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* app module is now used for CLI. Classes and options created * log4j is now used instead of 'simple' and log4j.properties created in resources * core module package renamed
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| #!/bin/bash | ||
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| if [ $# -eq 1 ]; then | ||
| if [ $1 == 'run-maven' ]; then | ||
| mvn clean install -DskipTests | ||
| fi | ||
| fi | ||
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| ## Check if 'build' folder exists to delete the content. If not it is created. | ||
| if [ -d build ]; then | ||
| rm -rf build/* | ||
| else | ||
| mkdir build | ||
| fi | ||
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| ## Copy all the binaries, dependencies and files | ||
| cp -r hpg-bigdata-app/target/appassembler/* build/ | ||
| cp README.md build/ | ||
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62 changes: 62 additions & 0 deletions
62
hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/BigDataMain.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| package org.opencb.hpg.bigdata.app; | ||
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| import org.opencb.hpg.bigdata.app.cli.*; | ||
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| /** | ||
| * Created by imedina on 15/03/15. | ||
| */ | ||
| public class BigDataMain { | ||
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| public static void main(String[] args) { | ||
| CliOptionsParser cliOptionsParser = new CliOptionsParser(); | ||
| cliOptionsParser.parse(args); | ||
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| String parsedCommand = cliOptionsParser.getCommand(); | ||
| if (parsedCommand == null || parsedCommand.isEmpty()) { | ||
| if (cliOptionsParser.getGeneralOptions().help) { | ||
| cliOptionsParser.printUsage(); | ||
| } | ||
| if (cliOptionsParser.getGeneralOptions().version) { | ||
| System.out.println("version = 3.1.0"); | ||
| } | ||
| } else { | ||
| CommandExecutor commandExecutor = null; | ||
| switch (parsedCommand) { | ||
| case "fastq": | ||
| if (cliOptionsParser.getFastqCommandOptions().commonOptions.help) { | ||
| cliOptionsParser.printUsage(); | ||
| } else { | ||
| commandExecutor = new FastqCommandExecutor(cliOptionsParser.getFastqCommandOptions()); | ||
| } | ||
| break; | ||
| case "bam": | ||
| if (cliOptionsParser.getBamCommandOptions().commonOptions.help) { | ||
| cliOptionsParser.printUsage(); | ||
| } else { | ||
| commandExecutor = new BamCommandExecutor(cliOptionsParser.getBamCommandOptions()); | ||
| } | ||
| break; | ||
| case "ga4gh": | ||
| if (cliOptionsParser.getGa4ghCommandOptions().commonOptions.help) { | ||
| cliOptionsParser.printUsage(); | ||
| } else { | ||
| commandExecutor = new Ga4ghCommandExecutor(cliOptionsParser.getGa4ghCommandOptions()); | ||
| } | ||
| break; | ||
| case "align": | ||
| if (cliOptionsParser.getAlignCommandOptions().commonOptions.help) { | ||
| cliOptionsParser.printUsage(); | ||
| } else { | ||
| commandExecutor = new AlignCommandExecutor(cliOptionsParser.getAlignCommandOptions()); | ||
| } | ||
| break; | ||
| default: | ||
| break; | ||
| } | ||
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| if (commandExecutor != null) { | ||
| commandExecutor.parse(); | ||
| } | ||
| } | ||
| } | ||
| } |
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27
hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/AlignCommandExecutor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| package org.opencb.hpg.bigdata.app.cli; | ||
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| /** | ||
| * Created by imedina on 16/03/15. | ||
| */ | ||
| public class AlignCommandExecutor extends CommandExecutor { | ||
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| private CliOptionsParser.AlignCommandOptions alignCommandOptions; | ||
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| public AlignCommandExecutor(CliOptionsParser.AlignCommandOptions alignCommandOptions) { | ||
| super(alignCommandOptions.commonOptions.logLevel, alignCommandOptions.commonOptions.verbose, | ||
| alignCommandOptions.commonOptions.conf); | ||
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| this.alignCommandOptions = alignCommandOptions; | ||
| } | ||
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| /** | ||
| * Parse specific 'align' command options | ||
| */ | ||
| public void parse() { | ||
| logger.info("Executing {} CLI options", "align"); | ||
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| logger.debug("Input file: {}", alignCommandOptions.input); | ||
| } | ||
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| } |
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hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/BamCommandExecutor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| package org.opencb.hpg.bigdata.app.cli; | ||
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| /** | ||
| * Created by imedina on 15/03/15. | ||
| */ | ||
| public class BamCommandExecutor extends CommandExecutor { | ||
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| private CliOptionsParser.BamCommandOptions bamCommandOptions; | ||
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| public BamCommandExecutor(CliOptionsParser.BamCommandOptions bamCommandOptions) { | ||
| super(bamCommandOptions.commonOptions.logLevel, bamCommandOptions.commonOptions.verbose, | ||
| bamCommandOptions.commonOptions.conf); | ||
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| this.bamCommandOptions = bamCommandOptions; | ||
| } | ||
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| /** | ||
| * Parse specific 'bam' command options | ||
| */ | ||
| public void parse() { | ||
| logger.info("Executing {} CLI options", "bam"); | ||
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| logger.debug("Input file: {}", bamCommandOptions.input); | ||
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| } | ||
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| } |
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