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fix(template): ReferenceBundleId in EMBRC data
1 parent acae40b commit 386044e

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15 files changed

+3215
-1837
lines changed

15 files changed

+3215
-1837
lines changed

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/embrc/CpmEmbrcTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -57,7 +57,7 @@ private static Stream<Object[]> dataSetProvider() {
5757

5858
private static Stream<Object[]> documentProvider() {
5959
return Stream.of(
60-
new Object[]{Dataset1Transformer.class, 1, 6, 35, 2},
60+
new Object[]{Dataset1Transformer.class, 1, 7, 35, 2},
6161
new Object[]{Dataset2Transformer.class, 2, 4, 11, 2},
6262
new Object[]{Dataset3Transformer.class, 3, 4, 7, 2},
6363
new Object[]{Dataset4Transformer.class, 4, 3, 41, 2}

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/embrc/transform/cpm/Dataset1Transformer.java‎

Lines changed: 30 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -8,16 +8,21 @@
88

99
import java.util.List;
1010

11-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset2Transformer.PROCESSED_SAMPLE_CON;
11+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset2Transformer.PROCESSING;
1212
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset3Transformer.IDENTIFIED_SPECIES_CON;
13-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset4Transformer.FILTERED_SEQUENCES_CON;
13+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset3Transformer.SPECIES_IDENTIFICATION;
14+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset4Transformer.DNA_SEQUENCING;
1415

1516
public class Dataset1Transformer extends DatasetTransformer {
16-
static final String SAMPLING = "sampling";
17-
static final String STORED_SAMPLE = "stored-sample-";
18-
static final String STORED_SAMPLE_CON = "stored-sample-con-";
19-
static final String STORED_SAMPLE_CON_R1 = STORED_SAMPLE_CON + "r1";
20-
static final String STORED_SAMPLE_CON_R2_3UM = STORED_SAMPLE_CON + "r2-3um";
17+
static final String SAMPLING = "Sampling";
18+
19+
static final String STORED_SAMPLE = "StoredSample";
20+
static final String STORED_SAMPLE_R1 = STORED_SAMPLE + "_r1";
21+
static final String STORED_SAMPLE_R2_3UM = STORED_SAMPLE + "_r2_3um";
22+
23+
static final String STORED_SAMPLE_CON = "StoredSampleCon";
24+
static final String STORED_SAMPLE_CON_R1 = STORED_SAMPLE_CON + "_r1";
25+
static final String STORED_SAMPLE_CON_R2_3UM = STORED_SAMPLE_CON + "_r2_3um";
2126

2227
private static final String STORING_ACTIVITY_R1 = "09a6f65fe087c3806631e8926fa3cae8e049cfdfa2b0b63fe6de04bc88144e80";
2328
private static final String STORING_ACTIVITY_R2_3um = "67c557a442ca2446b987928fb47c4bbbd59c54395e61f01949d76c06e0106925";
@@ -32,7 +37,7 @@ public Dataset1Transformer(ProvFactory pF, ICpmProvFactory cPF) {
3237
@Override
3338
protected Document createTI(IndexedDocument indexedDS) {
3439
TraversalInformation ti = new TraversalInformation();
35-
ti.setBundleName(newQNWithBlankNS(SAMPLING + "-bundle"));
40+
ti.setBundleName(newQNWithBlankNS(SAMPLING + "Bundle"));
3641

3742
MainActivity mA = new MainActivity(newQNWithBlankNS(SAMPLING));
3843
ti.setMainActivity(mA);
@@ -41,40 +46,46 @@ protected Document createTI(IndexedDocument indexedDS) {
4146

4247
ForwardConnector fcR1 = new ForwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R1));
4348

44-
SpecializationOf specR1 = pF.newSpecializationOf(newQNWithBlankNS(STORED_SAMPLE + "r1"), fcR1.getId());
49+
ForwardConnector fcR1Spec = new ForwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R1 + "_Spec"));
50+
fcR1Spec.setReferencedBundleId(newQNWithBlankNS(PROCESSING + "Bundle"));
51+
fcR1Spec.setSpecializationOf(fcR1.getId());
52+
53+
SpecializationOf specR1 = pF.newSpecializationOf(newQNWithBlankNS(STORED_SAMPLE_R1), fcR1.getId());
4554
indexedDS.add(specR1);
4655

