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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@131699 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2016-09-23 08:39:21 +00:00
parent a1cb85737b
commit 3f5287800f
1 changed files with 105 additions and 96 deletions
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39
src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/AbstractEcologicalEngineMapper.java
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@ -238,7 +238,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
for (File file : generatedFiles) { for (File file : generatedFiles) {
if (file.exists()) { if (file.exists()) {
AnalysisLogger.getLogger().debug("Deleting File " + file.getAbsolutePath()); AnalysisLogger.getLogger().debug("Deleting File " + file.getAbsolutePath());
try{AnalysisLogger.getLogger().debug("Deleting File Check " + file.delete());}catch(Exception e){} try {
AnalysisLogger.getLogger().debug("Deleting File Check " + file.delete());
} catch (Exception e) {
}
} else } else
AnalysisLogger.getLogger().debug("Deleting File - File does not exist " + file.getAbsolutePath()); AnalysisLogger.getLogger().debug("Deleting File - File does not exist " + file.getAbsolutePath());
} }
@ -249,19 +252,23 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
public void manageUserToken() { public void manageUserToken() {
String scope = null; String scope = null;
String username = null; String username = null;
String token = null;
// DONE get scope and username from SmartGears // DONE get scope and username from SmartGears
// get scope from SmartGears // get scope from SmartGears
TokenManager tokenm = new TokenManager(); TokenManager tokenm = new TokenManager();
tokenm.getCredentials(); tokenm.getCredentials();
scope = tokenm.getScope(); scope = tokenm.getScope();
username = tokenm.getUserName(); username = tokenm.getUserName();
token = tokenm.getToken();
// set parameters // set parameters
inputs.put(ConfigurationManager.scopeParameter, scope); inputs.put(ConfigurationManager.scopeParameter, scope);
inputs.put(ConfigurationManager.usernameParameter, username); inputs.put(ConfigurationManager.usernameParameter, username);
inputs.put(ConfigurationManager.tokenParameter, token);
} }
long statusInterrupt = 0; long statusInterrupt = 0;
float previousStatus = -3; float previousStatus = -3;
public void updateStatus(float status) { public void updateStatus(float status) {
if (agent != null) { if (agent != null) {
long stream = 0; long stream = 0;
@ -278,21 +285,31 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
agent = null; agent = null;
status = -1f; status = -1f;
super.update(new Integer((int) status)); super.update(new Integer((int) status));
try {
updateComputationOnWS(status, null); updateComputationOnWS(status, null);
} catch (Exception e) {
}
System.gc(); System.gc();
} }
if (status != previousStatus) { if (status != previousStatus) {
AnalysisLogger.getLogger().debug("STATUS update to:" + status + " - status interrupt " + statusInterrupt); AnalysisLogger.getLogger().debug("STATUS update to:" + status + " - status interrupt " + statusInterrupt);
previousStatus = status; previousStatus = status;
super.update(new Integer((int) status)); super.update(new Integer((int) status));
try {
updateComputationOnWS(status, null); updateComputationOnWS(status, null);
} catch (Exception e) {
}
} }
} catch (Exception e) { } catch (Exception e) {
AnalysisLogger.getLogger().debug("WARNING: STATUS RETRIEVAL EXCEPTION "+e.getLocalizedMessage()); AnalysisLogger.getLogger().debug("WARNING - STATUS RETRIEVAL EXCEPTION " + e.getLocalizedMessage());
AnalysisLogger.getLogger().debug(e);
// stream = statusInterrupt; // stream = statusInterrupt;
} }
} }
} }
public void updateComputationOnWS(float status, String exception) { public void updateComputationOnWS(float status, String exception) {
updateComputationOnWS(status, exception, null, null); updateComputationOnWS(status, exception, null, null);
} }
@ -409,8 +426,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
// run the computation // run the computation
AnalysisLogger.getLogger().info("9 - Running the computation and updater"); AnalysisLogger.getLogger().info("9 - Running the computation and updater");
AnalysisLogger.getLogger().info("Initializing the computation"); AnalysisLogger.getLogger().info("Initializing the WPS status of the computation");
updateStatus(0); updateStatus(0);
AnalysisLogger.getLogger().info("Initializing the computation");
agent.init(); agent.init();
AnalysisLogger.getLogger().info("Updating status"); AnalysisLogger.getLogger().info("Updating status");
runStatusUpdater(); runStatusUpdater();
@ -542,7 +560,6 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
} }
private void cleanResources() { private void cleanResources() {
times = null; times = null;
agent = null; agent = null;
@ -575,19 +592,12 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
System.gc(); System.gc();
} }
public static List<String> command(final String cmdline, final String directory) {
public static List<String> command(final String cmdline,
final String directory) {
try { try {
Process process = Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true).directory(new File(directory)).start();
new ProcessBuilder(new String[] {"bash", "-c", cmdline})
.redirectErrorStream(true)
.directory(new File(directory))
.start();
List<String> output = new ArrayList<String>(); List<String> output = new ArrayList<String>();
BufferedReader br = new BufferedReader( BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
new InputStreamReader(process.getInputStream()));
String line = null; String line = null;
while ((line = br.readLine()) != null) while ((line = br.readLine()) != null)
output.add(line); output.add(line);
@ -603,5 +613,4 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
} }
} }
} }