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sabrineChesabrineChe
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Revert "Fixed issue #4"
This reverts commit 15eb0ec.
1 parent 93f826d commit e54c7f3

21 files changed

+878
-970
lines changed

‎src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java

Lines changed: 325 additions & 332 deletions
Large diffs are not rendered by default.

‎src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java

Lines changed: 356 additions & 385 deletions
Large diffs are not rendered by default.

‎src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java

Lines changed: 4 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -48,14 +48,12 @@ public class ImportFromDataCite {
4848
https://api.datacite.org/application/vnd.datacite.datacite+json/10.1594/pangaea.149669
4949
* @param name the name the crate should have.
5050
* @param description the description of the crate.
51-
* @param datePublished the published date of the crate.
52-
* @param licenseId the license identifier of the crate.
5351
* @return the created crate.
5452
*/
5553
public static Crate createCrateFromDataCiteResource(
56-
String url, String name, String description, String datePublished, String licenseId) {
54+
String url, String name, String description) {
5755

58-
Crate crate = new RoCrate.RoCrateBuilder(name, description, datePublished, licenseId)
56+
Crate crate = new RoCrate.RoCrateBuilder(name, description)
5957
.build();
6058
addDataCiteToCrate(url, crate);
6159
return crate;
@@ -80,13 +78,11 @@ public static void addDataCiteToCrate(String url, Crate crate) {
8078
* @param json the Json object of the DataCite resource.
8179
* @param name the name of the crate that will be created.
8280
* @param description the description of the crate that will be created.
83-
* @param datePublished the published date of the crate.
84-
* @param licenseId the license identifier of the crate.
8581
* @return the created crate.
8682
*/
8783
public static Crate createCrateFromDataCiteJson(
88-
JsonNode json, String name, String description, String datePublished, String licenseId) {
89-
Crate crate = new RoCrate.RoCrateBuilder(name, description, datePublished, licenseId)
84+
JsonNode json, String name, String description) {
85+
Crate crate = new RoCrate.RoCrateBuilder(name, description)
9086
.build();
9187
addDataCiteToCrateFromJson(json, crate);
9288
return crate;

‎src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -32,12 +32,10 @@ public class ImportFromZenodo {
3232
* @param url the url of the zenodo resource.
3333
* @param name the name of the crate created.
3434
* @param description the description of the crate created.
35-
* @param datePublished the published date of the crate.
36-
* @param licenseId the license identifier of the crate.
3735
* @return the created crate.
3836
*/
39-
public static Crate createCrateWithItem(String url, String name, String description, String datePublished, String licenseId) {
40-
RoCrate crate = new RoCrate.RoCrateBuilder("name", "description", "datePublished", "licenseId").build();
37+
public static Crate createCrateWithItem(String url, String name, String description) {
38+
RoCrate crate = new RoCrate.RoCrateBuilder("name", "description").build();
4139
addToCrateFromZotero(url, crate);
4240
return crate;
4341
}

‎src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java

Lines changed: 87 additions & 91 deletions
Original file line numberDiff line numberDiff line change
@@ -19,102 +19,98 @@
1919
import java.util.Map;
2020
import java.util.function.Function;
2121
import java.util.stream.Collectors;
22-
import static org.junit.jupiter.api.Assertions.assertEquals;
2322

