Merge pull request #2 from endtb/ED-94

ED-94: Customize the exports functionality of endTB Bahmni for non-st…

scripts/rpm/bahmni-batch

@@ -2,6 +2,10 @@
 
 . /etc/bahmni-installer/bahmni.conf
 
+# change to this directory explicitly so that any properties set up in applicatin.properties here or the config subdirectory will get picked up
+# (see: https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-external-config.html)
+cd /opt/bahmni-batch
+
 echo "Running bahmni-batch..."
 java -DOPENMRS_DB_SERVER=${OPENMRS_DB_SERVER} -DOPENMRS_DB_USER=${OPENMRS_DB_USERNAME} -DOPENMRS_DB_PASSWORD=${OPENMRS_DB_PASSWORD} -jar /opt/bahmni-batch/libs/bahmni-batch-*.jar >> /opt/bahmni-batch/log/bahmni-batch.log
 echo "Done"

src/main/java/org/bahmni/batch/exports/BaseExportStep.java

@@ -1,41 +1,49 @@
 package org.bahmni.batch.exports;
 
-import org.bahmni.batch.BatchUtils;
+import org.bahmni.batch.helper.FreeMarkerEvaluator;
 import org.springframework.batch.core.Step;
 import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
 import org.springframework.batch.item.database.JdbcCursorItemReader;
 import org.springframework.batch.item.file.FlatFileHeaderCallback;
 import org.springframework.batch.item.file.FlatFileItemWriter;
 import org.springframework.batch.item.file.transform.DelimitedLineAggregator;
 import org.springframework.batch.item.file.transform.PassThroughFieldExtractor;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.Resource;
 import org.springframework.jdbc.core.ColumnMapRowMapper;
 
-import javax.annotation.PostConstruct;
 import javax.sql.DataSource;
 import java.io.IOException;
 import java.io.Writer;
+import java.util.HashMap;
+import java.util.Map;
 
 
 public class BaseExportStep {
+
+    @Value("${restrictByTreatmentInitiationCohort:false}")
+    public Boolean restrictByTreatmentInitiationCohort;
+
     private DataSource dataSource;
 
     private StepBuilderFactory stepBuilderFactory;
 
-    private Resource sqlResource;
+    private String ftlFilename;
 
     private Resource outputFolder;
 
     private String exportName;
 
     private String headers;
 
-    private String sql;
+    @Autowired
+    private FreeMarkerEvaluator<Map<String, Object>> freeMarkerEvaluator;
 
-    public BaseExportStep(StepBuilderFactory stepBuilderFactory, DataSource dataSource, Resource sqlResource, Resource outputFolder, String exportName, String headers) {
+    public BaseExportStep(StepBuilderFactory stepBuilderFactory, DataSource dataSource, String ftlFilename, Resource outputFolder, String exportName, String headers) {
         this.dataSource = dataSource;
         this.stepBuilderFactory = stepBuilderFactory;
-        this.sqlResource = sqlResource;
+        this.ftlFilename = ftlFilename;
         this.outputFolder = outputFolder;
         this.exportName = exportName;
         this.headers = headers;
@@ -51,6 +59,11 @@ public Step getStep() {
     }
 
     private JdbcCursorItemReader jdbcItemReader() {
+
+        Map<String, Object> input = new HashMap<String,Object>();
+        input.put("restrictByTreatmentInitiationCohort", restrictByTreatmentInitiationCohort);
+        String sql = freeMarkerEvaluator.evaluate(ftlFilename, input);
+
         JdbcCursorItemReader reader = new JdbcCursorItemReader();
         reader.setDataSource(dataSource);
         reader.setSql(sql);
@@ -78,8 +91,4 @@ public String getHeaders() {
         return headers;
     }
 
-    @PostConstruct
-    public void postConstruct(){
-        this.sql = BatchUtils.convertResourceOutputToString(sqlResource);
-    }
 }

src/main/java/org/bahmni/batch/exports/MetaDataCodeDictionaryExportStep.java

@@ -13,10 +13,9 @@ public class MetaDataCodeDictionaryExportStep extends BaseExportStep {
     @Autowired
     public MetaDataCodeDictionaryExportStep(StepBuilderFactory stepBuilderFactory,
                                             DataSource dataSource,
-                                            @Value("classpath:sql/metaDataCodeDictionary.sql") Resource sqlResource,
                                             @Value("${outputFolder}/metaDataCodeDictionary.csv") Resource outputFolder,
                                             @Value("${metaDataCodeDictionaryHeaders}") String headers) {
-        super(stepBuilderFactory, dataSource, sqlResource, outputFolder, "metaDataCodeDictionary", headers);
+        super(stepBuilderFactory, dataSource, "metaDataCodeDictionary.sql.ftl", outputFolder, "metaDataCodeDictionary", headers);
     }
 
