Merge pull request #5 from aleksandr-isaev/master

Brackets fix and additional scripts to setup umea data in neo4j
stacs-srg · Sep 19, 2024 · 5c02cd9 · 5c02cd9
2 parents 8541ae6 + f58ceaa
commit 5c02cd9
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Showing 20 changed files with 234 additions and 25 deletions.
diff --git a/.gitignore b/.gitignore
@@ -9,4 +9,4 @@ application.properties
 *.meta
 src/main/scripts/R/.Rhistory
 !/properties/application.properties
-!/src/main/scripts/R/.RData
+!/src/main/scripts/R/.RData
diff --git a/...ingBundleThenBirthDeathExperiment.run.xml → .run/BirthSiblingBundleBuilder.run.xml b/...ingBundleThenBirthDeathExperiment.run.xml → .run/BirthSiblingBundleBuilder.run.xml
@@ -2,7 +2,7 @@
   <configuration default="false" name="BirthSiblingBundleBuilder" type="Application" factoryName="Application">
     <option name="MAIN_CLASS_NAME" value="uk.ac.standrews.cs.population_linkage.endToEnd.builders.BirthSiblingBundleBuilder" />
     <module name="population-linkage" />
-    <option name="PROGRAM_PARAMETERS" value="umea 10" />
+    <option name="PROGRAM_PARAMETERS" value="umea EVERYTHING" />
     <option name="VM_PARAMETERS" value="-Xmx16G" />
     <method v="2">
       <option name="Make" enabled="true" />

diff --git a/.run/SiblingBirthTriangleResolver.run.xml → .../SiblingBirthOpenTriangleResolver.run.xml b/.run/SiblingBirthTriangleResolver.run.xml → .../SiblingBirthOpenTriangleResolver.run.xml
@@ -2,7 +2,7 @@
   <configuration default="false" name="SiblingBirthOpenTriangleResolver" type="Application" factoryName="Application" nameIsGenerated="true">
     <option name="MAIN_CLASS_NAME" value="uk.ac.standrews.cs.population_linkage.resolver.triangles.SiblingBirthOpenTriangleResolver" />
     <module name="population-linkage" />
-    <option name="PROGRAM_PARAMETERS" value="umea" />
+    <option name="PROGRAM_PARAMETERS" value="umea EVERYTHING" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>

diff --git a/.../ac/standrews/cs/population_linkage/endToEnd/builders/BirthBrideSiblingBundleBuilder.java b/.../ac/standrews/cs/population_linkage/endToEnd/builders/BirthBrideSiblingBundleBuilder.java
@@ -28,6 +28,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Birth;
 import uk.ac.standrews.cs.population_records.record_types.Death;
+import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
  * This class attempts to perform birth-marriage sibling linkage.
@@ -59,8 +60,8 @@ public static void main(String[] args) throws Exception {
     public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
 
-            String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
-            String std_id2 = link.getRecord2().getReferend(Birth.class).getString(Birth.STANDARDISED_ID );
+            String std_id1 = link.getRecord1().getReferend(Birth.class).getString(Birth.STANDARDISED_ID);
+            String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID );
 
                 if (!Query.BMBrideSiblingReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {
                     Query.createBMBrideSiblingReference(

diff --git a/.../ac/standrews/cs/population_linkage/endToEnd/builders/BirthGroomSiblingBundleBuilder.java b/.../ac/standrews/cs/population_linkage/endToEnd/builders/BirthGroomSiblingBundleBuilder.java
@@ -28,6 +28,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Birth;
 import uk.ac.standrews.cs.population_records.record_types.Death;
+import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
  * This class attempts to perform birth-marriage sibling linkage.
@@ -39,8 +40,7 @@ public static void main(String[] args) throws Exception {
         String sourceRepo = args[0];  // e.g. umea
         String number_of_records = args[1]; // e.g. EVERYTHING or 10000 etc.
 