4756
ForwardConnector fcR23UM = new ForwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R2_3UM));
4857

49-
SpecializationOf specR23UM = pF.newSpecializationOf(newQNWithBlankNS(STORED_SAMPLE + "r2_3um"), fcR23UM.getId());
58+
ForwardConnector fcR23UMSpec = new ForwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R2_3UM + "_Spec"));
59+
fcR23UMSpec.setReferencedBundleId(newQNWithBlankNS(DNA_SEQUENCING + "Bundle"));
60+
fcR23UMSpec.setSpecializationOf(fcR23UM.getId());
61+
62+
SpecializationOf specR23UM = pF.newSpecializationOf(newQNWithBlankNS(STORED_SAMPLE_R2_3UM), fcR23UM.getId());
5063
indexedDS.add(specR23UM);
5164

5265
mA.setGenerated(List.of(fcR1.getId(), fcR23UM.getId()));
5366

54-
ForwardConnector fCProc = new ForwardConnector(newQNWithBlankNS(PROCESSED_SAMPLE_CON));
55-
fCProc.setDerivedFrom(List.of(fcR1.getId()));
56-
5767
ForwardConnector fCIden = new ForwardConnector(newQNWithBlankNS(IDENTIFIED_SPECIES_CON));
58-
fCIden.setDerivedFrom(List.of(fCProc.getId()));
68+
fCIden.setDerivedFrom(List.of(fcR1.getId()));
5969

60-
ForwardConnector fCFil = new ForwardConnector(newQNWithBlankNS(FILTERED_SEQUENCES_CON));
61-
fCFil.setDerivedFrom(List.of(fcR23UM.getId()));
70+
ForwardConnector fCIdenSpec = new ForwardConnector(newQNWithBlankNS(IDENTIFIED_SPECIES_CON + "Spec"));
71+
fCIdenSpec.setReferencedBundleId(newQNWithBlankNS(SPECIES_IDENTIFICATION + "Bundle"));
72+
fCIdenSpec.setSpecializationOf(fCIden.getId());
6273

63-
ti.getForwardConnectors().addAll(List.of(fcR1, fcR23UM, fCProc, fCIden, fCFil));
74+
ti.getForwardConnectors().addAll(List.of(fcR1, fcR1Spec, fcR23UM, fcR23UMSpec, fCIden, fCIdenSpec));
6475

6576
return mapper.map(ti);
6677
}
6778

6879
@Override
6980
protected void modifyDS(IndexedDocument indexedDS) {
70-
Entity storedR1 = pF.newEntity(newQNWithBlankNS(STORED_SAMPLE + "r1"));
81+
Entity storedR1 = pF.newEntity(newQNWithBlankNS(STORED_SAMPLE_R1));
7182
storedR1.getType().addAll(indexedDS.getEntity(newQNWithBlankNS(SAMPLE_R1)).getType());
7283
indexedDS.add(storedR1);
7384

7485
WasGeneratedBy storingGenR1 = pF.newWasGeneratedBy(null, storedR1.getId(), newQnWithGenNS(STORING_ACTIVITY_R1));
7586
indexedDS.add(storingGenR1);
7687

77-
Entity storedR23UM = pF.newEntity(newQNWithBlankNS(STORED_SAMPLE + "r2_3um"));
88+
Entity storedR23UM = pF.newEntity(newQNWithBlankNS(STORED_SAMPLE_R2_3UM));
7889
storedR23UM.getType().addAll(indexedDS.getEntity(newQNWithBlankNS(SAMPLE_R2_3UM)).getType());
7990
indexedDS.add(storedR23UM);
8091

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/embrc/transform/cpm/Dataset2Transformer.java‎

