From 00ed6fb40301a0e50c78a3e154089421301e42ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C5=81ukasz=20Szeremeta?= <l.szeremeta.dev@gmail.com>
Date: Sat, 3 Apr 2021 22:20:52 +0200
Subject: [PATCH] Add subject type option

---
 README.md                                     |   1 +
 .../java/pl/edu/uwb/ii/sdfeater/File.java     |  11 +-
 .../java/pl/edu/uwb/ii/sdfeater/Molecule.java |  43 ++-
 .../java/pl/edu/uwb/ii/sdfeater/SDFEater.java |  50 ++-
 .../pl/edu/uwb/ii/sdfeater/OutputTest.java    | 325 ++++++++++++++++--
 5 files changed, 365 insertions(+), 65 deletions(-)

diff --git a/README.md b/README.md
index 82dd2a8..7405bd8 100644
--- a/README.md
+++ b/README.md
@@ -93,6 +93,7 @@ Running SDFEater without parameters displays help.
 * `-i,--input <arg>` - input SDF file path (required)
 * `-f,--format <arg>` - output format (e.g. `cypher`, `jsonld`, `cvme`, `smiles`, `inchi`) (required; full list below)
 * `-p,--periodic` - add additional atoms data from [periodic table](https://github.com/lszeremeta/SDFEater/blob/master/src/main/resources/pl/edu/uwb/ii/sdfeater/periodic_table.json) (for `cypher` output format)
+* `-s,--subject <arg>` - subject type (`iri`, `uuid`, `bnode`; `iri` by default; for all formats excluding cypher, cvme, smiles, inchi)
 * `-u,--urls` - try to generate full database URLs instead of IDs (for `cypher` output format, always enabled in `cvme`)
 
 Remember about the appropriate file path when using Docker image. Suppose you mounted your local directory `/home/user/input` under `/app/input` and the path to the SDF file you want to use in SDFEater is `/home/user/input/file.sdf`. In this case, enter the path `/app/input/file.sdf` or `input/file.sdf` as the value of the `-i` argument.
diff --git a/src/main/java/pl/edu/uwb/ii/sdfeater/File.java b/src/main/java/pl/edu/uwb/ii/sdfeater/File.java
index 7ab1e64..d097577 100644
--- a/src/main/java/pl/edu/uwb/ii/sdfeater/File.java
+++ b/src/main/java/pl/edu/uwb/ii/sdfeater/File.java
@@ -58,9 +58,10 @@ class File {
      * appropriate program structures
      *
      * @param molecule Molecule object to which values from the file will be entered
-     * @param format   Output format from Format enum
+     * @param format   Output format
+     * @param subject  Subject type
      */
-    void parse(Molecule molecule, SDFEater.Format format) {
+    void parse(Molecule molecule, SDFEater.Format format, SDFEater.Subject subject) {
         try {
             FileInputStream fstream = new FileInputStream(filename);
             BufferedReader br = new BufferedReader(new InputStreamReader(fstream));
@@ -156,13 +157,13 @@ void parse(Molecule molecule, SDFEater.Format format) {
                             case jsonldhtml:
                             case rdfxml:
                             case rdfthrift:
-                                molecule.addToJenaModel();
+                                molecule.addToJenaModel(subject);
                                 break;
                             case rdfa:
-                                molecule.printRDFaMolecule();
+                                molecule.printRDFaMolecule(subject);
                                 break;
                             case microdata:
-                                molecule.printMicrodataMolecule();
+                                molecule.printMicrodataMolecule(subject);
                                 break;
                             default:
                                 break;
diff --git a/src/main/java/pl/edu/uwb/ii/sdfeater/Molecule.java b/src/main/java/pl/edu/uwb/ii/sdfeater/Molecule.java
index f55e3eb..bfb04f8 100644
--- a/src/main/java/pl/edu/uwb/ii/sdfeater/Molecule.java
+++ b/src/main/java/pl/edu/uwb/ii/sdfeater/Molecule.java
@@ -324,9 +324,20 @@ void printChemSKOSMolecule() {
 
