Merge pull request #26 from hkuich/attributes_in_relation

Attributes in relation

README.md

@@ -22,7 +22,7 @@ Use GraMi (**Gra**kn**Mi**grator) to take care of your data migration for you. G
     - supports any tabular data file with your separator of choice (i.e.: csv, tsv, whatever-sv...)
     - supports gzipped files
     - ignores unnecessary columns
- - [Entity](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Entities), [Relation](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Relations), and [Nested Relations](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Nested-Relations) Migration:
+ - [Attribute](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Attributes), [Entity](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Entities), [Relation](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Relations), [Nested Relations](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Nested-Relations), [Attribute-Player Relations](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Attribute-Player-Relations) Migration:
     - migrate required/optional attributes of any grakn type (string, boolean, long, double, datetime)
     - migrate required/optional role players (entity & relations)
     - migrate list-like attribute columns as n attributes (recommended procedure until attribute lists are fully supported by Grakn)
@@ -53,9 +53,11 @@ The processor configuration file describes how you want data to be migrated give
 
 Depending on what you would like to migrate, see here:
 
+ - [Attribute Processor Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Attributes#processor-config)
  - [Entity Processor Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Entities#processor-config)
  - [Relation Processor Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Relations#processor-config)
  - [Nested Relation Processor Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Nested-Relations#processor-config)
+ - [Attribute-Player Relation](https://github.com/bayer-science-for-a-better-life/grami/wiki/Attribute-Player-Relations#processor-config)
 
 ### Data Configuration
 
@@ -65,10 +67,13 @@ A good point to start the performance optimization is to set the number of threa
 
 See Example here:
 
+ - [Attribute Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Attributes#data-config)
  - [Entity Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Entities#data-config)
  - [Relation Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Relations#data-config)
  - [Nested Relation - Match by Attribute(s) - Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Nested-Relations#data-config---attribute-matching)
  - [Nested Relation - Match by Player(s) - Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Migrating-Nested-Relations#data-config---player-matching)
+ - [Attribute-Player Relation - Data Config Example](https://github.com/bayer-science-for-a-better-life/grami/wiki/Attribute-Player-Relations#data-config)
+ - [Custom Migration Order](https://github.com/bayer-science-for-a-better-life/grami/wiki/Custom-Migration-Order)
 
