airavata-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From shame...@apache.org
Subject airavata git commit: Added UGE Configuration class and rename SGE to UGE to resolve name conflicts.
Date Thu, 14 May 2015 19:23:47 GMT
Repository: airavata
Updated Branches:
  refs/heads/master acf30c013 -> 86a79b669


Added UGE Configuration class and rename SGE to UGE to resolve name conflicts.


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/86a79b66
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/86a79b66
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/86a79b66

Branch: refs/heads/master
Commit: 86a79b669c51bb1d464d860256057d793de38fca
Parents: acf30c0
Author: shamrath <shameerainfo@gmail.com>
Authored: Thu May 14 15:23:45 2015 -0400
Committer: shamrath <shameerainfo@gmail.com>
Committed: Thu May 14 15:23:45 2015 -0400

----------------------------------------------------------------------
 .../server/src/main/resources/SGETemplate.xslt  |  78 ---------
 .../server/src/main/resources/UGETemplate.xslt  |  78 +++++++++
 .../gsi/ssh/api/job/SGEOutputParser.java        | 173 -------------------
 .../gsi/ssh/api/job/UGEJobConfiguration.java    | 119 +++++++++++++
 .../gsi/ssh/api/job/UGEOutputParser.java        | 173 +++++++++++++++++++
 .../airavata/gsi/ssh/util/CommonUtils.java      |   3 +-
 .../gsissh/src/main/resources/SGETemplate.xslt  |  74 --------
 .../gsissh/src/main/resources/UGETemplate.xslt  |  74 ++++++++
 8 files changed, 445 insertions(+), 327 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/modules/configuration/server/src/main/resources/SGETemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/configuration/server/src/main/resources/SGETemplate.xslt b/modules/configuration/server/src/main/resources/SGETemplate.xslt
deleted file mode 100644
index 7005295..0000000
--- a/modules/configuration/server/src/main/resources/SGETemplate.xslt
+++ /dev/null
@@ -1,78 +0,0 @@
-<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license
agreements. See the NOTICE file
-	distributed with this work for additional information regarding copyright ownership. The
ASF licenses this file to you under
-	the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance
with the License. You may
-	obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to
-	in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF
-	ANY ~ KIND, either express or implied. See the License for the specific language governing
permissions and limitations under
-	the License. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-    <xsl:param name="quote">"</xsl:param>
-#! /bin/bash
-# Grid Engine batch job script built by Apache Airavata
-#   <xsl:choose>
-    <xsl:when test="ns:shellName != ''">
-#$ -S <xsl:value-of select="ns:shellName"/>
-    </xsl:when></xsl:choose>
-#$ -V
-    <xsl:choose>
-    <xsl:when test="ns:queueName != ''">
-#$ -q <xsl:value-of select="ns:queueName"/>
-    </xsl:when>
-    </xsl:choose>
-#$ -m beas <xsl:choose>
-    <xsl:when test="ns:mailAddress != ''">
-#$ -M <xsl:value-of select="ns:mailAddress"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-<xsl:when test="ns:acountString != ''">
-#$ -A <xsl:value-of select="ns:acountString"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:maxWallTime != ''">
-#$ -l h_rt=<xsl:value-of select="ns:maxWallTime"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:jobName != ''">
-#$ -N <xsl:value-of select="ns:jobName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile != ''">
-#$ -o <xsl:value-of select="ns:standardOutFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile != ''">
-#$ -e <xsl:value-of select="ns:standardErrorFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
-#$ -pe <xsl:value-of select="ns:processesPerNode"/>way <xsl:value-of select="12
* ns:nodes"/>
-<xsl:text>&#xa;</xsl:text>
-    </xsl:when>
-    </xsl:choose>
-<xsl:for-each select="ns:exports/ns:name">
-<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
-export<xsl:text>   </xsl:text><xsl:value-of select="."/>
-<xsl:text>&#xa;</xsl:text>
-</xsl:for-each>
-<xsl:for-each select="ns:preJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of
select="ns:executablePath"/><xsl:text>   </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-<xsl:for-each select="ns:postJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-</xsl:for-each>
-</xsl:template>
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/modules/configuration/server/src/main/resources/UGETemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/configuration/server/src/main/resources/UGETemplate.xslt b/modules/configuration/server/src/main/resources/UGETemplate.xslt
new file mode 100644
index 0000000..7005295
--- /dev/null
+++ b/modules/configuration/server/src/main/resources/UGETemplate.xslt
@@ -0,0 +1,78 @@
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license
agreements. See the NOTICE file
+	distributed with this work for additional information regarding copyright ownership. The