     /**
      * Add main molecule data to Jena model
+     *
+     * @param subject subject type
      */
-    void addToJenaModel() {
-        Resource me = ResourceFactory.createResource("http://example.com/molecule#entity" + createID());
+    void addToJenaModel(SDFEater.Subject subject) {
+        Resource me = ResourceFactory.createResource();
+
+        if (subject == SDFEater.Subject.iri) {
+            me = ResourceFactory.createResource("http://example.com/molecule#entity" + createID());
+        } else if (subject == SDFEater.Subject.uuid) {
+            me = ResourceFactory.createResource("urn:uuid:" + uuid);
+        } else if (subject == SDFEater.Subject.bnode) {
+            me = ResourceFactory.createResource();
+        }
+
         for (Map.Entry<String, List<String>> entry : properties.entrySet()) {
 
             String key = entry.getKey();
@@ -381,7 +392,7 @@ void addToJenaModel() {
     /**
      * Print main molecule data in RDFa
      */
-    void printRDFaMolecule() {
+    void printRDFaMolecule(SDFEater.Subject subject) {
         StringBuilder output_str = new StringBuilder();
         for (Map.Entry<String, List<String>> entry : properties.entrySet()) {
             String key = entry.getKey();
@@ -421,8 +432,15 @@ void printRDFaMolecule() {
         }
 
         if (output_str.length() > 0) {
-            String mID = createID();
-            System.out.println("    <div typeof='schema:MolecularEntity' about='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
+            if (subject == SDFEater.Subject.iri) {
+                String mID = createID();
+                System.out.println("    <div typeof='schema:MolecularEntity' about='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
+            } else if (subject == SDFEater.Subject.uuid) {
+                System.out.println("    <div typeof='schema:MolecularEntity' about='urn:uuid:" + uuid + "'>");
+            } else if (subject == SDFEater.Subject.bnode) {
+                System.out.println("    <div typeof='schema:MolecularEntity' about='_:b" + createID() + "'>");
+            }
+
             System.out.print(output_str);
             System.out.println("    </div>");
         }
@@ -431,8 +449,10 @@ void printRDFaMolecule() {
 
     /**
      * Print main molecule data in Microdata
+     *
+     * @param subject subject type
      */
-    void printMicrodataMolecule() {
+    void printMicrodataMolecule(SDFEater.Subject subject) {
         StringBuilder output_str = new StringBuilder();
         for (Map.Entry<String, List<String>> entry : properties.entrySet()) {
             String key = entry.getKey();
@@ -472,8 +492,15 @@ void printMicrodataMolecule() {
         }
 