 }

src/main/java/org/bahmni/batch/exports/NonTBDrugOrderBaseExportStep.java

@@ -14,9 +14,8 @@ public class NonTBDrugOrderBaseExportStep extends BaseExportStep {
     @Autowired
     public NonTBDrugOrderBaseExportStep(StepBuilderFactory stepBuilderFactory,
                                         DataSource dataSource,
-                                        @Value("classpath:sql/nonTbDrugOrder.sql") Resource sqlResource,
                                         @Value("${outputFolder}/nonTbDrugOrder.csv") Resource outputFolder,
                                         @Value("${nonTbDrugOrderHeaders}") String headers ) {
-        super(stepBuilderFactory, dataSource, sqlResource, outputFolder, "nonTbDrugOrder", headers);
+        super(stepBuilderFactory, dataSource, "nonTbDrugOrder.sql.ftl", outputFolder, "nonTbDrugOrder", headers);
     }
 }

src/main/java/org/bahmni/batch/exports/ObservationExportStep.java

@@ -26,6 +26,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.Writer;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -44,8 +45,11 @@ public class ObservationExportStep {
     @Value("${outputFolder}")
     public Resource outputFolder;
 
+    @Value("${restrictByTreatmentInitiationCohort:false}")
+    public Boolean restrictByTreatmentInitiationCohort;
+
     @Autowired
-    private FreeMarkerEvaluator<BahmniForm> freeMarkerEvaluator;
+    private FreeMarkerEvaluator<Map<String, Object>> freeMarkerEvaluator;
 
     private BahmniForm form;
 
@@ -66,7 +70,10 @@ public Step getStep() {
     }
 
     private JdbcCursorItemReader<Map<String, Object>> obsReader() {
-        String sql = freeMarkerEvaluator.evaluate("obsWithParentSql.ftl",form);
+        Map<String, Object> input = new HashMap<String,Object>();
+        input.put("form", form);
+        input.put("restrictByTreatmentInitiationCohort", restrictByTreatmentInitiationCohort);
+        String sql = freeMarkerEvaluator.evaluate("obsWithParentSql.ftl", input);
         JdbcCursorItemReader<Map<String, Object>> reader = new JdbcCursorItemReader<>();
         reader.setDataSource(dataSource);
         reader.setSql(sql);

src/main/java/org/bahmni/batch/exports/TBDrugOrderBaseExportStep.java

@@ -15,10 +15,9 @@ public class TBDrugOrderBaseExportStep extends  BaseExportStep{
     @Autowired
     public TBDrugOrderBaseExportStep(StepBuilderFactory stepBuilderFactory,
                                      DataSource dataSource,
-                                     @Value("classpath:sql/tbDrugOrder.sql") Resource sqlResource,
                                      @Value("${outputFolder}/tbDrugOrder.csv") Resource outputFolder,
                                      @Value("${tbDrugOrderHeaders}")String headers) {
-        super(stepBuilderFactory, dataSource, sqlResource, outputFolder, "tbDrugOrder", headers);
+        super(stepBuilderFactory, dataSource, "tbDrugOrder.sql.ftl", outputFolder, "tbDrugOrder", headers);
     }
 
 

src/main/java/org/bahmni/batch/exports/TreatmentRegistrationBaseExportStep.java

@@ -14,9 +14,8 @@ public class TreatmentRegistrationBaseExportStep extends BaseExportStep {
 
     @Autowired
     public TreatmentRegistrationBaseExportStep(StepBuilderFactory stepBuilderFactory, DataSource dataSource,
-                                               @Value("classpath:sql/treatmentRegistration.sql") Resource sqlResource,
                                                @Value("${outputFolder}/treatmentRegistration.csv") Resource outputFolder,
                                                @Value("${treatmentRegistrationHeaders}")String headers ) {
-        super(stepBuilderFactory, dataSource, sqlResource, outputFolder, "treatmentRegistration", headers);
+        super(stepBuilderFactory, dataSource, "treatmentRegistration.sql.ftl", outputFolder, "treatmentRegistration", headers);
     }
 }

src/main/resources/sql/nonTbDrugOrder.sql → src/main/resources/templates/nonTbDrugOrder.sql.ftl

