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#492 fix ping + download after install
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@pavelToman
pavelToman committed Jan 28, 2025
1 parent 4901d6f commit 3de2e4e
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15 changes: 15 additions & 0 deletions 492_UFCG/UFCG-1.0.6_fix-ping.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
Fix function internetConnection to prevent run ping and internet connection error.
https://github.com/steineggerlab/ufcg/blob/cf9cfe3c2950c8d17447864da4574014db5a90f7/src/module/DownloadModule.java#L121
--- src/module/DownloadModule.java.orig 2025-01-28 18:06:36.553823000 +0100
+++ src/module/DownloadModule.java 2025-01-28 18:28:36.023487000 +0100
@@ -119,9 +119,7 @@
}

private boolean internetConnection(){
- String[] raw = Shell.exec(String.format("ping -c 1 -W %d ufcg.steineggerlab.workers.dev", GenericConfig.OS.equals("Linux") ? 1 : 1000), true, 0);
- if(raw == null || raw.length < 2) return false;
- return raw[raw.length - 2].contains(GenericConfig.OS.equals("Linux") ? "1 received" : "1 packets received");
+ return true;
}
private void printManual() {
System.out.println(ANSIHandler.wrapper(" UFCG - download", 'G'));
334 changes: 334 additions & 0 deletions 492_UFCG/patch1_fix-ping/DownloadModule.java
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package module;

import java.io.File;
import java.io.IOException;
import java.util.Arrays;

import envs.config.PathConfig;
import envs.toolkit.Shell;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.MissingArgumentException;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.UnrecognizedOptionException;

import envs.config.GenericConfig;
import envs.toolkit.ANSIHandler;
import envs.toolkit.Prompt;
import pipeline.ExceptionHandler;
import pipeline.UFCGMainPipeline;

public class DownloadModule {
private static final String[] targets = {"full", "minimum", "config", "core", "busco", "sample"};
private final String[] args;
private String target, dir = PathConfig.JarPath;
private boolean dirGiven = false;

public DownloadModule(String[] args) {
this.args = args;
switch(parseArguments()){
case 0: break;
case -1: printManual(); break;
case -2: checkStatus(); break;
default: ExceptionHandler.handle(ExceptionHandler.UNEXPECTED_ERROR);
}
}

private int parseArguments() {
Options opts = new Options();
opts.addOption("h", "help", false, "helper route");
opts.addOption(null, "notime", false, "no timestamp with prompt");
opts.addOption(null, "nocolor", false, "disable ANSI escapes");
opts.addOption("v", "verbose", false, "verbosity");
opts.addOption(null, "developer", false, "developer tool");
opts.addOption(null, "test", false, "for test");

opts.addOption("t", "target", true, "download target");
opts.addOption("d", "dir", true, "download directory");
opts.addOption("c", "check", false, "check files");

CommandLineParser clp = new DefaultParser();
CommandLine cmd = null;
try{ cmd = clp.parse(opts, args); }
catch(UnrecognizedOptionException uoe) {
ExceptionHandler.pass(uoe.getOption());
ExceptionHandler.handle(ExceptionHandler.UNKNOWN_OPTION);
}
catch(MissingArgumentException mae) {
ExceptionHandler.pass(mae.getOption().getOpt() != null ?
mae.getOption().getOpt() :
mae.getOption().getLongOpt());
ExceptionHandler.handle(ExceptionHandler.MISSING_ARGUMENT);
}
catch(ParseException pe) {
ExceptionHandler.handle(pe);
}

assert cmd != null;
if(cmd.hasOption("developer")) {
GenericConfig.DEV = true;
GenericConfig.VERB = true;
GenericConfig.TSTAMP = true;
}
if(cmd.hasOption("test")) GenericConfig.TEST = true;

/* parse user friendly options; return ID and finish routine if necessary */
if(cmd.hasOption("v")) GenericConfig.VERB = true;
if(cmd.hasOption("notime")) GenericConfig.TSTAMP = false;
if(cmd.hasOption("nocolor")) GenericConfig.NOCOLOR = true;
if(cmd.hasOption("h")) return -1;

Prompt.debug(ANSIHandler.wrapper("Developer mode activated.", 'Y'));
Prompt.talk("Verbose option check.");
if(GenericConfig.TSTAMP) Prompt.talk("Timestamp printing option check.");

/* parse arguments */
if(cmd.hasOption("d")){
dirGiven = true;
dir = cmd.getOptionValue("d");
if(!dir.endsWith("/")) dir += "/";
if(new File(dir).exists()) {
if(!new File(dir).isDirectory()) {
ExceptionHandler.pass(dir);
ExceptionHandler.handle(ExceptionHandler.INVALID_DIRECTORY);
return 1;
}
}
else {
if(!new File(dir).mkdirs()) {
ExceptionHandler.pass(dir);
ExceptionHandler.handle(ExceptionHandler.INVALID_DIRECTORY);
return 1;
}
}
}
if(cmd.hasOption("c")) return -2;
if(cmd.hasOption("t")) target = cmd.getOptionValue("t");
else {
ExceptionHandler.handle(ExceptionHandler.NO_TARGET);
return 1;
}
if(!Arrays.asList(targets).contains(target)){
ExceptionHandler.pass(target);
ExceptionHandler.handle(ExceptionHandler.INVALID_TARGET);
return 1;
}
return 0;
}

private boolean internetConnection(){
return true;
}
private void printManual() {
System.out.println(ANSIHandler.wrapper(" UFCG - download", 'G'));
System.out.println(ANSIHandler.wrapper(" List or download resources", 'g'));
System.out.println();