ASF licenses this file to you under
+	the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance
with the License. You may
+	obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to
+	in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF
+	ANY ~ KIND, either express or implied. See the License for the specific language governing
permissions and limitations under
+	the License. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<xsl:output method="text" />
+<xsl:template match="/ns:JobDescriptor">
+    <xsl:param name="quote">"</xsl:param>
+#! /bin/bash
+# Grid Engine batch job script built by Apache Airavata
+#   <xsl:choose>
+    <xsl:when test="ns:shellName != ''">
+#$ -S <xsl:value-of select="ns:shellName"/>
+    </xsl:when></xsl:choose>
+#$ -V
+    <xsl:choose>
+    <xsl:when test="ns:queueName != ''">
+#$ -q <xsl:value-of select="ns:queueName"/>
+    </xsl:when>
+    </xsl:choose>
+#$ -m beas <xsl:choose>
+    <xsl:when test="ns:mailAddress != ''">
+#$ -M <xsl:value-of select="ns:mailAddress"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+<xsl:when test="ns:acountString != ''">
+#$ -A <xsl:value-of select="ns:acountString"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:maxWallTime != ''">
+#$ -l h_rt=<xsl:value-of select="ns:maxWallTime"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:jobName != ''">
+#$ -N <xsl:value-of select="ns:jobName"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:standardOutFile != ''">
+#$ -o <xsl:value-of select="ns:standardOutFile"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:standardOutFile != ''">
+#$ -e <xsl:value-of select="ns:standardErrorFile"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
+#$ -pe <xsl:value-of select="ns:processesPerNode"/>way <xsl:value-of select="12
* ns:nodes"/>
+<xsl:text>&#xa;</xsl:text>
+    </xsl:when>
+    </xsl:choose>
+<xsl:for-each select="ns:exports/ns:name">
+<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
+export<xsl:text>   </xsl:text><xsl:value-of select="."/>
+<xsl:text>&#xa;</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+    </xsl:for-each>
+cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
+    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of
select="ns:executablePath"/><xsl:text>   </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+    </xsl:for-each>
+<xsl:for-each select="ns:postJobCommands/ns:command">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+</xsl:for-each>
+</xsl:template>
+</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java
b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java
deleted file mode 100644
index 884b7f3..0000000
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java
+++ /dev/null
@@ -1,173 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.gsi.ssh.api.job;
-
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.impl.JobStatus;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-public class SGEOutputParser implements OutputParser{
-    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
-
-    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String[] line;
-        for (int i = 0; i < info.length; i++) {
-            if (info[i].contains("=")) {
-                line = info[i].split("=", 2);
-            } else {
-                line = info[i].split(":", 2);
-            }
-            if (line.length >= 2) {
-                String header = line[0].trim();
-                log.debug("Header = " + header);
-                String value = line[1].trim();
-                log.debug("value = " + value);
-
-                if (header.equals("Variable_List")) {
-                    while (info[i + 1].startsWith("\t")) {
-                        value += info[i + 1];
-                        i++;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setVariableList(value);
-                } else if ("Job Id".equals(header)) {
-                    jobDescriptor.setJobID(value);
-                } else if ("Job_Name".equals(header)) {
-                    jobDescriptor.setJobName(value);
-                } else if ("Account_Name".equals(header)) {
-                    jobDescriptor.setAcountString(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("Job_Owner".equals(header)) {
-                    jobDescriptor.setOwner(value);
-                } else if ("resources_used.cput".equals(header)) {
-                    jobDescriptor.setUsedCPUTime(value);
-                } else if ("resources_used.mem".equals(header)) {
-                    jobDescriptor.setUsedMemory(value);
-                } else if ("resources_used.walltime".equals(header)) {
-                    jobDescriptor.setEllapsedTime(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("queue".equals(header))
-                    jobDescriptor.setQueueName(value);
-                else if ("ctime".equals(header)) {
-                    jobDescriptor.setCTime(value);
