adds footers to report files

src/main/java/org/reactome/DuplicateChecker.java

@@ -41,6 +41,8 @@ public void findAndLogDuplicates() throws Exception {
                     referenceMolecule.getDisplayName()
                 );
             }
+
+            this.duplicateReferenceMoleculeReporter.writeFooterIfInitialized();
         }
     }
 

src/main/java/org/reactome/Main.java

@@ -64,6 +64,10 @@ private static void updateReferenceMolecules(List<GKInstance> referenceMolecules
             processedCount += referenceMoleculeBatch.size();
             logger.info("Finished processing " + processedCount + " reference molecules");
         }
+
+        failedChEBILookupReporter.writeFooterIfInitialized();
+        referenceMoleculeChEBIIdentifierChangeReporter.writeFooterIfInitialized();
+        dbInteractor.closeReports();
     }
 
     private static void updateReferenceMoleculeBatch(List<GKInstance> referenceMoleculeBatch) throws Exception {

src/main/java/org/reactome/database/DBInteractor.java

@@ -12,6 +12,7 @@
 import org.reactome.reports.ReferenceMoleculeNameChangeReporter;
 import org.reactome.reports.SimpleEntityNameChangeReporter;
 
+import java.io.IOException;
 import java.sql.SQLException;
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
@@ -177,6 +178,12 @@ public boolean updateModifiedInstanceEdits(GKInstance instance) throws Exception
         return true;
     }
 
+    public void closeReports() throws IOException {
+        this.referenceMoleculeNameChangeReporter.writeFooterIfInitialized();
+        this.referenceMoleculeFormulaChangeReporter.writeFooterIfInitialized();
+        this.simpleEntityNameChangeReporter.writeFooterIfInitialized();
+    }
+
     GKInstance getInstanceEdit() throws Exception {
         if (instanceEdit == null) {
             instanceEdit = new GKInstance(getSchema().getClassByName(ReactomeJavaConstants.InstanceEdit));

src/main/java/org/reactome/reports/AbstractReporter.java

@@ -0,0 +1,74 @@
+package org.reactome.reports;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+
+public abstract class AbstractReporter {
+
+    private boolean initialized;
+
+    public abstract String getHeader();
+
+    public abstract String getFooter();
+
+    public abstract Path getFilePath();
+
+    public Path getReportDirectory() {
+        return Paths.get("reports");
+    }
+
+    public void report(String ...values) throws IOException {
+        initializeIfNeeded();
+
+        String reportLine = String.join("\t", values).concat(System.lineSeparator());
+        Files.write(
+            getFilePath(),
+            reportLine.getBytes(),
+            StandardOpenOption.APPEND
+        );
+    }
+
+    public void writeFooterIfInitialized() throws IOException {
+        if (!initialized) {
+            return;
+        }
+
+        String footerWithPrependedNewLines = ""
+            .concat(System.lineSeparator())
+            .concat(System.lineSeparator())
+            .concat(getFooter());
+
+        Files.write(
+            getFilePath(),
+            footerWithPrependedNewLines.getBytes(),
+            StandardOpenOption.APPEND
+        );
+    }
+
+    private void writeHeader() throws IOException {
+        Files.write(
+            getFilePath(),
+            getHeader().concat(System.lineSeparator()).getBytes(),
+            StandardOpenOption.CREATE, StandardOpenOption.APPEND
+        );
+    }
+
+    private void initializeIfNeeded() throws IOException {
+        if (initialized) {
+            return;
+        }
+
+        if (Files.notExists(getReportDirectory())) {
+            Files.createDirectories(getReportDirectory());
+        }
+
+        if (Files.notExists(getFilePath())) {
+            writeHeader();
+        }
+
+        initialized = true;
+    }
+}

src/main/java/org/reactome/reports/DuplicateReferenceMoleculeReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class DuplicateReferenceMoleculeReporter implements Reportable {
+public class DuplicateReferenceMoleculeReporter extends AbstractReporter {
 