         if (output_str.length() > 0) {
-            String mID = createID();
-            System.out.println("    <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
+            if (subject == SDFEater.Subject.iri) {
+                String mID = createID();
+                System.out.println("    <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='http://example.com/molecule#entity" + mID + "' id='entity" + mID + "'>");
+            } else if (subject == SDFEater.Subject.uuid) {
+                System.out.println("    <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='urn:uuid:" + uuid + "'>");
+            } else if (subject == SDFEater.Subject.bnode) {
+                System.out.println("    <div itemscope itemtype='http://schema.org/MolecularEntity' itemid='_:b" + createID() + "'>");
+            }
+
             System.out.print(output_str);
             System.out.println("    </div>");
         }
diff --git a/src/main/java/pl/edu/uwb/ii/sdfeater/SDFEater.java b/src/main/java/pl/edu/uwb/ii/sdfeater/SDFEater.java
index b2ffc1e..9073335 100644
--- a/src/main/java/pl/edu/uwb/ii/sdfeater/SDFEater.java
+++ b/src/main/java/pl/edu/uwb/ii/sdfeater/SDFEater.java
@@ -87,6 +87,9 @@ public static void main(String[] args) {
         Option formatarg = new Option("f", "format", true, "output format (cypher, cvme, smiles, inchi, turtle, ntriples, rdfxml, rdfthrift, jsonldhtml, jsonld, rdfa, microdata)");
         formatarg.setRequired(true);
         options.addOption(formatarg);
+        Option subject = new Option("s", "subject", true, "subject type (iri, uuid, bnode; iri by default); for all formats excluding cypher, cvme, smiles, inchi");
+        subject.setRequired(false);
+        options.addOption(subject);
         Option urls = new Option("u", "urls", false, "try to generate full database URLs instead of IDs (for cypher output format, always enabled in cvme)");
         urls.setRequired(false);
         options.addOption(urls);
@@ -103,51 +106,57 @@ public static void main(String[] args) {
             if (cmd.hasOption("format")) {
                 String format = cmd.getOptionValue("format");
                 if (format.equalsIgnoreCase("cypher") && !cmd.hasOption("urls") && !cmd.hasOption("periodic")) {
-                    file.parse(molecule, Format.cypher);
+                    file.parse(molecule, Format.cypher, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("cypher") && cmd.hasOption("urls") && !cmd.hasOption("periodic")) {
-                    file.parse(molecule, Format.cypheru);
+                    file.parse(molecule, Format.cypheru, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("cypher") && cmd.hasOption("periodic") && !cmd.hasOption("urls")) {
                     loadPeriodicTableData();
-                    file.parse(molecule, Format.cypherp);
+                    file.parse(molecule, Format.cypherp, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("cypher") && cmd.hasOption("urls") && cmd.hasOption("periodic")) {
                     loadPeriodicTableData();
-                    file.parse(molecule, Format.cypherup);
+                    file.parse(molecule, Format.cypherup, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("cvme")) {
-                    file.parse(molecule, Format.cvme);
+                    file.parse(molecule, Format.cvme, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("smiles")) {
-                    file.parse(molecule, Format.smiles);
+                    file.parse(molecule, Format.smiles, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("inchi")) {
-                    file.parse(molecule, Format.inchi);
+                    file.parse(molecule, Format.inchi, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("turtle")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.turtle);
+                    file.parse(molecule, Format.turtle, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("ntriples")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.ntriples);
+                    file.parse(molecule, Format.ntriples, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("jsonldhtml")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.jsonldhtml);
+                    file.parse(molecule, Format.jsonldhtml, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("jsonld")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.jsonld);
+                    file.parse(molecule, Format.jsonld, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("rdfxml")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.rdfxml);
+                    file.parse(molecule, Format.rdfxml, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("rdfthrift")) {
                     initializeJenaModel();
-                    file.parse(molecule, Format.rdfthrift);
+                    file.parse(molecule, Format.rdfthrift, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("rdfa")) {
-                    file.parse(molecule, Format.rdfa);
+                    file.parse(molecule, Format.rdfa, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else if (format.equalsIgnoreCase("microdata")) {
-                    file.parse(molecule, Format.microdata);
+                    file.parse(molecule, Format.microdata, Subject.valueOf(cmd.getOptionValue("subject", Subject.iri.toString())));
                 } else {
                     System.err.println("The selected format is not supported");
                     formatter.printHelp("SDFEater.jar", options);
                 }
 
             }
+        } catch (IllegalArgumentException e) {
+            System.err.println("Incorrect option selected");
+            formatter.printHelp("SDFEater.jar", options);
         } catch (ParseException e) {
-            System.err.println(e.getMessage());
+            System.err.println("Parse error: " + e.getMessage());
+            formatter.printHelp("SDFEater.jar", options);
+        } catch (Exception e) {
+            System.err.println("Error: " + e.getMessage());
             formatter.printHelp("SDFEater.jar", options);
         }
     }
@@ -172,4 +181,13 @@ public enum Format {
         rdfa,
         microdata
     }
+
+    /**
+     * Subject type
+     */
+    public enum Subject {
+        iri,
+        uuid,
+        bnode
+    }
 }
diff --git a/src/test/java/pl/edu/uwb/ii/sdfeater/OutputTest.java b/src/test/java/pl/edu/uwb/ii/sdfeater/OutputTest.java
index a44045f..b5f4cb5 100644
--- a/src/test/java/pl/edu/uwb/ii/sdfeater/OutputTest.java
+++ b/src/test/java/pl/edu/uwb/ii/sdfeater/OutputTest.java
@@ -7,6 +7,7 @@
 import java.io.PrintStream;
 import java.nio.file.Paths;
 
