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fix(template): MOU rename store to storage
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‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/CpmMouTest.java‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@
88
import cz.muni.fi.cpm.template.deserialization.mou.schema.Patient;
99
import cz.muni.fi.cpm.template.deserialization.mou.transform.acquisition.CpmAcquisitionTransformer;
1010
import cz.muni.fi.cpm.template.deserialization.mou.transform.acquisition.ProvAcquisitionTransformer;
11-
import cz.muni.fi.cpm.template.deserialization.mou.transform.store.CpmStoreTransformer;
12-
import cz.muni.fi.cpm.template.deserialization.mou.transform.store.ProvStoreTransformer;
11+
import cz.muni.fi.cpm.template.deserialization.mou.transform.storage.CpmStorageTransformer;
12+
import cz.muni.fi.cpm.template.deserialization.mou.transform.storage.ProvStorageTransformer;
1313
import cz.muni.fi.cpm.template.deserialization.pbm.PbmFactory;
1414
import cz.muni.fi.cpm.template.util.GraphvizChecker;
1515
import cz.muni.fi.cpm.vanilla.CpmProvFactory;
@@ -27,7 +27,7 @@
2727

2828
import static cz.muni.fi.cpm.template.constants.PathConstants.TEST_RESOURCES;
2929
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.ACQUISITION;
30-
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.STORE;
30+
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.STORAGE;
3131
import static org.junit.jupiter.api.Assertions.assertEquals;
3232
import static org.junit.jupiter.api.Assertions.fail;
3333

@@ -90,7 +90,7 @@ private void assertAcquisition(Document doc) {
9090
}
9191

9292
@Test
93-
public void toDocument_withMouTestDataStore_serialisesSuccessfully() {
93+
public void toDocument_withMouTestDataStorage_serialisesSuccessfully() {
9494
ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
9595

9696
Patient patient;
@@ -103,29 +103,29 @@ public void toDocument_withMouTestDataStore_serialisesSuccessfully() {
103103
}
104104

105105
InteropFramework interop = new InteropFramework();
106-
List<Document> pATDocs = new ProvStoreTransformer(patient, pF, cPF, pbmF).toDocuments();
107-
List<Document> cATDocs = new CpmStoreTransformer(patient, pF, cPF, pbmF).toDocuments();
106+
List<Document> pATDocs = new ProvStorageTransformer(patient, pF, cPF, pbmF).toDocuments();
107+
List<Document> cATDocs = new CpmStorageTransformer(patient, pF, cPF, pbmF).toDocuments();
108108
for (int i = 0; i < pATDocs.size(); i++) {
109109
Document pATDoc = pATDocs.get(i);
110-
assertStore(pATDoc);
110+
assertStorage(pATDoc);
111111

112112
Document cATDoc = cATDocs.get(i);
113-
assertStore(cATDoc);
113+
assertStorage(cATDoc);
114114

115115
Bundle pATBundle = (Bundle) pATDoc.getStatementOrBundle().getFirst();
116116
Bundle cATBundle = (Bundle) cATDoc.getStatementOrBundle().getFirst();
117117
assertEquals(new HashSet<>(pATBundle.getStatement()), new HashSet<>(cATBundle.getStatement()));
118118

119119
Bundle bundle = (Bundle) cATDoc.getStatementOrBundle().getFirst();
120-
String fileName = TEST_RESOURCES + MOU_FOLDER + STORE + File.separator + bundle.getId().getLocalPart().replace(":", "-");
120+
String fileName = TEST_RESOURCES + MOU_FOLDER + STORAGE + File.separator + bundle.getId().getLocalPart().replace(":", "-");
121121
interop.writeDocument(fileName + ".provn", cATDoc);
122122
if (GraphvizChecker.isGraphvizInstalled()) {
123123
interop.writeDocument(fileName + ".svg", cATDoc);
124124
}
125125
}
126126
}
127127

128-
private void assertStore(Document doc) {
128+
private void assertStorage(Document doc) {
129129
CpmDocument cpmDoc = new CpmDocument(doc, pF, cPF, cF);
130130
assertEquals(4, cpmDoc.getTraversalInformationPart().size());
131131
assertEquals(5, cpmDoc.getDomainSpecificPart().size());

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/constants/NameConstants.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,6 @@ public class NameConstants {
44
public static final String ACQUISITION = "acquisition";
55
public static final String ACQUISITION_CON = "sampleAcqConnector";
66

7-
public static final String STORE = "store";
8-
public static final String STORE_CON = "sampleStoreConnector";
7+
public static final String STORAGE = "storage";
8+
public static final String STOR_CON = "sampleStorConnector";
99
}

