How to import other source code files in dm script - import

Is there a way to use multiple code files in dm-script to structure the code? Something like:
import "path/to/utility_functions.s";
utility_functions.do_something_general();
Note that I do not want to have the code as a menu item if possible. The code contains only functions that I use in the main script.
I tried the following:
File 1: test.s
void test(){
result("test\n");
}
File 2: require-test.s
AddScriptFileToPackage("path/to/test.s", "test", 3, "test-function", "", "", 1);
ExecuteScriptString("test()"); // works immediately but feels wrong
test(); // works after restart
Now I have the following problems:
I have to restart DigitalMicrograph after executing this script, otherwise test() does not work (ExecuteScriptString("test()"); works but it feels wrong to use strings for invoking code, if possible I'd like to avoid that)
When I restart DigitalMicrograph another time AddScriptFileToPackage() sais 'The script cannot be added because the package exists and is read-only. [...]'. Is there a way around it or do I have to use try blocks?
I feel like I am not doing this wrong at some place.

DM script does not support on-demand-loading of packages, but there are two different ways to achieve what you want:
Using library packages
When you "install" a script, you can choose to either install it as menu-command or as a library. This is true for both installing scripts via the menu command (which get stored in the global preferences file) or via the scripting-command (which can be used to
create .gtk files which one can then add/remove from the plugins
folder as needed).
The "menu" option will install a script such that it is invoked once via the menu-item but does not stay in memory otherwise.
The "library" option will execute a script once on startup and keep the script itself in scope. So you can define methods (or classes) in a library file and have it generally available. And you can put some executable code in a library if you need some startup-action.
Using script libraries as .gtk plugins is possibly the recommended way to achieve what you want. They are, however, always loaded.
Piece of advise: If you make libraries ensure you use very unique class and method names to avoid any conflict. I would recommend pre-fixing all class/method names with some library-name, i.e. use MyLib_MyClass instead of MyClass and the like.
Clarification: Scripts added as library packages are permanently added to the software, i.e. those packages get created once and are then placed in the plugins-folder. They will always load on startup of DM and be available. The Library package method is not suitable for temporarily 'loading' external scripts. Such 'on demand import' is not supported by DM-scripting.
The script commands to create packages are utility commands to help one create packages in an easy and manageable way. Typically, one would create a "Create package XY" script with several such commands adding all scripts from a location into a package. The script would be called once to create the package-file (It is already in the plugins folder afterwards.)
Only when the included scripts change and the package therefore requires to be updated, is the create-package script called again. Note, that in this case it is first required to remove the package-file from the plugins folder and start DigitalMicrograph without loading it, so that a new package is created. Otherwise the script would append to the package, which would not be possible if methods of the same name already exist in the package.
The F1 help documentation has an example script:
A typical examples, using GMS 3.4.0:
Script stored at: C:\Tmp\testLib.s
void TestCall()
{
Result("\nTest")
}
Script stored at: C:\Tmp\menuAction.s
Result("\nPerforming an action here.")
One-time run script to install a package:
// General package parameters
// *********************************************
string pkNa = "myPkg" // Filename of plugin
number pkLe = 3 // level 3 (.gtk) only needed for load order
string pkLo = "user_plugin" // plugin location
string scriptRoot = "C:\\Temp\\"
// List of Scripts to be installed as menu items
// *********************************************
// Each entry needs a (unique) command-name, a menu-name and an optional sub-menu name.
// The "isLibary" flag is set to 0
// It is possible to add the same script multiple times. The script will be executed when the menu item
// is chosen. Methods and Classes of the script are not available otherwise
// A separator can be added by installing and empty script with a (unique) command name starting with "-"
AddScriptFileToPackage( scriptRoot + "menuAction.s", pkNa, pkLe, pkLo, "Call 1", "MyMenu", "MySubMenu", 0 )
AddScriptFileToPackage( scriptRoot + "menuAction.s", pkNa, pkLe, pkLo, "Call 2", "MyMenu", "", 0 )
AddScriptToPackage( "", pkNa, pkLe, pkLo, "-sep1", "MyMenu", "", 0 )
AddScriptFileToPackage( scriptRoot + "menuAction.s", pkNa, pkLe, pkLo, "Call 3", "MyMenu", "", 0 )
// List of Scripts to be installed as library
// *********************************************
// Each entry needs a (unique) command-name. Menu-name and sub-menu name are "".
// The "isLibary" flag is set to 1
// The script will be executed once on startup (if there is executable code). It is also executed once
// here during the install.
// Methods and Classes of the script are permanently available and need unique names.
// Adding a script to the package as libary can be used to create on-load-version info output.
AddScriptFileToPackage( scriptRoot + "testLib.s", pkNa, pkLe, pkLo, "library-1", "", "", 1 )
AddScriptToPackage( "Result(\"Script packages myPkg loaded.\\n\")", pkNa, pkLe, pkLo, "myPkg-versionInfo", "", "", 1 )
After running the install-script there will be:
A menu like this:
Output in the results window like this:
A package file in the folder C:\Users\USERNAME\AppData\Local\Gatan\Plugins\myPkg.gtk
The script command TestCall() generally available in all scripts.
The package will load each time when DM starts as long as the .gtk file remains in the plugins folder.
Calling script code from within scripts
The scripting language supports two commands to call a script from within a script:
Number ExecuteScriptString( String text )
Number ExecuteScriptFile( String file_path )
Using the command to execute scripts form disc can do what you want, but maintaining a useful 'library' that way could be tedious. It also does not allow you to install classes.
Example of calling a script from within a script:
// Direct example
void Demo()
{
ClearResults()
Result( "I am a test call.\n")
number n = 5
Result( "I am working on the number: " + n )
}
Demo()
//Having the script as a string
number otherNumber = 11 // To show how you can modify a script call as an example
string scriptStr
scriptStr += "void Demo()\n{" + "\n"
scriptStr += "ClearResults()" + "\n"
scriptStr += "Result( \"I am a test call.\\n\")" + "\n"
scriptStr += "number n = " + otherNumber + "\n"
scriptStr += "Result( \"I am working on the number: \" + n )"+ "\n"
scriptStr += "}\n"
scriptStr += "Demo()\n"
If ( TwoButtonDialog("Script-call","Show it", "Run it") )
{
ClearResults()
Result( scriptStr )
}
else
ExecuteScriptString( scriptStr )

