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@amontenegro
amontenegro committed Jun 29, 2023
1 parent 117971b commit 1524148
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88 changes: 61 additions & 27 deletions orcid-core/src/main/java/org/orcid/core/groupIds/issn/IssnClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ public class IssnClient {
private static final String START_OF_STRING = "\u0098";
private static final String STRING_TERMINATOR = "\u009C";

private static final String RESOURCE_MAIN = "resource/ISSN/%issn";
private static final String RESOURCE_KEY_TITLE = "resource/ISSN/%issn#KeyTitle";

@Resource
private IssnPortalUrlBuilder issnPortalUrlBuilder;

Expand All @@ -44,7 +47,7 @@ public IssnData getIssnData(String issn) {
}
try {
if (json != null) {
IssnData data = extractIssnData(json);
IssnData data = extractIssnData(issn.toUpperCase(), json);
data.setIssn(issn);
return data;
} else {
Expand All @@ -56,41 +59,72 @@ public IssnData getIssnData(String issn) {
}
}

private IssnData extractIssnData(String json) throws JSONException {
private IssnData extractIssnData(String issn, String json) throws JSONException {
LOG.info("Extracting json data from " + issn);
JSONObject jsonObject = new JSONObject(json);
JSONArray jsonArray = jsonObject.getJSONArray("@graph");
IssnData issnData = new IssnData();
if (issnData != null) {
JSONArray jsonArray = jsonObject.getJSONArray("@graph");
if (jsonArray != null) {
IssnData issnData = new IssnData();
// Look for the KeyTitle element
for (int i = 0; i < jsonArray.length(); i++) {
if (jsonArray.getJSONObject(i).has("mainTitle")) {
String title = jsonArray.getJSONObject(i).getString("mainTitle");
String cleanTitle = cleanText(title);
issnData.setMainTitle(cleanTitle);
return issnData;
}
JSONObject obj = jsonArray.getJSONObject(i);
if (obj.has("@id")) {
String idName = obj.getString("@id");
if (idName.equals(RESOURCE_KEY_TITLE.replace("%issn", issn))) {
String title = obj.getString("value");
String cleanTitle = cleanText(title);
issnData.setMainTitle(cleanTitle);
LOG.debug("Found KeyTitle for '" + issn + "' " + cleanTitle);
return issnData;
}
}
}
// If we reach this point it means the mainTitle was not available.
// Lets iterate again now looking for key

// If it can't find it, look for the main resource and extract the
// mainTitle from it or the first element in the name array
for (int i = 0; i < jsonArray.length(); i++) {
if (jsonArray.getJSONObject(i).has("name")) {
try {
String title = jsonArray.getJSONObject(i).getString("name");
issnData.setMainTitle(cleanText(title));
} catch (JSONException e) {
// may be an array
try {
String title = jsonArray.getJSONObject(i).getJSONArray("name").getString(0);
issnData.setMainTitle(cleanText(title));
} catch(Exception ee) {
// Nothing else to try, propagate the exception
throw ee;
JSONObject obj = jsonArray.getJSONObject(i);
if (obj.has("@id")) {
String idName = obj.getString("@id");
if (idName.equals(RESOURCE_MAIN.replace("%issn", issn))) {
LOG.debug("Found main resource for " + issn);
// Look for the mainTitle
if (obj.has("mainTitle")) {
String title = obj.getString("mainTitle");
String cleanTitle = cleanText(title);
issnData.setMainTitle(cleanTitle);
LOG.debug("Found mainTitle for '" + issn + "' " + cleanTitle);
return issnData;
} else if (obj.has("name")) {
LOG.debug("Found name array for " + issn);
// If the mainTitle is not available, look for the
// name array
Object nameObject = jsonArray.getJSONObject(i).get("name");
if (nameObject instanceof JSONArray) {
String title = jsonArray.getJSONObject(i).getJSONArray("name").getString(0);
String cleanTitle = cleanText(title);
issnData.setMainTitle(cleanTitle);
LOG.debug("Found KeyTitle for '" + issn + "' " + cleanTitle);
return issnData;
} else if (nameObject instanceof String) {
String title = jsonArray.getJSONObject(i).getString("name");
String cleanTitle = cleanText(title);
issnData.setMainTitle(cleanTitle);
LOG.debug("Found name for '" + issn + "' " + cleanTitle);
return issnData;
} else {
LOG.warn("Unable to extract name, it is not a string nor an array for " + issn);
throw new IllegalArgumentException("Unable to extract name, it is not a string nor an array for " + issn);
}
} else {
LOG.warn("Unable to extract name, couldn't find the mainTitle nor the name for " + issn);
throw new IllegalArgumentException("Unable to extract name, couldn't find the mainTitle nor the name for " + issn);
}
}
return issnData;
}
}
}
return null;
throw new IllegalArgumentException("Unable to extract name, couldn't find the Key Title nor the main resource for " + issn);
}

