Add BioGtUnixSubprocess and tests

repository/BioTools-Tests/BioGtUnixSubprocessTest.class.st

@@ -0,0 +1,88 @@
+"
+Tests for BioGtUnixSubprocess execution API compatibility.
+"
+Class {
+	#name : 'BioGtUnixSubprocessTest',
+	#superclass : 'BioAbstractTest',
+	#category : 'BioTools-Tests-Adapters',
+	#package : 'BioTools-Tests',
+	#tag : 'Adapters'
+}
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandChained [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo bio&&echo smalltalk"' ]
+		ifFalse: [ 'sh -c ''echo bio; echo smalltalk''' ].
+	output := BioGtUnixSubprocess executeCommand: command.
+	self assert: (output includesSubstring: 'bio').
+	self assert: (output includesSubstring: 'smalltalk')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandEcho [
+	| output |
+
+	output := BioGtUnixSubprocess executeCommand: 'echo biosmalltalk'.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandFailureReturnsErrorOutput [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "nonexistent_command_12345"' ]
+		ifFalse: [ 'sh -c ''nonexistent_command_12345''' ].
+	output := BioGtUnixSubprocess executeCommand: command.
+	self deny: output isEmpty
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandParameter [
+	| output |
+
+	output := BioGtUnixSubprocess
+		executeCommand: 'echo'
+		parameter: 'biosmalltalk'.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandPipeline [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo biosmalltalk | findstr /c:biosmalltalk"' ]
+		ifFalse: [ 'sh -c ''echo biosmalltalk | grep biosmalltalk''' ].
+	output := BioGtUnixSubprocess executeCommand: command.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandQuotedParameter [
+	| output |
+
+	output := BioGtUnixSubprocess
+		executeCommand: 'echo'
+		parameter: '"bio smalltalk"'.
+	self assert: (output includesSubstring: 'bio smalltalk')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testExecuteCommandStderrOutput [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo errormsg 1>&2 & exit /b 1"' ]
+		ifFalse: [ 'sh -c ''echo errormsg 1>&2; exit 1''' ].
+	output := BioGtUnixSubprocess executeCommand: command.
+	self assert: (output includesSubstring: 'errormsg')
+]
+
+{ #category : 'tests' }
+BioGtUnixSubprocessTest >> testProviderClass [
+	self assert: BioGtUnixSubprocess providerClass equals: #GtUnixSubprocess
+]

repository/BioTools-Tests/BioOSSubProcessExecutorTest.class.st

@@ -0,0 +1,88 @@
+"
+Tests for BioOSSubProcessExecutor execution behavior.
+"
+Class {
+	#name : 'BioOSSubProcessExecutorTest',
+	#superclass : 'BioAbstractTest',
+	#category : 'BioTools-Tests-Adapters',
+	#package : 'BioTools-Tests',
+	#tag : 'Adapters'
+}
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandChained [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo bio&&echo smalltalk"' ]
+		ifFalse: [ 'sh -c ''echo bio; echo smalltalk''' ].
+	output := BioOSSubProcessExecutor executeCommand: command.
+	self assert: (output includesSubstring: 'bio').
+	self assert: (output includesSubstring: 'smalltalk')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandEcho [
+	| output |
+
+	output := BioOSSubProcessExecutor executeCommand: 'echo biosmalltalk'.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandFailureReturnsErrorOutput [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "nonexistent_command_12345"' ]
+		ifFalse: [ 'sh -c ''nonexistent_command_12345''' ].
+	output := BioOSSubProcessExecutor executeCommand: command.
+	self deny: output isEmpty
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandParameter [
+	| output |
+
+	output := BioOSSubProcessExecutor
+		executeCommand: 'echo'
+		parameter: 'biosmalltalk'.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandPipeline [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo biosmalltalk | findstr /c:biosmalltalk"' ]
+		ifFalse: [ 'sh -c ''echo biosmalltalk | grep biosmalltalk''' ].
+	output := BioOSSubProcessExecutor executeCommand: command.
+	self assert: (output includesSubstring: 'biosmalltalk')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandQuotedParameter [
+	| output |
+
+	output := BioOSSubProcessExecutor
+		executeCommand: 'echo'
+		parameter: '"bio smalltalk"'.
+	self assert: (output includesSubstring: 'bio smalltalk')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testExecuteCommandStderrOutput [
+	| command output |
+
+	command := Smalltalk os isWindows
+		ifTrue: [ 'cmd /c "echo errormsg 1>&2 & exit /b 1"' ]
+		ifFalse: [ 'sh -c ''echo errormsg 1>&2; exit 1''' ].
+	output := BioOSSubProcessExecutor executeCommand: command.
+	self assert: (output includesSubstring: 'errormsg')
+]
+
+{ #category : 'tests' }
+BioOSSubProcessExecutorTest >> testProviderClass [
+	self assert: BioOSSubProcessExecutor providerClass equals: #OSSUnixSubprocess
+]

repository/BioTools/BioAbstractAdapter.class.st

@@ -42,13 +42,21 @@ BioAbstractAdapter class >> adapter [
 	^ self adapterClass new
 ]
 