 ### Migrate Data
 
@@ -104,7 +109,7 @@ public class Migration {
 
     public static void main(String[] args) throws IOException {
         GraknMigrator mig = new GraknMigrator(migrationConfig, migrationStatus, true);
-        mig.migrate(true, true, true, true);
+        mig.migrate();
     }
 }
 ```
@@ -122,13 +127,11 @@ There is this [example repository](https://github.com/bayer-science-for-a-better
 
 ## Compatibility
 
-GraMi version >= 0.1.0-alpha-12 is tested for:
-- [grakn-core](https://github.com/graknlabs/grakn) >= 2.0-alpha-9
-- using [client-java](https://github.com/graknlabs/client-java) >= 2.0.0-alpha-12
+GraMi version == 0.1.1 is tested for:
+- [grakn-core](https://github.com/graknlabs/grakn) == 2.0.1
 
 GraMi version < 0.1.0 is tested for: 
- - [grakn-core](https://github.com/graknlabs/grakn) >= 1.8.2 
- - [client-java](https://github.com/graknlabs/client-java) >= 1.8.3
+ - [grakn-core](https://github.com/graknlabs/grakn) >= 1.8.2
 
 Find the Readme for GraMi for grakn < 2.0 [here](https://github.com/bayer-science-for-a-better-life/grami/blob/b3d6d272c409d6c40254354027b49f90b255e1c3/README.md)
 

build.gradle

@@ -5,7 +5,7 @@ plugins {
 }
 
 group 'com.github.bayer-science-for-a-better-life'
-version '0.1.0'
+version '0.1.1'
 
 repositories {
     mavenCentral()

src/main/java/cli/GramiCLI.java

@@ -8,7 +8,7 @@
 
 import java.io.IOException;
 
-@CommandLine.Command(description="Welcome to the CLI of GraMi - your grakn data migration tool", name = "grami", version = "0.1.0-alpha-12", mixinStandardHelpOptions = true)
+@CommandLine.Command(description="Welcome to the CLI of GraMi - your grakn data migration tool", name = "grami", version = "0.1.1", mixinStandardHelpOptions = true)
 public class GramiCLI {
 
     public static void main(String[] args) {
@@ -46,9 +46,6 @@ class MigrateCommand implements Runnable {
     @CommandLine.Option(names = {"-cm", "--cleanMigration"}, description = "optional - delete old schema and data and restart migration from scratch - default: continue previous migration, if exists")
     private boolean cleanMigration;
 
-    @CommandLine.Option(names = {"-sc", "--scope"}, description = "optional - set migration scope: 0 - apply schema only (Note: this has no effect unless you also set the cleanMigration flag to true.); 1 - migrate entities; 2 - migrate entities & relations; 3 - migrate entites, relations, & relation-with-relations; everything else defaults to 4 - migrate all (entities, relations, relation-with-relations, append-attributes")
-    private int scope = 4;
-
     @Override
     public void run() {
         spec.commandLine().getOut().println("############## GraMi migration ###############");
@@ -60,24 +57,12 @@ public void run() {
         spec.commandLine().getOut().println("\tdatabase: " + databaseName);
         spec.commandLine().getOut().println("\tgrakn server: " + graknURI);
         spec.commandLine().getOut().println("\tdelete database and all data in it for a clean new migration?: " + cleanMigration);
-        spec.commandLine().getOut().println("\tmigration scope: " + scope);
 
         final MigrationConfig migrationConfig = new MigrationConfig(graknURI, databaseName, schemaFilePath, dataConfigFilePath, processorConfigFilePath);
 
         try {
             GraknMigrator mig = new GraknMigrator(migrationConfig, migrationStatusFilePath, cleanMigration);
-
-            if (scope != 0 && scope != 1 && scope != 2 && scope != 3) {
-                scope = 4;
-            }
-
-            switch (scope) {
-                case 0: mig.migrate(false, false, false, false); break;
-                case 1: mig.migrate(true, false, false, false); break;
-                case 2: mig.migrate(true, true, false, false); break;
-                case 3: mig.migrate(true, true, true, false); break;
-                case 4: mig.migrate(true, true, true, true); break;
-            }
+            mig.migrate();
         } catch (IOException e) {
             e.printStackTrace();
         }

src/main/java/configuration/DataConfigEntry.java

@@ -13,6 +13,8 @@ public class DataConfigEntry {
     private DataConfigGeneratorMapping[] relationPlayers;
     private int batchSize;
     private int threads;
+    private Integer orderBefore;
+    private Integer orderAfter;
 
     public String getDataPath() {
         return dataPath;
@@ -46,6 +48,14 @@ public int getThreads() {
         return threads;
     }
 
+    public Integer getOrderBefore() {
+        return orderBefore;
+    }
+
+    public Integer getOrderAfter() {
+        return orderAfter;
+    }
+
     public ArrayList<DataConfigEntry.DataConfigGeneratorMapping> getMatchAttributes() {
         ArrayList<DataConfigEntry.DataConfigGeneratorMapping> matchAttributes = new ArrayList<>();
         for (DataConfigEntry.DataConfigGeneratorMapping attributeMapping: getAttributes()) {

