integrated Tracer through CLIRecordable for test observability

virtualcell · Nov 21, 2024 · 6cec020 · 6cec020
1 parent e775967
commit 6cec020
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Showing 49 changed files with 332 additions and 116 deletions.
diff --git a/vcell-cli/src/main/java/org/vcell/cli/CLIRecordable.java b/vcell-cli/src/main/java/org/vcell/cli/CLIRecordable.java
@@ -5,16 +5,16 @@
 
 public interface CLIRecordable {
 
-    public void writeDetailedErrorList(String message) throws IOException;
+    public void writeDetailedErrorList(Exception e, String message) throws IOException;
 
     public void writeFullSuccessList(String message) throws IOException;
 
-    public void writeErrorList(String message) throws IOException;
+    public void writeErrorList(Exception e, String message) throws IOException;
 
     public void writeDetailedResultList(String message) throws IOException;
 
     // we make a list with the omex files that contain (some) spatial simulations (FVSolverStandalone solver)
     public void writeSpatialList(String message) throws IOException;
 
-    public void writeImportErrorList(String message) throws IOException;
+    public void writeImportErrorList(Exception e, String message) throws IOException;
 }
diff --git a/vcell-cli/src/main/java/org/vcell/cli/CLIRecorder.java b/vcell-cli/src/main/java/org/vcell/cli/CLIRecorder.java
@@ -121,7 +121,8 @@ private void writeToFileLog(TextFileRecord log, String message) throws IOExcepti
      * 
      * @param message string to write to file
      */
-    public void writeDetailedErrorList(String message) throws IOException {
+    @Override
+    public void writeDetailedErrorList(Exception _e, String message) throws IOException {
         this.writeToFileLog(this.detailedErrorLog, message);     
     }
 
@@ -130,6 +131,7 @@ public void writeDetailedErrorList(String message) throws IOException {
      * 
      * @param message string to write to file
      */
+    @Override
     public void writeFullSuccessList(String message) throws IOException {
         this.writeToFileLog(this.fullSuccessLog, message);
     }
@@ -139,7 +141,8 @@ public void writeFullSuccessList(String message) throws IOException {
      * 
      * @param message string to write to file
      */
-    public void writeErrorList(String message) throws IOException {
+    @Override
+    public void writeErrorList(Exception _e, String message) throws IOException {
         this.writeToFileLog(this.errorLog, message);
     }
 
@@ -148,6 +151,7 @@ public void writeErrorList(String message) throws IOException {
      * 
      * @param message string to write to file
      */
+    @Override
     public void writeDetailedResultList(String message) throws IOException {
         this.writeToFileLog(this.detailedResultsLog, message);
     }
@@ -168,7 +172,8 @@ public void writeSpatialList(String message) throws IOException {
      * 
      * @param message string to write to file
      */
-    public void writeImportErrorList(String message) throws IOException {
+    @Override
+    public void writeImportErrorList(Exception _e, String message) throws IOException {
         this.writeToFileLog(this.importErrorLog, message);
     }
 

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java
@@ -92,15 +92,15 @@ public void preprocessArchive() throws PythonStreamException, IOException {
             this.sedmlLocations = this.omexHandler.getSedmlLocationsAbsolute();
         } catch (IOException e){
             String error = e.getMessage() + ", error for OmexHandler with " + this.inputFilePath;
-            this.cliRecorder.writeErrorList(this.bioModelBaseName);
+            this.cliRecorder.writeErrorList(e, this.bioModelBaseName);
             this.cliRecorder.writeDetailedResultList(this.bioModelBaseName + ", " + "IO error with OmexHandler");
             logger.error(error);
             throw new RuntimeException(error, e);
         } catch (Exception e) {
             String error = e.getMessage() + ", error for archive " + this.inputFilePath;
             logger.error(error);
             if (this.omexHandler != null) this.omexHandler.deleteExtractedOmex();
-            this.cliRecorder.writeErrorList(this.bioModelBaseName);
+            this.cliRecorder.writeErrorList(e, this.bioModelBaseName);
             this.cliRecorder.writeDetailedResultList(this.bioModelBaseName + ", " + "unknown error with the archive file");
 
             throw new RuntimeException(error, e);
@@ -183,7 +183,7 @@ public void postProcessessArchive() throws InterruptedException, PythonStreamExc
             PythonCalls.updateOmexStatusYml(Status.FAILED, outputDir, duration + "");
             logger.error(error);
             logOmexMessage.append(error);
-            cliRecorder.writeErrorList(bioModelBaseName);
+            cliRecorder.writeErrorList(new Exception("exception not recorded"), bioModelBaseName);
         } else {
             PythonCalls.updateOmexStatusYml(Status.SUCCEEDED, outputDir, duration + "");
             cliRecorder.writeFullSuccessList(bioModelBaseName);

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/SedmlJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/SedmlJob.java
@@ -173,9 +173,11 @@ public boolean preProcessDoc() throws PythonStreamException, InterruptedExceptio
             this.plotFile = new File(this.PLOTS_DIRECTORY, "simulation_" + this.sedmlName);
             Path path = Paths.get(this.plotFile.getAbsolutePath());
             if (!Files.exists(path)) {
-                String message = "Failed to create file " + this.plotFile.getAbsolutePath();
+                String message = "Failed to create plot file " + this.plotFile.getAbsolutePath();
                 this.CLI_RECORDER.writeDetailedResultList(this.BIOMODEL_BASE_NAME + "," + this.sedmlName + "," + message);
-                throw new RuntimeException(message);
+                RuntimeException exception = new RuntimeException(message);
+                Tracer.failure(exception, this.BIOMODEL_BASE_NAME + "," + this.sedmlName + "," + message);
+                throw exception;
             }
 
             // Converting pseudo SED-ML to biomodel
@@ -462,7 +464,7 @@ private void reportProblem(Exception e) throws PythonStreamException, Interrupte
         String type = e.getClass().getSimpleName();
         PythonCalls.setOutputMessage(this.SEDML_LOCATION, this.sedmlName, this.RESULTS_DIRECTORY_PATH, "sedml", this.logDocumentMessage);
         PythonCalls.setExceptionMessage(this.SEDML_LOCATION, this.sedmlName, this.RESULTS_DIRECTORY_PATH, "sedml", type, this.logDocumentError);
-        this.CLI_RECORDER.writeDetailedErrorList(this.BIOMODEL_BASE_NAME + ",  doc:    " + type + ": " + this.logDocumentError);
+        this.CLI_RECORDER.writeDetailedErrorList(e, this.BIOMODEL_BASE_NAME + ",  doc:    " + type + ": " + this.logDocumentError);
         PythonCalls.updateSedmlDocStatusYml(this.SEDML_LOCATION, Status.FAILED, this.RESULTS_DIRECTORY_PATH);
     }
 

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java
@@ -545,11 +545,11 @@ public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, CLIRe
 							if (!bTimeoutFound) {        // don't repeat this for each task
 								String str = logTaskError.substring(0, logTaskError.indexOf("Process timed out"));
 								str += "Process timed out";        // truncate the rest of the spam
-								cliLogger.writeDetailedErrorList(bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + str);
+								cliLogger.writeDetailedErrorList(e, bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + str);
 								bTimeoutFound = true;
 							}
 						} else {
-							cliLogger.writeDetailedErrorList(bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + logTaskError);
+							cliLogger.writeDetailedErrorList(e,bioModelBaseName + ",  solver: " + sdl + ": " + type + ": " + logTaskError);
 						}
 						RunUtils.drawBreakLine("-", 100);
 					} finally {