-                } else if ("qtime".equals(header)) {
-                    jobDescriptor.setQTime(value);
-                } else if ("mtime".equals(header)) {
-                    jobDescriptor.setMTime(value);
-                } else if ("start_time".equals(header)) {
-                    jobDescriptor.setSTime(value);
-                } else if ("comp_time".equals(header)) {
-                    jobDescriptor.setCompTime(value);
-                } else if ("exec_host".equals(header)) {
-                    jobDescriptor.setExecuteNode(value);
-                } else if ("Output_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardOutFile(value);
-                    else {
-                        jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
-                        i++;
-                    }
-                } else if ("Error_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardErrorFile(value);
-                    else {
-                        String st = info[i + 1].trim();
-                        jobDescriptor.setStandardErrorFile(value + st);
-                        i++;
-                    }
-
-                } else if ("submit_args".equals(header)) {
-                    while (i + 1 < info.length) {
-                        if (info[i + 1].startsWith("\t")) {
-                            value += info[i + 1];
-                            i++;
-                        } else
-                            break;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setSubmitArgs(value);
-                }
-            }
-        }
-    }
-
-	public String parseJobSubmission(String rawOutput) {
-		log.debug(rawOutput);
-		if (rawOutput != null && !rawOutput.isEmpty()) {
-			String[] info = rawOutput.split("\n");
-			String lastLine = info[info.length - 1];
-			return lastLine.split(" ")[2]; // In PBS stdout is going to be directly the jobID
-		} else {
-			return "";
-		}
-	}
-
-    public JobStatus parseJobStatus(String jobID, String rawOutput) {
-       // not implemented to sun grid engine
-        return JobStatus.U;
-    }
-
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap,
String rawOutput) {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            for(int i=lastStop;i<info.length;i++){
-               if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split("
")[0])){
-                   // now starts processing this line
-                   log.info(info[i]);
-                   String correctLine = info[i];
-                   String[] columns = correctLine.split(" ");
-                   List<String> columnList = new ArrayList<String>();
-                   for (String s : columns) {
-                       if (!"".equals(s)) {
-                           columnList.add(s);
-                       }
-                   }
-                   lastStop = i+1;
-                   if ("E".equals(columnList.get(4))) {
-                       // There is another status with the same letter E other than error
status
-                       // to avoid that we make a small tweek to the job status
-                       columnList.set(4, "Er");
-                   }
-                   statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
-                   break;
-               }
-            }
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        return null; // TODO: Implement the parse logic ( with regex if possible ).
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
new file mode 100644
index 0000000..8817c06
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEJobConfiguration.java
@@ -0,0 +1,119 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gsi.ssh.api.job;
+
+import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.File;
+
+public class UGEJobConfiguration implements JobManagerConfiguration {
+
+    private String jobDescriptionTemplateName;
+
+    private String scriptExtension;
+
+    private String installedPath;
+
+    private OutputParser parser;
+
+    public UGEJobConfiguration() {
+        // this can be used to construct and use setter methods to set all the params in
order
+    }
+
+    public UGEJobConfiguration(String jobDescriptionTemplateName,
+                               String scriptExtension, String installedPath, OutputParser
parser) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+        this.scriptExtension = scriptExtension;
+        this.parser = parser;
+        if (installedPath.endsWith("/")) {
+            this.installedPath = installedPath;
+        } else {
+            this.installedPath = installedPath + "/";
+        }
+    }
+
+    public RawCommandInfo getCancelCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "qdel " + jobID);
+    }
+
+    public String getJobDescriptionTemplateName() {
+        return jobDescriptionTemplateName;
+    }
+
+    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
+        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
