annotate envs in algorithms

applied-systems-biology · Oct 21, 2024 · c3bd4db · c3bd4db
1 parent 34dca16
commit c3bd4db
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diff --git a/...main/java/org/hkijena/jipipe/plugins/cellpose/algorithms/Cellpose2InferenceAlgorithm.java b/...main/java/org/hkijena/jipipe/plugins/cellpose/algorithms/Cellpose2InferenceAlgorithm.java
@@ -29,6 +29,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -188,6 +189,7 @@ public void setEnable3DSegmentation(boolean enable3DSegmentation) {
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Cellpose is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(showCategory = "Cellpose", allowArtifact = true, artifactFilters = {"com.github.mouseland.cellpose:*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/.../main/java/org/hkijena/jipipe/plugins/cellpose/algorithms/Cellpose2TrainingAlgorithm.java b/.../main/java/org/hkijena/jipipe/plugins/cellpose/algorithms/Cellpose2TrainingAlgorithm.java
@@ -27,6 +27,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -198,6 +199,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Cellpose is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(showCategory = "Cellpose", allowArtifact = true, artifactFilters = {"com.github.mouseland.cellpose:*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...k/src/main/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikAutoContextAlgorithm.java b/...k/src/main/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikAutoContextAlgorithm.java
@@ -32,6 +32,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -358,6 +359,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Ilastik environment", description = "If enabled, a different Ilastik environment is used for this node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Ilastik is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.embl.ilastik:*"})
     public OptionalIlastikEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...n/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikObjectClassificationAlgorithm.java b/...n/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikObjectClassificationAlgorithm.java
@@ -29,6 +29,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -332,6 +333,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Ilastik environment", description = "If enabled, a different Ilastik environment is used for this node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Ilastik is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.embl.ilastik:*"})
     public OptionalIlastikEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...in/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikPixelClassificationAlgorithm.java b/...in/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikPixelClassificationAlgorithm.java
@@ -32,6 +32,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -303,6 +304,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Ilastik environment", description = "If enabled, a different Ilastik environment is used for this node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Ilastik is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.embl.ilastik:*"})
     public OptionalIlastikEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...jena/jipipe/plugins/ilastik/nodes/IlastikPredictionMapsObjectClassificationAlgorithm.java b/...jena/jipipe/plugins/ilastik/nodes/IlastikPredictionMapsObjectClassificationAlgorithm.java
@@ -29,6 +29,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -368,6 +369,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Ilastik environment", description = "If enabled, a different Ilastik environment is used for this node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Ilastik is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.embl.ilastik:*"})
     public OptionalIlastikEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...a/jipipe/plugins/ilastik/nodes/IlastikSegmentationImageObjectClassificationAlgorithm.java b/...a/jipipe/plugins/ilastik/nodes/IlastikSegmentationImageObjectClassificationAlgorithm.java
@@ -29,6 +29,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -370,6 +371,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Ilastik environment", description = "If enabled, a different Ilastik environment is used for this node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Ilastik is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.embl.ilastik:*"})
     public OptionalIlastikEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...main/java/org/hkijena/jipipe/plugins/omnipose/algorithms/Omnipose0InferenceAlgorithm.java b/...main/java/org/hkijena/jipipe/plugins/omnipose/algorithms/Omnipose0InferenceAlgorithm.java
@@ -29,6 +29,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -187,6 +188,7 @@ public void setEnable3DSegmentation(boolean enable3DSegmentation) {
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Cellpose is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(showCategory = "Omnipose", allowArtifact = true, artifactFilters = {"com.github.kevinjohncutler.omnipose:*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/.../main/java/org/hkijena/jipipe/plugins/omnipose/algorithms/Omnipose0TrainingAlgorithm.java b/.../main/java/org/hkijena/jipipe/plugins/omnipose/algorithms/Omnipose0TrainingAlgorithm.java
@@ -27,6 +27,7 @@
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -196,6 +197,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Omnipose is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(showCategory = "Omnipose", allowArtifact = true, artifactFilters = {"com.github.kevinjohncutler.omnipose:*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...a/org/hkijena/jipipe/plugins/python/algorithms/python/IteratingPythonScriptAlgorithm.java b/...a/org/hkijena/jipipe/plugins/python/algorithms/python/IteratingPythonScriptAlgorithm.java
@@ -18,6 +18,7 @@
 import org.hkijena.jipipe.api.SetJIPipeDocumentation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.JIPipeDefaultMutableSlotConfiguration;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.JIPipeGraphNodeRunContext;
 import org.hkijena.jipipe.api.nodes.JIPipeNodeInfo;
@@ -97,6 +98,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
 