-        try(
-            BirthGroomSiblingLinkageRecipe linkageRecipe = new BirthGroomSiblingLinkageRecipe(sourceRepo, number_of_records, BirthGroomSiblingBundleBuilder.class.getName() ) ) {
+        try(BirthGroomSiblingLinkageRecipe linkageRecipe = new BirthGroomSiblingLinkageRecipe(sourceRepo, number_of_records, BirthGroomSiblingBundleBuilder.class.getName() ) ) {
 
             BitBlasterLinkageRunner runner = new BitBlasterLinkageRunner();
 
@@ -60,8 +60,8 @@ public static void main(String[] args) throws Exception {
     public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
 
-            String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
-            String std_id2 = link.getRecord2().getReferend(Birth.class).getString(Birth.STANDARDISED_ID );
+            String std_id1 = link.getRecord1().getReferend(Birth.class).getString(Birth.STANDARDISED_ID);
+            String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID );
 
                 if (!Query.BMGroomSiblingReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {
                     Query.createBMGroomSiblingReference(

diff --git a/...tandrews/cs/population_linkage/endToEnd/builders/BrideMarriageParentsMarriageBuilder.java b/...tandrews/cs/population_linkage/endToEnd/builders/BrideMarriageParentsMarriageBuilder.java
@@ -27,6 +27,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageQuality;
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Death;
+import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
  *  This class attempts to find marriage-marriage links: links a groom's parents on a marriage record to the parents marriage.
@@ -60,8 +61,8 @@ public static void main(String[] args) throws Exception {
     @Override
     public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
-            String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
-            String std_id2 = link.getRecord2().getReferend(Death.class).getString( Death.STANDARDISED_ID );
+            String std_id1 = link.getRecord1().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID);
+            String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID);
 
             if (!std_id1.equals(std_id2)) {
                 if( ! Query.MMBrideMarriageParentsMarriageReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {

diff --git a/...uk/ac/standrews/cs/population_linkage/endToEnd/builders/DeathGroomOwnMarriageBuilder.java b/...uk/ac/standrews/cs/population_linkage/endToEnd/builders/DeathGroomOwnMarriageBuilder.java
@@ -27,6 +27,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageQuality;
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Birth;
+import uk.ac.standrews.cs.population_records.record_types.Death;
 import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
@@ -61,7 +62,7 @@ public static void main(String[] args) throws Exception {
     @Override
     public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
-            final String std_id1 = link.getRecord1().getReferend(Birth.class).getString(Birth.STANDARDISED_ID);
+            final String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
             final String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID);
 
             if( ! Query.DMDeathGroomOwnMarriageReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {

diff --git a/.../ac/standrews/cs/population_linkage/endToEnd/builders/DeathGroomSiblingBundleBuilder.java b/.../ac/standrews/cs/population_linkage/endToEnd/builders/DeathGroomSiblingBundleBuilder.java
@@ -28,6 +28,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Birth;
 import uk.ac.standrews.cs.population_records.record_types.Death;
+import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
  * This class attempts to perform birth-marriage sibling linkage.
@@ -62,7 +63,7 @@ public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
 
             String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
-            String std_id2 = link.getRecord2().getReferend(Birth.class).getString(Birth.STANDARDISED_ID );
+            String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID );
 
                 if (!Query.DMGroomSiblingReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {
                     Query.createDMGroomSiblingReference(

diff --git a/...tandrews/cs/population_linkage/endToEnd/builders/GroomMarriageParentsMarriageBuilder.java b/...tandrews/cs/population_linkage/endToEnd/builders/GroomMarriageParentsMarriageBuilder.java
@@ -27,6 +27,7 @@
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageQuality;
 import uk.ac.standrews.cs.population_linkage.supportClasses.LinkageResult;
 import uk.ac.standrews.cs.population_records.record_types.Death;
+import uk.ac.standrews.cs.population_records.record_types.Marriage;
 