private String getJsonDataFromIssnPortal(String issn) throws IOException, InterruptedException, URISyntaxException {
Expand Down
128 changes: 87 additions & 41 deletions orcid-core/src/test/java/org/orcid/core/issn/IssnClientTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;
Expand Down Expand Up @@ -41,90 +42,135 @@ public void setUp() throws IOException {
Mockito.when(mockUrlBuilder.buildJsonIssnPortalUrlForIssn(Mockito.anyString())).thenReturn("anything");
ReflectionTestUtils.setField(issnClient, "issnPortalUrlBuilder", mockUrlBuilder);
ReflectionTestUtils.setField(issnClient, "httpRequestUtils", mockHttpRequestUtils);
}

@Test
public void testGetIssnDataUseKeyTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamKeyTitle());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("1755-4349");
assertEquals("Nature chemistry (Online) - Key Title", data.getMainTitle());
assertEquals("1755-4349", data.getIssn());
}

@Test
public void testGetIssnData() throws IOException, JSONException, InterruptedException, URISyntaxException {
public void testGetIssnDataUseMainTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStream());
when(mockResponse.body()).thenReturn(getJsonInputStreamFallbackToMainTitle());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("my-issn-0");
assertEquals("Nature chemistry.", data.getMainTitle());
// Should ignore ISSN from the metadata
assertEquals("my-issn-0", data.getIssn());
IssnData data = issnClient.getIssnData("0260-8774");
assertEquals("Journal of food engineering - Main title", data.getMainTitle());
assertEquals("0260-8774", data.getIssn());
}

@Test
public void testGetIssnDataWhenNoIssnInMetadata() throws IOException, JSONException, InterruptedException, URISyntaxException {
public void testGetIssnDataUseNameArray() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamNoIssnInMetadata());
when(mockResponse.body()).thenReturn(getJsonInputStreamFallbackToNameArray());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("my-issn-1");
assertEquals("Nature chemistry.", data.getMainTitle());
// Should ignore ISSN from the metadata
assertEquals("my-issn-1", data.getIssn());
IssnData data = issnClient.getIssnData("0260-8774");
assertEquals("Journal of food engineering - Array", data.getMainTitle());
assertEquals("0260-8774", data.getIssn());
}

@Test
public void testGetIssnDataNoMainTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
public void testGetIssnDataUseNameArrayAsString() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamNoMainTitle());
when(mockResponse.body()).thenReturn(getJsonInputStreamFallbackToNameArrayAsString());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("my-issn-2");
assertEquals("Journal of food engineering", data.getMainTitle());
// Should ignore ISSN from the metadata
assertEquals("my-issn-2", data.getIssn());
IssnData data = issnClient.getIssnData("0260-8774");
assertEquals("Journal of food engineering - String", data.getMainTitle());
assertEquals("0260-8774", data.getIssn());
}

@Test
public void testGetIssnDataNoMainTitleNameArray() throws IOException, JSONException, InterruptedException, URISyntaxException {
public void testGetIssnDataNoTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamNoMainTitleNameArray());
when(mockResponse.body()).thenReturn(getJsonInputStreamNoTitle());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("my-issn-3");
assertEquals("Shalom (Glyvrar)", data.getMainTitle());
// Should ignore ISSN from the metadata
assertEquals("my-issn-3", data.getIssn());
IssnData data = issnClient.getIssnData("0260-8774");
assertNull(data);
}

@Test
public void testGetIssnDataBadCharacters() throws IOException, JSONException, InterruptedException, URISyntaxException {
public void testGetIssnDataBadCharactersKeyTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamBadCharacters());
when(mockResponse.body()).thenReturn(getJsonInputStreamBadCharactersKeyTitle());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("my-issn-2");
assertFalse("\u0098The \u009CJournal of cell biology.".equals(data.getMainTitle()));
assertEquals("The Journal of cell biology.", data.getMainTitle());
assertTrue("\u0098The \u009CJournal of cell biology.".getBytes().length != data.getMainTitle().getBytes().length);
IssnData data = issnClient.getIssnData("0021-9525");
assertFalse("\u0098The \u009CJournal of cell biology - Key Title".equals(data.getMainTitle()));
assertEquals("The Journal of cell biology - Key Title", data.getMainTitle());
assertTrue("\u0098The \u009CJournal of cell biology - Key Title".getBytes().length != data.getMainTitle().getBytes().length);
}

private String getJsonInputStream() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response.json");
@Test
public void testGetIssnDataBadCharactersMainTitle() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamBadCharactersMainTitle());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("0021-9525");
assertFalse("\u0098The \u009CJournal of cell biology - Main Title".equals(data.getMainTitle()));
assertEquals("The Journal of cell biology - Main Title", data.getMainTitle());
assertTrue("\u0098The \u009CJournal of cell biology - Main Title".getBytes().length != data.getMainTitle().getBytes().length);
}