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.python.*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...ava/org/hkijena/jipipe/plugins/python/algorithms/python/MergingPythonScriptAlgorithm.java b/...ava/org/hkijena/jipipe/plugins/python/algorithms/python/MergingPythonScriptAlgorithm.java
@@ -18,6 +18,7 @@
 import org.hkijena.jipipe.api.SetJIPipeDocumentation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.JIPipeDefaultMutableSlotConfiguration;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.JIPipeGraphNodeRunContext;
 import org.hkijena.jipipe.api.nodes.JIPipeNodeInfo;
@@ -97,6 +98,7 @@ public void setCleanUpAfterwards(boolean cleanUpAfterwards) {
 
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.python.*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/.../main/java/org/hkijena/jipipe/plugins/python/algorithms/python/PythonScriptAlgorithm.java b/.../main/java/org/hkijena/jipipe/plugins/python/algorithms/python/PythonScriptAlgorithm.java
@@ -19,6 +19,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.JIPipeDefaultMutableSlotConfiguration;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.JIPipeGraphNodeRunContext;
 import org.hkijena.jipipe.api.nodes.JIPipeNodeInfo;
@@ -97,6 +98,7 @@ public void setSuppressLogs(boolean suppressLogs) {
     @SetJIPipeDocumentation(name = "Override Python environment", description = "If enabled, a different Python environment is used for this Node. Otherwise " +
             "the one in the Project > Application settings > Extensions > Python is used.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.python.*"})
     public OptionalPythonEnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...ugin-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/ImportRDatasetAlgorithm.java b/...ugin-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/ImportRDatasetAlgorithm.java
@@ -16,6 +16,7 @@
 import org.hkijena.jipipe.api.ConfigureJIPipeNode;
 import org.hkijena.jipipe.api.JIPipeProgressInfo;
 import org.hkijena.jipipe.api.SetJIPipeDocumentation;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
 import org.hkijena.jipipe.api.nodes.JIPipeGraphNodeRunContext;
@@ -75,6 +76,7 @@ public void getEnvironmentDependencies(List<JIPipeEnvironment> target) {
 
     @SetJIPipeDocumentation(name = "Override R environment", description = "If enabled, a different R environment is used for this Node.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.r.*"})
     public OptionalREnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...in-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/IteratingRScriptAlgorithm.java b/...in-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/IteratingRScriptAlgorithm.java
@@ -22,6 +22,7 @@
 import org.hkijena.jipipe.api.data.serialization.JIPipeDataTableMetadata;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemReadDataStorage;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -130,6 +131,7 @@ public void reportValidity(JIPipeValidationReportContext reportContext, JIPipeVa
 
     @SetJIPipeDocumentation(name = "Override R environment", description = "If enabled, a different R environment is used for this Node.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.r.*"})
     public OptionalREnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }

diff --git a/...ugin-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/MergingRScriptAlgorithm.java b/...ugin-r/src/main/java/org/hkijena/jipipe/plugins/r/algorithms/MergingRScriptAlgorithm.java
@@ -22,6 +22,7 @@
 import org.hkijena.jipipe.api.data.serialization.JIPipeDataTableMetadata;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemReadDataStorage;
 import org.hkijena.jipipe.api.data.storage.JIPipeFileSystemWriteDataStorage;
+import org.hkijena.jipipe.api.environments.ExternalEnvironmentParameterSettings;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
 import org.hkijena.jipipe.api.nodes.AddJIPipeOutputSlot;
@@ -130,6 +131,7 @@ public void reportValidity(JIPipeValidationReportContext reportContext, JIPipeVa
 
     @SetJIPipeDocumentation(name = "Override R environment", description = "If enabled, a different R environment is used for this Node.")
     @JIPipeParameter("override-environment")
+    @ExternalEnvironmentParameterSettings(allowArtifact = true, artifactFilters = {"org.r.*"})
     public OptionalREnvironment getOverrideEnvironment() {
         return overrideEnvironment;
     }