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base repository: Bahmni/openmrs-module-bahmniendtb
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head repository: endtb/deprecated-openmrs-module-bahmniendtb
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  • 19 commits
  • 28 files changed
  • 4 contributors

Commits on Jan 29, 2017

  1. Added Milestone for End of Treatment in FlowshetUI

    Modified Highlighted milestone for continuation 6 months after treatment
    end date
    Omar Ahmed committed Jan 29, 2017
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Commits on Feb 1, 2017

  1. Omar Ahmed |ED-4|Patient Monitoring tool improvments for configurable

    status tracking
    Omar Ahmed committed Feb 1, 2017
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Commits on Feb 6, 2017

  1. Re-organize Poms a bit to pull version numbers into a centralized pro…

    …perty, and order dependencies alphabetically
    mseaton committed Feb 6, 2017
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Commits on Feb 7, 2017

  1. Upgrade to version 4.2.3 of dataintegrity, mainly to take advantage o…

    …f fixed project organization so that hbm files can be referenced in unit tests
    mseaton committed Feb 7, 2017
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  3. Include remaining bahmni-specific tables in test metadata set that re…

    …quired ensuring hibernate mapping files were available in the pom.
    mseaton committed Feb 7, 2017
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Commits on Feb 15, 2017

  1. ED-4 - Improvements to monitoring tool. Follow up commit to remove th…

    …e configuration for months past treatment end, as we plan to show the treatment data and current month up to month 30. Add in some changes to hide the legend elements for pending and planned if these are not configured to display on the chart.
    mseaton committed Feb 15, 2017
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Commits on Mar 8, 2017

  1. Merge remote-tracking branch 'bahmni/master' into master-merge

    # Conflicts:
    #	api/pom.xml
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/BaselineSecondlineDSTViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/CultureStatusAtStartMissing.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/EndTBStudyConsentSignedViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/FirstLineDSTViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingCaseDefinitionViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingEventBecameSeriousSAEViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOnsetDateAEViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOnsetDateSAEViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOutcomeViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingTreatmentStartDate.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingTreatmentStopDate.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/NewDrugConsentSignedViolation.java
    #	api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/TreatmentTBDrugRule.java
    #	omod/pom.xml
    #	pom.xml
    mogoodrich committed Mar 8, 2017
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  2. fix poms

    mogoodrich committed Mar 8, 2017
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Commits on Mar 9, 2017

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Commits on Mar 10, 2017

  1. Merge pull request #2 from Bahmni/master

    Merging latest from Bahmni fork
    mogoodrich authored Mar 10, 2017
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Commits on Apr 4, 2017

  1. Merge pull request #3 from Bahmni/master

    Swathi | #3331 | Removing SAE Form, Is SAE related to TB drugs condit…
    mogoodrich authored Apr 4, 2017
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Commits on Apr 19, 2017