2423
public class HelpFunctions {
2524

26-
public static void compareEntityWithFile(AbstractEntity entity, String string) throws IOException {
27-
InputStream inputStream
28-
= HelpFunctions.class.getResourceAsStream(string);
29-
JsonNode expectedJson = MyObjectMapper.getMapper().readTree(inputStream);
30-
JsonNode node = MyObjectMapper.getMapper().convertValue(entity, JsonNode.class);
31-
//compare the size of the expected and actual node. Both nodes should have the same number of properties.
32-
assertEquals(expectedJson.size(), node.size());
33-
compare(expectedJson, node, true);
25+
public static void compareEntityWithFile(AbstractEntity entity, String string) throws IOException {
26+
InputStream inputStream =
27+
HelpFunctions.class.getResourceAsStream(string);
28+
JsonNode expectedJson = MyObjectMapper.getMapper().readTree(inputStream);
29+
JsonNode node = MyObjectMapper.getMapper().convertValue(entity, JsonNode.class);
30+
compare(expectedJson, node, true);
31+
}
32+
33+
public static void compare(JsonNode node1, JsonNode node2, Boolean equals) {
34+
var comparator = new JsonComparator() {
35+
public boolean compareValues(Object expected, Object actual) {
36+
return expected.equals(actual);
37+
}
38+
39+
public boolean compareFields(String expected, String actual) {
40+
return expected.equals(actual);
41+
}
42+
};
43+
if (equals) {
44+
JSONCompare.assertMatches(node1, node2, comparator);
45+
} else {
46+
JSONCompare.assertNotMatches(node1, node2, comparator);
3447
}
35-
36-
public static void compare(JsonNode node1, JsonNode node2, Boolean equals) {
37-
var comparator = new JsonComparator() {
38-
public boolean compareValues(Object expected, Object actual) {
39-
40-
return expected.equals(actual);
41-
}
42-
43-
public boolean compareFields(String expected, String actual) {
44-
return expected.equals(actual);
45-
}
46-
};
47-
if (equals) {
48-
JSONCompare.assertMatches(node1, node2, comparator);
49-
} else {
50-
JSONCompare.assertNotMatches(node1, node2, comparator);
51-
}
52-
}
53-
54-
public static void compareTwoMetadataJsonNotEqual(Crate crate1, Crate crate2) throws JsonProcessingException {
55-
ObjectMapper objectMapper = MyObjectMapper.getMapper();
56-
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
57-
JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata());
58-
compare(node1, node2, false);
59-
}
60-
61-
public static void compareTwoMetadataJsonNotEqual(Crate crate1, String jsonFileString) throws IOException {
62-
InputStream inputStream = HelpFunctions.class.getResourceAsStream(
63-
jsonFileString);
64-
ObjectMapper objectMapper = MyObjectMapper.getMapper();
65-
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
66-
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream));
67-
compare(node1, node2, false);
68-
}
69-
70-
public static void compareTwoCrateJson(Crate crate1, Crate crate2) throws JsonProcessingException {
71-
ObjectMapper objectMapper = MyObjectMapper.getMapper();
72-
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
73-
JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata());
74-
compare(node1, node2, true);
48+
}
49+
50+
public static void compareTwoMetadataJsonNotEqual(Crate crate1, Crate crate2) throws JsonProcessingException {
51+
ObjectMapper objectMapper = MyObjectMapper.getMapper();
52+
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
53+
JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata());
54+
compare(node1, node2, false);
55+
}
56+
57+
public static void compareTwoMetadataJsonNotEqual(Crate crate1, String jsonFileString) throws IOException {
58+
InputStream inputStream = HelpFunctions.class.getResourceAsStream(
59+
jsonFileString);
60+
ObjectMapper objectMapper = MyObjectMapper.getMapper();
61+
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
62+
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream));
63+
compare(node1, node2, false);
64+
}
65+
66+
public static void compareTwoCrateJson(Crate crate1, Crate crate2) throws JsonProcessingException {
67+
ObjectMapper objectMapper = MyObjectMapper.getMapper();
