Working draft, minimal styling

.gitignore

@@ -22,4 +22,7 @@
 /nbbuild/
 /dist/
 /nbdist/
-/.nb-gradle/
+/.nb-gradle/
+
+/application.properties
+

pom.xml

@@ -70,6 +70,11 @@
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-configuration-processor</artifactId>
+            <optional>true</optional>
+        </dependency>
     </dependencies>
 
     <build>

src/main/java/com/jacobsonmt/idrbind/controllers/JobController.java

@@ -0,0 +1,123 @@
+package com.jacobsonmt.idrbind.controllers;
+
+import com.jacobsonmt.idrbind.model.IDRBindJob;
+import com.jacobsonmt.idrbind.model.IDRBindJobResult;
+import com.jacobsonmt.idrbind.services.JobManager;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.multipart.MultipartFile;
+import org.springframework.web.servlet.mvc.support.RedirectAttributes;
+
+import javax.servlet.http.HttpServletRequest;
+import java.io.IOException;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
+
+@Log4j2
+@Controller
+public class JobController {
+
+    @Autowired
+    private JobManager jobManager;
+
+
+
+    @PostMapping("/")
+    public String handleFileUpload(@RequestParam("pdbFile") MultipartFile pdbFile,
+                                   @RequestParam("sequence") MultipartFile sequence,
+                                   @RequestParam("label") String label,
+                                   @RequestParam(value = "email", required = false, defaultValue = "") String email,
+                                   @RequestParam(value = "hidden", required = false, defaultValue = "false") boolean hidden,
+                                   HttpServletRequest request,
+                                   RedirectAttributes redirectAttributes) throws IOException {
+
+        String ipAddress = request.getHeader( "X-FORWARDED-FOR" );
+        if ( ipAddress == null ) {
+            ipAddress = request.getRemoteAddr();
+        }
+
+        IDRBindJob job = jobManager.createJob( ipAddress,
+                label,
+                IDRBindJob.inputStreamToString( pdbFile.getInputStream() ),
+                IDRBindJob.inputStreamToString( sequence.getInputStream() ),
+                email,
+                hidden );
+        jobManager.submit( job );
+
+        redirectAttributes.addFlashAttribute("message",
+                "Job Submitted! View job <a href='job/" + job.getJobId() + "' target='_blank'>here</a>.");
+
+        return "redirect:/";
+    }
+
+    @GetMapping("/job/{jobId}")
+    public String job( @PathVariable("jobId") String jobId,
+                       Model model) throws IOException {
+
+        IDRBindJob job = jobManager.getSavedJob( jobId );
+
+        if (job==null) {
+            return "/";
+        }
+
+        model.addAttribute("job", jobManager.getSavedJob( jobId ).toValueObject( true ) );
+
+        return "job";
+    }
+
+    @GetMapping("/job/{jobId}/resultPDB")
+    public ResponseEntity<String> jobResultPDB( @PathVariable("jobId") String jobId) {
+        IDRBindJob job = jobManager.getSavedJob( jobId );
+
+        // test for not null and complete
+        if ( job != null && job.isComplete() && !job.isFailed() ) {
+            try {
+                IDRBindJobResult result = job.getFuture().get( 1, TimeUnit.SECONDS );
+
+                    return ResponseEntity.ok()
+                            .contentType( MediaType.parseMediaType("application/octet-stream"))
+                            .header( HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + job.getLabel() + "-result.pdb\"")
+                            .body(result.getResultPDB());
+
+            } catch ( InterruptedException | ExecutionException | TimeoutException e ) {
+                log.warn( e );
+                ResponseEntity.status( 500 ).body( "" );
+            }
+        }
+        return ResponseEntity.badRequest().body( "" );
+    }
+
+    @GetMapping("/job/{jobId}/resultCSV")
+    public ResponseEntity<String> jobResultCSV( @PathVariable("jobId") String jobId) {
+        IDRBindJob job = jobManager.getSavedJob( jobId );
+
+        // test for not null and complete
+        if ( job != null && job.isComplete() && !job.isFailed() ) {
+            try {
+                IDRBindJobResult result = job.getFuture().get( 1, TimeUnit.SECONDS );
+
+                return ResponseEntity.ok()
+                        .contentType( MediaType.parseMediaType("application/octet-stream"))
+                        .header( HttpHeaders.CONTENT_DISPOSITION, "attachment; filename=\"" + job.getLabel() + "-result.csv\"")
+                        .body(result.getResultCSV());
+
+            } catch ( InterruptedException | ExecutionException | TimeoutException e ) {
+                log.warn( e );
+                ResponseEntity.status( 500 ).body( "" );
+            }
+        }
+        return ResponseEntity.badRequest().body( "" );
+    }
+
+
+}