+    }
+
+    public RawCommandInfo getMonitorCommand(String jobID) {
+        return new RawCommandInfo(this.installedPath + "qstat -j " + jobID);
+    }
+
+    public String getScriptExtension() {
+        return scriptExtension;
+    }
+
+    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
+        return new RawCommandInfo(this.installedPath + "qsub " +
+                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
+    }
+
+    public String getInstalledPath() {
+        return installedPath;
+    }
+
+    public void setInstalledPath(String installedPath) {
+        this.installedPath = installedPath;
+    }
+
+    public OutputParser getParser() {
+        return parser;
+    }
+
+    public void setParser(OutputParser parser) {
+        this.parser = parser;
+    }
+
+    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
+        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+    }
+
+    @Override
+    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
+        // For PBS there is no option to get jobDetails by JobName, so we search with userName
+        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+    }
+
+    @Override
+    public String  getBaseCancelCommand() {
+        return "qdel";
+    }
+
+    @Override
+    public String  getBaseMonitorCommand() {
+        return "qstat";
+    }
+
+    @Override
+    public String getBaseSubmitCommand() {
+        return "qsub ";
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
new file mode 100644
index 0000000..645b975
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/UGEOutputParser.java
@@ -0,0 +1,173 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gsi.ssh.api.job;
+
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.impl.JobStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public class UGEOutputParser implements OutputParser{
+    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
+
+    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
+        log.debug(rawOutput);
+        String[] info = rawOutput.split("\n");
+        String[] line;
+        for (int i = 0; i < info.length; i++) {
+            if (info[i].contains("=")) {
+                line = info[i].split("=", 2);
+            } else {
+                line = info[i].split(":", 2);
+            }
+            if (line.length >= 2) {
+                String header = line[0].trim();
+                log.debug("Header = " + header);
+                String value = line[1].trim();
+                log.debug("value = " + value);
+
+                if (header.equals("Variable_List")) {
+                    while (info[i + 1].startsWith("\t")) {
+                        value += info[i + 1];
+                        i++;
+                    }
+                    value = value.replaceAll("\t", "");
+                    jobDescriptor.setVariableList(value);
+                } else if ("Job Id".equals(header)) {
+                    jobDescriptor.setJobID(value);
+                } else if ("Job_Name".equals(header)) {
+                    jobDescriptor.setJobName(value);
+                } else if ("Account_Name".equals(header)) {
+                    jobDescriptor.setAcountString(value);
+                } else if ("job_state".equals(header)) {
+                    jobDescriptor.setStatus(value);
+                } else if ("Job_Owner".equals(header)) {
+                    jobDescriptor.setOwner(value);
+                } else if ("resources_used.cput".equals(header)) {
+                    jobDescriptor.setUsedCPUTime(value);
+                } else if ("resources_used.mem".equals(header)) {
+                    jobDescriptor.setUsedMemory(value);
+                } else if ("resources_used.walltime".equals(header)) {
+                    jobDescriptor.setEllapsedTime(value);
+                } else if ("job_state".equals(header)) {
+                    jobDescriptor.setStatus(value);
+                } else if ("queue".equals(header))
+                    jobDescriptor.setQueueName(value);
+                else if ("ctime".equals(header)) {
+                    jobDescriptor.setCTime(value);
+                } else if ("qtime".equals(header)) {
+                    jobDescriptor.setQTime(value);
+                } else if ("mtime".equals(header)) {
+                    jobDescriptor.setMTime(value);
+                } else if ("start_time".equals(header)) {
+                    jobDescriptor.setSTime(value);
+                } else if ("comp_time".equals(header)) {
+                    jobDescriptor.setCompTime(value);
+                } else if ("exec_host".equals(header)) {
+                    jobDescriptor.setExecuteNode(value);
+                } else if ("Output_Path".equals(header)) {
+                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+                        jobDescriptor.setStandardOutFile(value);
+                    else {