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/acquisition/CpmAcquisitionTransformer.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,7 @@ protected Document createTI(String suffix) {
4040
QualifiedName fcSpecId = ti.getNamespace().qualifiedName(BBMRI_PREFIX, ACQUISITION_CON + "Spec" + suffix, pF);
4141
ForwardConnector fCSpec = new ForwardConnector(fcSpecId);
4242
fCSpec.setSpecializationOf(fcID);
43-
fCSpec.setReferencedBundleId(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORE + "Bundle" + suffix, pF));
43+
fCSpec.setReferencedBundleId(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORAGE + "Bundle" + suffix, pF));
4444
ti.getForwardConnectors().add(fCSpec);
4545

4646
QualifiedName agentId = ti.getNamespace().qualifiedName(BBMRI_PREFIX, patient.getBiobank(), pF);

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/acquisition/ProvAcquisitionTransformer.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ protected Document createTI(String suffix) {
3131
"receiver_id", newQDescriptor(BBMRI_PREFIX + ":" + patient.getBiobank()),
3232
"forward_conn_id_spec", newQDescriptor(BBMRI_PREFIX + ":" + ACQUISITION_CON + "Spec" + suffix),
3333
"bndl", newQDescriptor(BBMRI_PREFIX + ":" + ACQUISITION + "Bundle" + suffix),
34-
"ref_id", newQDescriptor(BBMRI_PREFIX + ":" + STORE + "Bundle" + suffix)
34+
"ref_id", newQDescriptor(BBMRI_PREFIX + ":" + STORAGE + "Bundle" + suffix)
3535
);
3636

3737
bindings.context = Map.of(

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/store/CpmStoreTransformer.java‎ renamed to ‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/storage/CpmStorageTransformer.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package cz.muni.fi.cpm.template.deserialization.mou.transform.store;
1+
package cz.muni.fi.cpm.template.deserialization.mou.transform.storage;
22

33
import cz.muni.fi.cpm.model.ICpmProvFactory;
44
import cz.muni.fi.cpm.template.deserialization.mou.schema.Patient;
@@ -15,18 +15,18 @@
1515
import static cz.muni.fi.cpm.template.deserialization.pbm.PbmNamespaceConstants.PBM_NS;
1616
import static cz.muni.fi.cpm.template.deserialization.pbm.PbmNamespaceConstants.PBM_PREFIX;
1717

18-
public class CpmStoreTransformer extends StoreTransformer {
19-
public CpmStoreTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
18+
public class CpmStorageTransformer extends StorageTransformer {
19+
public CpmStorageTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
2020
super(patient, pF, cPF, pbmF);
2121
}
2222

2323
@Override
2424
protected Document createTI(String suffix) {
2525
TraversalInformation ti = new TraversalInformation();
2626
ti.setPrefixes(Map.of(BBMRI_PREFIX, BBMRI_NS, PBM_PREFIX, PBM_NS));
27-
ti.setBundleName(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORE + "Bundle" + suffix, pF));
27+
ti.setBundleName(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORAGE + "Bundle" + suffix, pF));
2828

29-
MainActivity mA = new MainActivity(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORE + suffix, pF));
29+
MainActivity mA = new MainActivity(ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORAGE + suffix, pF));
3030
ti.setMainActivity(mA);
3131

3232
QualifiedName aCID = ti.getNamespace().qualifiedName(BBMRI_PREFIX, ACQUISITION_CON + suffix, pF);
@@ -38,7 +38,7 @@ protected Document createTI(String suffix) {
3838
MainActivityUsed used = new MainActivityUsed(aCID);
3939
mA.setUsed(List.of(used));
4040

41-
QualifiedName fcID = ti.getNamespace().qualifiedName(BBMRI_PREFIX, STORE_CON + suffix, pF);
41+
QualifiedName fcID = ti.getNamespace().qualifiedName(BBMRI_PREFIX, STOR_CON + suffix, pF);
4242
mA.setGenerated(List.of(fcID));
4343

4444
ForwardConnector fC = new ForwardConnector(fcID);

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/store/ProvStoreTransformer.java‎ renamed to ‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/storage/ProvStorageTransformer.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package cz.muni.fi.cpm.template.deserialization.mou.transform.store;
1+
package cz.muni.fi.cpm.template.deserialization.mou.transform.storage;
22

