Merge pull request #15 from BiBiServ/feature/running-docker-containers

Feature running docker containers
BiBiServ · Nov 8, 2016 · 6817a55 · 6817a55
2 parents e8c0b00 + f05067a
commit 6817a55
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Showing 4 changed files with 34 additions and 39 deletions.
diff --git a/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/BiBiTools.java b/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/BiBiTools.java
@@ -22,15 +22,9 @@
  */
 package de.unibi.techfak.bibiserv;
 
-import de.unibi.techfak.bibiserv.cms.TenumParam;
-import de.unibi.techfak.bibiserv.cms.TenumValue;
-import de.unibi.techfak.bibiserv.cms.Tfunction;
-import de.unibi.techfak.bibiserv.cms.TinputOutput;
-import de.unibi.techfak.bibiserv.cms.Tparam;
+import de.unibi.techfak.bibiserv.cms.*;
 import de.unibi.techfak.bibiserv.cms.Tparam.Max;
 import de.unibi.techfak.bibiserv.cms.Tparam.Min;
-import de.unibi.techfak.bibiserv.cms.TparamGroup;
-import de.unibi.techfak.bibiserv.cms.TrunnableItem;
 import de.unibi.techfak.bibiserv.debug.DDataSource;
 import de.unibi.techfak.bibiserv.exception.BiBiToolsException;
 import de.unibi.techfak.bibiserv.exception.DBConnectionException;
@@ -932,8 +926,8 @@ public File getTmpDir() throws FileNotFoundException {
      *
      * @return
      */
-    public Element getToolDescription() {
-        return (Element) runnableitem;
+    public TrunnableItem getToolDescription() {
+        return runnableitem;
     }
 
     /**
@@ -2285,7 +2279,7 @@ public String generateCmdLineString(String id, Map<String, String> hash, String
         StringBuffer cmdline = new StringBuffer(getExecCmd());
 
         // test if cmdline describe a valid executable (only if 'UseDocker' is unset)
-        if (getProperty("UseDocker") == null || !getProperty("UseDocker").equalsIgnoreCase("true")) {
+        if (!getToolDescription().getExecutable().getExecInfo().getExecutableType().equalsIgnoreCase("docker")) {
 
             File test = new File(cmdline.toString());
             if (testexec && !(test.exists() && test.isFile() && test.canExecute())) {
@@ -2949,35 +2943,31 @@ private TinputOutput search_for_input(String id) {
      */
     private String getExecCmd() {
         StringBuffer cmdbuf = new StringBuffer();
-        if (getProperty("UseDocker") == null || !getProperty("UseDocker").equalsIgnoreCase("true")) {
-            if (getProperty("executable.rootpath") != null) {
-                cmdbuf.append(getProperty("executable.rootpath"));
-                if (!endWithFileSeparator(cmdbuf)) {
-                    cmdbuf.append(this.separator);
-                }
-                if (getProperty("executable.path.isrelativ").equalsIgnoreCase("true")) {
-                    cmdbuf.append(runnableitem.getExecutable().getExecInfo().getPath());
-                    if (!endWithFileSeparator(cmdbuf)) {
-                        cmdbuf.append(this.separator);
-                    }
-                }
-            } else {
+
+        Texecutable executable = getToolDescription().getExecutable();
+        boolean isDocker = getToolDescription().getExecutable().getExecInfo().getExecutableType().equalsIgnoreCase("docker");
+        if (getProperty("executable.rootpath") != null && !isDocker) {
+            cmdbuf.append(getProperty("executable.rootpath"));
+            if (!endWithFileSeparator(cmdbuf)) {
+                cmdbuf.append(this.separator);
+            }
+            if (getProperty("executable.path.isrelativ").equalsIgnoreCase("true")) {
                 cmdbuf.append(runnableitem.getExecutable().getExecInfo().getPath());
                 if (!endWithFileSeparator(cmdbuf)) {
                     cmdbuf.append(this.separator);
                 }
             }
         } else {
-            String orga = getProperty("DockerHubOrganization");
-            if (orga != null) {
-                cmdbuf.append("docker run ");
-                cmdbuf.append(" --rm=true");
-                cmdbuf.append(" -v ").append(getProperty("spooldir.base")).append(":").append(getProperty("spooldir.base"));
-                cmdbuf.append(" ").append(orga).append("/").append(runnableitem.getId());
-                cmdbuf.append(" /usr/local/bin/");
-            } else {
-                cmdbuf.append("# BiBiTool.properties doesn't contain a property named 'DockerHubOrganization'!");
+            cmdbuf.append("docker ");
+            cmdbuf.append("run ");
+            cmdbuf.append("--entrypoint='" + runnableitem.getExecutable().getExecInfo().getPath() + "' ");
+            try {
+                cmdbuf.append("-v ");
+                cmdbuf.append(getSpoolDir().toString() + ":" + getSpoolDir().toString() + ":rw ");
+            } catch (FileNotFoundException e) {
+                e.printStackTrace();
             }
+            cmdbuf.append(executable.getExecInfo().getImage() + " ");
         }
         cmdbuf.append(runnableitem.getExecutable().getExecInfo().getCallingInformation());
         return cmdbuf.toString();

diff --git a/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/impl/JobProxyCall.java b/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/impl/JobProxyCall.java
@@ -29,7 +29,6 @@
 import de.unibi.techfak.bibiserv.exception.IdNotFoundException;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
@@ -39,7 +38,6 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
-import java.util.logging.Level;
 import org.apache.log4j.Logger;
 import org.json.*;
 
@@ -77,7 +75,16 @@ public JobProxyCall() {
      */
     public JobProxyCall(BiBiTools wsstools) {
         this(wsstools, wsstools.getStatus());
-        // get servr JobProxyServer from 
+        setUri(wsstools);
+    }
+
+    @Override
+    public void setBiBiTools(BiBiTools bibitools) {
+        super.setBiBiTools(bibitools);
+        setUri(bibitools);
+    }
+
+    private void setUri(BiBiTools biBiTools){
         try {
             uri = new URI(wsstools.getProperty("JobProxyServer.URI", "http://localhost:9999/"));
         } catch (URISyntaxException e) {
@@ -88,7 +95,6 @@ public JobProxyCall(BiBiTools wsstools) {
                 // should not occure
             }
         }
-
     }
 
     public JobProxyCall(BiBiTools submitted_wsstools, Status submitted_status) {

diff --git a/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/impl/LocalCall.java b/libs/bibitools/src/main/java/de/unibi/techfak/bibiserv/impl/LocalCall.java
@@ -29,7 +29,6 @@
 
 import de.unibi.techfak.bibiserv.exception.DBConnectionException;
 import java.io.File;
-import java.io.FileInputStream;
 
 /**
  * Implements the Call interface executing a program directly on the local

diff --git a/libs/ontoaccess/pom.xml b/libs/ontoaccess/pom.xml
@@ -34,13 +34,13 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>2.10.1</version>
+            <version>2.7.1</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/com.github.ansell.pellet/pellet-jena -->
         <dependency>
             <groupId>com.github.ansell.pellet</groupId>
             <artifactId>pellet-jena</artifactId>
-            <version>2.3.6-ansell</version>
+            <version>2.3.2</version>
         </dependency>
 
     </dependencies>