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Headless import and export
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@frothga
frothga committed Dec 8, 2023
1 parent f0ac23b commit 793c468
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Showing 48 changed files with 653 additions and 290 deletions.
162 changes: 129 additions & 33 deletions N2A/src/gov/sandia/n2a/Main.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,15 @@
import gov.sandia.n2a.eqset.MPart;
import gov.sandia.n2a.host.Host;
import gov.sandia.n2a.host.Remote;
import gov.sandia.n2a.plugins.ExtensionPoint;
import gov.sandia.n2a.plugins.PluginManager;
import gov.sandia.n2a.plugins.extpoints.Backend;
import gov.sandia.n2a.plugins.extpoints.Export;
import gov.sandia.n2a.plugins.extpoints.ExportModel;
import gov.sandia.n2a.plugins.extpoints.ShutdownHook;
import gov.sandia.n2a.ui.MainFrame;
import gov.sandia.n2a.ui.eq.PanelEquations;
import gov.sandia.n2a.ui.eq.PanelModel;
import gov.sandia.n2a.ui.jobs.NodeJob;
import gov.sandia.n2a.ui.jobs.OutputParser;
import gov.sandia.n2a.ui.jobs.OutputParser.Column;
Expand All @@ -41,6 +46,7 @@
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;

import javax.swing.JFrame;
Expand All @@ -56,26 +62,32 @@ public static void main (String[] args)
ArrayList<Path> pluginDirs = new ArrayList<Path> ();
MNode record = new MVolatile ();
String headless = "";
String format = null;
Path path = null;
for (String arg : args)
{
if (arg.startsWith ("-plugin=" )) pluginClassNames.add (arg.substring (8));
else if (arg.startsWith ("-pluginDir=" )) pluginDirs .add (Paths.get (arg.substring (11)).toAbsolutePath ());
else if (arg.startsWith ("-param=" )) processParamFile (arg.substring (7), record);
else if (arg.startsWith ("-install" )) headless = "install";
else if (arg.startsWith ("-csv" )) record.set (true, "$meta", "csv");
else if (arg.startsWith ("-run="))
else if (arg.equals ("-install" )) headless = "install";
else if (arg.equals ("-csv" )) record.set (true, "$meta", "csv");
else if (arg.equals ("-run" )) headless = "run";
else if (arg.equals ("-study" )) headless = "study";
else if (arg.startsWith ("-export" )) headless = "export";
else if (arg.startsWith ("-import" )) headless = "import";
else if (arg.startsWith ("-model=" ))
{
MNode temp = new MVolatile ("", arg.substring (5));
MNode temp = new MVolatile ("", arg.substring (7));
temp.merge (record);
record = temp;
headless = "run";
}
else if (arg.startsWith ("-study="))
else if (arg.startsWith ("-file="))
{
MNode temp = new MVolatile ("", arg.substring (7));
temp.merge (record);
record = temp;
headless = "study";
path = Paths.get (arg.substring (6));
}
else if (arg.startsWith ("-format="))
{
format = arg.substring (8);
}
else if (! arg.startsWith ("-"))
{
Expand Down Expand Up @@ -110,28 +122,47 @@ else if (! arg.startsWith ("-"))

if (! headless.isEmpty ())
{
if (headless.equals ("run" )) runHeadless (record);
else if (headless.equals ("study" )) studyHeadless (record);
else if (headless.equals ("install"))
switch (headless)
{
try
{
JobC jobC = new JobC (new MVolatile ());
jobC.runtimeDir = resourceDir.resolve ("backend").resolve ("c");
jobC.unpackRuntime ();

JobPython jobPython = new JobPython ();
jobPython.runtimeDir = resourceDir.resolve ("backend").resolve ("python");
jobPython.unpackRuntime ();
}
catch (Exception e)
{
e.printStackTrace ();
System.err.println ("Failed to unpack runtime resources.");
}
case "run":
runHeadless (record);
break;
case "study":
studyHeadless (record);
break;
case "import":
String name = record.key ();
if (name.isBlank ()) name = null;
importHeadless (path, format, name);
break;
case "export":
exportHeadless (record, format, path);
break;
case "install":
try
{
JobC jobC = new JobC (new MVolatile ());
jobC.runtimeDir = resourceDir.resolve ("backend").resolve ("c");
jobC.unpackRuntime ();

AppData.quit (); // Flush new DB data.
JobPython jobPython = new JobPython ();
jobPython.runtimeDir = resourceDir.resolve ("backend").resolve ("python");
jobPython.unpackRuntime ();
}
catch (Exception e)
{
e.printStackTrace ();
System.err.println ("Failed to unpack runtime resources.");
}
break;
}