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Commits on May 15, 2017

  1. Merge branch 'bahmni-master'

    # Conflicts:
    #	pom.xml
    mogoodrich committed May 15, 2017
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Showing with 15,241 additions and 331 deletions.
  1. +2 −1 .gitignore
  2. +48 −37 api/pom.xml
  3. +1 −8 .../main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/BaselineSecondlineDSTViolation.java
  4. +1 −9 ...src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/CultureStatusAtStartMissing.java
  5. +2 −9 ...ain/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/EndTBStudyConsentSignedViolation.java
  6. +14 −0 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/EndTbRuleDefinition.java
  7. +1 −8 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/FirstLineDSTViolation.java
  8. +2 −12 .../main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingCaseDefinitionViolation.java
  9. +2 −9 ...ava/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingEventBecameSeriousSAEViolation.java
  10. +2 −9 ...src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOnsetDateAEViolation.java
  11. +2 −9 ...rc/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOnsetDateSAEViolation.java
  12. +3 −12 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingOutcomeViolation.java
  13. +2 −9 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingTreatmentStartDate.java
  14. +2 −9 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/MissingTreatmentStopDate.java
  15. +2 −9 ...c/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/NewDrugConsentSignedViolation.java
  16. +1 −10 api/src/main/java/org/openmrs/module/bahmniendtb/dataintegrity/rules/TreatmentTBDrugRule.java
  17. +57 −0 api/src/test/java/org/openmrs/module/bahmniendtb/EndTbContextSensitiveTest.java
  18. +148 −0 api/src/test/java/org/openmrs/module/bahmniendtb/test/CreateEndTBMetadata.java
  19. +14,663 −0 api/src/test/resources/endtbMetadata.xml
  20. +7 −0 api/src/test/resources/test-hibernate.cfg.xml
  21. +64 −84 omod/pom.xml
  22. +25 −0 omod/src/main/java/org/bahmni/flowsheet/config/FlowsheetConfig.java
  23. +4 −1 omod/src/main/java/org/bahmni/flowsheet/constants/FlowsheetConstant.java
  24. +24 −8 omod/src/main/java/org/bahmni/flowsheet/ui/FlowsheetUI.java
  25. +52 −22 ...n/java/org/openmrs/module/endtb/flowsheet/service/impl/PatientMonitoringFlowsheetServiceImpl.java
  26. +1 −1 omod/src/main/resources/config.xml
  27. +2 −2 ...java/org/openmrs/module/endtb/flowsheet/service/impl/PatientMonitoringFlowsheetServiceImplIT.java
  28. +107 −53 pom.xml
3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -13,4 +13,5 @@ hs_err_pid*

.idea
target/
*.iml
*.iml
/bin/
85 changes: 48 additions & 37 deletions api/pom.xml
Original file line number Diff line number Diff line change
@@ -16,22 +16,8 @@
<version>${bahmniEndTbVersion}</version>

<dependencies>
<!-- Begin OpenMRS modules -->

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>emrapi-api</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>emrapi-api-1.12</artifactId>
</dependency>

<!-- End OpenMRS modules -->


<!-- Begin OpenMRS core -->
<!-- OpenMRS core -->

<dependency>
<groupId>org.openmrs.api</groupId>
@@ -63,61 +49,86 @@
<groupId>org.openmrs.test</groupId>
<artifactId>openmrs-test</artifactId>
<type>pom</type>
<scope>test</scope>
</dependency>

<!-- OpenMRS Modules -->

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>calculation-api</artifactId>
<scope>test</scope>
<groupId>org.bahmni.module</groupId>
<artifactId>bahmni-emr-api</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>reporting-api</artifactId>
<scope>test</scope>
<artifactId>dataintegrity-api</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>serialization.xstream-api-2.0</artifactId>
<scope>test</scope>
<artifactId>emrapi-api-1.12</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>providermanagement-api</artifactId>
<version>1.1.3</version>
<artifactId>emrapi-api</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>episodes-api</artifactId>
<version>${episodes.version}</version>
<scope>provided</scope>
</dependency>
<!-- End OpenMRS core -->

<!-- Test Module Dependencies -->

<dependency>
<groupId>org.bahmni.module</groupId>
<artifactId>bahmnicore-api</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.bahmni.module</groupId>
<artifactId>bahmnicore-api</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.bahmni.module</groupId>
<artifactId>bahmni-mapping</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>legacyui-omod</artifactId>
<artifactId>calculation-api</artifactId>
</dependency>

<!-- Begin Data Integrity omod -->
<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>dataintegrity-omod</artifactId>
<version>${dataintegrityVersion}</version>
<scope>provided</scope>
<artifactId>serialization.xstream-api-2.0</artifactId>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>dataintegrity-api</artifactId>
<version>${dataintegrityVersion}</version>
<scope>provided</scope>
<artifactId>reporting-api</artifactId>
</dependency>

<dependency>
<groupId>org.ict4h.openmrs</groupId>
<artifactId>openmrs-atomfeed-api</artifactId>
</dependency>
<!-- End Data Integrity omod -->

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>providermanagement-api</artifactId>
</dependency>

<!-- Other dependencies -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>

</dependencies>

</project>
Original file line number Diff line number Diff line change
@@ -7,8 +7,6 @@
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.DrugDSTViolationHelper;
import org.openmrs.module.bahmniendtb.dataintegrity.service.DataintegrityRuleService;
import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;
import org.openmrs.module.episodes.Episode;

