Repository: kestra-io/kestra (java)

Issue:
UploadFiles task doesn't upload Namespace Files as expected
### Describe the issue

I'm trying to download scripts from Git and upload them to my namespace. Both approaches resulted in a successful execution but without files being actually uploaded:

```yaml
id: upload_from_git
namespace: dev

tasks:
  - id: wdir
    type: io.kestra.plugin.core.flow.WorkingDirectory
    tasks:
      - id: git
        type: io.kestra.plugin.git.Clone
        url: https://github.com/kestra-io/scripts
        branch: main
  
      - id: upload
        type: io.kestra.plugin.core.namespace.UploadFiles
        namespace: dev
        destination: /etl
        files: 
          - etl/
```

zip approach:

```yaml
id: upload
namespace: dev

tasks:
  - id: download
    type: io.kestra.plugin.core.http.Download
    uri: https://github.com/kestra-io/scripts/archive/refs/heads/main.zip
  
  - id: unzip
    type: io.kestra.plugin.compress.ArchiveDecompress
    from: "{{ outputs.download.uri }}"
    algorithm: ZIP
  
  - id: upload
    type: io.kestra.plugin.core.namespace.UploadFiles
    namespace: dev
    # destination: /scripts/
    files: "{{ outputs.unzip.files }}"
```

### Environment

- Kestra Version:
- Operating System (OS/Docker/Kubernetes):
- Java Version (if you don't run kestra in Docker):


Pull request description:
feat(): simplified uploadfiles
close #3919


Patch:
diff --git a/core/src/main/java/io/kestra/plugin/core/namespace/UploadFiles.java b/core/src/main/java/io/kestra/plugin/core/namespace/UploadFiles.java
index 1aa001b9f..3e07aa8f2 100644
--- a/core/src/main/java/io/kestra/plugin/core/namespace/UploadFiles.java
+++ b/core/src/main/java/io/kestra/plugin/core/namespace/UploadFiles.java
@@ -1,7 +1,5 @@
 package io.kestra.plugin.core.namespace;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonMappingException;
 import io.kestra.core.exceptions.IllegalVariableEvaluationException;
 import io.kestra.core.models.annotations.Example;
 import io.kestra.core.models.annotations.Plugin;
@@ -11,7 +9,6 @@ import io.kestra.core.models.tasks.Task;
 import io.kestra.core.runners.RunContext;
 import io.kestra.core.serializers.JacksonMapper;
 import io.kestra.core.storages.Namespace;
-import io.kestra.core.utils.FileUtils;
 import io.swagger.v3.oas.annotations.media.Schema;
 import lombok.Builder;
 import lombok.Getter;
@@ -21,14 +18,14 @@ import org.codehaus.commons.nullanalysis.NotNull;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.IOException;
 import java.net.URI;
-import java.nio.file.InvalidPathException;
+import java.net.URISyntaxException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 
 import static io.kestra.core.utils.PathUtil.checkLeadingSlash;
 
@@ -42,29 +39,69 @@ import static io.kestra.core.utils.PathUtil.checkLeadingSlash;
 @Plugin(
     examples = {
         @Example(
-            title = "Upload a custom Python script to the `dev` namespace and execute it.",
+            title = "Upload files output from a previous task",
             full = true,
             code = """
-id: upload_inputfile
+id: upload2
 namespace: company.team
-
-inputs:
-  - id: my_python_script
-    type: FILE
+                
+tasks:
+  - id: download
+    type: io.kestra.plugin.core.http.Download
+    uri: https://github.com/kestra-io/scripts/archive/refs/heads/main.zip
+ \s
+  - id: unzip
+    type: io.kestra.plugin.compress.ArchiveDecompress
+    from: "{{ outputs.download.uri }}"
+    algorithm: ZIP
+                
+  - id: upload
+    type: io.kestra.plugin.core.namespace.UploadFiles
+    filesMap: "{{ outputs.unzip.files }}"
+    namespace: company.team"""
+        ),
+        @Example(
+            title = "Upload a specific file and rename it.",
+            full = true,
+            code = """
+id: upload-a-file
+namespace: dwh
 