// Save all data and exit.
// See MainFrame window close listener
AppData.quit ();
List<ExtensionPoint> exps = PluginManager.getExtensionsForPoint (ShutdownHook.class);
for (ExtensionPoint exp : exps) ((ShutdownHook) exp).shutdown ();
Host.quit (); // Close down any ssh sessions.
return;
}

Expand Down Expand Up @@ -298,7 +329,7 @@ public static void studyHeadless (MNode record)
MPart collated = new MPart (record);
if (! collated.containsKey ("study")) return;

// Start host monitor threads (see PanelRun constructor for non-headless procedure)
// Start host monitor threads (see PanelRun constructor for GUI procedure)
Host.restartAssignmentThread ();
for (Host h : Host.getHosts ()) h.restartMonitorThread ();

Expand Down Expand Up @@ -352,10 +383,75 @@ public static void studyHeadless (MNode record)
e.printStackTrace ();
}
}
}

public static void importHeadless (Path path, String format, String name)
{
if (path == null)
{
System.err.println ("Import requires at least the path to the source file.");
return;
}
if (! path.isAbsolute ()) path = Paths.get (System.getProperty ("user.dir")).resolve (path);

try
{
PanelModel.importFile (path, format, name);
}
catch (Exception e)
{
System.err.println ("Import failed");
e.printStackTrace();
}
}

// See MainFrame window close listener
AppData.quit (); // Save any modified data, particularly the study record.
Host.quit (); // Close down any ssh sessions.
public static void exportHeadless (MNode record, String format, Path path)
{
// See PanelEquations.listenerExport(). The code here is highly stripped down because we're not dealing with a GUI.
String key = record.key ();
MNode doc = AppData.docs.childOrEmpty ("models", key);
record.mergeUnder (doc);

if (format == null) format = "";
if (path == null)
{
path = Paths.get (System.getProperty ("user.dir"));
path = path.resolve (key); // The exporter will add an appropriate suffix to this.
}
else if (! path.isAbsolute ())
{
path = Paths.get (System.getProperty ("user.dir")).resolve (path);
}

Export exporter = null;
Export n2a = null;
List<ExtensionPoint> exps = PluginManager.getExtensionsForPoint (Export.class);
for (ExtensionPoint exp : exps)
{
if (! (exp instanceof ExportModel)) continue;
Export em = ((ExportModel) exp);
String name = em.getName ();
if (name.contains ("N2A")) n2a = em;
if (name.equalsIgnoreCase (format)) exporter = em;
if (exporter == null && em.accept (path)) exporter = em; // Suffix match
}
if (exporter == null) exporter = n2a;
if (exporter == null)
{
System.err.println ("No matching export method");
return;
}

try
{
Files.createDirectories (path.getParent ());
exporter.process (record, path);
}
catch (Exception e)
{
System.err.println ("Export failed");
e.printStackTrace ();
}
}

public static void setUncaughtExceptionHandler (final JFrame parent)
Expand Down
18 changes: 9 additions & 9 deletions N2A/src/gov/sandia/n2a/N2APlugin.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
Copyright 2013-2021 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
Copyright 2013-2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
Under the terms of Contract DE-NA0003525 with NTESS,
the U.S. Government retains certain rights in this software.
*/
Expand Down Expand Up @@ -98,18 +98,18 @@ public ExtensionPoint[] getExtensions ()
Windows.factory (),
RemoteUnix.factory (),
RemoteSlurm.factory (),
RemoteLSF.factory ()
RemoteLSF.factory (),
new ExportNative (),
gov.sandia.n2a.ui.ref.PanelSearch.exportBibTeX,
new ImportNative (),
new ImportBibTeX (),
new ImportEndNote (),
new ImportPubMed (),
new ImportRIS ()
);
if (! AppData.properties.getBoolean ("headless"))
{
Collections.addAll (result,
new ExportNative (),
gov.sandia.n2a.ui.ref.PanelSearch.exportBibTeX,
new ImportNative (),
new ImportBibTeX (),
new ImportEndNote (),
new ImportPubMed (),
new ImportRIS (),
new ActivityModel (),
new ActivityRun (),
new ActivityReference (),
Expand Down
22 changes: 22 additions & 0 deletions N2A/src/gov/sandia/n2a/backend/c/ExportCbinary.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
/*
Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
Under the terms of Contract DE-NA0003525 with NTESS,
the U.S. Government retains certain rights in this software.
*/

package gov.sandia.n2a.backend.c;

public class ExportCbinary extends ExportCstatic
{
public ExportCbinary ()
{
shared = true; // Default choice for binaries, unless overridden by metadata in model itself.
lib = false;
}

@Override
public String getName ()
{
return "C binary";
}
}
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