The following explicit example of build script usage may be closer to what you are looking for. It shows that in the course of a single DM session, one can edit the module source files and repeatedly rebuild the package without having to relaunch DM, contrary to the clarification about package creation provided in the answer from BmyGuest. This example also makes use of the very convenient GetCurrentScriptSourceFilePath function which greatly simplifies file path references when one can locate the build script and module source files in the same folder (this is the approach I take with my own development projects).
Here is the arrangement of my files for this example:
The two source modules are very simple function and class libraries.
Here is Module1:
void Module1SayHello()
{
OKDialog("Hello from module 1");
}
And here is Module2:
class Module2TestClass
{
void Module2SayHello(Object self)
{
OKDialog("Hello from module 2");
}
}
Here is the build script:
void main()
{
// Establish the source code directory relative to the current build script location
String buildScriptSourceFilePath;
GetCurrentScriptSourceFilePath(buildScriptSourceFilePath);
String sourceFileDir = buildScriptSourceFilePath.PathExtractDirectory(0);
// Add the modules
AddScriptFileToPackage(sourceFileDir.PathConcatenate("Module1.s"), "MultiModuleTest", 3, "Module1", "", "", 1);
AddScriptFileToPackage(sourceFileDir.PathConcatenate("Module2.s"), "MultiModuleTest", 3, "Module2", "", "", 1);
}
main();
Contrary to the above-mentioned clarification, this build script can be run multiple times during a DM session and the content of the package file gets replaced each time. So now one has a very nice development environment where one can open the source file for a module, edit it as desired, save it, and then rebuild the package file. One can use the following test script to see that the behavior changes as one edits, saves, and rebuilds the implementation of any function or method in the module source files:
void main()
{
Module1SayHello();
Alloc(Module2TestClass).Module2SayHello();
}
main();
Because of the way the DM script interpreter parses, tokenizes, and executes code, all functions and methods invoked anywhere in a script must have been previously defined before a script is executed. This is why the above test script, or any other script that uses the added modules, cannot simply be appended to the end of the build script (except if embedded in a string passed to the ExecuteScriptString function, as pointed out in the posed question). The concept of imported code modules (e.g. as in Python) is therefore not really possible in DM scripting (as pointed out in a comment to the answer by BmyGuest). In this sense, DM scripting shows its roots in 1990’s coding concepts, which commonly involved separate compilation, linking, and execution phases.
Nevertheless, the build script approach described here allows one to take advantage of the features of a true integrated development environment (IDE). For example, one can add the module source files (and build script) to a project in Visual Studio and get all the benefits of a modern multi-file code editor and revision control (e.g. via Git). This is what I do with the Enabler framework.
The one caveat is that once the DM session is closed, the plug-in (package) file does become finalized in some way so that it can no longer be replaced by the build script in a future DM session. In this case, one does have to remove the package file from the plug-ins folder before resuming another development session in DM (as covered in the clarification from BmyGuest).

