created structured json file with url + metadata

virtual-imaging-platform · Oct 19, 2023 · 741b0d6 · 741b0d6
1 parent e7e6fae
commit 741b0d6
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Showing 6 changed files with 79 additions and 34 deletions.
diff --git a/...ication/src/main/java/fr/insalyon/creatis/vip/application/client/rpc/ReproVipService.java b/...ication/src/main/java/fr/insalyon/creatis/vip/application/client/rpc/ReproVipService.java
@@ -25,7 +25,7 @@ public static ReproVipServiceAsync getInstance() {
     void addExecution(Execution execution) throws CoreException;
     void updateExecution(String executionID, String newStatus) throws CoreException;
     void executionOutputData(String executionID) throws CoreException;
-    String downloadJsonOutputData(String executionID) throws CoreException;
+    String downloadJsonOutputData(String executionName, String executionID, String version) throws CoreException;
     void createReproVipDirectory(String executionName, String executionID, String version) throws CoreException;
 }
 
diff --git a/...on/src/main/java/fr/insalyon/creatis/vip/application/client/rpc/ReproVipServiceAsync.java b/...on/src/main/java/fr/insalyon/creatis/vip/application/client/rpc/ReproVipServiceAsync.java
@@ -9,7 +9,7 @@ public interface ReproVipServiceAsync {
     void addExecution(Execution execution, AsyncCallback<Void> asyncCallback);
     void updateExecution(String executionID, String newStatus, AsyncCallback<Void> asyncCallback);
     void executionOutputData(String executionID, AsyncCallback<Void> callback);
-    void downloadJsonOutputData(String executionID, AsyncCallback<String> callback);
+    void downloadJsonOutputData(String executionName, String executionID, String version, AsyncCallback<String> callback);
     void createReproVipDirectory(String executionName, String execution, String version, AsyncCallback<Void> callback);
 }
 
diff --git a/...nsalyon/creatis/vip/application/client/view/system/application/ExecutionsContextMenu.java b/...nsalyon/creatis/vip/application/client/view/system/application/ExecutionsContextMenu.java
@@ -41,7 +41,7 @@ public void onClick(MenuItemClickEvent event) {
         DownloadOutputDataItem.addClickHandler(new ClickHandler() {
             @Override
             public void onClick(MenuItemClickEvent event) {
-                DownloadOutputDataExecution();
+                DownloadOutputDataExecution(executionName, executionID, version);
             }
         });
 
@@ -63,7 +63,7 @@ public void onSuccess(Void result) {
         modal.show("Make execution public", true);
         reproVipServiceAsync.updateExecution(executionID, "Public", callback);
     }
-    private void DownloadOutputDataExecution() {
+    private void DownloadOutputDataExecution(String executionName, String executionID, String version) {
         final AsyncCallback<String> callback = new AsyncCallback<String>() {
             @Override
             public void onFailure(Throwable caught) {
@@ -77,7 +77,7 @@ public void onSuccess(String s) {
             }
         };
         modal.show("Download Outputs", true);
-        reproVipServiceAsync.downloadJsonOutputData(executionID, callback);
+        reproVipServiceAsync.downloadJsonOutputData(executionName, executionID, version,  callback);
     }
     public void createReproVipDirectory(String executionName, String executionID, String version) {
         reproVipServiceAsync.createReproVipDirectory(executionName, executionID, version, new AsyncCallback<Void>() {

diff --git a/...n/src/main/java/fr/insalyon/creatis/vip/application/server/business/ReproVipBusiness.java b/...n/src/main/java/fr/insalyon/creatis/vip/application/server/business/ReproVipBusiness.java
@@ -23,10 +23,7 @@
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import java.io.File;
-import java.io.FileWriter;
-import java.io.FilenameFilter;
-import java.io.IOException;
+import java.io.*;
 import java.nio.file.Files;
 import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
@@ -112,37 +109,51 @@ public ExecutionJobTaskData getExecutionJobTaskData(String executionID) throws B
         }
         return new ExecutionJobTaskData(jobList);
     }
-
-    public String createJsonOutputData(String executionID, User currentUser)
+    public String createJsonOutputData(String executionName, String executionID, String version, User currentUser)
             throws ApplicationException, BusinessException {
-        ExecutionInOutData inOutData = executionOutputData(executionID, currentUser);
-        //ExecutionJobTaskData jobTaskData = getExecutionJobTaskData(executionID);
+        List<String> filesToDownload = getFilesToCopyPaths(executionName, executionID, version, currentUser);
+
+        Map<String, Object> structuredJson = new HashMap<>();
+
+        structuredJson.put("files_to_download", filesToDownload);
+
+        Map<String, Object> metadataOuter = new HashMap<>();
+        Map<String, Object> metadataInner = new HashMap<>();
+
+        metadataInner.put("title", "your title");
+        metadataInner.put("upload_type", "workflow");
+        metadataInner.put("description", "your description");
 
-        //Map<String, Object> combinedData = new HashMap<>();
-        //combinedData.put("inOutData", inOutData);
-        //combinedData.put("jobs", jobTaskData.getJobs());
+        List<Map<String, String>> creators = new ArrayList<>();
+        Map<String, String> creator = new HashMap<>();
+        creator.put("name", currentUser.getFullName());
+        creator.put("affiliation", "your affiliation");
+        creators.add(creator);
+
+        metadataInner.put("creators", creators);
+        metadataOuter.put("metadata", metadataInner);
+
+        structuredJson.put("metadata", metadataOuter);
 
