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Custom properties vip:dot #480

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merged 11 commits into from
Jul 9, 2024
Merged

Custom properties vip:dot #480

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694a964
Update BoutiquesApplication.java
sandepat Jun 21, 2024
26440b8
Update BoutiquesParser.java
sandepat Jun 21, 2024
ac94b72
Update DisplayTab.java
sandepat Jun 21, 2024
f7619a2
Update
sandepat Jun 26, 2024
f78e43e
Update DisplayTab.java
sandepat Jul 1, 2024
301a78b
Update BoutiquesApplication.java
sandepat Jul 1, 2024
72795d4
Update gwendia-standalone.vm
sandepat Jul 1, 2024
357563f
Update BoutiquesParser.java
sandepat Jul 1, 2024
a2c7841
Resolution of review comment and display of results-directory
sandepat Jul 1, 2024
11992a0
removed unused field - inputIds
sandepat Jul 3, 2024
9a9297c
update gwendia.vm
sandepat Jul 8, 2024
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34 changes: 34 additions & 0 deletions ...r/insalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/DisplayTab.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@
*/
package fr.insalyon.creatis.vip.applicationimporter.client.view.applicationdisplay;

import java.util.HashSet;
import java.util.Set;

import com.google.gwt.user.client.rpc.AsyncCallback;
import com.smartgwt.client.widgets.Canvas;
import com.smartgwt.client.widgets.IButton;
Expand All @@ -39,6 +42,7 @@
import com.smartgwt.client.widgets.layout.HLayout;
import com.smartgwt.client.widgets.layout.VLayout;
import com.smartgwt.client.widgets.tab.Tab;

import fr.insalyon.creatis.vip.application.client.bean.boutiquesTools.BoutiquesApplication;
import fr.insalyon.creatis.vip.application.client.view.boutiquesParsing.BoutiquesParser;
import fr.insalyon.creatis.vip.application.client.view.boutiquesParsing.InvalidBoutiquesDescriptorException;
Expand All @@ -49,6 +53,7 @@
import fr.insalyon.creatis.vip.core.client.view.layout.Layout;
import fr.insalyon.creatis.vip.core.client.view.util.WidgetUtil;


public class DisplayTab extends Tab {

// Layouts
Expand Down Expand Up @@ -158,6 +163,35 @@ private static void verifyBoutiquesTool(BoutiquesApplication boutiquesTool)
if (boutiquesTool.getAuthor() == null) {
throw new ApplicationImporterException("Boutiques file must have an author");
}
checkvipdot(boutiquesTool);
}

/**
* display warning message if any.
*
* @param application BoutiquesApplication object to cehck warning message
* **/
private static void checkvipdot(BoutiquesApplication application) {
Set<String> commandLineFlags = application.getCommandLineFlag();
Set<String> vipDotInputIds = application.getVipDotInputIds();
Set<String> commonValues = new HashSet<>(application.getVipDotInputIds());

commonValues.retainAll(commandLineFlags);

if (!commonValues.isEmpty()) {
String warningMessage = "<b>" + String.join(", ", commonValues) + "</b> appears as command-line flag input(s), it should not be included in Dot iteration. Importing it may cause functionality issues, although the application will still be imported.";
Layout.getInstance().setWarningMessage(warningMessage);
}

// Extract the IDs from inputs
Set<String> inputIds = application.getInputs().stream().map(BoutiquesInput::getId).collect(Collectors.toSet());
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You may add this as a BoutiquesApplication method. (optionally)

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Added the getinputIds method to BoutiquesApplication

// Check if all vipDotInputIds are in inputs
if (!inputIds.containsAll(vipDotInputIds)) {
Set<String> incorrectInputs = new HashSet<>(vipDotInputIds);
incorrectInputs.removeAll(inputIds);
String warningMessage = "<b>" + String.join(", ", incorrectInputs) + "</b> appears in vipDotInputIds but not in inputs. Please ensure all ids are correct.";
Layout.getInstance().setWarningMessage(warningMessage);
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in this case, it should be a error with an exception thrown.

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throwing ApplicationImporterException

}
}

/**
Expand Down
7 changes: 5 additions & 2 deletions ...nsalyon/creatis/vip/applicationimporter/client/view/applicationdisplay/GeneralLayout.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,8 @@ public class GeneralLayout extends AbstractFormLayout {
version,
schemaVersion,
description,
vipContainer;
vipContainer,
dotInputs;

public GeneralLayout(String width, String height) {
super(width, height);
Expand All @@ -63,8 +64,9 @@ public GeneralLayout(String width, String height) {
schemaVersion = new LocalTextField("Schema Version", false, false);
description = new LocalTextField("Description", false, false);
vipContainer = new LocalTextField("VIP Container", false, false);
dotInputs = new LocalTextField("DOT Inputs", false, false);

this.addMembers(name, commandLine, dockerImage, dockerIndex, version, schemaVersion, description, vipContainer);
this.addMembers(name, commandLine, dockerImage, dockerIndex, version, schemaVersion, description, vipContainer, dotInputs);
}