For everybody else who needs this, I am using AddScriptFileToPackage() now, inspired by both, #BmyGuest and #MikeKundmann.
The following main.s is always open in my GMS. The real code I'm working on is in program.s. To test your code execute the main.s. This file can be executed multiple times in one session!
For opening GMS I use the (Windows) batch file below. This deleteds registered plugins automatically which makes the main.s usable again. For debugging I created a python script that combines all the files listed in the main.s. This way GMS jumps to the errors. This python program can be downloaded from my github page.
/**
* File: main.s
*/
String __file__;
GetCurrentScriptSourceFilePath(__file__);
String __base__ = __file__.PathExtractDirectory(0);
/**
* Load and add the file `filename`, the name will be the `filename` without
* the extension.
*
* This is dynamic only for the current session. If GMS is restarted, using
* this will create errors except if the plugins folder does not contain the
* required files (delete `%LOCALAPPDATA%\Gatan\Plugins\` before starting).
*
* #param filename The filename (or path) relative to the path of this file
* #param name The internal name to register the script with
*/
void require(String filename, String name){
// AddScriptFileToPackage(
// <file_path>,
// <packageName: filename of .gtk file in plugins>,
// <packageLevel: load order [0..3]>,
// <command_name: id/name of the libary/command>,
// <menu_name: name of the menu, ignored if isLibrary=1>
// <sub_menu_name: name of the submenu, ignored if isLibrary=1>,
// <isLibrary: wheter to add as library (1) or as menu item (0)>
// )
AddScriptFileToPackage(__base__.PathConcatenate(filename), "__require_main_" + name, 3, name, "", "", 1);
}
/**
* Require the file `filename` with the basename of the `filename` as the name.
*
* #see require(String filename, String name);
*
* #param filename The filename (or path) relative to the path of this file
*/
void require(String filename){
require(filename, PathExtractBaseName(filename, 0));
}
void main(){
// add libaries
require("string-lib.s");
// add main file
require("program.s");
}
main();
The (Windows) batch file to start GMS. This deletes the plugins folder automatically. Then the main.s does not cause any problems.
#echo off
rem
rem File: start-gatan.bat
rem ---------------------
echo Deleting GMS cached libaries...
SET plugins_path=%LOCALAPPDATA%\Gatan\Plugins\
SET gms_path=%PROGRAMFILES%\Gatan\DigitalMicrograph.exe
if exist %plugins_path% (
echo Deleting all .gtk files in %plugins_path%...
del %plugins_path%__require_main_*.gtk /F /Q
del %plugins_path%__require_main_*.gt1 /F /Q
del %plugins_path%__require_main_*.gt2 /F /Q
del %plugins_path%__require_main_*.gt3 /F /Q
if exist "%gms_path%" (
echo Starting GMS
start "" "%gms_path%"
) else (
echo GMS path %gms_path% does not exist.
pause
)
) else (
echo Plugins path %plugins_path% does not exist.
pause
)

Related

SCP command not working in karate project - it throws command error:cannot run program scp.exe: CreateProcess error=2 [duplicate]

I'm trying to execute bash script using karate. I'm able to execute the script from karate-config.js and also from .feature file. I'm also able to pass the arguments to the script.
The problem is, that if the script fails (exits with something else than 0) the test execution continues and finishes as succesfull.
I found out that when the script echo-es something then i can access it as a result of the script so I could possibly echo the exit value and do assertion on it (in some re-usable feature), but this seems like a workaround rather than a valid clean solution. Is there some clean way of accessing the exit code without echo-ing it? Am I missing on something?
script
#!/bin/bash
#possible solution
#echo 3
exit 3;
karate-config.js
var result = karate.exec('script.sh arg1')
feture file
def result = karate.exec('script.sh arg1')
Great timing. We very recently did some work for CLI testing which I am sure you can use effectively. Here is a thread on Twitter: https://twitter.com/maxandersen/status/1276431309276151814
And we have just released version 0.9.6.RC4 and new we have a new karate.fork() option that returns an instance of Command on which you can call exitCode
Here's an example:
* def proc = karate.fork('script.sh arg1')
* proc.waitSync()
* match proc.exitCode == 0
You can get more ideas here: https://github.com/intuit/karate/issues/1191#issuecomment-650087023
Note that the argument to karate.fork() can take multiple forms. If you are using karate.exec() (which will block until the process completes) the same arguments work.
string - full command line as seen above
string array - e.g. ['script.sh', 'arg1']
json where the keys can be
line - string (OR)
args - string array
env - optional environment properties (as JSON)
redirectErrorStream - boolean, true by default which means Sys.err appears in Sys.out
workingDir - working directory
useShell - default false, auto-prepend cmd /c or sh -c depending on OS
And since karate.fork() is async, you need to call waitSync() if needed as in the example above.
Do provide feedback and we can tweak further if needed.
EDIT: here's a very advanced example that shows how to listen to the process output / log, collect the log, and conditionally exit: fork-listener.feature
Another answer which can be a useful reference: Conditional match based on OS
And here's how to use cURL for advanced HTTP tests ! https://stackoverflow.com/a/73230200/143475
In case you need to do a lot of local file manipulation, you can use the karate.toJavaFile() utility so you can convert a relative path or a "prefixed" path to an absolute path.
* def file = karate.toJavaFile('classpath:some/file.txt')
* def path = file.getPath()