src/main/java/com/jacobsonmt/idrbind/controllers/MainController.java

@@ -0,0 +1,47 @@
+package com.jacobsonmt.idrbind.controllers;
+
+import com.jacobsonmt.idrbind.services.JobManager;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
+
+import java.io.IOException;
+
+@Log4j2
+@Controller
+public class MainController {
+
+    @Autowired
+    private JobManager jobManager;
+
+    @GetMapping("/")
+    public String index( Model model) throws IOException {
+
+        return "index";
+    }
+
+    @GetMapping("/queue")
+    public String queue( Model model) throws IOException {
+
+        model.addAttribute("jobs", jobManager.listPublicJobs() );
+
+        return "queue";
+    }
+
+    @GetMapping("/documentation")
+    public String documentation( Model model) throws IOException {
+        return "documentation";
+    }
+
+    @GetMapping("/faq")
+    public String faq( Model model) throws IOException {
+        return "faq";
+    }
+
+    @GetMapping("/contact")
+    public String contact( Model model) throws IOException {
+        return "contact";
+    }
+}

src/main/java/com/jacobsonmt/idrbind/model/IDRBindJob.java

@@ -0,0 +1,194 @@
+package com.jacobsonmt.idrbind.model;
+
+import com.jacobsonmt.idrbind.services.JobManager;
+import lombok.*;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.util.StopWatch;
+
+import javax.ws.rs.core.StreamingOutput;
+import java.io.*;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.util.Date;
+import java.util.concurrent.*;
+
+@Log4j2
+@Getter
+@Setter
+@Builder
+@ToString(of = {"jobId", "userId", "label", "hidden"})
+@EqualsAndHashCode(of = {"jobId"})
+public class IDRBindJob implements Callable<IDRBindJobResult> {
+
+    // Path to resources
+    private String command;
+    private String commandWorkingDirectory;
+    private String inputPDBFullPath;
+    private String inputProteinChainFullPath;
+    private String outputScoredPDBFullPath;
+    private String outputCSVFullPath;
+
+
+    // Information on creation of job
+    private String userId;
+    private String jobId;
+    private String label;
+    private String inputPDBContent;
+    private String inputProteinChainIds;
+    @Builder.Default private boolean hidden = true;
+    private Date submittedDate;
+    private String email;
+
+    // Information on running / completion
+    @Builder.Default private boolean running = false;
+    @Builder.Default private boolean failed = false;
+    @Builder.Default private boolean complete = false;
+    private Integer position;
+    private String status;
+
+    // Results
+    private Future<IDRBindJobResult> future;
+    private StreamingOutput resultFile;
+    private long executionTime;
+
+    // Saving Job information / results for later
+    @Builder.Default private boolean saved = false;
+    private Long saveExpiredDate;
+
+    // Back-reference to owning JobManager
+    private JobManager jobManager;
+
+    @Override
+    public IDRBindJobResult call() throws Exception {
+
+        try {
+
+            log.info( "Starting job (" + label + ") for user: (" + userId + ")" );
+
+            this.running = true;
+            this.status = "Processing";
+
+            jobManager.onJobStart( this );
+
+            // Write content to input
+            File pdbFile = new File( inputPDBFullPath );
+            writeToFile( pdbFile, inputPDBContent );
+
+            File chainFile = new File( inputProteinChainFullPath );
+            writeToFile( chainFile, inputProteinChainIds );
+
+            // Execute script
+            StopWatch sw = new StopWatch();
+            sw.start();
+            executeCommand( "./" + command, commandWorkingDirectory );
+            sw.stop();
