@Override
public boolean processQuery(String query, ImportInspector dialog, OutputPrinter status) {
stopFetching = false;
try {
List<String> citations = getCitations(query);
if (citations == null) {
return false;
}
if (citations.isEmpty()) {
status.showMessage(
Localization.lang("No entries found for the search string '%0'", query),
Localization.lang("Search %0", SCIENCE_DIRECT),
JOptionPane.INFORMATION_MESSAGE);
return false;
}
int i = 0;
for (String cit : citations) {
if (stopFetching) {
break;
}
BibsonomyScraper.getEntry(cit).ifPresent(dialog::addEntry);
dialog.setProgress(++i, citations.size());
}
return true;
} catch (IOException e) {
LOGGER.warn("Communcation problems", e);
status.showMessage(
Localization.lang("Error while fetching from %0", SCIENCE_DIRECT)
+ ": "
+ e.getMessage());
}
return false;
}
@Override
public boolean processQuery(String query, ImportInspector iIDialog, OutputPrinter frameOP) {
shouldContinue = true;
query = query.trim().replace(';', ',');
if (query.matches("\\d+[,\\d+]*")) {
frameOP.setStatus(Localization.lang("Fetching Medline by id..."));
List<BibtexEntry> bibs = MedlineImporter.fetchMedline(query, frameOP);
if (bibs.isEmpty()) {
frameOP.showMessage(Localization.lang("No references found"));
}
for (BibtexEntry entry : bibs) {
iIDialog.addEntry(entry);
}
return true;
}
if (!query.isEmpty()) {
frameOP.setStatus(Localization.lang("Fetching Medline by term..."));
String searchTerm = toSearchTerm(query);
// get the ids from entrez
SearchResult result = getIds(searchTerm, 0, 1);
if (result.count == 0) {
frameOP.showMessage(Localization.lang("No references found"));
return false;
}
int numberToFetch = result.count;
if (numberToFetch > MedlineFetcher.PACING) {
while (true) {
String strCount =
JOptionPane.showInputDialog(
Localization.lang("References found")
+ ": "
+ numberToFetch
+ " "
+ Localization.lang("Number of references to fetch?"),
Integer.toString(numberToFetch));
if (strCount == null) {
frameOP.setStatus(Localization.lang("Medline import canceled"));
return false;
}
try {
numberToFetch = Integer.parseInt(strCount.trim());
break;
} catch (RuntimeException ex) {
frameOP.showMessage(Localization.lang("Please enter a valid number"));
}
}
}
for (int i = 0; i < numberToFetch; i += MedlineFetcher.PACING) {
if (!shouldContinue) {
break;
}
int noToFetch = Math.min(MedlineFetcher.PACING, numberToFetch - i);
// get the ids from entrez
result = getIds(searchTerm, i, noToFetch);
List<BibtexEntry> bibs = MedlineImporter.fetchMedline(result.ids, frameOP);
for (BibtexEntry entry : bibs) {
iIDialog.addEntry(entry);
}
iIDialog.setProgress(i + noToFetch, numberToFetch);
}
return true;
}
frameOP.showMessage(
Localization.lang(
"Please enter a comma separated list of Medline IDs (numbers) or search terms."),
Localization.lang("Input error"),
JOptionPane.ERROR_MESSAGE);
return false;
}
@Override
public boolean processQuery(String query, ImportInspector inspector, OutputPrinter status) {
shouldContinue = true;
try {
status.setStatus(Localization.lang("Searching..."));
HttpResponse<JsonNode> jsonResponse;
query = URLEncoder.encode(query, "UTF-8");
jsonResponse =
Unirest.get(API_URL + query + "&api_key=" + API_KEY + "&p=1")
.header("accept", "application/json")
.asJson();
JSONObject jo = jsonResponse.getBody().getObject();
int hits = jo.getJSONArray("result").getJSONObject(0).getInt("total");
int numberToFetch = 0;
if (hits > 0) {
if (hits > maxPerPage) {
while (true) {
String strCount =
JOptionPane.showInputDialog(
Localization.lang("References found")
+ ": "
+ hits
+ " "
+ Localization.lang("Number of references to fetch?"),
Integer.toString(hits));
if (strCount == null) {
status.setStatus(Localization.lang("Search canceled"));
return false;
}
try {
numberToFetch = Integer.parseInt(strCount.trim());
break;
} catch (RuntimeException ex) {
status.showMessage(Localization.lang("Please enter a valid number"));
}
}
} else {
numberToFetch = hits;
}
int fetched = 0; // Keep track of number of items fetched for the progress bar
for (int startItem = 1; startItem <= numberToFetch; startItem += maxPerPage) {
if (!shouldContinue) {
break;
}
int noToFetch = Math.min(maxPerPage, numberToFetch - startItem);
jsonResponse =
Unirest.get(
API_URL
+ query
+ "&api_key="
+ API_KEY
+ "&p="
+ noToFetch
+ "&s="
+ startItem)
.header("accept", "application/json")
.asJson();
jo = jsonResponse.getBody().getObject();
if (jo.has("records")) {
JSONArray results = jo.getJSONArray("records");
for (int i = 0; i < results.length(); i++) {
JSONObject springerJsonEntry = results.getJSONObject(i);
BibtexEntry entry = jep.SpringerJSONtoBibtex(springerJsonEntry);
inspector.addEntry(entry);
fetched++;
inspector.setProgress(fetched, numberToFetch);
}
}
}
return true;
} else {
status.showMessage(
Localization.lang("No entries found for the search string '%0'", query),
Localization.lang("Search %0", "Springer"),
JOptionPane.INFORMATION_MESSAGE);
return false;
}
} catch (UnirestException e) {
LOGGER.warn("Problem searching Springer", e);
} catch (UnsupportedEncodingException e) {
LOGGER.warn("Cannot encode query", e);
}
return false;
}