33
import cz.muni.fi.cpm.model.ICpmProvFactory;
44
import cz.muni.fi.cpm.template.deserialization.mou.schema.Patient;
@@ -15,8 +15,8 @@
1515
import static cz.muni.fi.cpm.template.deserialization.pbm.PbmNamespaceConstants.PBM_NS;
1616
import static cz.muni.fi.cpm.template.deserialization.pbm.PbmNamespaceConstants.PBM_PREFIX;
1717

18-
public class ProvStoreTransformer extends StoreTransformer {
19-
public ProvStoreTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
18+
public class ProvStorageTransformer extends StorageTransformer {
19+
public ProvStorageTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
2020
super(patient, pF, cPF, pbmF);
2121
}
2222

@@ -25,19 +25,19 @@ protected Document createTI(String suffix) {
2525

2626
Bindings bindings = new Bindings();
2727
bindings.var = Map.of(
28-
"main_activity_id", newQDescriptor(BBMRI_PREFIX + ":" + STORE + suffix),
29-
"forward_conn_id", newQDescriptor(BBMRI_PREFIX + ":" + STORE_CON + suffix),
28+
"main_activity_id", newQDescriptor(BBMRI_PREFIX + ":" + STORAGE + suffix),
29+
"forward_conn_id", newQDescriptor(BBMRI_PREFIX + ":" + STOR_CON + suffix),
3030
"sender_id", newQDescriptor(BBMRI_PREFIX + ":UNI"),
3131
"backward_conn_id", newQDescriptor(BBMRI_PREFIX + ":" + ACQUISITION_CON + suffix),
32-
"bndl", newQDescriptor(BBMRI_PREFIX + ":" + STORE + "Bundle" + suffix),
32+
"bndl", newQDescriptor(BBMRI_PREFIX + ":" + STORAGE + "Bundle" + suffix),
3333
"ref_id", newQDescriptor(BBMRI_PREFIX + ":" + ACQUISITION + "Bundle" + suffix)
3434
);
3535

3636
bindings.context = Map.of(
3737
BBMRI_PREFIX, BBMRI_NS, PBM_PREFIX, PBM_NS, DCT_PREFIX, DCT_NS
3838
);
3939

40-
return newDocument(pF, bindings, "backbone_tmpl_store");
40+
return newDocument(pF, bindings, "backbone_tmpl_stor");
4141
}
4242

4343
}

‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/store/StoreTransformer.java‎ renamed to ‎cpm-template/src/test/java/cz/muni/fi/cpm/template/deserialization/mou/transform/storage/StorageTransformer.java‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
package cz.muni.fi.cpm.template.deserialization.mou.transform.store;
1+
package cz.muni.fi.cpm.template.deserialization.mou.transform.storage;
22

33
import cz.muni.fi.cpm.constants.CpmType;
44
import cz.muni.fi.cpm.model.CpmUtilities;
@@ -19,14 +19,14 @@
1919
import static cz.muni.fi.cpm.constants.DctNamespaceConstants.DCT_NS;
2020
import static cz.muni.fi.cpm.constants.DctNamespaceConstants.DCT_PREFIX;
2121
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.ACQUISITION_CON;
22-
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.STORE_CON;
22+
import static cz.muni.fi.cpm.template.deserialization.mou.constants.NameConstants.STOR_CON;
2323

24-
public abstract class StoreTransformer extends PatientTransformer implements ProvTemplateHandler {
25-
public StoreTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
24+
public abstract class StorageTransformer extends PatientTransformer implements ProvTemplateHandler {
25+
public StorageTransformer(Patient patient, ProvFactory pF, ICpmProvFactory cPF, PbmFactory pbmF) {
2626
super(patient, pF, cPF, pbmF);
2727
}
2828

29-
private void addStoreDSToDocument(Document doc, String suffix, String sampleId, Function<Entity, Void> populateStore) {
29+
private void addStorageDSToDocument(Document doc, String suffix, String sampleId, Function<Entity, Void> populateStor) {
3030
Type sampleType = pbmF.newType(PbmType.SAMPLE);
3131

3232
QualifiedName patientQN = pF.newQualifiedName(BBMRI_NS, "patient-" + patient.getId(), BBMRI_PREFIX);
@@ -51,26 +51,26 @@ private void addStoreDSToDocument(Document doc, String suffix, String sampleId,
5151

5252
WasGeneratedBy transGeneratedBy = pF.newWasGeneratedBy(null, sampleTransQN, transActivity);
5353

54-
QualifiedName storeActivity = pF.newQualifiedName(BBMRI_NS, "storeAct" + suffix, BBMRI_PREFIX);
55-
Activity storeAc = pF.newActivity(storeActivity);
56-
storeAc.getType().add(pbmF.newType(PbmType.STORAGE_ACTIVITY));
54+
QualifiedName storActivity = pF.newQualifiedName(BBMRI_NS, "storageAct" + suffix, BBMRI_PREFIX);
55+
Activity storAc = pF.newActivity(storActivity);
56+
storAc.getType().add(pbmF.newType(PbmType.STORAGE_ACTIVITY));
5757