+            this.executionTime = sw.getTotalTimeMillis() / 1000;
+
+            // Get output
+            String resultPDB = inputStreamToString( new FileInputStream( outputScoredPDBFullPath ) );
+            String resultCSV = inputStreamToString( new FileInputStream( outputCSVFullPath ) );
+
+            log.info( "Finished job (" + label + ") for user: (" + userId + ")" );
+            this.running = false;
+            this.complete = true;
+
+            jobManager.onJobComplete( this );
+            jobManager = null;
+
+            return new IDRBindJobResult( resultPDB, resultCSV );
+        } catch ( Exception e ) {
+            log.error( e );
+            this.complete = true;
+            this.running = false;
+            this.failed = true;
+            jobManager = null;
+            this.status = "Failed";
+            return new IDRBindJobResult( "", "" );
+        }
+
+    }
+
+    private static void writeToFile(File file, String fileContents) throws IOException {
+
+        try (FileOutputStream fop = new FileOutputStream( file )) {
+
+            // if file doesn't exists, then create it
+            if (!file.exists()) {
+                file.createNewFile();
+            }
+
+            BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fop));
+            writer.write(fileContents);
+            writer.newLine();
+            writer.flush();
+            writer.close();
+
+        }
+
+    }
+
+    private static String executeCommand( String command, String path ) {
+
+        StringBuffer output = new StringBuffer();
+
+        Process p;
+        try {
+            p = Runtime.getRuntime().exec( command, null, new File( path ) );
+            p.waitFor();
+            BufferedReader reader = new BufferedReader( new InputStreamReader( p.getInputStream() ) );
+
+            String line = "";
+            while ( ( line = reader.readLine() ) != null ) {
+                output.append( line + "\r\n" );
+            }
+
+        } catch ( Exception e ) {
+            e.printStackTrace();
+        }
+
+        return output.toString();
+    }
+
+    public static String inputStreamToString(InputStream inputStream) throws IOException {
+        StringBuilder textBuilder = new StringBuilder();
+        try (Reader reader = new BufferedReader(new InputStreamReader
+                (inputStream, Charset.forName(StandardCharsets.UTF_8.name())))) {
+            int c = 0;
+            while ((c = reader.read()) != -1) {
+                textBuilder.append((char) c);
+            }
+        }
+        return textBuilder.toString();
+    }
+
+    @Getter
+    @AllArgsConstructor
+    public static final class IDRBindJobVO {
+        private final String jobId;
+        private final String label;
+        private final String status;
+        private final boolean running;
+        private final boolean failed;
+        private final boolean complete;
+        private Integer position;
+        private final String email;
+        private final boolean hidden;
+        private final Date submitted;
+        private final IDRBindJobResult result;
+    }
+
+    public IDRBindJobVO toValueObject(boolean obfuscateEmail) {
+
+        IDRBindJobResult result = null;
+        if ( this.isComplete() ) {
+            try {
+                result = this.getFuture().get( 1, TimeUnit.SECONDS );
+            } catch ( InterruptedException | ExecutionException | TimeoutException e ) {
+                log.error( e );
+            }
+        }
+
+        return new IDRBindJobVO( jobId, label, status, running, failed, complete, position, obfuscateEmail ? email.replaceAll("(\\w{0,3})(\\w+.*)(@.*)", "$1****$3") :  email, hidden, submittedDate, result );
+    }
+
+}