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -6,13 +6,12 @@
66

77
import java.util.List;
88

9-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.SAMPLE_R1;
10-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.STORED_SAMPLE_CON_R1;
11-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset3Transformer.IDENTIFIED_SPECIES_CON;
9+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.*;
10+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset3Transformer.SPECIES_IDENTIFICATION;
1211

1312
public class Dataset2Transformer extends DatasetTransformer {
14-
static final String PROCESSING = "processing";
15-
static final String PROCESSED_SAMPLE_CON = "processed-sample-con-r1";
13+
static final String PROCESSING = "Processing";
14+
static final String PROCESSED_SAMPLE_CON = "ProcessedSampleCon";
1615

1716
private static final String IMAGES = "5017bc3edda5006a4c29737b48585fefdfd4ef740bed03ab10730ec86e4153d7";
1817

@@ -23,14 +22,15 @@ public Dataset2Transformer(ProvFactory pF, ICpmProvFactory cPF) {
2322
@Override
2423
protected Document createTI(IndexedDocument indexedDS) {
2524
TraversalInformation ti = new TraversalInformation();
26-
ti.setBundleName(newQNWithBlankNS(PROCESSING + "-bundle"));
25+
ti.setBundleName(newQNWithBlankNS(PROCESSING + "Bundle"));
2726

2827
MainActivity mA = new MainActivity(newQNWithBlankNS(PROCESSING));
2928
ti.setMainActivity(mA);
3029

3130
mA.setHasPart(indexedDS.getActivities().stream().map(Identifiable::getId).toList());
3231

3332
BackwardConnector bC = new BackwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R1));
33+
bC.setReferencedBundleId(newQNWithBlankNS(SAMPLING + "Bundle"));
3434
ti.setBackwardConnectors(List.of(bC));
3535

3636
SpecializationOf specBc = pF.newSpecializationOf(newQNWithBlankNS(SAMPLE_R1), bC.getId());
@@ -41,15 +41,16 @@ protected Document createTI(IndexedDocument indexedDS) {
4141
ForwardConnector fC = new ForwardConnector(newQNWithBlankNS(PROCESSED_SAMPLE_CON));
4242
fC.setDerivedFrom(List.of(bC.getId()));
4343

44+
ForwardConnector fCSpec = new ForwardConnector(newQNWithBlankNS(PROCESSED_SAMPLE_CON + "Spec"));
45+
fCSpec.setReferencedBundleId(newQNWithBlankNS(SPECIES_IDENTIFICATION + "Bundle"));
46+
fCSpec.setSpecializationOf(fC.getId());
47+
4448
SpecializationOf specFc = pF.newSpecializationOf(newQnWithGenNS(IMAGES), fC.getId());
4549
indexedDS.add(specFc);
4650

4751
mA.setGenerated(List.of(fC.getId()));
4852

49-
ForwardConnector fCIden = new ForwardConnector(newQNWithBlankNS(IDENTIFIED_SPECIES_CON));
50-
fCIden.setDerivedFrom(List.of(fC.getId()));
51-
52-
ti.setForwardConnectors(List.of(fC, fCIden));
53+
ti.setForwardConnectors(List.of(fC, fCSpec));
5354

5455
return mapper.map(ti);
5556
}

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/embrc/transform/cpm/Dataset3Transformer.java‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,14 @@
66

77
import java.util.List;
88

9+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.SAMPLING;
910
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.STORED_SAMPLE_CON_R1;
1011
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset2Transformer.PROCESSED_SAMPLE_CON;
12+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset2Transformer.PROCESSING;
1113

1214
public class Dataset3Transformer extends DatasetTransformer {
13-
static final String SPECIES_IDENTIFICATION = "species-identification";
14-
static final String IDENTIFIED_SPECIES_CON = "identified-species-con";
15+
static final String SPECIES_IDENTIFICATION = "SpeciesIdentification";
16+
static final String IDENTIFIED_SPECIES_CON = "IdentifiedSpeciesCon";
1517