68+
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
69+
JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata());
70+
compare(node1, node2, true);
71+
}
72+
73+
public static void compareCrateJsonToFileInResources(File file1, File file2) throws IOException {
74+
ObjectMapper objectMapper = MyObjectMapper.getMapper();
75+
JsonNode node1 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file1));
76+
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file2));
77+
compare(node1, node2, true);
78+
}
79+
80+
public static void compareCrateJsonToFileInResources(Crate crate1, String jsonFileString) throws IOException {
81+
InputStream inputStream = HelpFunctions.class.getResourceAsStream(
82+
jsonFileString);
83+
ObjectMapper objectMapper = MyObjectMapper.getMapper();
84+
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
85+
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream));
86+
compare(node1, node2, true);
87+
}
88+
89+
public static boolean compareTwoDir(File dir1, File dir2) throws IOException {
90+
// compare the content of the two directories
91+
List<File> a = (List<java.io.File>) FileUtils.listFiles(dir1, null, true);
92+
Map<String, File> result_map = a.stream()
93+
.collect(Collectors.toMap(java.io.File::getName, Function.identity()));
94+
95+
List<java.io.File> b = (List<java.io.File>) FileUtils.listFiles(dir2, null, true);
96+
Map<String, java.io.File> input_map = b.stream()
97+
.collect(Collectors.toMap(java.io.File::getName, Function.identity()));
98+
99+
if (result_map.size() != input_map.size()) {
100+
return false;
75101
}
76-
77-
public static void compareCrateJsonToFileInResources(File file1, File file2) throws IOException {
78-
ObjectMapper objectMapper = MyObjectMapper.getMapper();
79-
JsonNode node1 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file1));
80-
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file2));
81-
compare(node1, node2, true);
82-
}
83-
84-
public static void compareCrateJsonToFileInResources(Crate crate1, String jsonFileString) throws IOException {
85-
InputStream inputStream = HelpFunctions.class.getResourceAsStream(
86-
jsonFileString);
87-
ObjectMapper objectMapper = MyObjectMapper.getMapper();
88-
JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata());
89-
JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream));
90-
compare(node1, node2, true);
91-
}
92-
93-
public static boolean compareTwoDir(File dir1, File dir2) throws IOException {
94-
// compare the content of the two directories
95-
List<File> a = (List<java.io.File>) FileUtils.listFiles(dir1, null, true);
96-
Map<String, File> result_map = a.stream()
97-
.collect(Collectors.toMap(java.io.File::getName, Function.identity()));
98-
99-
List<java.io.File> b = (List<java.io.File>) FileUtils.listFiles(dir2, null, true);
100-
Map<String, java.io.File> input_map = b.stream()
101-
.collect(Collectors.toMap(java.io.File::getName, Function.identity()));
102-
103-
if (result_map.size() != input_map.size()) {
104-
return false;
105-
}
106-
for (String s : input_map.keySet()) {
107-
// we do that because the ro-crate-metadata.json can be differently formatted,
108-
// or the order of the entities may be different
109-
// the same holds for the html file
110-
if (s.equals("ro-crate-preview.html") || s.equals("ro-crate-metadata.json")) {
111-
if (!result_map.containsKey(s)) {
112-
return false;
113-
}
114-
} else if (!FileUtils.contentEqualsIgnoreEOL(input_map.get(s), result_map.get(s), null)) {
115-
return false;
116-
}
102+
for (String s : input_map.keySet()) {
103+
// we do that because the ro-crate-metadata.json can be differently formatted,
104+
// or the order of the entities may be different
105+
// the same holds for the html file
106+
if (s.equals("ro-crate-preview.html") || s.equals("ro-crate-metadata.json")) {
107+
if (!result_map.containsKey(s)) {
108+
return false;
117109
}
118-
return true;
110+
} else if (!FileUtils.contentEqualsIgnoreEOL(input_map.get(s), result_map.get(s), null)) {
111+
return false;
112+
}
119113
}
114+
return true;
115+
}
120116
}

