Develop (#134)

* Mepts 264 data quality report issues (#123)

* Remove null pointers in ERDSI

* Proper labels naming in the excel template for EC3 to match the web view

* Proper labelling of the EC5 to match the labels as provided by the java code

* proper date format for EC15 and only filter them per ART program workflows

* Clarifying the specifications for the EC13 to avoid confusion

* Filter EC3 to only per the ART program workflow states

* Add ART state filters to EC4 report

* Reverting changes to match the latest develop branch

* MEPTS-266 bug for for txML: changed the untraced composition string a… (#124)

* [maven-release-plugin] prepare release 1.6.0

* [maven-release-plugin] prepare for next development iteration

* MEPTS-266 bug for for txML: changed the untraced composition string and updated one of the queries

* TxML fixed typo

* MEPTS-266: updated dead concept for txML and disabled EC20 Data quality report

* Fixed bug in visit card dead query for txML

* Updated txML untraced composition query and SQL for patients without visitcard

* MEPTS-266: updated untraced withvisit and with obs query

* MEPTS-280: added mastercard ficha resumo encounter type to base cohort (#126)

* Revert "MEPTS-280: added mastercard ficha resumo encounter type to base cohort (#126)" (#128)

This reverts commit ed7abd7.

* MEPTS-282: RM Dev: Updates in Tx-NEW IM-ER Report (#130)

* Fix matchCalculationResults

* Fix failing test

* Add mastercard encounter type and drug pickup to ART Start Date criterias

* Add mastercard transferred-in to exclusion

* Correct program workflow state name

* Add support for onOrAfter to JembiPatientStateDefinition

* Fix formatting

* Update TX_NEW breastfeeding cohort

* Add key population columns

* Update IM_ER report template

* Remove nulls

* Test TxNewBreastfeedingDateCalculation

* Add missing scenarios

* Test TX_NEW exclusion criteria

* Test key population cohorts

* Revert "MEPTS-282: RM Dev: Updates in Tx-NEW IM-ER Report (#130)" (#132)

This reverts commit 9bcac62.

* Mepts 263 (#125)

* E1: Number of active patients in ART at the end of current month who performed Viral Load Test (Annual Notification)

* Added the functionality to exclude the patients who had a VL with the year of reporting for E1

* Adding a generic way to easly pull the common indicators of E1 E2 and E3

* Initial work for the E2 indicators

* Add the E2 indicator and it required definitions

* Adding E3 indicators and its definitions

* Added the F1 indicator

* Added F2 indicator definitions

* Initial work on the F3 indicators

* Finish work on the section F of the report

* Proper mapping of end date so that it can be picked in a claculation

* Fix the exclusion criteria so that those outside should be included in our indicators

* Replacing the for each loop to iterators

* Proper calulation of the date required as start date

* Change from using reporting ORM to native sql

* Proper parameter mappings and proper nagations

* Preparing to start converting ExcludeCriteriaForEandFCalculation into sql equivalent

* Initial work on the exclusion for E1

* Complete change of the calculation for exclusion criteria for E and F done

* Replacing java code for the start date exclution criteria with sql

* General code clean up

* MEPTS-263: updated comment blocks for E-F sections in master card resumo report to match indicator names in the specs

* Combine union of the E2 exclusion into one query

* Using the visit date as encounter date as oppossed to end date for F2 exclusion

* Fix the F2 and F3 exclusion criteria to base on visit date as end date as oppossed to when we were applying the end of reporting period

* Proper E1 exclusion end date set based on the lab results date as oppossed to the end of reporting period

* E2 exclusion done including the date from the encounter date as oppossed to the end of reporting period

* Include the lab visit date for the criteria 3 exclusion instead of using reporting end period

* Fix for Total 0-14 bringing in some case +15

* Fix B.4 where not calculating correctly for total +15

* Fix B.7, B.8,B.10 and B.12 where the references to excel file where wrong, where all pointing to female desagregation