1618
private static final String IMAGES = "db2aef1f9e9cdf745897953efba7931099655ee21f323526decd0ad11b4cc0e0";
1719
private static final String RESULTS = "ac6f25ecc17ae20cbb5789ee654db6d401c771b4ad4c9e971a0d960c3b596ac4";
@@ -23,21 +25,23 @@ public Dataset3Transformer(ProvFactory pF, ICpmProvFactory cPF) {
2325
@Override
2426
protected Document createTI(IndexedDocument indexedDS) {
2527
TraversalInformation ti = new TraversalInformation();
26-
ti.setBundleName(newQNWithBlankNS(SPECIES_IDENTIFICATION + "-bundle"));
28+
ti.setBundleName(newQNWithBlankNS(SPECIES_IDENTIFICATION + "Bundle"));
2729

2830
MainActivity mA = new MainActivity(newQNWithBlankNS(SPECIES_IDENTIFICATION));
2931
ti.setMainActivity(mA);
3032

3133
mA.setHasPart(indexedDS.getActivities().stream().map(Identifiable::getId).toList());
3234

3335
BackwardConnector bC = new BackwardConnector(newQNWithBlankNS(PROCESSED_SAMPLE_CON));
36+
bC.setReferencedBundleId(newQNWithBlankNS(PROCESSING + "Bundle"));
3437

3538
SpecializationOf specBc = pF.newSpecializationOf(newQnWithGenNS(IMAGES), bC.getId());
3639
indexedDS.add(specBc);
3740

3841
mA.setUsed(List.of(new MainActivityUsed(bC.getId())));
3942

4043
BackwardConnector bcStored = new BackwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R1));
44+
bcStored.setReferencedBundleId(newQNWithBlankNS(SAMPLING + "Bundle"));
4145
bC.setDerivedFrom(List.of(bcStored.getId()));
4246

4347
ti.setBackwardConnectors(List.of(bC, bcStored));

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/embrc/transform/cpm/Dataset4Transformer.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,12 +7,11 @@
77
import java.util.List;
88
import java.util.Objects;
99

10-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.SAMPLE_R2_3UM;
11-
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.STORED_SAMPLE_CON_R2_3UM;
10+
import static cz.muni.fi.cpm.template.deserialization.embrc.transform.cpm.Dataset1Transformer.*;
1211

1312
public class Dataset4Transformer extends DatasetTransformer {
14-
static final String DNA_SEQUENCING = "dna-sequencing";
15-
static final String FILTERED_SEQUENCES_CON = "filtered-sequences-con";
13+
static final String DNA_SEQUENCING = "DnaSequencing";
14+
static final String FILTERED_SEQUENCES_CON = "FilteredSequencesCon";
1615

1716
private static final String STORING_ACTIVITY_1 = "StoringActivity";
1817
private static final String STORING_ACTIVITY_2 = "StoringActivity2";
@@ -32,14 +31,15 @@ public Dataset4Transformer(ProvFactory pF, ICpmProvFactory cPF) {
3231
@Override
3332
protected Document createTI(IndexedDocument indexedDS) {
3433
TraversalInformation ti = new TraversalInformation();
35-
ti.setBundleName(newQNWithBlankNS(DNA_SEQUENCING + "-bundle"));
34+
ti.setBundleName(newQNWithBlankNS(DNA_SEQUENCING + "Bundle"));
3635

3736
MainActivity mA = new MainActivity(newQNWithBlankNS(DNA_SEQUENCING));
3837
ti.setMainActivity(mA);
3938

4039
mA.setHasPart(indexedDS.getActivities().stream().map(Identifiable::getId).toList());
4140

4241
BackwardConnector bC = new BackwardConnector(newQNWithBlankNS(STORED_SAMPLE_CON_R2_3UM));
42+
bC.setReferencedBundleId(newQNWithBlankNS(SAMPLING + "Bundle"));
4343
ti.setBackwardConnectors(List.of(bC));
4444

4545
mA.setUsed(List.of(new MainActivityUsed(bC.getId())));

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