@Test
public void testGetIssnDataBadCharactersNameArray() throws IOException, JSONException, InterruptedException, URISyntaxException {
when(mockHttpRequestUtils.doGet(any())).thenReturn(mockResponse);
when(mockResponse.body()).thenReturn(getJsonInputStreamBadCharactersNameArray());
when(mockResponse.statusCode()).thenReturn(200);

IssnData data = issnClient.getIssnData("0021-9525");
assertFalse("\u0098The \u009CJournal of cell biology - Name Array".equals(data.getMainTitle()));
assertEquals("The Journal of cell biology - Name Array", data.getMainTitle());
assertTrue("\u0098The \u009CJournal of cell biology - Name Array".getBytes().length != data.getMainTitle().getBytes().length);
}

private String getJsonInputStreamKeyTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-key-title.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamNoIssnInMetadata() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-no-issn-in-metadata.json");
private String getJsonInputStreamFallbackToMainTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-fallback-to-main-title.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamNoMainTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-no-mainTitle.json");
private String getJsonInputStreamFallbackToNameArray() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-fallback-to-name-array.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamNoMainTitleNameArray() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-no-mainTitle-name-array.json");
private String getJsonInputStreamFallbackToNameArrayAsString() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-fallback-to-name-array-as-string.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamNoTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-no-title.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamBadCharacters() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-bad-characters.json");
private String getJsonInputStreamBadCharactersKeyTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-bad-characters-key-title.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}
}

private String getJsonInputStreamBadCharactersMainTitle() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-bad-characters-main-title.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}

private String getJsonInputStreamBadCharactersNameArray() throws IOException {
InputStream is = getClass().getResourceAsStream("/issn-response-bad-characters-name-array.json");
return new String(is.readAllBytes(), StandardCharsets.UTF_8);
}
}
6 changes: 3 additions & 3 deletions ...sources/issn-response-bad-characters.json → ...sn-response-bad-characters-key-title.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
"@id" : "resource/ISSN/0021-9525",
"@type" : [ "http://id.loc.gov/ontologies/bibframe/Work", "http://id.loc.gov/ontologies/bibframe/Instance", "http://schema.org/Periodical" ],
"identifiedBy" : [ "resource/ISSN/0021-9525#KeyTitle", "resource/ISSN/0021-9525#ISSN", "resource/ISSN/0021-9525#ISSN-L" ],
"mainTitle" : "˜\u0098The \u009CJournal of cell biology.",
"mainTitle" : "˜\u0098The \u009CJournal of cell biology - Main Title",
"otherPhysicalFormat" : "resource/ISSN/1540-8140",
"title" : "resource/ISSN/0021-9525#KeyTitle",
"format" : "vocabularies/medium#Print",
Expand All @@ -22,7 +22,7 @@
"http://purl.org/ontology/bibo/issn" : "0021-9525",
"isPartOf" : "resource/ISSN-L/0021-9525",
"issn" : "0021-9525",
"name" : [ "˜The œJournal of cell biology.", "˜The œJournal of cell biology" ],
"name" : [ "˜\u0098The \u009CJournal of cell biology - Name Array"],
"publication" : "resource/ISSN/0021-9525#ReferencePublicationEvent",
"url" : [ "http://www.jcb.org/", "http://www.jstor.org/journals/00219525.html", "http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=482&action=archive", "http://bibpurl.oclc.org/web/21389" ]
}, {
Expand All @@ -38,7 +38,7 @@
}, {
"@id" : "resource/ISSN/0021-9525#KeyTitle",
"@type" : [ "http://id.loc.gov/ontologies/bibframe/Identifier", "http://id.loc.gov/ontologies/bibframe/KeyTitle" ],
"value" : "˜The œJournal of cell biology"
"value" : "˜\u0098The \u009CJournal of cell biology - Key Title"
}, {
"@id" : "resource/ISSN/0021-9525#Record",
"@type" : "http://schema.org/CreativeWork",
Expand Down
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