     @Override
     public String getHeader() {
@@ -15,6 +15,12 @@ public String getHeader() {
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This report specifies Reference Molecule instances with duplicated ChEBI identifiers.  " +
+            "Where possible, these should be merged and/or all but one removed from the curator database.";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("duplicates.tsv"));

src/main/java/org/reactome/reports/FailedChEBILookupReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class FailedChEBILookupReporter implements Reportable {
+public class FailedChEBILookupReporter extends AbstractReporter {
 
     @Override
     public String getHeader() {
@@ -14,6 +14,13 @@ public String getHeader() {
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This report specifies Reference Molecule instances whose ChEBI identifier couldn't be retrieved " +
+            "from the external ChEBI API.  This may have been due to an intermittent service interruption or an " +
+            "invalid ChEBI identifier.  The identifiers reported should be checked manually in ChEBI to verify them.";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("failed-chebi-lookups.tsv"));

src/main/java/org/reactome/reports/ReferenceMoleculeChEBIIdentifierChangeReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class ReferenceMoleculeChEBIIdentifierChangeReporter implements Reportable {
+public class ReferenceMoleculeChEBIIdentifierChangeReporter extends AbstractReporter {
 
     @Override
     public String getHeader() {
@@ -13,12 +13,20 @@ public String getHeader() {
             "Reference Molecule",
             "Deprecated Identifier",
             "Replacement Identifier",
-            "Affected referenceEntity DB_IDs",
-            "DB_ID of Molecule with Replacement Identifier",
-            "DB_IDs of referenceEntities of Molecule with Replacement Identifier"
+            "Affected Simple Entity DB_IDs",
+            "DB_ID of Reference Molecule with Replacement Identifier",
+            "DB_IDs of Simple Entities of Reference Molecule with Replacement Identifier"
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This reports specifies Reference Molecule instances whose ChEBI identifier has changed. " +
+            "For any instances reported, it is necessary to move the SimpleEntity referrers to the new " +
+            "Reference Molecule with the replacement identifier and remove the old Reference Molecule with " +
+            "deprecated identifier";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("reference-molecule-chebi-identifier-changes.tsv"));

src/main/java/org/reactome/reports/ReferenceMoleculeFormulaChangeReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class ReferenceMoleculeFormulaChangeReporter implements Reportable {
+public class ReferenceMoleculeFormulaChangeReporter extends AbstractReporter {
     @Override
     public String getHeader() {
         return String.join("\t",
@@ -15,6 +15,13 @@ public String getHeader() {
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This report specifies when a Reference Molecule instance has a new chemical formula. " +
+            "This report is only informational as the changes have already been applied in the database - " +
+            " nothing need be done.";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("reference-molecule-formula-changes.tsv"));

src/main/java/org/reactome/reports/ReferenceMoleculeNameChangeReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class ReferenceMoleculeNameChangeReporter implements Reportable {
+public class ReferenceMoleculeNameChangeReporter extends AbstractReporter {
     @Override
     public String getHeader() {
         return String.join("\t",
@@ -15,6 +15,13 @@ public String getHeader() {
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This report specifies when a Reference Molecule instance has a new name. " +
+            "This report is only informational as the changes have already been applied in the database - " +
+            " nothing need be done.";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("reference-molecule-name-changes.tsv"));

src/main/java/org/reactome/reports/SimpleEntityNameChangeReporter.java

@@ -3,7 +3,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public class SimpleEntityNameChangeReporter implements Reportable {
+public class SimpleEntityNameChangeReporter extends AbstractReporter {
 
     @Override
     public String getHeader() {
@@ -18,6 +18,13 @@ public String getHeader() {
         );
     }
 
+    @Override
+    public String getFooter() {
+        return "This report specifies Simple Entities with updated names.  If the update is applied automatically " +
+            "(true for the last column), nothing need be done.  If the update is not applied automatically, it is " +
+            "a suggestion for curators to apply what is given in the 'Update Simple Entity Names' column.";
+    }
+
     @Override
     public Path getFilePath() {
         return getReportDirectory().resolve(Paths.get("simple-entity-name-changes.tsv"));