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static pl.edu.uwb.ii.sdfeater.SDFEater.initializeJenaModel;
 import static pl.edu.uwb.ii.sdfeater.SDFEater.loadPeriodicTableData;
@@ -53,7 +54,7 @@ void setUp() {
      */
     @Test
     void cypherRawContainsRequiredStrings() {
-        file.parse(molecule, SDFEater.Format.cypher);
+        file.parse(molecule, SDFEater.Format.cypher, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"CREATE (", "{", "}", ",", ")", ":", "[", "]", "'", ":", "->", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:"};
         assertTrue(stringContainsAllValues(out, required));
@@ -64,7 +65,7 @@ void cypherRawContainsRequiredStrings() {
      */
     @Test
     void cypherRawContainsAllMoleculeData() {
-        file.parse(molecule, SDFEater.Format.cypher);
+        file.parse(molecule, SDFEater.Format.cypher, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -76,7 +77,7 @@ void cypherRawContainsAllMoleculeData() {
      */
     @Test
     void cypherURLContainsRequiredStrings() {
-        file.parse(molecule, SDFEater.Format.cypheru);
+        file.parse(molecule, SDFEater.Format.cypheru, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "http", "//", "/"};
         assertTrue(stringContainsAllValues(out, required));
@@ -87,7 +88,7 @@ void cypherURLContainsRequiredStrings() {
      */
     @Test
     void cypherURLContainsAllMoleculeData() {
-        file.parse(molecule, SDFEater.Format.cypheru);
+        file.parse(molecule, SDFEater.Format.cypheru, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -100,7 +101,7 @@ void cypherURLContainsAllMoleculeData() {
     @Test
     void cypherPeriodicContainsRequiredStrings() {
         loadPeriodicTableData();
-        file.parse(molecule, SDFEater.Format.cypherp);
+        file.parse(molecule, SDFEater.Format.cypherp, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "atomicNumber:", "name:", "Carbon", "atomicMass:", "bondingType:"};
         assertTrue(stringContainsAllValues(out, required));
@@ -112,7 +113,7 @@ void cypherPeriodicContainsRequiredStrings() {
     @Test
     void cypherPeriodicContainsAllMoleculeData() {
         loadPeriodicTableData();
-        file.parse(molecule, SDFEater.Format.cypherp);
+        file.parse(molecule, SDFEater.Format.cypherp, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -125,7 +126,7 @@ void cypherPeriodicContainsAllMoleculeData() {
     @Test
     void cypherAllContainsRequiredStrings() {
         loadPeriodicTableData();
-        file.parse(molecule, SDFEater.Format.cypherup);
+        file.parse(molecule, SDFEater.Format.cypherup, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "http", "//", "/", "atomicNumber:", "name:", "Carbon", "atomicMass:", "bondingType:"};
         assertTrue(stringContainsAllValues(out, required));
@@ -137,7 +138,7 @@ void cypherAllContainsRequiredStrings() {
     @Test
     void cypherAllContainsAllMoleculeData() {
         loadPeriodicTableData();
-        file.parse(molecule, SDFEater.Format.cypherup);
+        file.parse(molecule, SDFEater.Format.cypherup, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -149,7 +150,7 @@ void cypherAllContainsAllMoleculeData() {
      */
     @Test
     void cvmeContainsRequiredStrings() {
-        file.parse(molecule, SDFEater.Format.cvme);
+        file.parse(molecule, SDFEater.Format.cvme, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"skos:altLabel", "skos:definition", "skos:notation", "skos:prefLabel", "rdfs:seeAlso", "dbo:inchi", "dbp:inchikey", "dbo:casNumber", "skos:hiddenLabel", "skos:example", "urn:uuid:", "^^", "@", "chemskos:SMILES", ".", "<", ">", "http", ":", "//", "\"\"\"", "END", "C"};
         assertTrue(stringContainsAllValues(out, required));
@@ -160,7 +161,7 @@ void cvmeContainsRequiredStrings() {
      */
     @Test
     void cvmeContainsAllMoleculeData() {
-        file.parse(molecule, SDFEater.Format.cvme);
+        file.parse(molecule, SDFEater.Format.cvme, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -172,7 +173,7 @@ void cvmeContainsAllMoleculeData() {
      */
     @Test
     void smilesContainsSMILES() {
-        file.parse(molecule, SDFEater.Format.smiles);
+        file.parse(molecule, SDFEater.Format.smiles, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"[H][C@@]1(Oc2cc(O)cc(O)c2C[C@H]1O)c1ccc(O)c(O)c1", "CC1(C)[C@@H]2CC[C@@](C)(C2)C1=O"};
         assertTrue(stringContainsAllValues(out, required));
@@ -185,7 +186,7 @@ void smilesContainsSMILES() {
      */
     @Test
     void inchiContainsInChI() {
-        file.parse(molecule, SDFEater.Format.inchi);
+        file.parse(molecule, SDFEater.Format.inchi, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m1/s1", "InChI=1S/C10H16O/c1-9(2)7-4-5-10(3,6-7)8(9)11/h7H,4-6H2,1-3H3/t7-,10+/m1/s1"};
         assertTrue(stringContainsAllValues(out, required));
@@ -199,7 +200,7 @@ void inchiContainsInChI() {
     @Test
     void turtleContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.turtle);
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"@prefix", "schema.org", "rdf", "MolecularEntity", "[", ";", "]", ".", "<", ">", "http", "//", ":", "\""};
         assertTrue(stringContainsAllValues(out, required));
@@ -211,7 +212,7 @@ void turtleContainsRequiredStrings() {
     @Test
     void turtleContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.turtle);
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -222,11 +223,47 @@ void turtleContainsAllMoleculeDataFields() {
     @Test
     void turtleContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.turtle);
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if Turtle output have IRI subject
+     */
+    @Test
+    void turtleHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if Turtle output have uuid subject
+     */
+    @Test
+    void turtleHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if Turtle output have bNode subject
+     */
+    @Test
+    void turtleHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.turtle, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"[", "]"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
     // N-Triples
 