         ObjectMapper objectMapper = new ObjectMapper();
         try {
-            String json = objectMapper.writeValueAsString(inOutData);
-            //saveJsonToFile(json, executionID);
+            String json = objectMapper.writeValueAsString(structuredJson);
             logger.info(json);
+
+            String filePath = "/vip/ReproVip/structuredOutput.json";
+            saveJsonToFile(json, filePath);
+
             return json;
         } catch (JsonProcessingException e) {
-            throw new ApplicationException(ApplicationException.ApplicationError.valueOf("Failed to convert Output to JSON"), e);
+            throw new ApplicationException(ApplicationException.ApplicationError.valueOf("Failed to convert structured output to JSON"), e);
+        } catch (IOException e) {
+            throw new BusinessException("Failed to save JSON to file", e);
         }
     }
-
-    public void saveJsonToFile(String jsonContent, String executionID) throws IOException {
-        String filePath = server.getWorkflowsPath() + "/" + executionID + "/inOutPut.json";
-        File file = new File(filePath);
-
-        if (!file.exists()) {
-            file.createNewFile();
-        }
-
-        try (FileWriter fileWriter = new FileWriter(file)) {
-            fileWriter.write(jsonContent);
+    public void saveJsonToFile(String jsonContent, String filePath) throws IOException {
+        try (FileWriter fileWriter = new FileWriter(filePath);
+             BufferedWriter bufferedWriter = new BufferedWriter(fileWriter)) {
+            bufferedWriter.write(jsonContent);
         }
     }
     public void createReproVipDirectory(String executionName, String executionID, String version, User currentUser) {
@@ -165,7 +176,7 @@ public void createReproVipDirectory(String executionName, String executionID, St
             logger.info(outputData.get(0).getPath());
 
             if (outputData != null && !outputData.isEmpty()) {
-                String outputPath = outputData.get(0).getPath();
+                String outputPath = "/vip/grida/downloads" + outputData.get(0).getPath();
                 if (outputPath != null) {
                     File outputFile = new File(outputPath);
                     if (outputFile.exists()) {
@@ -234,4 +245,38 @@ public boolean accept(File dir, String name) {
             throw new RuntimeException(e);
         }
     }
+
+    public List<String> getFilesToCopyPaths(String executionName, String executionID, String version, User currentUser) throws BusinessException {
+        List<String> paths = new ArrayList<>();
+
+        List<InOutData> outputData = workflowBusiness.getOutputData(executionID, currentUser.getFolder(), true);
+        if (outputData != null && !outputData.isEmpty()) {
+            String outputPath = outputData.get(0).getPath();
+            if (outputPath != null) {
+                paths.add(outputPath);
+            }
+        }
+
+        String workflowPath = String.valueOf(workflowBusiness.getRawApplicationDescriptorPath(currentUser, executionName, version));
+        if (workflowPath != null && !workflowPath.isEmpty()) {
+            paths.add(workflowPath);
+        }
+
+        String provenanceDirPath = server.getWorkflowsPath() + "/" + executionID + "/provenance";
+        File provenanceDir = new File(provenanceDirPath);
+        if (provenanceDir.exists()) {
+            FilenameFilter filter = new FilenameFilter() {
+                @Override
+                public boolean accept(File dir, String name) {
+                    return name.endsWith(".sh.provenance.json");
+                }
+            };
+            File[] matchingFiles = provenanceDir.listFiles(filter);
+            if (matchingFiles != null && matchingFiles.length > 0) {
+                paths.add(matchingFiles[0].getAbsolutePath());
+            }
+        }
+
+        return paths;
+    }
 }
diff --git a/...n/src/main/java/fr/insalyon/creatis/vip/application/server/business/WorkflowBusiness.java b/...n/src/main/java/fr/insalyon/creatis/vip/application/server/business/WorkflowBusiness.java
@@ -452,7 +452,7 @@ public String getRawApplicationDescriptorPath(User user, String applicationName,
 
         try {
             AppVersion version = applicationDAO.getVersion(applicationName, applicationVersion);
-            return dataManagerBusiness.getRemoteFile(user, version.getLfn());
+            return dataManagerBusiness.getRemoteFile(user, version.getJsonLfn());
         } catch (DAOException | BusinessException ex) {
             throw new BusinessException(WRONG_APPLICATION_DESCRIPTOR, ex, applicationName + "/" + applicationVersion);
         }

diff --git a/...ion/src/main/java/fr/insalyon/creatis/vip/application/server/rpc/ReproVipServiceImpl.java b/...ion/src/main/java/fr/insalyon/creatis/vip/application/server/rpc/ReproVipServiceImpl.java
@@ -65,10 +65,10 @@ public void executionOutputData(String executionID) throws CoreException {
             throw new RuntimeException(e);
         }
     }
-    public String downloadJsonOutputData(String executionID) throws CoreException {
+    public String downloadJsonOutputData(String executionName, String executionID, String version) throws CoreException {
         try {
             User currentUser = getSessionUser();
-            String json = reproVipBusiness.createJsonOutputData(executionID, currentUser);
+            String json = reproVipBusiness.createJsonOutputData(executionName, executionID, version, currentUser);
             return json;
         } catch (BusinessException | ApplicationException e) {
             throw new RuntimeException(e);