Cudafy chapter 3 example has path issue how to fix?

Using Cudafy version 1.29, which can be downloaded from here
I am executing the examples that are found in the install folder CudafyV1.29\CudafyByExample\
Specifically, "chapter 3" example that begins line 42 of program.cs calls the following:
simple_kernel.Execute();
which is this:
public static void Execute()
{
CudafyModule km = CudafyTranslator.Cudafy(); // <--exception thrown!
GPGPU gpu = CudafyHost.GetDevice(CudafyModes.Target, CudafyModes.DeviceId);
gpu.LoadModule(km);
gpu.Launch().thekernel(); // or gpu.Launch(1, 1, "kernel");
Console.WriteLine("Hello, World!");
}
The indicated line throws this exception:
Compilation error: CUDAFYSOURCETEMP.cu
'C:\Program' is not recognized as an internal or external command,
operable program or batch file. .
Which is immediately obvious that the path has spaces and the programmer did not double quote or use ~ to make it operational.
So, I did not write this code. And I cannot step through the sealed code contained within CudafyModule km = CudafyTranslator.Cudafy();In fact I don't even know the full path that is causing the exception, it is cut-off in the exception message.
Does anyone have a suggestion for how to fix this issue?
Update #1: I discovered where CUDAFYSOURCETEMP.cu lives on my computer, here it is:
C:\Users\humphrt\Desktop\Active Projects\Visual Studio
Projects\CudafyV1.29\CudafyByExample\bin\Debug
...I'm still trying to determine what the program is looking for along the path to 'C:\Program~'.
I was able to apply a workaround to bypass this issue. The workaround is to reinstall all components of cudafy in to folders with paths with no ' ' (spaces). My setup looks like the below screenshot. Notice that I also installed the CUDA TOOLKIT from NVIDIA in the same folder - also with no spaces in folder names.
I created a folder named "C:\CUDA" and installed all components within it, here is the folder structure:

How to do File creation and manipulation in functional style?

I need to write a program where I run a set of instructions and create a file in a directory. Once the file is created, when the same code block is run again, it should not run the same set of instructions since it has already been executed before, here the file is used as a guard.
var Directory: String = "Dir1"
var dir: File = new File("Directory");
dir.mkdir();
var FileName: String = Directory + File.separator + "samplefile" + ".log"
val FileObj: File = new File(FileName)
if(!FileObj.exists())
// blahblah
else
{
// set of instructions to create the file
}
When the programs runs initially, the file won't be present, so it should run the set of instructions in else and also create the file, and after the first run, the second run it should exit since the file exists.
The problem is that I do not understand new File, and when the file is created? Should I use file.CreateNewFile? Also, how to write this in functional style using case?
It's important to understand that a java.io.File is not a physical file on the file system, but a representation of a pathname -- per the javadoc: "An abstract representation of file and directory pathnames". So new File(...) has nothing to do with creating an actual file - you are just defining a pathname, which may or may not correspond to an existing file.
To create an empty file, you can use:
val file = new File("filepath/filename")
file.createNewFile();
If running on JRE 7 or higher, you can use the new java.nio.file API:
val path = Paths.get("filepath/filename")
Files.createFile(path)
If you're not happy with the default IO APIs, you an consider a number of alternative. Scala-specific ones that I know of are:
scala-io
rapture.io
Or you can use libraries from the Java world, such as Google Guava or Apache Commons IO.
Edit: One thing I did not consider initially: I understood "creating a file" as "creating an empty file"; but if you intend to write something immediately in the file, you generally don't need to create an empty file first.

How to access static resources in jar (that correspond to src/main/resources folder)?