System.out.println(ANSIHandler.wrapper("\n USAGE :", 'Y') + " ufcg download -t <TARGET> [...]");
System.out.println();

System.out.println(ANSIHandler.wrapper("\n Required options", 'Y'));
System.out.println(ANSIHandler.wrapper(" Argument Description", 'c'));
System.out.println(ANSIHandler.wrapper(" -t ", 'x') + ANSIHandler.wrapper("full ", 'x') + ANSIHandler.wrapper("Full download", 'x'));
System.out.println(ANSIHandler.wrapper(" minimum ", 'x') + ANSIHandler.wrapper("Minimum download (config, core)", 'x'));
System.out.println(ANSIHandler.wrapper(" config ", 'x') + ANSIHandler.wrapper("Download config files", 'x'));
System.out.println(ANSIHandler.wrapper(" core ", 'x') + ANSIHandler.wrapper("Download core gene database", 'x'));
System.out.println(ANSIHandler.wrapper(" busco ", 'x') + ANSIHandler.wrapper("Download BUSCO odb_fungi_v10 database", 'x'));
System.out.println(ANSIHandler.wrapper(" sample ", 'x') + ANSIHandler.wrapper("Download sample files", 'x'));
System.out.println();

System.out.println(ANSIHandler.wrapper("\n Configurations", 'y'));
System.out.println(ANSIHandler.wrapper(" Argument Description", 'c'));
System.out.println(ANSIHandler.wrapper(" -d STR Download directory [auto]", 'x'));
System.out.println(ANSIHandler.wrapper(" -c Check download status", 'x'));
System.out.println();

UFCGMainPipeline.printGeneral();

System.exit(0);
}
private void checkStatus(){
boolean ping = internetConnection();
if(PathConfig.EnvironmentPathSet && !dirGiven) dir = PathConfig.EnvironmentPath;
String sampleDir = dir;
if(!dirGiven) sampleDir = PathConfig.CurrPath;

System.out.println(ANSIHandler.wrapper(" System status", 'Y'));
System.out.println(ANSIHandler.wrapper(" OS : " + GenericConfig.OS, 'x'));
System.out.println(ANSIHandler.wrapper(" Path : ", 'x') + ANSIHandler.wrapper(dir, 'y'));
System.out.println(ANSIHandler.wrapper(" Internet : ", 'x') + (ping ? ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
if(!ping) System.exit(0);

System.out.println(ANSIHandler.wrapper("\n Download status", 'Y'));
System.out.println(ANSIHandler.wrapper(" Target Status", 'c'));
System.out.println(ANSIHandler.wrapper(" config ", 'x') + (new File(dir + "config/ppx.cfg").exists() ?
ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
System.out.println(ANSIHandler.wrapper(" core ", 'x') + (new File(dir + "config/seq/pro/ACT1.fa").exists() ?
ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
System.out.println(ANSIHandler.wrapper(" busco ", 'x') + (new File(dir + "config/seq/busco/100957at4751.fa").exists() ?
ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
System.out.println(ANSIHandler.wrapper(" sample ", 'x') + (new File(sampleDir + "sample/meta_full.tsv").exists() ?
ANSIHandler.wrapper("OK", 'G') : ANSIHandler.wrapper("NO", 'R')));
System.out.println();

System.exit(0);
}
private void download() throws IOException {
boolean ping = internetConnection();
if(PathConfig.EnvironmentPathSet && !dirGiven) dir = PathConfig.EnvironmentPath;

if(!ping) {
ExceptionHandler.handle(ExceptionHandler.NO_INTERNET);
return;
}

switch (target) {
case "full": downloadConfig(); downloadCore(); downloadBusco(); downloadSample(); break;
case "minimum": downloadConfig(); downloadCore(); break;
case "config": downloadConfig(); break;
case "core": downloadCore(); break;
case "busco": downloadBusco(); break;
case "sample": downloadSample(); break;
}
}

private void downloadConfig(){
// download payload
Prompt.print("Downloading config package on " + ANSIHandler.wrapper(dir + "config.tar.gz", 'y') + " ...");
Shell.exec(String.format("wget -q -O %sconfig.tar.gz https://ufcg.steineggerlab.workers.dev/payload/config.tar.gz", dir));

// check download
if(!new File(dir + "config.tar.gz").exists()){
ExceptionHandler.pass(dir + "config.tar.gz");
ExceptionHandler.handle(ExceptionHandler.DOWNLOAD_FAILED);
return;
}

