OpenMRS

Timestamp:

08/04/08 16:57:21 (5 months ago)

Author:

jegg

Message:

in patientmatching module, updated class to read patient objects from OpenMRS and convert them to matching Record objects without using external database. Code not tested yet

Files:

• openmrs-modules/patientmatching/src/org/regenstrief/linkage/io/OrderedOpenMRSReader.java (modified) (6 diffs)

openmrs-modules/patientmatching/src/org/regenstrief/linkage/io/OrderedOpenMRSReader.java

@@ -4 +4 @@
-import java.util.Iterator;
-import java.util.List;
-import java.util.Properties;
-
-import org.hibernate.Query;
-import org.hibernate.SessionFactory;
-import org.hibernate.cfg.Configuration;
-import org.openmrs.Patient;
+import org.openmrs.PatientIdentifierType;
-import org.openmrs.PersonAttributeType;
-import org.openmrs.api.context.Context;
@@ -16 +15 @@
-import org.regenstrief.linkage.util.MatchingConfig;
-
+/**
+ * identifier and attribute convention and examples:
+ * 
+ * (Attribute) Birthplace
+ * (Identifer) OpenMRS Identification Number
+ * (Attribute) Credit Card Number
+ * 
+ * Object fields convention and examples:
+ * 
+ * org.openmrs.Person.gender
+ * org.openmrs.PersonAddress.cityVillage
+ * 
+ * 
+ * @author jegg
+ *
+ */
+
-public class OrderedOpenMRSReader implements OrderedDataSourceReader{
-        
-        String[] blocking_cols;
-String
-String
-List<String>
+Object
+Object
+Object[]
-        List<Integer> value_set;
-        
+        public final static String ATTRIBUTE_PREFIX = "(Attribute) ";
+        public final static String IDENT_PREFIX = "(Identifier)";
+        
-        private SessionFactory sessionFactory;
-        
-
-// need to initialize sessionFactory to avoid null pointer exception when issuing query
-
-String
+, SessionFactory session_factory
+sessionFactory = session_factory;
+
+Object
-                value_set = new ArrayList<Integer>();
-                current_blocking_values = new ArrayList<String>();
-                
-                blocking_cols = mc.getBlockingColumns();
-
+
+
+
-                
-                for(int i = 0; i < blocking_cols.length; i++){
-
+
+
+
+
+
+
+
-                        blocking_values.add(values);
-                        values_iterators.add(values.iterator());
-                }
+                
+                // initial increment and blocking value assignment
+                for(int i = values_iterators.size() - 1; i >= 0; i--){
+                        Iterator<Object> it = values_iterators.get(i);
+                        Object new_block_val = it.next();
+                        current_blocking_values[i] = new_block_val;
+                }
+                
+                while(fillIDValueSet() < 1 && incrementIterators()){
+                        // do until IDs are set, or iterators are all incremented
+                }
+                
-        }
-        
@@ -68 +106 @@
-        }
-        
+        protected int fillIDValueSet(){
+                value_set = getPatientIDs(blocking_cols[0], current_blocking_values[0]);
+                int col = 1;
+                while(value_set.size() > 0 && col < blocking_cols.length){
+                        value_set.retainAll(getPatientIDs(blocking_cols[col], current_blocking_values[col]));
+                        col++;
+                }
+                
+                return value_set.size();
+        }
+        
-        public Record nextRecord(){
-                // possible future optimization - remove values from blocking_values if all references
-                // to a value has been read
-                
-                boolean has_record = value_set.size() > 0;
-                while(!has_record){
-                        // need to increment the least significant iterator, or restart iterators, until we find
-                        // IDs at the combination, or 
-                        if(incrementedIterators()){
-                                // get the set of IDs at the current values
-                                value_set = getPatientIDs(blocking_cols[0], current_blocking_values.get(0));
-                                int col = 1;
-                                while(value_set.size() > 0 && col < blocking_cols.length){
-                                        value_set.retainAll(getPatientIDs(blocking_cols[1], current_blocking_values.get(1)));
-                                }
-                                if(value_set.size() > 0){
-                                        has_record = true;
-                                }
-                        } else {
-                                // at the end of values
-                                return null;
-                        }
-                }
-                
-                // if there are IDs in the value_set, then return a Record of one of the IDs
-                if(value_set.size() > 0){
-                        Integer id = value_set.remove(0);
-                        Patient p = Context.getPatientService().getPatient(id);
+                        
+                        if(value_set.size() == 0){
+                                // removed last ID at this point in blocking values, need to increment iterators and refill
+                                // value_set
+                                while(incrementIterators() && fillIDValueSet() < 1){
+                                        // do until IDs are set, or iterators are all incremented
+                                }
+                        }
-                        return PatientMatchingActivator.patientToRecord(p);
-                }
@@ -102 +138 @@
-        }
-        
-ed
+
-                for(int i = values_iterators.size() - 1; i >= 0; i--){
-String
+Object
-                        if(it.hasNext()){
-String
-.set(i, new_block_val)
+Object
+[i] =  new_block_val
-                                return true;
-                        } else {
@@ -121 +157 @@
-         * @return
-         */
-
-
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+
-                if(demographic.contains(".")){
-                        // need to query the table name before the . for the field
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-                } else {
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-                return ret;
+        }
+        
+        private String stripType(String type_name){
+                // method strips the first 
+                if(type_name.indexOf(ATTRIBUTE_PREFIX) != -1){
+                        return type_name.replaceFirst(ATTRIBUTE_PREFIX,"");
+                } else if(type_name.indexOf(IDENT_PREFIX) != -1){
+                        return type_name.replaceFirst(IDENT_PREFIX, "");
+                }
+                return type_name;
-        }
-        
@@ -155 +222 @@
-         * @return
-         */
-String
+Object
-                List<Integer> ret = null;
+                String query_text = new String();
-                // get patient IDs using HQL that have this value for
-                // this demographic
-                if(demographic.contains(".")){
-                        // need to query the table name before the . for the field
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-                } else {
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-                return ret;
-        }
+        
-}