+                        jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
+                        i++;
+                    }
+                } else if ("Error_Path".equals(header)) {
+                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+                        jobDescriptor.setStandardErrorFile(value);
+                    else {
+                        String st = info[i + 1].trim();
+                        jobDescriptor.setStandardErrorFile(value + st);
+                        i++;
+                    }
+
+                } else if ("submit_args".equals(header)) {
+                    while (i + 1 < info.length) {
+                        if (info[i + 1].startsWith("\t")) {
+                            value += info[i + 1];
+                            i++;
+                        } else
+                            break;
+                    }
+                    value = value.replaceAll("\t", "");
+                    jobDescriptor.setSubmitArgs(value);
+                }
+            }
+        }
+    }
+
+	public String parseJobSubmission(String rawOutput) {
+		log.debug(rawOutput);
+		if (rawOutput != null && !rawOutput.isEmpty()) {
+			String[] info = rawOutput.split("\n");
+			String lastLine = info[info.length - 1];
+			return lastLine.split(" ")[2]; // In PBS stdout is going to be directly the jobID
+		} else {
+			return "";
+		}
+	}
+
+    public JobStatus parseJobStatus(String jobID, String rawOutput) {
+       // not implemented to sun grid engine
+        return JobStatus.U;
+    }
+
+    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap,
String rawOutput) {
+        log.debug(rawOutput);
+        String[] info = rawOutput.split("\n");
+        int lastStop = 0;
+        for (String jobID : statusMap.keySet()) {
+            for(int i=lastStop;i<info.length;i++){
+               if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split("
")[0])){
+                   // now starts processing this line
+                   log.info(info[i]);
+                   String correctLine = info[i];
+                   String[] columns = correctLine.split(" ");
+                   List<String> columnList = new ArrayList<String>();
+                   for (String s : columns) {
+                       if (!"".equals(s)) {
+                           columnList.add(s);
+                       }
+                   }
+                   lastStop = i+1;
+                   if ("E".equals(columnList.get(4))) {
+                       // There is another status with the same letter E other than error
status
+                       // to avoid that we make a small tweek to the job status
+                       columnList.set(4, "Er");
+                   }
+                   statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
+                   break;
+               }
+            }
+        }
+    }
+
+    @Override
+    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+        return null; // TODO: Implement the parse logic ( with regex if possible ).
+    }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/CommonUtils.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/CommonUtils.java
b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/CommonUtils.java
index e5ab739..f1086d7 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/CommonUtils.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/CommonUtils.java
@@ -22,7 +22,6 @@ package org.apache.airavata.gsi.ssh.util;
 
 import org.apache.airavata.gsi.ssh.api.job.*;
 import org.apache.airavata.gsi.ssh.impl.JobStatus;
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
 
 public class CommonUtils {
     /**
@@ -73,7 +72,7 @@ public class CommonUtils {
     }
 
      public static JobManagerConfiguration getSGEJobManager(String installedPath) {
-        return new PBSJobConfiguration("SGETemplate.xslt", ".pbs", installedPath, new SGEOutputParser());
+        return new UGEJobConfiguration("UGETemplate.xslt", ".pbs", installedPath, new UGEOutputParser());
     }
 
     public static JobManagerConfiguration getLSFJobManager(String installedPath) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/resources/SGETemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/SGETemplate.xslt b/tools/gsissh/src/main/resources/SGETemplate.xslt
deleted file mode 100644
index 5b57265..0000000
--- a/tools/gsissh/src/main/resources/SGETemplate.xslt
+++ /dev/null
@@ -1,74 +0,0 @@
-<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license
agreements. See the NOTICE file
-	distributed with this work for additional information regarding copyright ownership. The
ASF licenses this file to you under
-	the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance
with the License. You may
-	obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to
-	in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF
-	ANY ~ KIND, either express or implied. See the License for the specific language governing