 tasks:
-  - id: upload_and_rename
+  - id: download
+    type: io.kestra.plugin.core.http.Download
+    uri: https://github.com/kestra-io/scripts/archive/refs/heads/main.zip
+ \s
+  - id: unzip
+    type: io.kestra.plugin.compress.ArchiveDecompress
+    from: "{{ outputs.download.uri }}"
+    algorithm: ZIP
+
+  - id: upload
     type: io.kestra.plugin.core.namespace.UploadFiles
-    files:
-      /scripts/main.py: "{{ inputs.my_python_script }}"
-    namespace: dev
-
-  - id: python
-    type: io.kestra.plugin.scripts.python.Commands
-    namespace:
-      enabled: true
-    commands:
-      - python scripts/main.py"""
+    filesMap:
+      LICENCE: "{{ outputs.unzip.files['scripts-main/LICENSE'] }}"
+    namespace: dwh"""
+        ),
+        @Example(
+            title = "Upload a folder",
+            full = true,
+            code = """
+id: dbt_setup
+namespace: dwh
+tasks:
+  - id: wdir
+    type: io.kestra.plugin.core.flow.WorkingDirectory
+    tasks:
+      - id: git_clone
+        type: io.kestra.plugin.git.Clone
+        url: https://github.com/kestra-io/dbt-example
+        branch: master
+      - id: upload
+        type: io.kestra.plugin.core.namespace.UploadFiles
+        files:
+          - "glob:**/dbt/**"
+        namespace: dwh"""
         )
     }
 )
@@ -76,16 +113,22 @@ public class UploadFiles extends Task implements RunnableTask<UploadFiles.Output
     @PluginProperty(dynamic = true)
     private String namespace;
 
-    @NotNull
     @Schema(
-        title = "A list of files.",
-        description = "This can be a list of strings, where each string can be either a regex glob pattern or a file path. Providing a list requires specifying a `destination` where files will be stored.\n" +
-                    "This can also be a map where you can provide a specific destination path for a URI, which can be useful if you need to rename a file or move it to a different folder.\n" +
-                    "Finally, this can also be a string if its a pebble expression that render to a list or a map, or a single URI (that will be handle like a list of one).",
-        anyOf = {List.class, Map.class, String.class}
+        title = "A list of regex that match files in the current directory.",
+        description = "This should be a list of regex matching **ant-style patterns**." +
+            "This one is intended to be used with the WorkingDirectory task"
     )
     @PluginProperty(dynamic = true)
-    private Object files;
+    private List<String> files;
+
+    @Schema(
+        title = "A map of URI.",
+        description = "This should be a map of URI, with the key being the filename that will be upload, and the key the URI." +
+            "This one is intended to be used with output files of other tasks",
+        anyOf = {List.class, String.class}
+    )
+    @PluginProperty(dynamic = true)
+    private Object filesMap;
 
     @Schema(
         title = "The destination folder.",
@@ -111,64 +154,54 @@ public class UploadFiles extends Task implements RunnableTask<UploadFiles.Output
 
         final Namespace storageNamespace = runContext.storage().namespace(renderedNamespace);
 
-        if (files instanceof String filesString) {
-            // check if rendered filesString is a map, a list or a string
-            files = renderFilesString(runContext, filesString);
+        if (files == null && filesMap == null) {
+            throw new IllegalArgumentException("files or filesMap is required");
         }
 
-        if (files instanceof List<?> filesList) {
-            filesList = runContext.render((List<String>) filesList);
+        if (files != null) {
+            this.uploadFiles(runContext, files, storageNamespace, renderedDestination);
+        }
 
-            final List<String> regexs = new ArrayList<>();
+        if (filesMap != null) {
+            Map<String, Object> readFilesMap = new HashMap<>();
+            if (filesMap instanceof String) {
+                String renderedFilesMap = runContext.render((String) filesMap);
+                readFilesMap = JacksonMapper.ofJson().readValue(renderedFilesMap, Map.class);
+            } else {
+                readFilesMap = (Map<String, Object>) filesMap;
+            }
+            this.uploadFilesMap(runContext, readFilesMap, storageNamespace, renderedDestination);
+        }
 
-            for (Object file : filesList) {
-                Optional<URI> uri = FileUtils.getURI(file.toString());
-                // Immediately handle strings that are full URI
-                try {
+        return Output.builder().build();
+    }
 