api/src/main/java/org/openmrs/module/eptsreports/metadata/HivMetadata.java

@@ -49,6 +49,7 @@ public Concept getReturnVisitDateForArvDrugConcept() {
             .getGlobalProperty("eptsreports.returnVisitDateForArvDrugConceptUuid");
     return getConcept(uuid);
   }
+
   // concept_id=6123
   public Concept getDateOfHivDiagnosisConcept() {
     String uuid =
@@ -98,69 +99,80 @@ public Concept getAzt3tcAbcEfvConcept() {
             .getGlobalProperty("eptsreports.AZT_3TC_ABC_EFV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 6327
   public Concept getD4t3tcAbcEfvConcept() {
     String uuid =
         Context.getAdministrationService()
             .getGlobalProperty("eptsreports.D4T_3TC_ABC_EFV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 6326
   public Concept getAzt3tcAbcLpvConcept() {
     String uuid =
         Context.getAdministrationService()
             .getGlobalProperty("eptsreports.AZT_3TC_ABC_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 6325
   public Concept getD4t3tcAbcLpvConcept() {
     String uuid =
         Context.getAdministrationService()
             .getGlobalProperty("eptsreports.D4T_3TC_ABC_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 6109
   public Concept getAztDdiLpvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.AZT_DDI_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 1315
   public Concept getTdf3tcEfvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.TDF_3TC_EFV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 1314
   public Concept getAzt3tcLpvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.AZT_3TC_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 1313
   public Concept getAbc3tcEfvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.ABC_3TC_EFV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 1312
   public Concept getAbc3tcNvpConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.ABC_3TC_NVP_ConceptUuid");
     return getConcept(uuid);
   }
+
   // 1311
   public Concept getAbc3tcLpvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.ABC_3TC_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   //
   public Concept getTdf3tcLpvConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.TDF_3TC_LPV_ConceptUuid");
     return getConcept(uuid);
   }
+
   // concept id 6306
   public Concept getAcceptContactConcept() {
     String uuid =
@@ -195,6 +207,7 @@ public Concept getIsoniazidUsageConcept() {
         Context.getAdministrationService().getGlobalProperty("eptsreports.isoniazidUseConceptUuid");
     return getConcept(uuid);
   }
+
   // concept_id=1695
   public Concept getCD4AbsoluteOBSConcept() {
     String uuid =
@@ -216,6 +229,7 @@ public Concept getcurrentWhoHivStageConcept() {
         Context.getAdministrationService().getGlobalProperty("eptsreports.currentWhoHivStageUuid");
     return getConcept(uuid);
   }
+
   // concept_id=1205
   public Concept getWho2AdultStageConcept() {
     String uuid =
@@ -229,6 +243,7 @@ public Concept getWho3AdultStageConcept() {
         Context.getAdministrationService().getGlobalProperty("eptsreports.who3AdultStageUuid");
     return getConcept(uuid);
   }
+
   // concept_id=1207
   public Concept getWho4AdultStageConcept() {
     String uuid =
@@ -268,46 +283,54 @@ public Concept getBuscaConcept() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.busca");
     return getConcept(uuid);
   }
+
   // concept_id = 6254
   public Concept getSecondAttemptConcept() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.secondAttempt");
     return getConcept(uuid);
   }
+
   // concept_id = 6255
   public Concept getThirdAttemptConcept() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.thirdAttempt");
     return getConcept(uuid);
   }
+
   // concept_id = 2016
   public Concept getDefaultingMotiveConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.defaultingMotive");
     return getConcept(uuid);
   }
+
   // concept_id = 2158
   public Concept getReportOfVisitSupportConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.reportOfVisitSupport");
     return getConcept(uuid);
   }
+
   // concept_id = 2157
   public Concept getPatientHadDifficultyConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.patientHadDifficulty");
     return getConcept(uuid);
   }
+
   // concept_id = 1272
   public Concept getPatientFoundForwardedConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.patientFoundForwarded");
     return getConcept(uuid);
   }
+
   // concept_id = 2037
   public Concept getWhoGaveInformationConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.whoGaveInformation");
     return getConcept(uuid);
   }
+
   // concept_id = 2180
   public Concept getCardDeliveryDateConcept() {
     String uuid =
@@ -377,145 +400,171 @@ public Concept getAdherenceCoucelingConcept() {
         Context.getAdministrationService().getGlobalProperty("eptsreports.adherenceCounselingUuid");
     return getConcept(uuid);
   }
+
   // concept_id=5497
   public Concept getCD4AbsoluteConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.cd4AbsolutoUuid");
     return getConcept(uuid);
   }
+
   // concept_id=730
   public Concept getCD4PercentConcept() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.cd4PercentUuid");
     return getConcept(uuid);
   }
+
   // concept_id=1714
   public Concept getAdherence() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.poorAdherenceUuid");
     return getConcept(uuid);
   }
+
   // concept_id=2015
   public Concept getAdverseReaction() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.adverseReactionUuid");
     return getConcept(uuid);
   }
+
   // Concept 6292
   public Concept getNeutropenia() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.neutropenia");
     return getConcept(uuid);
   }
+
   // Concept 6293
   public Concept getPancreatitis() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.pancreatitis");
     return getConcept(uuid);
   }
+
   // Concept 6294
   public Concept getHepatotoxicity() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.hepatotoxicity");
     return getConcept(uuid);
   }
+
   // Concept 6295
   public Concept getPsychologicalChanges() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.psychologicalChanges");
     return getConcept(uuid);
   }
+
   // Concept 6296
   public Concept getMyopathy() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.myopathy");
     return getConcept(uuid);
   }
+
   // Concept 6297
   public Concept getSkinAllergy() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.skinAllergy");
     return getConcept(uuid);
   }
+
   // Concept 6298
   public Concept getLipodystrophy() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.lipodystrophy");
     return getConcept(uuid);
   }
+
   // Concept 6299
   public Concept getLacticAcidosis() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.lacticAcidosis");
     return getConcept(uuid);
   }
+
   // Concept 821
   public Concept getPeripheralNeuropathy() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.peripheralNeuropathy");
     return getConcept(uuid);
   }
+
   // Concept 16
   public Concept getDiarrhea() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.diarrhea");
     return getConcept(uuid);
   }
+
   // Concept 1406
   public Concept getOtherDiagnosis() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.otherDiagnosis");
     return getConcept(uuid);
   }
+
   // Concept 23724 GAAC
   public Concept getGaac() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.gaac");
     return getConcept(uuid);
   }
+
   // Concept 23725 AF
   public Concept getFamilyApproach() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.familyApproach");
     return getConcept(uuid);
   }
+
   // Concept 23726 CA
   public Concept getAccessionClubs() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.accessionClubs");
     return getConcept(uuid);
   }
+
   // Concept 23727 PU
   public Concept getSingleStop() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.singleStop");
     return getConcept(uuid);
   }
+
   // Concept 23729 FR
   public Concept getRapidFlow() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.rapidFlow");
     return getConcept(uuid);
   }
+
   // Concept 23730 DT
   public Concept getQuarterlyDispensation() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.quarterlyDispensation");
     return getConcept(uuid);
   }
+
   // Concept 23731 DC
   public Concept getCommunityDispensation() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.communityDispensation");
     return getConcept(uuid);
   }
+
   // Concept 23732 Other Model
   public Concept getAnotherModel() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.anotherModel");
     return getConcept(uuid);
   }
+
   // Concept 1256 Start Drugs
   public Concept getStartDrugs() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.startDrugs");
     return getConcept(uuid);
   }
+
   // Concept 1257 Continue Regimen
   public Concept getContinueRegimen() {
     String uuid =
         Context.getAdministrationService().getGlobalProperty("eptsreports.continueRegimen");
     return getConcept(uuid);
   }
+
   // Concept 23808 Pre-ART Start Date
   public Concept getPreArtStartDate() {
     String uuid =
@@ -552,8 +601,15 @@ public Concept getReasonPatientNotFound() {
     return getConcept(uuid);
   }
 