@@ -64,5 +64,11 @@ FROM
   LEFT OUTER JOIN program_attribute_type pat ON o.attribute_type_id = pat.program_attribute_type_id
   LEFT JOIN concept_name cn on cn.name=o.reason_for_administration and cn.voided = 0
   LEFT JOIN concept_reference_term_map_view reason_admin on reason_admin.concept_id=cn.concept_id AND reason_admin.concept_reference_source_name='EndTB-Export' and reason_admin.concept_map_type_name= 'SAME-AS'
+
+<#if input.restrictByTreatmentInitiationCohort>
+WHERE patient_id in
+(select distinct person_id from obs where concept_id in (SELECT concept_id from concept_name where name='Treatment Initiation')  and obs_group_id IS NULL and voided=0)
+</#if>
+
 GROUP BY patient_id, program_id, order_id
 ORDER BY patient_id, date_enrolled;

src/main/resources/templates/obsWithParentSql.ftl

@@ -1,12 +1,19 @@
-SELECT obs0.obs_id,obs${input.depthToParent}.obs_id as parent_obs_id
+SELECT obs0.obs_id,obs${input.form.depthToParent}.obs_id as parent_obs_id
 FROM obs obs0
-<#if input.depthToParent &gt; 0>
-<#list 1..input.depthToParent as x>
+<#if input.form.depthToParent &gt; 0>
+<#list 1..input.form.depthToParent as x>
 INNER JOIN obs obs${x} on ( obs${x}.obs_id=obs${x-1}.obs_group_id and obs${x}.voided=0 )
 </#list>
 </#if>
-WHERE obs0.concept_id=${input.formName.id?c}
+WHERE obs0.concept_id=${input.form.formName.id?c}
 AND obs0.voided = 0
-<#if input.parent?has_content>
-AND obs${input.depthToParent}.concept_id=${input.parent.formName.id?c}
+<#if input.form.parent?has_content>
+AND obs${input.form.depthToParent}.concept_id=${input.form.parent.formName.id?c}
 </#if>
+<#if input.restrictByTreatmentInitiationCohort>
+AND obs0.person_id in
+(select distinct person_id from obs where concept_id in (SELECT concept_id from concept_name where name='Treatment Initiation')  and obs_group_id IS NULL and voided=0)
+</#if>
+
+
+

src/main/resources/sql/tbDrugOrder.sql → src/main/resources/templates/tbDrugOrder.sql.ftl

@@ -68,5 +68,12 @@ FROM
      LEFT JOIN concept_reference_term_map_view stopped_reason ON stopped_order.order_reason = stopped_reason.concept_id and stopped_reason.concept_reference_source_name='EndTB-Export' and stopped_reason.concept_map_type_name= 'SAME-AS'
 ) o
   LEFT OUTER JOIN program_attribute_type pat ON o.attribute_type_id = pat.program_attribute_type_id
+
+<#if input.restrictByTreatmentInitiationCohort>
+WHERE patient_id in
+(select distinct person_id from obs where concept_id in (SELECT concept_id from concept_name where name='Treatment Initiation')  and obs_group_id IS NULL and voided=0)
+</#if>
+
+
 GROUP BY patient_id, program_id, order_id
 ORDER BY patient_id, date_enrolled;

src/main/resources/sql/treatmentRegistration.sql → src/main/resources/templates/treatmentRegistration.sql.ftl

@@ -45,5 +45,12 @@ FROM
      LEFT OUTER JOIN concept_name outcome_concept ON outcome_concept.concept_id = pp.outcome_concept_id and outcome_concept.concept_name_type='FULLY_SPECIFIED' AND outcome_concept.voided = 0
   ) o
   LEFT OUTER JOIN program_attribute_type pat ON o.attribute_type_id = pat.program_attribute_type_id
+
+
+<#if input.restrictByTreatmentInitiationCohort>
+WHERE patient_id in
+(select distinct person_id from obs where concept_id in (SELECT concept_id from concept_name where name='Treatment Initiation')  and obs_group_id IS NULL and voided=0)
+</#if>
+
 GROUP BY patient_id, patient_program_id
 ORDER BY patient_id, date_enrolled;