src/main/java/configuration/ProcessorConfigEntry.java

@@ -66,7 +66,7 @@ public ConceptGenerator getRelationPlayerGenerator(String key) {
 
     public HashMap<String,ConceptGenerator> getRelationRequiredPlayers() {
         HashMap<String,ConceptGenerator> relationPlayers = new HashMap<>();
-        if (processorType.equals("relation") || processorType.equals("relation-with-relation")) {
+        if (processorType.equals("relation") || processorType.equals("nested-relation") || processorType.equals("attribute-relation")) {
             HashMap<String, ConceptGenerator> playerGenerators = getConceptGenerators().get("players");
             for (Map.Entry<String, ConceptGenerator> pg: playerGenerators.entrySet()) {
                 if (pg.getValue().isRequired()) {

src/main/java/generator/AppendAttributeGenerator.java

@@ -15,14 +15,15 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import static generator.GeneratorUtil.*;
+import static generator.GeneratorUtil.addAttribute;
+import static generator.GeneratorUtil.malformedRow;
 
 public class AppendAttributeGenerator extends InsertGenerator {
 
-    private final DataConfigEntry dce;
-    private final ProcessorConfigEntry pce;
     private static final Logger appLogger = LogManager.getLogger("com.bayer.dt.grami");
     private static final Logger dataLogger = LogManager.getLogger("com.bayer.dt.grami.data");
+    private final DataConfigEntry dce;
+    private final ProcessorConfigEntry pce;
 
     public AppendAttributeGenerator(DataConfigEntry dataConfigEntry,
                                     ProcessorConfigEntry processorConfigEntry) {
@@ -33,24 +34,25 @@ public AppendAttributeGenerator(DataConfigEntry dataConfigEntry,
     }
 
     public HashMap<String, ArrayList<ArrayList<ThingVariable<?>>>> graknAppendAttributeInsert(ArrayList<String> rows,
-                                                                                              String header) throws Exception {
+                                                                                              String header, int rowCounter) throws Exception {
         HashMap<String, ArrayList<ArrayList<ThingVariable<?>>>> matchInsertPatterns = new HashMap<>();
 
         ArrayList<ArrayList<ThingVariable<?>>> matchPatterns = new ArrayList<>();
         ArrayList<ArrayList<ThingVariable<?>>> insertPatterns = new ArrayList<>();
 
         int insertCounter = 0;
-
+        int batchCounter = 1;
         for (String row : rows) {
-            ArrayList<ArrayList<ThingVariable<?>>> tmp = graknAppendAttributeQueryFromRow(row, header, insertCounter);
+
+            ArrayList<ArrayList<ThingVariable<?>>> tmp = graknAppendAttributeQueryFromRow(row, header, insertCounter, rowCounter + batchCounter);
             if (tmp != null) {
                 if (tmp.get(0) != null && tmp.get(1) != null) {
                     matchPatterns.add(tmp.get(0));
                     insertPatterns.add(tmp.get(1));
                     insertCounter++;
                 }
             }
-
+            batchCounter = batchCounter + 1;
         }
         matchInsertPatterns.put("match", matchPatterns);
         matchInsertPatterns.put("insert", insertPatterns);
@@ -59,7 +61,8 @@ public HashMap<String, ArrayList<ArrayList<ThingVariable<?>>>> graknAppendAttrib
 
     public ArrayList<ArrayList<ThingVariable<?>>> graknAppendAttributeQueryFromRow(String row,
                                                                                    String header,
-                                                                                   int insertCounter) throws Exception {
+                                                                                   int insertCounter,
+                                                                                   int rowCounter) throws Exception {
         String fileSeparator = dce.getSeparator();
         String[] rowTokens = row.split(fileSeparator);
         String[] columnNames = header.split(fileSeparator);
@@ -77,7 +80,7 @@ public ArrayList<ArrayList<ThingVariable<?>>> graknAppendAttributeQueryFromRow(S
         Thing appendAttributeMatchPattern = addEntityToMatchPattern(insertCounter);
         for (DataConfigEntry.DataConfigGeneratorMapping generatorMappingForMatchAttribute : dce.getAttributes()) {
             if (generatorMappingForMatchAttribute.isMatch()) {
-                appendAttributeMatchPattern = addAttribute(rowTokens, appendAttributeMatchPattern, columnNames, generatorMappingForMatchAttribute, pce, generatorMappingForMatchAttribute.getPreprocessor());
+                appendAttributeMatchPattern = addAttribute(rowTokens, appendAttributeMatchPattern, columnNames, rowCounter, generatorMappingForMatchAttribute, pce, generatorMappingForMatchAttribute.getPreprocessor());