58-
Used storeUsed = pF.newUsed(storeActivity, sampleTransQN);
58+
Used storUsed = pF.newUsed(storActivity, sampleTransQN);
5959

60-
Other sampleIdStoreOther = newOther("sampleId", sampleId);
61-
QualifiedName sampleStoreQN = pF.newQualifiedName(BBMRI_NS, "sampleStore" + suffix, BBMRI_PREFIX);
62-
Entity sampleStore = pF.newEntity(sampleStoreQN, List.of(sampleType, sampleIdStoreOther));
60+
Other sampleIdStorOther = newOther("sampleId", sampleId);
61+
QualifiedName sampleStorQN = pF.newQualifiedName(BBMRI_NS, "sampleStorage" + suffix, BBMRI_PREFIX);
62+
Entity sampleStor = pF.newEntity(sampleStorQN, List.of(sampleType, sampleIdStorOther));
6363

64-
WasDerivedFrom sampleStoreDer = pF.newWasDerivedFrom(sampleStoreQN, patientQN);
64+
WasDerivedFrom sampleStorDer = pF.newWasDerivedFrom(sampleStorQN, patientQN);
6565

66-
populateStore.apply(sampleStore);
66+
populateStor.apply(sampleStor);
6767

68-
WasGeneratedBy storeGeneratedBy = pF.newWasGeneratedBy(null, sampleStoreQN, storeActivity);
68+
WasGeneratedBy storGeneratedBy = pF.newWasGeneratedBy(null, sampleStorQN, storActivity);
6969

70-
SpecializationOf fcSpec = pF.newSpecializationOf(sampleStoreQN, doc.getNamespace().qualifiedName(BBMRI_PREFIX, STORE_CON + suffix, pF));
70+
SpecializationOf fcSpec = pF.newSpecializationOf(sampleStorQN, doc.getNamespace().qualifiedName(BBMRI_PREFIX, STOR_CON + suffix, pF));
7171

7272
Bundle bundle = (Bundle) doc.getStatementOrBundle().getFirst();
73-
bundle.getStatement().addAll(List.of(bcSpec, trans, sampleTrans, transGeneratedBy, storeAc, storeUsed, sampleStore, storeGeneratedBy, fcSpec, patientE, sampleTransDer, sampleStoreDer));
73+
bundle.getStatement().addAll(List.of(bcSpec, trans, sampleTrans, transGeneratedBy, storAc, storUsed, sampleStor, storGeneratedBy, fcSpec, patientE, sampleTransDer, sampleStorDer));
7474

7575
for (Statement s : bundle.getStatement()) {
7676
if (CpmUtilities.hasCpmType(s, CpmType.MAIN_ACTIVITY)) {
@@ -81,15 +81,15 @@ private void addStoreDSToDocument(Document doc, String suffix, String sampleId,
8181
pF.getName().PROV_QUALIFIED_NAME));
8282
mainActivity.getOther().add(pF.newOther(
8383
pF.newQualifiedName(DCT_NS, HAS_PART, DCT_PREFIX),
84-
storeActivity,
84+
storActivity,
8585
pF.getName().PROV_QUALIFIED_NAME));
8686
}
8787
}
8888
}
8989

9090
@Override
9191
protected void addTissueDSToDoc(Document doc, String suffix, Tissue tissue) {
92-
addStoreDSToDocument(doc, suffix, tissue.getSampleId(), entity ->
92+
addStorageDSToDocument(doc, suffix, tissue.getSampleId(), entity ->
9393
{
9494
entity.getType().add(pF.newType(
9595
pF.newQualifiedName(BBMRI_NS, "tissue", BBMRI_PREFIX),
@@ -111,7 +111,7 @@ protected void addTissueDSToDoc(Document doc, String suffix, Tissue tissue) {
111111

112112
@Override
113113
protected void addDMDSToDoc(Document doc, String suffix, DiagnosisMaterial dM) {
114-
addStoreDSToDocument(doc, suffix, dM.getSampleId(), entity ->
114+
addStorageDSToDocument(doc, suffix, dM.getSampleId(), entity ->
115115
{
116116
entity.getType().add(pF.newType(
117117
pF.newQualifiedName(BBMRI_NS, "diagnosticMaterial", BBMRI_PREFIX),

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