permissions and limitations under
-	the License. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-#! /bin/bash
-# Grid Engine batch job script built by Apache Airavata
-#   <xsl:choose>
-    <xsl:when test="ns:shellName">
-#$ -S <xsl:value-of select="ns:shellName"/>
-    </xsl:when></xsl:choose>
-#$ -V
-    <xsl:choose>
-    <xsl:when test="ns:queueName">
-#$ -q <xsl:value-of select="ns:queueName"/>
-    </xsl:when>
-    </xsl:choose>
-#$ -m beas <xsl:choose>
-<xsl:when test="ns:acountString">
-#$ -A <xsl:value-of select="ns:acountString"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:maxWallTime">
-#$ -l h_rt=<xsl:value-of select="ns:maxWallTime"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:jobName">
-#$ -N <xsl:value-of select="ns:jobName"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#$ -o <xsl:value-of select="ns:standardOutFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="ns:standardOutFile">
-#$ -e <xsl:value-of select="ns:standardErrorFile"/>
-    </xsl:when>
-    </xsl:choose>
-    <xsl:choose>
-    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
-#$ -pe <xsl:value-of select="ns:processesPerNode"/>way <xsl:value-of select="12
* ns:nodes"/>
-<xsl:text>&#xa;</xsl:text>
-    </xsl:when>
-    </xsl:choose>
-<xsl:for-each select="ns:exports/ns:name">
-<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
-export<xsl:text>   </xsl:text><xsl:value-of select="."/>
-<xsl:text>&#xa;</xsl:text>
-</xsl:for-each>
-<xsl:for-each select="ns:preJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
-    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of
select="ns:executablePath"/><xsl:text>   </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-    </xsl:for-each>
-<xsl:for-each select="ns:postJobCommands/ns:command">
-      <xsl:value-of select="."/><xsl:text>   </xsl:text>
-</xsl:for-each>
-
-</xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/86a79b66/tools/gsissh/src/main/resources/UGETemplate.xslt
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/resources/UGETemplate.xslt b/tools/gsissh/src/main/resources/UGETemplate.xslt
new file mode 100644
index 0000000..5b57265
--- /dev/null
+++ b/tools/gsissh/src/main/resources/UGETemplate.xslt
@@ -0,0 +1,74 @@
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license
agreements. See the NOTICE file
+	distributed with this work for additional information regarding copyright ownership. The
ASF licenses this file to you under
+	the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance
with the License. You may
+	obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to
+	in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF
+	ANY ~ KIND, either express or implied. See the License for the specific language governing
permissions and limitations under
+	the License. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<xsl:output method="text" />
+<xsl:template match="/ns:JobDescriptor">
+#! /bin/bash
+# Grid Engine batch job script built by Apache Airavata
+#   <xsl:choose>
+    <xsl:when test="ns:shellName">
+#$ -S <xsl:value-of select="ns:shellName"/>
+    </xsl:when></xsl:choose>
+#$ -V
+    <xsl:choose>
+    <xsl:when test="ns:queueName">
+#$ -q <xsl:value-of select="ns:queueName"/>
+    </xsl:when>
+    </xsl:choose>
+#$ -m beas <xsl:choose>
+<xsl:when test="ns:acountString">
+#$ -A <xsl:value-of select="ns:acountString"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:maxWallTime">
+#$ -l h_rt=<xsl:value-of select="ns:maxWallTime"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:jobName">
+#$ -N <xsl:value-of select="ns:jobName"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:standardOutFile">
+#$ -o <xsl:value-of select="ns:standardOutFile"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="ns:standardOutFile">
+#$ -e <xsl:value-of select="ns:standardErrorFile"/>
+    </xsl:when>
+    </xsl:choose>
+    <xsl:choose>
+    <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
+#$ -pe <xsl:value-of select="ns:processesPerNode"/>way <xsl:value-of select="12
* ns:nodes"/>
+<xsl:text>&#xa;</xsl:text>
+    </xsl:when>
+    </xsl:choose>
+<xsl:for-each select="ns:exports/ns:name">
+<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>&#xa;</xsl:text>
+export<xsl:text>   </xsl:text><xsl:value-of select="."/>
+<xsl:text>&#xa;</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+    </xsl:for-each>
+cd <xsl:text>   </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>&#xa;</xsl:text>
+    <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>   </xsl:text></xsl:when></xsl:choose><xsl:value-of
select="ns:executablePath"/><xsl:text>   </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+    </xsl:for-each>
+<xsl:for-each select="ns:postJobCommands/ns:command">
+      <xsl:value-of select="."/><xsl:text>   </xsl:text>
+</xsl:for-each>
+
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file


Mime
View raw message