-                    if (uri.isPresent() && runContext.storage().isFileExist(uri.get())) {
-                        Path targetFilePath = Path.of(renderedDestination, FileUtils.getFileName(uri.get()));
-                        storageNamespace.putFile(targetFilePath, runContext.storage().getFile(uri.get()), conflict);
-                    } else {
-                        regexs.add(file.toString());
-                    }
-                }
-                // If the string is not a valid URI, try to use it as a regex
-                catch (InvalidPathException | NullPointerException e) {
-                    runContext.logger().debug("File {} is not a valid URI, using it as a regex", file);
-                    regexs.add(file.toString());
-                }
-            }
+    private void uploadFiles(RunContext runContext, List<String> files, Namespace storageNamespace, String destination) throws IllegalVariableEvaluationException, IOException, URISyntaxException {
+        files = runContext.render(files);
 
-            // Check for files in the current WORKING_DIR that match the expressions
-            for (Path path : runContext.workingDir().findAllFilesMatching(regexs)) {
-                File file = path.toFile();
-                Path resolve = Paths.get("/").resolve(runContext.workingDir().path().relativize(file.toPath()));
+        for (Path path : runContext.workingDir().findAllFilesMatching(files)) {
+            File file = path.toFile();
+            Path resolve = Paths.get("/").resolve(runContext.workingDir().path().relativize(file.toPath()));
 
-                Path targetFilePath = Path.of(renderedDestination, resolve.toString());
-                storageNamespace.putFile(targetFilePath, new FileInputStream(file), conflict);
-            }
-        } else if (files instanceof Map map) {
-            // Using a Map for the `files` property, there must be only URI
-            Map<String, Object> renderedMap = runContext.render((Map<String, Object>) map);
-            for (Map.Entry<String, Object> entry : renderedMap.entrySet()) {
-                String key = entry.getKey();
-                Object value = entry.getValue();
-                if (key instanceof String targetFilePath && value instanceof String stringSourceFileURI) {
-                    URI sourceFileURI = URI.create(stringSourceFileURI);
-                    if (runContext.storage().isFileExist(sourceFileURI)) {
-                        storageNamespace.putFile(Path.of(targetFilePath), runContext.storage().getFile(sourceFileURI), conflict);
-                    }
-                } else {
-                    throw new IllegalArgumentException("files must be a List<String> or a Map<String, String>");
+            Path targetFilePath = Path.of(destination, resolve.toString());
+            storageNamespace.putFile(targetFilePath, new FileInputStream(file), conflict);
+        }
+    }
+
+    private void uploadFilesMap(RunContext runContext, Map<String, Object> filesMap, Namespace storageNamespace, String destination) throws IOException, URISyntaxException, IllegalVariableEvaluationException {
+        Map<String, Object> renderedMap = runContext.render(filesMap);
+        for (Map.Entry<String, Object> entry : renderedMap.entrySet()) {
+            String key = entry.getKey();
+            Object value = entry.getValue();
+            if (key instanceof String targetFilePath && value instanceof String stringSourceFileURI) {
+                URI sourceFileURI = URI.create(stringSourceFileURI);
+                if (runContext.storage().isFileExist(sourceFileURI)) {
+                    storageNamespace.putFile(Path.of(destination + targetFilePath), runContext.storage().getFile(sourceFileURI), conflict);
                 }
+            } else {
+                throw new IllegalArgumentException("filesMap must be a Map<String, String>");
             }
-        } else {
-            throw new IllegalArgumentException("Files must be a List<String> or a Map<String, String>");
-
         }
-
-        return Output.builder().build();
     }
 
     @Builder
@@ -176,18 +209,4 @@ public class UploadFiles extends Task implements RunnableTask<UploadFiles.Output
     public static class Output implements io.kestra.core.models.tasks.Output {
         private final Map<String, URI> files;
     }
-
-    private Object renderFilesString(RunContext runContext, String filesString) throws IllegalVariableEvaluationException, JsonProcessingException {
-        String rendered = runContext.render(filesString);
-        if (runContext.storage().isFileExist(URI.create(rendered))) {
-            return List.of(rendered);
-        } else {
-            try {
-                return JacksonMapper.ofJson().readValue(rendered, Map.class);
-            } catch (JsonMappingException e) {
-                return JacksonMapper.ofJson().readValue(rendered, List.class);
-            }
-        }
-    }
-
 }