‎src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java

Lines changed: 31 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -9,54 +9,37 @@
99
import edu.kit.datamanager.ro_crate.HelpFunctions;
1010
import edu.kit.datamanager.ro_crate.RoCrate;
1111
import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
12-
import java.io.IOException;
1312

1413
public class BuilderTest {
15-
@Test
16-
void testReadBuilder() throws JsonProcessingException {
17-
ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
18-
.addType("CreativeWork")
19-
.setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
20-
.addProperty("description",
21-
"This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
22-
.addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
23-
.addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
24-
.build();
25-
26-
RoCrate crate = new RoCrate.RoCrateBuilder().addContextualEntity(license).build();
27-
RoCrate crate1 = new RoCrate.RoCrateBuilder(crate).build();
28-
assertEquals(crate.getAllDataEntities(), crate1.getAllDataEntities());
29-
assertEquals(crate.getAllContextualEntities(), crate1.getAllContextualEntities());
30-
HelpFunctions.compareTwoCrateJson(crate1, crate);
31-
32-
}
33-
34-
@Test
35-
void testAddCrateWithOnlyRootDataEntity() throws IOException {
36-
ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
37-
.addType("CreativeWork")
38-
.setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
39-
.addProperty("description",
40-
"This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
41-
.addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
42-
.addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
43-
.build();
44-
RoCrate crate = new RoCrate.RoCrateBuilder("Data files", "Palliative care planning...", "2024-02-09T08:21:41Z", license.getId()).addContextualEntity(license).build();
45-
46-
HelpFunctions.compareEntityWithFile(crate.getRootDataEntity(), "/json/entities/data/rootMinimalExample.json");
47-
System.out.println("Sab "+crate.getRootDataEntity());
48-
HelpFunctions.compareEntityWithFile(crate.getContextualEntityById("https://creativecommons.org/licenses/by-nc-sa/3.0/au/"), "/json/entities/data/license.json");
49-
}
50-
51-
@Test
52-
void testEmptyCrates() throws JsonProcessingException {
53-
RoCrate built = new RoCrate.RoCrateBuilder().build();
54-
RoCrate constructed = new RoCrate();
55-
56-
assertEquals(built.getAllDataEntities(), constructed.getAllDataEntities());
57-
assertEquals(built.getAllContextualEntities(), constructed.getAllContextualEntities());
58-
assertEquals(built.getJsonDescriptor().getTypes(), constructed.getJsonDescriptor().getTypes());
59-
assertEquals(built.getJsonDescriptor().getProperties(), constructed.getJsonDescriptor().getProperties());
60-
HelpFunctions.compareTwoCrateJson(built, constructed);
61-
}
14+
@Test
15+
void testReadBuilder() throws JsonProcessingException {
16+
ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
17+
.addType("CreativeWork")
18+
.setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
19+
.addProperty("description",
20+
"This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
21+
.addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
22+
.addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
23+
.build();
24+
25+
RoCrate crate = new RoCrate.RoCrateBuilder().addContextualEntity(license).build();
26+
RoCrate crate1 = new RoCrate.RoCrateBuilder(crate).build();
27+
28+
assertEquals(crate.getAllDataEntities(), crate1.getAllDataEntities());
29+
assertEquals(crate.getAllContextualEntities(), crate1.getAllContextualEntities());
30+
HelpFunctions.compareTwoCrateJson(crate1, crate);
31+
32+
}
33+
34+
@Test
35+
void testEmptyCrates() throws JsonProcessingException {
36+
RoCrate built = new RoCrate.RoCrateBuilder().build();
37+
RoCrate constructed = new RoCrate();
38+
39+
assertEquals(built.getAllDataEntities(), constructed.getAllDataEntities());
40+
assertEquals(built.getAllContextualEntities(), constructed.getAllContextualEntities());
41+
assertEquals(built.getJsonDescriptor().getTypes(), constructed.getJsonDescriptor().getTypes());
42+
assertEquals(built.getJsonDescriptor().getProperties(), constructed.getJsonDescriptor().getProperties());
43+
HelpFunctions.compareTwoCrateJson(built, constructed);
44+
}
6245
}

‎src/test/java/edu/kit/datamanager/ro_crate/crate/OtherFilesTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ void testOtherFiles(@TempDir Path tempDir) throws IOException, URISyntaxExceptio
3333
FileUtils.touch(file2.toFile());
3434
FileUtils.writeStringToFile(file1.toFile(), "content of file 1", Charset.defaultCharset());
3535
FileUtils.writeStringToFile(file2.toFile(), "content of file 2", Charset.defaultCharset());
36-
RoCrate roCrate = new RoCrate.RoCrateBuilder("minimal", "minimal RO_crate", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
36+
RoCrate roCrate = new RoCrate.RoCrateBuilder("minimal", "minimal RO_crate")
3737
.addUntrackedFile(file1.toFile())
3838
.addUntrackedFile(file2.toFile())
3939
.build();

‎src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ void testReadingAndWriting(@TempDir Path path) throws IOException {
3030
Path fileInDir = htmlDir.resolve("file.html");
3131
FileUtils.writeStringToFile(fileInDir.toFile(), "fileN2", Charset.defaultCharset());
3232

33-
RoCrate crate = new RoCrate.RoCrateBuilder("name", "description", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
33+
RoCrate crate = new RoCrate.RoCrateBuilder("name", "description")
3434
.setPreview(new CustomPreview(htmlFile.toFile(), htmlDir.toFile()))
3535
.build();
3636

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