-{ #category : 'accessing-adapters' }
+{ #category : 'instance creation' }
 BioAbstractAdapter class >> adapterClass [
-	"Answer the preferred subclass for providing the receiver's services"
-
-	^ self validAdapters 
-			detect: [ : cls | cls isPreferredAdapter ]
-			ifNone: [ self validAdapters first ]
+	"Answer the preferred subclass for providing the receiver's services."
+
+	| preferred |
+	preferred := self preferredAdapterClassForCurrentPlatform.
+	preferred ifNotNil: [
+		(self validAdapters includes: preferred) ifTrue: [ ^ preferred ] ].
+
+	^ self validAdapters
+		detect: [ :cls | cls isPreferredAdapter ]
+		ifNone: [
+			self validAdapters
+			ifEmpty: [ self signalInvalidObject: 'No provider was found' ]
+			ifNotEmpty: [ :adapters | adapters first ] ]
 ]
 
 { #category : 'accessing' }
@@ -78,6 +86,20 @@ BioAbstractAdapter class >> hasAnyProvider [
 	^ self allFinalClasses anySatisfy: [ : cls | cls providerIsAvailable ]
 ]
 
+{ #category : 'testing' }
+BioAbstractAdapter class >> isGTImage [
+	"Answer whether the current image is a Glamorous Toolkit image."
+
+	^ Smalltalk globals includesKey: #GtImage
+]
+
+{ #category : 'testing' }
+BioAbstractAdapter class >> isPharoImage [
+	"Answer whether the current image is a standard Pharo image (including GT, unless explicitly handled)."
+
+	^ self isGTImage not
+]
+
 { #category : 'accessing' }
 BioAbstractAdapter class >> isPreferred [
 
@@ -92,6 +114,23 @@ BioAbstractAdapter class >> isPreferredAdapter [
 	^ false
 ]
 
+{ #category : 'private' }
+BioAbstractAdapter class >> preferredAdapterClassForCurrentPlatform [
+	"Answer the adapter class that best matches the current image/platform.
+	Prefer modern subprocess engines on Pharo/GToolkit, keep legacy engines as fallback."
+
+	| os |
+	os := BioOSInterfaceEngine adapter.
+
+	(self isGTImage and: [ os isRunningInUnix ]) ifTrue: [
+		^ BioGtUnixSubprocess ].
+
+	(self isPharoImage and: [ os isRunningInUnix ]) ifTrue: [
+		^ OSSUnixSubprocess ].
+
+	^ nil
+]
+
 { #category : 'accessing' }
 BioAbstractAdapter class >> providerClass [
 	" Answer a <Symbol>, the main external class name for this adapter "

repository/BioTools/BioGtUnixSubprocess.class.st

@@ -0,0 +1,87 @@
+"
+Execution engine backed by GToolkit subprocess API for running shell commands and retrieving output.
+"
+Class {
+	#name : 'BioGtUnixSubprocess',
+	#superclass : 'BioExecutionEngine',
+	#category : 'BioTools',
+	#package : 'BioTools'
+}
+
+{ #category : 'executing' }
+BioGtUnixSubprocess class >> executeCommand: aCommandName [
+	"See superimplementor's comment"
+
+	^ [ self executeGtSubprocessCommand: aCommandName ]
+		on: Warning
+		do: [ :ex | ex resume ]
+]
+
+{ #category : 'executing' }
+BioGtUnixSubprocess class >> executeCommand: aCommandName parameter: parameterName [
+	"See superimplementor's comment"
+
+	^ self executeGtSubprocessCommand: (String streamContents: [ :stream |
+		stream
+			<< aCommandName trimBoth;
+			space;
+			<< parameterName trimBoth ])
+]
+
+{ #category : 'private' }
+BioGtUnixSubprocess class >> executeGtSubprocessCommand: aCommandName [
+	"Private - Execute aCommandName and answer a <String> with any output returned"
+
+	| subprocess |
+
+	subprocess := (self classFor: self providerClass) new
+		shellCommand: aCommandName;
+		runAndWait;
+		yourself.
+
+	^ (subprocess stderr ifNotEmpty: [ subprocess stderr ] ifEmpty: [ subprocess stdout ]) trimBoth
+]
+
+{ #category : 'executing' }
+BioGtUnixSubprocess class >> executeMonitoring: aCommandName [
+	"See superimplementor's comment"
+
+	^ self executeCommand: aCommandName
+]
+
+{ #category : 'testing' }
+BioGtUnixSubprocess class >> isPreferredAdapter [
+	"Private - See superimplementor's comment"
+
+	^ self isRunningInUnix
+]
+
+{ #category : 'accessing' }
+BioGtUnixSubprocess class >> locateProgram: programName [
+	"Answer a <String> with the full qualified path to programName if can be located by the which command"
+
+	^ self programLocation isEmpty
+		ifTrue: [ self locateProgramNamed: programName ]
+		ifFalse: [ self programLocation ]
+]
+
+{ #category : 'accessing' }
+BioGtUnixSubprocess class >> locateProgramNamed: programName [
+	"Answer a <String> with the path to programName, if located, or an empty String otherwise"
+
+	| subprocess |
+
+	subprocess := GtSubprocessWithInMemoryOutput new
+		shellCommand: 'where ' , programName;
+		runAndWait;
+		yourself.
+
+	^ (subprocess stderr ifNotEmpty: [ subprocess stderr ] ifEmpty: [ subprocess stdout ]) trimBoth
+]
+
+{ #category : 'private' }
+BioGtUnixSubprocess class >> providerClass [
+	"Private - See superimplementor's comment"
+
+	^ #GtUnixSubprocess
+]