I have a Spark Streaming application built with Maven (as jar) and deployed with the spark-submit script. The application project layout follows the standard directory layout:
myApp
src
main
scala
com.mycompany.package
MyApp.scala
DoSomething.scala
...
resources
aPerlScript.pl
...
test
scala
com.mycompany.package
MyAppTest.scala
...
target
...
pom.xml
In the DoSomething.scala object I have a method (let's call it doSomething()) that tries to execute a Perl script -- aPerlScript.pl (from the resources folder) -- using scala.sys.process.Process and passing two arguments to the script (the first one is the absolute path to a binary file used as input, the second one is the path/name of the produced output file). I call then DoSomething.doSomething().
The issue is that I was not able to access the script, not with absolute paths, relative paths, getClass.getClassLoader.getResource, getClass.getResource, I have specified the resources folder in my pom.xml. None of my attempts succeeded. I don't know how to find the stuff I put in src/main/resources.
I will appreciate any help.
SIDE NOTES:
I use an external Process instead of a Spark pipe because, at this step of my workflow, I must handle binary files as input and output.
I'm using Spark-streaming 1.1.0, Scala 2.10.4 and Java 7. I build the jar with "Maven install" from within Eclipse (Kepler)
When I use the getClass.getClassLoader.getResource "standard" method to access resources I find that the actual classpath is the spark-submit script's one.
There are a few solutions. The simplest is to use Scala's process infrastructure:
import scala.sys.process._
object RunScript {
val arg = "some argument"
val stream = RunScript.getClass.getClassLoader.getResourceAsStream("aPerlScript.pl")
val ret: Int = (s"/usr/bin/perl - $arg" #< stream).!
}
In this case, ret is the return code for the process and any output from the process is directed to stdout.
A second (longer) solution is to copy the file aPerlScript.pl from the jar file to some temporary location and execute it from there. This code snippet should have most of what you need.
object RunScript {
// Set up copy destination from the Java temporary directory. This is /tmp on Linux
val destDir = System.getProperty("java.io.tmpdir") + "/"
// Get a stream to the script in the resources dir
val source = Channels.newChannel(RunScript.getClass.getClassLoader.getResourceAsStream("aPerlScript.pl"))
val fileOut = new File(destDir, "aPerlScript.pl")
val dest = new FileOutputStream(fileOut)
// Copy file to temporary directory
dest.getChannel.transferFrom(source, 0, Long.MaxValue)
source.close()
dest.close()
}
// Schedule the file for deletion for when the JVM quits
sys.addShutdownHook {
new File(destDir, "aPerlScript.pl").delete
}
// Now you can execute the script.
This approach allows you to bundle native libraries in JAR files. Copying them out allows the libraries to be loaded at runtime for whatever JNI mischief you have planned.

Where / how / in what context is ipython's configuration file executed?

Where is ipython's configuration file, which starts with c = get_config(), executed? I'm asking because I want to understand what order things are done in ipython, e.g. why certain commands will not work if included as c.InteractiveShellApp.exec_lines.
This is related to my other question, Log IPython output?, because I want access to a logger attribute, but I can't figure out how to access it in the configuration file, and by the time exec_lines are run, the logger has already started (it's too late).
EDIT: I've accepted a solution based on using a startup file in ipython0.12+. Here is my implementation of that solution:
from time import strftime
import os.path
ip = get_ipython()
#ldir = ip.profile_dir.log_dir
ldir = os.getcwd()
fname = 'ipython_log_' + strftime('%Y-%m-%d') + ".py"
filename = os.path.join(ldir, fname)
notnew = os.path.exists(filename)
try:
ip.magic('logstart -o %s append' % filename)
if notnew:
ip.logger.log_write( u"########################################################\n" )
else:
ip.logger.log_write( u"#!/usr/bin/env python\n" )
ip.logger.log_write( u"# " + fname + "\n" )
ip.logger.log_write( u"# IPython automatic logging file\n" )
ip.logger.log_write( u"# " + '# Started Logging At: '+ strftime('%Y-%m-%d %H:%M:%S\n') )
ip.logger.log_write( u"########################################################\n" )
print " Logging to "+filename
except RuntimeError:
print " Already logging to "+ip.logger.logfname
There are only two subtle differences from the proposed solution linked:
1. saves log to cwd instead of some log directory (though I like that more...)
2. ip.magic_logstart doesn't seem to exist, instead one should use ip.magic('logstart')
The config system sets up a special namespace containing the get_config() function, runs the config file, and collects the values to apply them to the objects as they're created. Referring to your previous question, it doesn't look like there's a configuration value for logging output. You may want to start logging yourself after config, when you can control it more precisely. See this example of starting logging automatically.
Your other question mentions that you're limited to 0.10.2 on one system: that has a completely different config system that won't even look at the same file.