     /**
@@ -235,7 +272,7 @@ void turtleContainsAllMoleculeData() {
     @Test
     void nTriplesContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.ntriples);
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"schema.org", "rdf", "MolecularEntity", ".", "<", ">", "http", "//", ":", "\""};
         assertTrue(stringContainsAllValues(out, required));
@@ -247,7 +284,7 @@ void nTriplesContainsRequiredStrings() {
     @Test
     void nTriplesContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.ntriples);
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -258,11 +295,47 @@ void nTriplesContainsAllMoleculeDataFields() {
     @Test
     void nTriplesContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.ntriples);
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if N-Triples output have IRI subject
+     */
+    @Test
+    void nTriplesHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if N-Triples output have uuid subject
+     */
+    @Test
+    void nTriplesHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if N-Triples output have bNode subject
+     */
+    @Test
+    void nTriplesHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.ntriples, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"_:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
     // RDF/XML
 
     /**
@@ -271,7 +344,7 @@ void nTriplesContainsAllMoleculeData() {
     @Test
     void rdfXMLContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfxml);
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"<", ">", "rdf:RDF", "xmlns:", "<rdf:Description", "type", "MolecularEntity", "schema", "</", "&lt;", "&gt;"};
         assertTrue(stringContainsAllValues(out, required));
@@ -283,7 +356,7 @@ void rdfXMLContainsRequiredStrings() {
     @Test
     void rdfXMLContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfxml);
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -294,11 +367,47 @@ void rdfXMLContainsAllMoleculeDataFields() {
     @Test
     void rdfXMLContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfxml);
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if RDF/XML output have IRI subject
+     */
+    @Test
+    void rdfXMLHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if RDF/XML output have uuid subject
+     */
+    @Test
+    void rdfXMLHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if RDF/XML output have bNode subject
+     */
+    @Test
+    void rdfXMLHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfxml, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"rdf:about"};
+        assertFalse(stringContainsAllValues(out, required));
+    }
+
     // RDF Binary encoding using Thrift (rdfthrift)
 
     /**
@@ -307,7 +416,7 @@ void rdfXMLContainsAllMoleculeData() {
     @Test
     void rdfthriftContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfthrift);
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"schema", "rdf"};
         assertTrue(stringContainsAllValues(out, required));
@@ -319,7 +428,7 @@ void rdfthriftContainsRequiredStrings() {
     @Test
     void rdfthriftContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfthrift);
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -330,11 +439,47 @@ void rdfthriftContainsAllMoleculeDataFields() {
     @Test
     void rdfthriftContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.rdfthrift);
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if rdfthrift output have IRI subject
+     */
+    @Test
+    void rdfthriftHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if rdfthrift output have uuid subject
+     */
+    @Test
+    void rdfthriftHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if rdfthrift output have bNode subject
+     */
+    @Test
+    void rdfthriftHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfthrift, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity", "urn:uuid:"};
+        assertFalse(stringContainsAllValues(out, required));
+    }
+
     // JSON-LD + HTML
 