             }
         }
         matchPatterns.add(appendAttributeMatchPattern);
@@ -87,7 +90,7 @@ public ArrayList<ArrayList<ThingVariable<?>>> graknAppendAttributeQueryFromRow(S
         Thing appendAttributeInsertPattern = null;
         for (DataConfigEntry.DataConfigGeneratorMapping generatorMappingForAppendAttribute : dce.getAttributes()) {
             if (!generatorMappingForAppendAttribute.isMatch()) {
-                appendAttributeInsertPattern = addAttribute(rowTokens, thingVar, columnNames, generatorMappingForAppendAttribute, pce, generatorMappingForAppendAttribute.getPreprocessor());
+                appendAttributeInsertPattern = addAttribute(rowTokens, thingVar, rowCounter, columnNames, generatorMappingForAppendAttribute, pce, generatorMappingForAppendAttribute.getPreprocessor());
             }
         }
         if (appendAttributeInsertPattern != null) {
@@ -100,10 +103,10 @@ public ArrayList<ArrayList<ThingVariable<?>>> graknAppendAttributeQueryFromRow(S
 
 
         if (isValid(assembledPatterns)) {
-            appLogger.debug("valid query: <" + assembleQuery(assembledPatterns).toString() + ">");
+            appLogger.debug("valid query: <" + assembleQuery(assembledPatterns) + ">");
             return assembledPatterns;
         } else {
-            dataLogger.warn("in datapath <" + dce.getDataPath() + ">: skipped row b/c does not contain at least one match attribute and one insert attribute. Faulty tokenized row: " + Arrays.toString(rowTokens));
+            dataLogger.warn("in datapath <" + dce.getDataPath() + ">: skipped row " + rowCounter + " b/c does not contain at least one match attribute and one insert attribute. Faulty tokenized row: " + Arrays.toString(rowTokens));
             return null;
         }
     }

src/main/java/generator/AttributeInsertGenerator.java

@@ -31,23 +31,25 @@ public AttributeInsertGenerator(DataConfigEntry dataConfigEntry, ProcessorConfig
     }
 
     public ArrayList<ThingVariable<?>> graknAttributeInsert(ArrayList<String> rows,
-                                                            String header) throws IllegalArgumentException {
+                                                            String header, int rowCounter) throws IllegalArgumentException {
         ArrayList<ThingVariable<?>> patterns = new ArrayList<>();
+        int batchCount = 1;
         for (String row : rows) {
             try {
-                ThingVariable<?> temp = graknAttributeQueryFromRow(row, header);
+                ThingVariable<?> temp = graknAttributeQueryFromRow(row, header, rowCounter + batchCount);
                 if (temp != null) {
                     patterns.add(temp);
                 }
             } catch (Exception e) {
                 e.printStackTrace();
             }
+            batchCount = batchCount + 1;
         }
         return patterns;
     }
 
     public ThingVariable<Attribute> graknAttributeQueryFromRow(String row,
-                                                               String header) throws Exception {
+                                                               String header, int rowCounter) throws Exception {
         String fileSeparator = dce.getSeparator();
         String[] rowTokens = row.split(fileSeparator);
         String[] columnNames = header.split(fileSeparator);
@@ -58,7 +60,7 @@ public ThingVariable<Attribute> graknAttributeQueryFromRow(String row,
         Attribute attributeInsertStatement = null;
 
         for (DataConfigEntry.DataConfigGeneratorMapping generatorMappingForAttribute : dce.getAttributes()) {
-            attributeInsertStatement = addValue(rowTokens, attributeInitialStatement, columnNames, generatorMappingForAttribute, pce, generatorMappingForAttribute.getPreprocessor());
+            attributeInsertStatement = addValue(rowTokens, attributeInitialStatement, rowCounter, columnNames, generatorMappingForAttribute, pce, generatorMappingForAttribute.getPreprocessor());
         }
 
         if (attributeInsertStatement != null) {
@@ -68,7 +70,7 @@ public ThingVariable<Attribute> graknAttributeQueryFromRow(String row,
                 appLogger.debug("valid query: <insert " + attributeInsertStatement.toString() + ";>");
                 return attributeInsertStatement;
             } else {
-                dataLogger.warn("in datapath <" + dce.getDataPath() + ">: skipped row b/c does not have a proper <isa> statement or is missing required attributes. Faulty tokenized row: " + Arrays.toString(rowTokens));
+                dataLogger.warn("in datapath <" + dce.getDataPath() + ">: skipped row " + rowCounter + " b/c does not have a proper <isa> statement or is missing required attributes. Faulty tokenized row: " + Arrays.toString(rowTokens));
                 return null;
             }
         } else {