 /**
  *  This class attempts to find marriage-marriage links: links a groom's parents on a marriage record to the parents marriage.
@@ -60,8 +61,8 @@ public static void main(String[] args) throws Exception {
     @Override
     public void makePersistent(LinkageRecipe recipe, Link link) {
         try {
-            String std_id1 = link.getRecord1().getReferend(Death.class).getString(Death.STANDARDISED_ID);
-            String std_id2 = link.getRecord2().getReferend(Death.class).getString( Death.STANDARDISED_ID );
+            String std_id1 = link.getRecord1().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID);
+            String std_id2 = link.getRecord2().getReferend(Marriage.class).getString(Marriage.STANDARDISED_ID);
 
             if (!std_id1.equals(std_id2)) {
                 if( ! Query.MMGroomMarriageParentsMarriageReferenceExists(recipe.getBridge(), std_id1, std_id2, recipe.getLinksPersistentName())) {

diff --git a/src/main/java/uk/ac/standrews/cs/population_linkage/graph/Query.java b/src/main/java/uk/ac/standrews/cs/population_linkage/graph/Query.java
@@ -58,8 +58,8 @@ public class Query {
 
     private static final String BD_DEATH_QUERY = "MATCH (a:Birth), (b:Death) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Child-Deceased\" } ]->(b)";
 
-    private static final String DM_DEATH_GROOM_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Groom\" } } ]->(b)";
-    private static final String DM_DEATH_BRIDE_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Bride\" } } ]->(b)";;
+    private static final String DM_DEATH_GROOM_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Groom\" } ]->(b)";
+    private static final String DM_DEATH_BRIDE_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Bride\" } ]->(b)";;
 
     private static final String MM_BB_SIBLING_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Bride-Bride\" } ]->(b)";
     private static final String MM_GG_SIBLING_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Groom-Groom\" } ]->(b)";
@@ -74,11 +74,11 @@ public class Query {
     private static final String BM_GROOM_SIBLING_QUERY = "MATCH (a:Birth), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Child-Groom\" } ]->(b)";
     private static final String BM_BRIDE_SIBLING_QUERY = "MATCH (a:Birth), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Child-Bride\" } ]->(b)";
 
-    private static final String MM_BRIDE_BRIDE_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Bride-Bride\" } } ]->(b)";
-    private static final String MM_GROOM_GROOM_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Groom-Groom\" } } ]->(b)";
+    private static final String MM_BRIDE_BRIDE_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Bride-Bride\" } ]->(b)";
+    private static final String MM_GROOM_GROOM_QUERY = "MATCH (a:Marriage), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:ID { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Groom-Groom\" } ]->(b)";
 
-    private static final String DM_DECEASED_BRIDE_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Bride\" } } ]->(b)";
-    private static final String DM_DECEASED_GROOM_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Groom\" } } ]->(b)";
+    private static final String DM_DECEASED_BRIDE_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Bride\" } ]->(b)";
+    private static final String DM_DECEASED_GROOM_QUERY = "MATCH (a:Death), (b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to CREATE (a)-[r:SIBLING { provenance: $prov, fields_populated: $fields, distance: $distance, actors: \"Deceased-Groom\" } ]->(b)";
 
     // queries for use in predicates - return a relationship if it exists
 
@@ -94,8 +94,8 @@ public class Query {
 
     private static final String BD_DEATH_EXISTS_QUERY = "MATCH (a:Birth)-[r:ID { actors: \"Child-Deceased\" }]-(b:Death) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to  RETURN r";
 
-    private static final String DM_DEATH_GROOM_EXISTS_QUERY = "MATCH (a:Death)-[r:ID actors: \"Deceased-Groom\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov RETURN r";
-    private static final String DM_DEATH_BRIDE_EXISTS_QUERY = "MATCH (a:Death)-[r:ID actors: \"Deceased-Bride\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov  RETURN r";
+    private static final String DM_DEATH_GROOM_EXISTS_QUERY = "MATCH (a:Death)-[r:ID { actors: \"Deceased-Groom\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov RETURN r";
+    private static final String DM_DEATH_BRIDE_EXISTS_QUERY = "MATCH (a:Death)-[r:ID { actors: \"Deceased-Bride\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov  RETURN r";
 
     private static final String MM_BB_SIBLING_EXISTS_QUERY = "MATCH (a:Marriage)-[r:SIBLING { actors: \"Bride-Bride\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov  RETURN r";
     private static final String MM_GG_SIBLING_EXISTS_QUERY = "MATCH (a:Marriage)-[r:SIBLING { actors: \"Groom-Groom\" }]-(b:Marriage) WHERE a.STANDARDISED_ID = $standard_id_from AND b.STANDARDISED_ID = $standard_id_to AND r.provenance = $prov  RETURN r";