public void setTool(BoutiquesApplication bt) {
Expand All @@ -76,5 +78,6 @@ public void setTool(BoutiquesApplication bt) {
dockerIndex.setValue(bt.getContainerIndex());
schemaVersion.setValue(bt.getSchemaVersion());
vipContainer.setValue(bt.getVipContainer());
dotInputs.setValue(String.join(", ", bt.getVipDotInputIds()));
}
}
33 changes: 32 additions & 1 deletion .../fr/insalyon/creatis/vip/application/client/bean/boutiquesTools/BoutiquesApplication.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package fr.insalyon.creatis.vip.application.client.bean.boutiquesTools;

import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
Expand All @@ -10,6 +11,8 @@

import com.google.gwt.user.client.rpc.IsSerializable;

import fr.insalyon.creatis.vip.application.client.bean.boutiquesTools.BoutiquesInput.InputType;

/**
* Representation of an application Boutiques descriptor
*
Expand Down Expand Up @@ -38,6 +41,8 @@ public class BoutiquesApplication implements IsSerializable {
private Set<BoutiquesOutputFile> outputFiles = new HashSet<>();
private Map<String, String> tags = new HashMap<>();
private String jsonFile;
private Set<String> vipDotInputIds;
private String resultDirs;
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rename field and getter/setter with vipDotIncludesResultsDir, and change type to boolean.

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@sandepat sandepat Jul 1, 2024 •
edited
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changed to boolean vipDotIncludesResultsDir


private BoutiquesApplicationExtensions boutiquesExtensions;

Expand Down Expand Up @@ -229,6 +234,24 @@ public String getVipContainer() {
return vipContainer;
}

public Set<String> getVipDotInputIds() {
if (vipDotInputIds == null) {
return Collections.emptySet();
}
return vipDotInputIds;
}

public Set<String> getCommandLineFlag() {
return inputs.stream()
.filter(i -> InputType.FLAG.equals(i.getType()))
.map(BoutiquesInput::getId)
.collect(Collectors.toSet());
}

public String getVipDotResultDirs() {
return resultDirs;
}

public void addInput(BoutiquesInput input){
this.inputs.add(input);
}
Expand Down Expand Up @@ -280,4 +303,12 @@ public void addTag(String key, String value) {
public void setVipContainer(String vipContainer) {
this.vipContainer = vipContainer;
}
}

public void setVipDotInputIds(Set<String> inputIds) {
this.vipDotInputIds = inputIds;
}

public void setVipDotResultDirs(String resultDirs) {
this.resultDirs = resultDirs;
}
}
7 changes: 3 additions & 4 deletions ...ava/fr/insalyon/creatis/vip/application/client/view/boutiquesParsing/BoutiquesParser.java
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Expand Up @@ -114,8 +114,9 @@ public BoutiquesApplication parseApplication(String descriptor) throws InvalidBo
// Custom property
JSONObject customObject = getObjectValue(parsedDescriptor, "custom", true);
if (customObject != null) {
String vipImagePath = getStringValue(customObject, "vip:imagepath", true);
application.setVipContainer(vipImagePath);
application.setVipContainer(getStringValue(customObject, "vip:imagepath", true));
application.setVipDotInputIds(getArrayValueAsStringSet(customObject, "vip:dot", true));
application.setVipDotResultDirs(getStringValue(customObject, "vip:dot-result-directory", true));
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Rename to vip:dot-with-results-directory.
Adapt to vip:dot-result-directory being a boolean.

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change to vip:dot-with-results-directory and adapt to the method getBooleanValue

}
// Json descriptor
application.setJsonFile(parsedDescriptor.toString());
Expand Down Expand Up @@ -241,6 +242,4 @@ private BoutiquesOutputFile parseBoutiquesOutputFile(JSONObject outputFile)
bof.setCommandLineFlag(commandLineFlag);
return bof;
}


}
149 changes: 85 additions & 64 deletions vip-portal/src/main/resources/vm/gwendia-standalone.vm
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Expand Up @@ -5,78 +5,99 @@
<source name="results-directory" type="URI" optional="false" default="/vip/Home" pretty-name="Results directory">
<source-comment>Directory where the results will be stored.</source-comment>
</source>
#foreach( $input in $tool.getInputs() )
#set($type="string")
#if($input.getType().getCamelName()=="File")
#set($type="URI")
#end
#if($input.getType().getCamelName()=="Flag")
#if($input.getDefaultValue() && $input.getDefaultValue()!="")
<source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
#foreach( $input in $tool.getInputs() )
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I thnk VS or something else changed the indentation of velocity code and it generetad a lot of diff.
Could it be possible to keep the original indentation ?

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indeed, restore original indentation.