     /**
@@ -343,7 +488,7 @@ void rdfthriftContainsAllMoleculeData() {
     @Test
     void jsonldHtmlContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonldhtml);
+        file.parse(molecule, SDFEater.Format.jsonldhtml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"<", ">", "</", "script>", "@id", "{", "}", ",", "MolecularEntity"};
         assertTrue(stringContainsAllValues(out, required));
@@ -355,7 +500,7 @@ void jsonldHtmlContainsRequiredStrings() {
     @Test
     void jsonldHtmlContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonldhtml);
+        file.parse(molecule, SDFEater.Format.jsonldhtml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -366,7 +511,7 @@ void jsonldHtmlContainsAllMoleculeDataFields() {
     @Test
     void jsonldHtmlContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonldhtml);
+        file.parse(molecule, SDFEater.Format.jsonldhtml, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
@@ -379,7 +524,7 @@ void jsonldHtmlContainsAllMoleculeData() {
     @Test
     void jsonldContainsRequiredStrings() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonld);
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"@id", "{", "}", ",", "MolecularEntity"};
         assertTrue(stringContainsAllValues(out, required));
@@ -391,7 +536,7 @@ void jsonldContainsRequiredStrings() {
     @Test
     void jsonldContainsAllMoleculeDataFields() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonld);
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -402,11 +547,47 @@ void jsonldContainsAllMoleculeDataFields() {
     @Test
     void jsonldContainsAllMoleculeData() {
         initializeJenaModel();
-        file.parse(molecule, SDFEater.Format.jsonld);
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if JSON-LD output have IRI subject
+     */
+    @Test
+    void jsonldHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if JSON-LD output have uuid subject
+     */
+    @Test
+    void jsonldHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if JSON-LD output have bNode subject
+     */
+    @Test
+    void jsonldHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.jsonld, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"_:b0"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
     // RDFa
 
     /**
@@ -414,7 +595,7 @@ void jsonldContainsAllMoleculeData() {
      */
     @Test
     void rdfaContainsRequiredStrings() {
-        file.parse(molecule, SDFEater.Format.rdfa);
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"<", ">", "</", "typeof", "property", "MolecularEntity", "&lt;", "&gt;"};
         assertTrue(stringContainsAllValues(out, required));
@@ -425,7 +606,7 @@ void rdfaContainsRequiredStrings() {
      */
     @Test
     void rdfaContainsAllMoleculeDataFields() {
-        file.parse(molecule, SDFEater.Format.rdfa);
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -435,11 +616,47 @@ void rdfaContainsAllMoleculeDataFields() {
      */
     @Test
     void rdfaContainsAllMoleculeData() {
-        file.parse(molecule, SDFEater.Format.rdfa);
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if RDFa output have IRI subject
+     */
+    @Test
+    void rdfaHaveIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if RDFa output have uuid subject
+     */
+    @Test
+    void rdfaHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if RDFa output have bNode subject
+     */
+    @Test
+    void rdfaHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.rdfa, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"_:b"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
     // Microdata
 
     /**
@@ -447,7 +664,7 @@ void rdfaContainsAllMoleculeData() {
      */
     @Test
     void microdataContainsRequiredStrings() {
-        file.parse(molecule, SDFEater.Format.microdata);
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         String[] required = {"<", ">", "</", "itemscope", "itemtype", "itemprop", "MolecularEntity", "&lt;", "&gt;"};
         assertTrue(stringContainsAllValues(out, required));
@@ -458,7 +675,7 @@ void microdataContainsRequiredStrings() {
      */
     @Test
     void microdataContainsAllMoleculeDataFields() {
-        file.parse(molecule, SDFEater.Format.microdata);
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeDataFields));
     }
@@ -468,9 +685,45 @@ void microdataContainsAllMoleculeDataFields() {
      */
     @Test
     void microdataContainsAllMoleculeData() {
-        file.parse(molecule, SDFEater.Format.microdata);
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.iri);
         String out = outputStreamCaptor.toString();
         assertTrue(stringContainsAllValues(out, testMoleculeData));
     }
 
+    /**
+     * Test if Microdata output have IRI subject
+     */
+    @Test
+    void microdataIRISubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.iri);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"http", "example.com", "molecule", "#", "entity"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if Microdata output have uuid subject
+     */
+    @Test
+    void microdataHaveUUIDSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.uuid);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"urn:uuid:"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
+    /**
+     * Test if Microdata output have bNode subject
+     */
+    @Test
+    void microdataHaveBNodeSubject() {
+        initializeJenaModel();
+        file.parse(molecule, SDFEater.Format.microdata, SDFEater.Subject.bnode);
+        String out = outputStreamCaptor.toString();
+        String[] required = {"_:b"};
+        assertTrue(stringContainsAllValues(out, required));
+    }
+
 }
\ No newline at end of file