@@ -19,7 +17,7 @@

import static org.openmrs.module.bahmniendtb.EndTBConstants.*;

public class BaselineSecondlineDSTViolation implements RuleDefinition<PatientProgram> {
public class BaselineSecondlineDSTViolation extends EndTbRuleDefinition<PatientProgram> {

private DataintegrityRuleService dataintegrityRuleService;
private ConceptService conceptService;
@@ -72,9 +70,4 @@ public List<RuleResult<PatientProgram>> evaluate() {
return drugDSTViolationHelper.getInconsistenciesForQuestion(episodesWithTreatmentStartDateAndCDRTB, BASELINE_FORM, BASELINE_DRUG_RESISTANCE, FIRST_LINE_RESISTANCE_RESULT_COMMENT);
}

@Override
public DataIntegrityRule getRule() {
return null;
}

}
Original file line number Diff line number Diff line change
@@ -5,18 +5,15 @@
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.CultureStatusAtStartMissingHelper;
import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;


import java.util.Arrays;
import java.util.List;

import static org.openmrs.module.bahmniendtb.EndTBConstants.*;


public class CultureStatusAtStartMissing implements RuleDefinition<PatientProgram> {
public class CultureStatusAtStartMissing extends EndTbRuleDefinition<PatientProgram> {

private ConceptService conceptService;
private CultureStatusAtStartMissingHelper cultureStatusAtStartMissingHelper;
@@ -39,9 +36,4 @@ public List<RuleResult<PatientProgram>> evaluate() {
Concept bacteriologyCultureResults = conceptService.getConceptByName(BACTERIOLOGY_CULTURE_RESULTS);
return cultureStatusAtStartMissingHelper.fetchCultureStatusAtStartMissing(Arrays.asList(mtbConfirmation, treatmentInitiationStartDate, bacteriologySpecimenCollectionDate, bacteriologyCultureResults));
}

@Override
public DataIntegrityRule getRule() {
return null;
}
}
Original file line number Diff line number Diff line change
@@ -1,13 +1,11 @@
package org.openmrs.module.bahmniendtb.dataintegrity.rules;

import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;
import org.openmrs.Concept;
import org.openmrs.PatientProgram;
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.TIFormInconsistencyHelper;
import org.openmrs.module.dataintegrity.rule.RuleResult;

import java.util.ArrayList;
import java.util.Arrays;
@@ -16,7 +14,7 @@
import static org.openmrs.module.bahmniendtb.EndTBConstants.*;


public class EndTBStudyConsentSignedViolation implements RuleDefinition<PatientProgram> {
public class EndTBStudyConsentSignedViolation extends EndTbRuleDefinition<PatientProgram> {
private ConceptService conceptService;

private TIFormInconsistencyHelper tiFormInconsistencyHelper;
@@ -39,11 +37,6 @@ public List<RuleResult<PatientProgram>> evaluate() {
return tiFormInconsistencyHelper.getInconsistenciesForQuestion(FSN_TREATMENT_INITIATION_FORM, FSN_TI_ENDTB_STUDY_CONSENT_QUESTION, unacceptableConsentResponses);
}

@Override
public DataIntegrityRule getRule() {
return null;
}

private void addConceptByNameToList(List<String> conceptNames, List<Concept> listToAdd) {
for (String concept : conceptNames) {
listToAdd.add(conceptService.getConceptByName(concept));
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
package org.openmrs.module.bahmniendtb.dataintegrity.rules;


import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;

public abstract class EndTbRuleDefinition<T> implements RuleDefinition<T> {

@Override
public DataIntegrityRule getRule() {
return null;
}

}
Original file line number Diff line number Diff line change
@@ -7,8 +7,6 @@
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.DrugDSTViolationHelper;
import org.openmrs.module.bahmniendtb.dataintegrity.service.DataintegrityRuleService;
import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;
import org.openmrs.module.episodes.Episode;

