted", true);

	Define a constant instead of duplicating this literal "updateJobStarted" 3 times. NEW String literals should not be duplicated
172	httpResponse.setContentType("text/html");

173	renderTemplate(REVIEW_CHANGES, referenceMap, httpResponse);

460	* @should return false if given user does not have the super user role

461	*/

462	protected boolean isSuperUser(Connection connection, Integer userId) throws Exception {

	Define and throw a dedicated exception instead of using a generic one. NEW Generic exceptions should never be thrown
463	// the 'Administrator' part of this string is necessary because if the database was upgraded

464	// by OpenMRS 1.6 alpha then System Developer was renamed to that. This has to be here so we

524	} else {

525	if (log.isDebugEnabled()) {

526	log.debug("Setting updates required to " + (model.changes.size() > 0)

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
527	+ " because of the size of unrun changes");

528	}

529	setUpdatesRequired(model.changes.size() > 0);

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
530	}

531	}

622	private List<String> updateWarnings = new LinkedList<String>();

623

624	synchronized public void reportError(String error, Object... params) {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
625	Map<String, Object[]> errors = new HashMap<String, Object[]>();

626	errors.put(error, params);

628	}

629

630	synchronized public void reportErrors(Map<String, Object[]> errs) {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
631	errors.putAll(errs);

632	erroneous = true;

633	}

634

635	synchronized public boolean hasErrors() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
636	return erroneous;

637	}

638

639	synchronized public Map<String, Object[]> getErrors() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
640	return errors;

641	}

659	}

660

661	synchronized public void setMessage(String message) {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
662	this.message = message;

663	}

664

665	synchronized public String getMessage() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
666	return message;

667	}

668

669	synchronized public void addChangesetId(String changesetid) {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
670	this.changesetIds.add(changesetid);

671	this.executingChangesetId = changesetid;

672	}

673

674	synchronized public List<String> getChangesetIds() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
675	return changesetIds;

676	}

677

678	synchronized public String getExecutingChangesetId() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
679	return executingChangesetId;

680	}

687	}

688

689	synchronized public boolean hasWarnings() {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
690	return hasUpdateWarnings;

691	}

692

693	synchronized public void reportWarnings(List<String> warnings) {

	Reorder the modifiers to comply with the Java Language Specification. NEW Modifiers should be declared in the correct order
694	updateWarnings.addAll(warnings);

695	hasUpdateWarnings = true;

openmrs-web - src/main/java/org/openmrs/web/filter/update/UpdateFilterModel.java

1
New issues

51

52	try {

53	if (changes != null && changes.size() > 0) {

	Use isEmpty() to check whether the collection is empty or not. NEW Collection.isEmpty() should be used to test for emptiness
54	updateRequired = true;

55	} else {