public static void main(String[] args) {
/////////////////////////////////////////////////////////////////////////////
// 複数の例外をマルチキャッチ
/////////////////////////////////////////////////////////////////////////////
try {
Date date = new SimpleDateFormat("yyyyMMdd").parse("20140401");
new File(String.format("新規ファイル%s.txt", date.getTime())).createNewFile();
// ParseExceptionまたはIOExceptionが発生した場合
} catch (ParseException | IOException e) {
System.out.println("例外発生: " + e.getMessage());
}
}
public void loadData() {
try {
JSONObject data =
(JSONObject)
new JSONParser()
.parse(new FileReader("plugins/Root/users/" + base.getUniqueId() + "/data.json"));
JSONObject user = (JSONObject) data.get("user");
JSONObject stat = (JSONObject) data.get("stat");
JSONObject attributes = (JSONObject) user.get("attributes");
fill = (boolean) attributes.get("fill");
muted = (boolean) attributes.get("muted");
frozen = (boolean) attributes.get("frozen"); // Let It Go
undercover = (boolean) attributes.get("undercover");
} catch (ParseException | IOException e) {
Bukkit.getLogger()
.warning("Error while loading data for " + getName() + ": " + e.getMessage());
}
}
@Override
public String save() {
SimpleDateFormat format = new SimpleDateFormat("yyyy");
Date data = null;
try {
data = new Date(format.parse(year).getTime());
if (file != null && !file.getFileName().equals("")) {
FacesMessage msg = new FacesMessage("Succesful" + file.getFileName() + " is uploaded.");
FacesContext.getCurrentInstance().addMessage(null, msg);
copyFile(file.getFileName(), file.getInputstream());
}
} catch (ParseException | IOException e) {
e.printStackTrace();
}
super.selectedEntity.setYear(data);
super.selectedEntity.setName(super.selectedEntity.getTitle());
super.selectedEntity.setDescription(super.selectedEntity.getAbstract());
saveAuthors(this.authors);
super.selectedEntity.setFilepath(destination + file.getFileName());
managePublicationsService.getDAO().save(super.selectedEntity);
super.selectedEntity = new Publication();
return list();
}
private JSONArray sendRequest(String param) {
List<BasicNameValuePair> params = new ArrayList<BasicNameValuePair>();
params.add(new BasicNameValuePair("content", param));
params.add(new BasicNameValuePair("longestOnly", "true"));
URI uri = null;
try {
uri = new URI(SCIGRAPH_ENTITIES_REQUEST_URL + "?" + URLEncodedUtils.format(params, "utf-8"));
} catch (URISyntaxException e) {
e.printStackTrace();
}
final HttpGet request = new HttpGet(uri);
final DefaultHttpClient client = new DefaultHttpClient();
HttpResponse response = null;
try {
response = new DefaultHttpClient().execute(request);
} catch (IOException e) {
JOptionPane.showMessageDialog(
null,
"Network connection unable to be established.",
"Network Error",
JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
return null;
}
client.getConnectionManager().shutdown();
String json = null;
try {
json = EntityUtils.toString(response.getEntity());
} catch (ParseException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
JSONArray responseJSON = new JSONArray(json);
return responseJSON;
}
/** @param args */
public static void main(String[] args) {
initOptions();
try {
parse(args, false);
String comm = args[1];
String buildOption = null;
// no needed to check as 'build' arg is required in Options
if (!commandLine.hasOption("build") || commandLine.getOptionValue("build").equals("")) {}
buildOption = commandLine.getOptionValue("build");
if (buildOption.equals("genome-sequence")) {
System.out.println("In genome-sequence");
String indir = commandLine.getOptionValue("indir");
String outfile = commandLine.getOptionValue("outfile", "/tmp/genome_sequence.json");
if (indir != null) {
GenomeSequenceFastaParser genomeSequenceFastaParser = new GenomeSequenceFastaParser();
genomeSequenceFastaParser.parseFastaGzipFilesToJson(new File(indir), new File(outfile));
}
}
if (buildOption.equals("core")) {
System.out.println("In core");
String gtfFile = commandLine.getOptionValue("gtf-file");
String geneDescriptionFile = commandLine.getOptionValue("gene-description", "");
String xrefFile = commandLine.getOptionValue("xref-file", "");
String tfbsFile = commandLine.getOptionValue("tfbs-file", "");
String mirnaFile = commandLine.getOptionValue("mirna-file", "");
String genomeSequenceDir = commandLine.getOptionValue("genome-sequence-dir", "");
String outfile = commandLine.getOptionValue("outfile", "/tmp/gene.json");
if (gtfFile != null) {
try {
GeneParser geneParser = new GeneParser();
geneParser.parse(
new File(gtfFile),
new File(geneDescriptionFile),
new File(xrefFile),
new File(tfbsFile),
new File(mirnaFile),
new File(genomeSequenceDir),
new File(outfile));
} catch (SecurityException | NoSuchMethodException | FileFormatException e) {
e.printStackTrace();
}
}
}
if (buildOption.equals("variation")) {
System.out.println("In variation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
System.out.println("chunksize: " + chunksize);
String outfile = commandLine.getOptionValue("outfile", "/tmp/variation.json");
if (indir != null) {
VariationParser vp = new VariationParser();
vp.createVariationDatabase(Paths.get(indir));
vp.connect(Paths.get(indir));
// List<String> res = vp.queryByVariationId(13, "variation_synonym",
// Paths.get(indir));
// System.out.println("a");
// res = vp.queryByVariationId(4, "variation_synonym", Paths.get(indir));
// System.out.println("b");
// res = vp.queryByVariationId(8, "variation_synonym", Paths.get(indir));
// System.out.println("c");
vp.parseVariationToJson("", "", "", "", Paths.get(indir), Paths.get(outfile));
vp.disconnect();
}
}
if (buildOption.equals("regulation")) {
System.out.println("In regulation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
System.out.println("chunksize: " + chunksize);
String outfile = commandLine.getOptionValue("outfile", "/tmp/regulations.json");
if (indir != null) {
try {
RegulatoryParser.parseRegulatoryGzipFilesToJson(
Paths.get(indir), chunksize, Paths.get(outfile));
} catch (ClassNotFoundException | NoSuchMethodException | SQLException e) {
e.printStackTrace();
}
}
}
if (buildOption.equals("conservation")) {
System.out.println("In conservation");
String indir = commandLine.getOptionValue("indir");
int chunksize = Integer.parseInt(commandLine.getOptionValue("chunksize", "0"));
String outfile = commandLine.getOptionValue("outfile", "/tmp/conservation.json");
if (indir != null) {
ConservedRegionParser.parseConservedRegionFilesToJson(
Paths.get(indir), chunksize, Paths.get(outfile));
}
}
} catch (ParseException | IOException | SQLException | ClassNotFoundException e) {
e.printStackTrace();
}
}