-  // Concept 2027 PATIENT IS DEAD
+  // Concept 1383 PATIENT IS DEAD - Incorrect
   public Concept getPatientIsDead() {
+    String uuid =
+        Context.getAdministrationService().getGlobalProperty("eptsreports.patientIsdeadIncorrect");
+    return getConcept(uuid);
+  }
+
+  // Concept 2027 PATIENT IS DEAD
+  public Concept getPatientIsDeadCorrect() {
     String uuid = Context.getAdministrationService().getGlobalProperty("eptsreports.patientIsdead");
     return getConcept(uuid);
   }
@@ -571,6 +627,21 @@ public Concept getTransferredOutConcept() {
             .getGlobalProperty("eptsreports.transferOutToAnotherFacilityConceptUuid");
     return getConcept(uuid);
   }
+
+  // Concept 23722 APPLICATION FOR LABORATORY RESEARCH
+  public Concept getApplicationForLaboratoryResearch() {
+    String uuid =
+        Context.getAdministrationService()
+            .getGlobalProperty("eptsreports.applicationForLaboratoryResearch");
+    return getConcept(uuid);
+  }
+  // Concept 1305 HIV VIRAL LOAD, QUALITATIVE
+  public Concept getHivViralLoadQualitative() {
+    String uuid =
+        Context.getAdministrationService()
+            .getGlobalProperty("eptsreports.viralLoadQualitativeConceptUuid");
+    return getConcept(uuid);
+  }
   // Encounter types
   // encounterType_id = 6
   public EncounterType getAdultoSeguimentoEncounterType() {
@@ -626,6 +697,7 @@ public EncounterType getEvaluationAndPrepForARTEncounterType() {
             .getGlobalProperty("eptsreports.evaluationAndPrepForARTEncounterTypeUuid");
     return getEncounterType(uuid);
   }
+
   // encounter_type 13
   public EncounterType getMisauLaboratorioEncounterType() {
     String uuid =
@@ -754,7 +826,8 @@ public ProgramWorkflowState getTransferredOutToAnotherHealthFacilityWorkflowStat
   }
 
   public ProgramWorkflowState getTransferredFromOtherHealthFacilityWorkflowState() {
-    // TODO Refactor this method, use #getTransferredFromOtherHealthFacilityWorkflowState(Program,
+    // TODO Refactor this method, use
+    // #getTransferredFromOtherHealthFacilityWorkflowState(Program,
     // ProgramWorkflow)
     String artProgramUuid = Context.getAdministrationService().getGlobalProperty(gpArtProgramUuid);
     String transferFromOtherUuid =