#set($type="string")
#if($input.getType().getCamelName()=="File")
#set($type="URI")
#end
#if($input.getType().getCamelName()=="Flag")
#if($input.getDefaultValue() && $input.getDefaultValue()!="")
<source name="$input.getId()" type="string" optional="$input.isOptional()" default="$input.getDefaultValue()" vip-type-restriction="flag" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="string" optional="$input.isOptional()" default="false" vip-type-restriction="flag" pretty-name="$input.getName()">
#end
#else
#if($input.getDefaultValue() && $input.getDefaultValue()!="")
#if($input.getType().getCamelName()=="Number" && $input.isInteger())
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
#end
#else
#if($input.isOptional()==true)
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
#end
#end
#end
#if($input.getDescription())
<source-comment>$esc.xml($input.getDescription())</source-comment>
#else
<source-comment></source-comment>
#end
</source>
#end
#else
#if($input.getDefaultValue() && $input.getDefaultValue()!="")
#if($input.getType().getCamelName()=="Number" && $input.isInteger())
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue().intValue()" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="$input.getDefaultValue()" pretty-name="$input.getName()">
#end
#else
#if($input.isOptional()==true)
<source name="$input.getId()" type="$type" optional="$input.isOptional()" default="No_value_provided" pretty-name="$input.getName()">
#else
<source name="$input.getId()" type="$type" optional="$input.isOptional()" pretty-name="$input.getName()">
#end
#foreach($output in $tool.getOutputFiles())
<sink name="$output.getId()" type="URI" />
#end
#end
#if($input.getDescription())
<source-comment>$esc.xml($input.getDescription())</source-comment>
#else
<source-comment></source-comment>
#end
</source>
#end
#foreach($output in $tool.getOutputFiles())
<sink name="$output.getId()" type="URI" />
#end
</interface>
<processors>
<processor name="append-date" >
<in name="dir" type="URI" depth="0" />
<out name="result" type="string" depth="0" />
<beanshell>/*----------Beginning of Beanshell------------*/
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
<beanshell>
/*----------Beginning of Beanshell------------*/
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;

String result = dir.toString();
if ( result.startsWith("/") || result.startsWith("lfn:") ) {
DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
}
/*------------End of Beanshell------------*/
String result = dir.toString();
if ( result.startsWith("/") || result.startsWith("lfn:") ) {
DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
result = result + "/" + (dateFormat.format(System.currentTimeMillis()));
}
/*------------End of Beanshell------------*/
</beanshell>
</processor>
<processor name="$tool.getName()" >
<in name="results-directory" type="string" depth="0"/>
#foreach($input in $tool.getInputs())
#if($input.getType().getCamelName()=="File" )
<in name="$input.getId()" type="URI" depth="0"/>
#else
<in name="$input.getId()" type="string" depth="0"/>
#end
#end
#foreach( $output in $tool.getOutputFiles() )
<out name="$output.getId()" type="URI" depth="0"/>
#end
#foreach($input in $tool.getInputs())
#if($input.getType().getCamelName()=="File" )
<in name="$input.getId()" type="URI" depth="0"/>
#else
<in name="$input.getId()" type="string" depth="0"/>
#end
#end
#foreach( $output in $tool.getOutputFiles() )
<out name="$output.getId()" type="URI" depth="0"/>
#end
<iterationstrategy>
<cross>
<port name="results-directory" />
#foreach($input in $tool.getInputs())
<port name="$input.getId()"/>
#end
#if($tools.getVipDotResultDirs)
<dot>
<port name="results-directory" />
#foreach($input in $tool.getInputs())
#if($tool.getVipDotInputIds().contains($input.getId()))
<port name="$input.getId()"/>
#end
#end
</dot>
#else
<port name="results-directory" />
#foreach($input in $tool.getInputs())
#if(!$tool.getVipDotInputIds().contains($input.getId()))
<port name="$input.getId()"/>
#end
#end
#end
#if($tool.getVipDotInputIds() && !$tool.getVipDotInputIds().isEmpty() && !$tools.getVipDotResultDirs)
<dot>
#foreach($dotInput in $tool.getVipDotInputIds())
<port name="$dotInput"/>
#end
</dot>
#end
</cross>
</iterationstrategy>
<gasw descriptor="$fileAccessProtocol:$tool.getGASWLFN()"/>
Expand All @@ -85,11 +106,11 @@ if ( result.startsWith("/") || result.startsWith("lfn:") ) {
<links>
<link from="results-directory" to="append-date:dir" />
<link from="append-date:result" to="$tool.getName():results-directory" />
#foreach( $input in $tool.getInputs() )
<link from="$input.getId()" to="$tool.getName():$input.getId()" />
#end
#foreach($output in $tool.getOutputFiles())
<link from="$tool.getName():$output.getId()" to="$output.getId()" />
#end
#foreach( $input in $tool.getInputs() )
<link from="$input.getId()" to="$tool.getName():$input.getId()" />
#end
#foreach($output in $tool.getOutputFiles())
<link from="$tool.getName():$output.getId()" to="$output.getId()" />
#end
</links>
</workflow>
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