@@ -19,7 +17,7 @@

import static org.openmrs.module.bahmniendtb.EndTBConstants.*;

public class FirstLineDSTViolation implements RuleDefinition<PatientProgram> {
public class FirstLineDSTViolation extends EndTbRuleDefinition<PatientProgram> {

private DataintegrityRuleService dataintegrityRuleService;
private ConceptService conceptService;
@@ -69,9 +67,4 @@ public List<RuleResult<PatientProgram>> evaluate() {
return drugDSTViolationHelper.getInconsistenciesForQuestion(episodesWithTreatmentStartDateAndCDRTB, BASELINE_FORM, BASELINE_DRUG_RESISTANCE, FIRST_LINE_RESISTANCE_RESULT_COMMENT);
}

@Override
public DataIntegrityRule getRule() {
return null;
}

}
Original file line number Diff line number Diff line change
@@ -5,19 +5,14 @@
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.MissingCaseDefnHelper;
import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;

import java.util.Arrays;
import java.util.List;

import static org.openmrs.module.bahmniendtb.EndTBConstants.BASELINE_CASEDEFINITION_CONFIRMATION;
import static org.openmrs.module.bahmniendtb.EndTBConstants.BASELINE_CASEDEFINITION_DISEASE_SITE;
import static org.openmrs.module.bahmniendtb.EndTBConstants.BASELINE_CASEDEFINITION_WHO_GROUP;
import static org.openmrs.module.bahmniendtb.EndTBConstants.BASELINE_FORM;
import static org.openmrs.module.bahmniendtb.EndTBConstants.*;

public class MissingCaseDefinitionViolation implements RuleDefinition<PatientProgram> {
public class MissingCaseDefinitionViolation extends EndTbRuleDefinition<PatientProgram> {

private ConceptService conceptService;

@@ -44,11 +39,6 @@ public List<RuleResult<PatientProgram>> evaluate() {
.getMissingObsInObsSetViolations(BASELINE_FORM,
Arrays.asList(whoGroupQuestion, siteDateQuestion, methodQuestion));
}

@Override
public DataIntegrityRule getRule() {
return null;
}
}


Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
package org.openmrs.module.bahmniendtb.dataintegrity.rules;

import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;
import org.openmrs.Concept;
import org.openmrs.PatientProgram;
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.MissingValuesHelper;
import org.openmrs.module.dataintegrity.rule.RuleResult;

import java.util.Arrays;
import java.util.List;

import static org.openmrs.module.bahmniendtb.EndTBConstants.*;

public class MissingEventBecameSeriousSAEViolation implements RuleDefinition<PatientProgram> {
public class MissingEventBecameSeriousSAEViolation extends EndTbRuleDefinition<PatientProgram> {

private ConceptService conceptService;

@@ -40,9 +38,4 @@ public List<RuleResult<PatientProgram>> evaluate() {
.getMissingObsInObsSetViolations(SAE_ADVERSE_EVENT_TEMPLATE, SAE_REPORTING_DATE,
Arrays.asList(reportingDateQuestion, eventBecameSeriousQuestion));
}

@Override
public DataIntegrityRule getRule() {
return null;
}
}
Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
package org.openmrs.module.bahmniendtb.dataintegrity.rules;

import org.openmrs.module.dataintegrity.DataIntegrityRule;
import org.openmrs.module.dataintegrity.rule.RuleDefinition;
import org.openmrs.module.dataintegrity.rule.RuleResult;
import org.openmrs.Concept;
import org.openmrs.PatientProgram;
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniendtb.dataintegrity.rules.helper.MissingValuesHelper;
import org.openmrs.module.dataintegrity.rule.RuleResult;

import java.util.Arrays;
import java.util.List;

import static org.openmrs.module.bahmniendtb.EndTBConstants.*;

public class MissingOnsetDateAEViolation implements RuleDefinition<PatientProgram> {
public class MissingOnsetDateAEViolation extends EndTbRuleDefinition<PatientProgram> {

private ConceptService conceptService;

@@ -40,11 +38,6 @@ public List<RuleResult<PatientProgram>> evaluate() {
.getMissingObsInObsSetViolations(AE_ADVERSE_EVENT_TEMPLATE, AE_REPORTING_DATE,
Arrays.asList(reportingDateQuestion, onsetDateQuestion));
}

@Override
public DataIntegrityRule getRule() {
return null;
}
}


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