// extract payload
Prompt.print("Extracting config package ...");
Shell.exec(String.format("tar -C %s -xzf %sconfig.tar.gz", dir, dir));

// check extraction
if(!new File(dir + "config/ppx.cfg").exists()){
ExceptionHandler.pass(dir + "config.tar.gz");
ExceptionHandler.handle(ExceptionHandler.EXTRACTION_FAILED);
return;
}

// delete payload
Prompt.print("Deleting config package ...");
if(!(new File(dir + "config.tar.gz")).delete()){
Prompt.warn("Failed to delete config package on " + ANSIHandler.wrapper(dir + "config.tar.gz", 'y'));
}

Prompt.print("Download success : target " + ANSIHandler.wrapper("config", 'G'));
}
private void downloadCore(){
// download payload
Prompt.print("Downloading core package on " + ANSIHandler.wrapper(dir + "core.tar.gz", 'y') + " ...");
Shell.exec(String.format("wget -q -O %score.tar.gz https://ufcg.steineggerlab.workers.dev/payload/core.tar.gz", dir));

// check download
if(!new File(dir + "core.tar.gz").exists()){
ExceptionHandler.pass(dir + "core.tar.gz");
ExceptionHandler.handle(ExceptionHandler.DOWNLOAD_FAILED);
return;
}

// extract payload
Prompt.print("Extracting core package ...");
Shell.exec(String.format("tar -C %s -xzf %score.tar.gz", dir, dir));

// check extraction
if(!new File(dir + "config/seq/pro/ACT1.fa").exists()){
ExceptionHandler.pass(dir + "core.tar.gz");
ExceptionHandler.handle(ExceptionHandler.EXTRACTION_FAILED);
return;
}

// delete payload
Prompt.print("Deleting core package ...");
if(!(new File(dir + "core.tar.gz")).delete()){
Prompt.warn("Failed to delete core package on " + ANSIHandler.wrapper(dir + "core.tar.gz", 'y'));
}

Prompt.print("Download success : target " + ANSIHandler.wrapper("core", 'G'));
}
private void downloadBusco(){
// download payload
Prompt.print("Downloading busco package on " + ANSIHandler.wrapper(dir + "busco.tar.gz", 'y') + " ...");
Shell.exec(String.format("wget -q -O %sbusco.tar.gz https://ufcg.steineggerlab.workers.dev/payload/busco.tar.gz", dir));

// check download
if(!new File(dir + "busco.tar.gz").exists()){
ExceptionHandler.pass(dir + "busco.tar.gz");
ExceptionHandler.handle(ExceptionHandler.DOWNLOAD_FAILED);
return;
}

// extract payload
Prompt.print("Extracting busco package ...");
Shell.exec(String.format("tar -C %s -xzf %sbusco.tar.gz", dir, dir));

// check extraction
if(!new File(dir + "config/seq/busco/100957at4751.fa").exists()){
ExceptionHandler.pass(dir + "busco.tar.gz");
ExceptionHandler.handle(ExceptionHandler.EXTRACTION_FAILED);
return;
}

// delete payload
Prompt.print("Deleting busco package ...");
if(!(new File(dir + "busco.tar.gz")).delete()){
Prompt.warn("Failed to delete busco package on " + ANSIHandler.wrapper(dir + "busco.tar.gz", 'y'));
}

Prompt.print("Download success : target " + ANSIHandler.wrapper("busco", 'G'));
}
private void downloadSample(){
if(!dirGiven) {
dir = PathConfig.CurrPath;
}

// download payload
Prompt.print("Downloading sample package on " + ANSIHandler.wrapper(dir + "sample.tar.gz", 'y') + " ...");
Shell.exec(String.format("wget -q -O %ssample.tar.gz https://ufcg.steineggerlab.workers.dev/payload/sample.tar.gz", dir));

// check download
if(!new File(dir + "sample.tar.gz").exists()){
ExceptionHandler.pass(dir + "sample.tar.gz");
ExceptionHandler.handle(ExceptionHandler.DOWNLOAD_FAILED);
return;
}

// extract payload
Prompt.print("Extracting sample package ...");
Shell.exec(String.format("tar -C %s -xzf %ssample.tar.gz", dir, dir));

// check extraction
if(!new File(dir + "sample/meta_full.tsv").exists()){
ExceptionHandler.pass(dir + "sample.tar.gz");
ExceptionHandler.handle(ExceptionHandler.EXTRACTION_FAILED);
return;
}

// delete payload
Prompt.print("Deleting sample package ...");
if(!(new File(dir + "sample.tar.gz")).delete()){
Prompt.warn("Failed to delete sample package on " + ANSIHandler.wrapper(dir + "sample.tar.gz", 'y'));
}

Prompt.print("Download success : target " + ANSIHandler.wrapper("sample", 'G'));
}

public static void run(String[] args){
DownloadModule dm = new DownloadModule(args);
try{
dm.download();
} catch (IOException e) {
ExceptionHandler.handle(e);
}
}
}
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