Test patch:
diff --git a/core/src/test/java/io/kestra/plugin/core/namespace/UploadFilesTest.java b/core/src/test/java/io/kestra/plugin/core/namespace/UploadFilesTest.java
index e777955d8..c363277eb 100644
--- a/core/src/test/java/io/kestra/plugin/core/namespace/UploadFilesTest.java
+++ b/core/src/test/java/io/kestra/plugin/core/namespace/UploadFilesTest.java
@@ -2,6 +2,7 @@ package io.kestra.plugin.core.namespace;
 
 import com.devskiller.friendly_id.FriendlyId;
 import com.google.common.collect.ImmutableMap;
+import io.kestra.core.junit.annotations.KestraTest;
 import io.kestra.core.runners.RunContext;
 import io.kestra.core.runners.RunContextFactory;
 import io.kestra.core.storages.Namespace;
@@ -9,9 +10,8 @@ import io.kestra.core.storages.NamespaceFile;
 import io.kestra.core.storages.StorageInterface;
 import io.kestra.core.utils.IdUtils;
 import io.kestra.core.utils.TestsUtils;
-import io.kestra.core.junit.annotations.KestraTest;
+import io.micrometer.core.instrument.util.IOUtils;
 import jakarta.inject.Inject;
-import org.apache.commons.io.IOUtils;
 import org.junit.jupiter.api.Test;
 
 import java.io.File;
@@ -51,7 +51,7 @@ public class UploadFilesTest {
         UploadFiles uploadFile = UploadFiles.builder()
             .id(UploadFiles.class.getSimpleName())
             .type(UploadFiles.class.getName())
-            .files(Map.of("/path/file.txt", fileStorage.toString()))
+            .filesMap(Map.of("/path/file.txt", fileStorage.toString()))
             .namespace(namespace)
             .conflict(Namespace.Conflicts.ERROR)
             .destination("/folder")
@@ -73,7 +73,7 @@ public class UploadFilesTest {
         UploadFiles uploadFile = UploadFiles.builder()
             .id(UploadFiles.class.getSimpleName())
             .type(UploadFiles.class.getName())
-            .files(Map.of("/path/file.txt", fileStorage.toString()))
+            .filesMap(Map.of("/path/file.txt", fileStorage.toString()))
             .namespace("{{ inputs.namespace }}")
             .destination("/folder")
             .build();
@@ -89,7 +89,7 @@ public class UploadFilesTest {
 
         fileStorage = addToStorage("logback.xml");
         uploadFile = uploadFile.toBuilder()
-                .files(Map.of("/path/file.txt", fileStorage.toString()))
+                .filesMap(Map.of("/path/file.txt", fileStorage.toString()))
                 .build();
 
         uploadFile.run(runContext);
@@ -111,7 +111,7 @@ public class UploadFilesTest {
         UploadFiles uploadFile = UploadFiles.builder()
             .id(UploadFiles.class.getSimpleName())
             .type(UploadFiles.class.getName())
-            .files(Map.of("/path/file.txt", fileStorage.toString()))
+            .filesMap(Map.of("/path/file.txt", fileStorage.toString()))
             .namespace(namespace)
             .conflict(Namespace.Conflicts.SKIP)
             .destination("/folder")
@@ -128,7 +128,7 @@ public class UploadFilesTest {
 
         fileStorage = addToStorage("logback.xml");
         uploadFile = uploadFile.toBuilder()
-            .files(Map.of("/path/file.txt", fileStorage.toString()))
+            .filesMap(Map.of("/path/file.txt", fileStorage.toString()))
             .build();
 
         uploadFile.run(runContext);
@@ -141,6 +141,29 @@ public class UploadFilesTest {
         assertThat(previousFile.equals(newFile), is(true));
     }
 
+    @Test
+    void shouldPutFileFromRegex() throws Exception {
+        String namespace = "io.kestra." + IdUtils.create();
+
+
+        UploadFiles uploadFile = UploadFiles.builder()
+            .id(UploadFiles.class.getSimpleName())
+            .type(UploadFiles.class.getName())
+            .files(List.of("glob:**application**"))
+            .namespace(namespace)
+            .conflict(Namespace.Conflicts.SKIP)
+            .destination("/folder/")
+            .build();
+
+        RunContext runContext = TestsUtils.mockRunContext(this.runContextFactory, uploadFile, ImmutableMap.of());
+        runContext.workingDir().createFile("application-test.yml");
+        uploadFile.run(runContext);
+
+        Namespace namespaceStorage = runContext.storage().namespace(namespace);
+        List<NamespaceFile> namespaceFiles = namespaceStorage.all();
+        assertThat(namespaceFiles.size(), is(1));
+    }
+
     private URI addToStorage(String fileToLoad) throws IOException, URISyntaxException {
         File file = new File(Objects.requireNonNull(UploadFilesTest.class.getClassLoader().getResource(fileToLoad)).toURI());