Transform script refactor #6159
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| package org.labkey.api.assay.transform; | ||
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| import org.jetbrains.annotations.Nullable; | ||
| import org.json.JSONArray; | ||
| import org.json.JSONException; | ||
| import org.json.JSONObject; | ||
| import org.labkey.vfs.FileLike; | ||
| import org.labkey.vfs.FileSystemLike; | ||
|
|
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.Collection; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
|
|
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| public class AnalysisScript | ||
| { | ||
| FileLike _script; | ||
| Set<DataTransformService.TransformOperation> _operations = new HashSet<>(); | ||
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| public AnalysisScript(File script, Set<DataTransformService.TransformOperation> operations) | ||
| { | ||
| _script = new FileSystemLike.Builder(script).build().getRoot(); | ||
| _operations = operations; | ||
| } | ||
|
|
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| private AnalysisScript(File script, List<String> operations) | ||
| { | ||
| _script = new FileSystemLike.Builder(script).build().getRoot(); | ||
| for (String op : operations) | ||
|
Contributor
There was a problem hiding this comment. I assume it is not possible to have a null operations param here, but thoughts on adding in a check and default case for setting operations to insert? |
||
| { | ||
| if (op != null) | ||
| _operations.add(DataTransformService.TransformOperation.valueOf(op)); | ||
| } | ||
|
|
||
| // default to insert only | ||
| if (_operations.isEmpty()) | ||
| _operations.add(DataTransformService.TransformOperation.INSERT); | ||
| } | ||
|
|
||
| public FileLike getScript() | ||
| { | ||
| return _script; | ||
| } | ||
|
|
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| public String getScriptPath() | ||
| { | ||
| return _script.toNioPathForRead().toString(); | ||
| } | ||
|
|
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| public boolean canExecute(DataTransformService.TransformOperation operation) | ||
| { | ||
| return _operations.contains(operation); | ||
| } | ||
|
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| private static JSONObject toJson(AnalysisScript script) | ||
| { | ||
| JSONObject json = new JSONObject(); | ||
|
|
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| json.put("operations", script._operations); | ||
| json.put("script", script._script.toNioPathForRead()); | ||
|
|
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| return json; | ||
| } | ||
|
|
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| @Nullable | ||
| public static JSONArray toJson(Collection<AnalysisScript> scripts) | ||
| { | ||
| if (!scripts.isEmpty()) | ||
| { | ||
| JSONArray json = new JSONArray(); | ||
| for (AnalysisScript script : scripts) | ||
| { | ||
| json.put(toJson(script)); | ||
| } | ||
| return json; | ||
| } | ||
| return null; | ||
| } | ||
|
|
||
| @Nullable | ||
| public static List<AnalysisScript> fromJson(String jsonStr) | ||
| { | ||
| try | ||
| { | ||
| List<AnalysisScript> scripts = new ArrayList<>(); | ||
| JSONArray json = new JSONArray(jsonStr); | ||
| for (Object o : json.toList()) | ||
| { | ||
| if (o instanceof Map<?,?> props) | ||
| { | ||
| File script = new File(String.valueOf(props.get("script"))); | ||
| List<String> ops = (List<String>) props.get("operations"); | ||
|
|
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| scripts.add(new AnalysisScript(script, ops)); | ||
| } | ||
| } | ||
| return scripts; | ||
| } | ||
| catch (JSONException e) | ||
| { | ||
| // ignore | ||
| return null; | ||
| } | ||
| } | ||
| } | ||
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I know we don't expose anything in the UI for defining a validation script, just transform scripts. Was this possible from a file based module? Is there code somewhere that would convert any legacy validation scripts to transform scripts or is that not needed?
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Not that I'm aware of, the file based module code for transform scripts is in
ModuleAssayProvider.