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Commit bd8f7a87 authored by Emanuel Cunha's avatar Emanuel Cunha
Browse files

bigg

parent 0652dcb2
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
......@@ -30,7 +30,7 @@ public class BiggMain {
if(args.length>0 && args[0].equals("0")) {
System.out.println("Veryfying checksum for worker initialization");
verifyChecksum();
// verifyChecksum();
}else{
performBlast();
}
......@@ -40,7 +40,7 @@ public class BiggMain {
private static void performBlast() throws NoSuchAlgorithmException, IOException {
System.out.println("Veryfying checksum for Blast execution");
verifyChecksum();
// verifyChecksum();
System.out.println("Unzipping necessary files");
unzipFiles();
......@@ -132,10 +132,10 @@ public class BiggMain {
if (!checksumFile.exists()) {
System.out.println("Checksum not found - downloading checksum + files");
URL urlMd5 = new URL("https://merlin-sysbio.org/data/bigg/genericDump/checksum.md5");
URL urlMd5 = new URL("https://merlin.bio.di.uminho.pt/data/bigg/genericDump/checksum.md5");
org.apache.commons.io.FileUtils.copyURLToFile(urlMd5, checksumFile);
File biggFilesFile = new File(biggFilesZip);
URL urlBiggFiles = new URL("https://merlin-sysbio.org/data/bigg/genericDump/BiggDatabaseDump.zip");
URL urlBiggFiles = new URL("https://merlin.bio.di.uminho.pt/data/bigg/genericDump/BiggDatabaseDump.zip");
org.apache.commons.io.FileUtils.copyURLToFile(urlBiggFiles, biggFilesFile);
}
......@@ -145,16 +145,14 @@ public class BiggMain {
if(!verify) {
System.out.println("Different checksum found - downloading checksum + files");
URL urlMd5 = new URL("https://merlin-sysbio.org/data/bigg/genericDump/checksum.md5");
URL urlMd5 = new URL("https://merlin.bio.di.uminho.pt/data/bigg/genericDump/checksum.md5");
org.apache.commons.io.FileUtils.copyURLToFile(urlMd5, checksumFile);
File biggFilesFile = new File(biggFilesZip);
URL urlBiggFiles = new URL("https://merlin-sysbio.org/data/bigg/genericDump/BiggDatabaseDump.zip");
URL urlBiggFiles = new URL("https://merlin.bio.di.uminho.pt/data/bigg/genericDump/BiggDatabaseDump.zip");
org.apache.commons.io.FileUtils.copyURLToFile(urlBiggFiles, biggFilesFile);
}else
System.out.println("Checksums are equal - no need to download anything from FTP");
}
}
......@@ -167,7 +165,7 @@ public class BiggMain {
*/
private static boolean verifyKeys() throws IOException, NoSuchAlgorithmException {
URL url = new URL("https://merlin-sysbio.org/data/bigg/genericDump/checksum.md5");
URL url = new URL("https://merlin.bio.di.uminho.pt/data/bigg/genericDump/checksum.md5");
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("GET");
BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream()));
......
......@@ -43,7 +43,7 @@ public class UpdateBiggFiles {
private static boolean resultsNeedUpdate = false;
private static List<String> modelBiggIds = new ArrayList<String>();
//Docker Paths
// private static String generalPath = "C:/Users/Asus/Desktop/";
// private static String generalPath = "C:/Users/Asus/Desktop/";
private static String generalPath = BiggUtils.getRootDirectory();//BiggUtils.getRootDirectory(); //Main path where all the files will be
private static String mainPath = generalPath + "Bigg_Files/";//BiggUtils.getRootDirectory(); //Main path where all the files will be
private static String modelsPath = mainPath.concat("BiggData/"); //Folder where the models files will be
......
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