Improve Excel2SBOL conversion error reporting

backend/sbs_server/app/views.py

@@ -13,6 +13,89 @@
 import sbol2 as sb2
 import pudu
 import subprocess
+import contextlib
+import io
+import traceback
+
+
+
+def classify_excel2sbol_error(exc):
+    if isinstance(exc, FileNotFoundError):
+        return {
+            "code": "E_INPUT_FILE",
+            "message": "The uploaded Excel file could not be read.",
+            "hint": "Check that the file was uploaded correctly.",
+            "status": 400,
+        }
+
+    if isinstance(exc, KeyError):
+        return {
+            "code": "E_WORKBOOK_STRUCTURE",
+            "message": "The Excel file is missing a required sheet, column, or SBOL mapping.",
+            "hint": "Check the Init sheet and column_definitions sheet.",
+            "status": 400,
+        }
+
+    if isinstance(exc, ValueError):
+        return {
+            "code": "E_WORKBOOK_VALUE",
+            "message": "A value in the Excel file could not be converted to SBOL.",
+            "hint": "Check the reported sheet, column, row, or pattern requirement.",
+            "status": 400,
+        }
+
+    return {
+        "code": "E_CONVERSION_FAILED",
+        "message": "Excel2SBOL failed during conversion.",
+        "hint": "Open More details and send the technical report to the developers.",
+        "status": 500,
+    }
+
+
+def redact_sensitive_values(text):
+    if text is None:
+        return ""
+
+    sensitive_values = [
+        os.getenv("SBOL_USERNAME"),
+        os.getenv("SBOL_PASSWORD"),
+        os.getenv("SBOL_URL"),
+        os.getenv("SYNBIOHUB_USERNAME"),
+        os.getenv("SYNBIOHUB_PASSWORD"),
+        os.getenv("SYNBIOHUB_URL"),
+    ]
+
+    for value in sensitive_values:
+        if value:
+            text = text.replace(value, "[REDACTED]")
+
+    return text
+
+
+def excel2sbol_error_response(exc, stdout_buffer, stderr_buffer):
+    app.logger.exception("Excel2SBOL conversion failed")
+    classified = classify_excel2sbol_error(exc)
+    terminal_output = "\n".join([
+        "STDOUT:",
+        stdout_buffer.getvalue(),
+        "",
+        "STDERR:",
+        stderr_buffer.getvalue(),
+    ])
+
+    return jsonify({
+        "status": "error",
+        "error": {
+            "code": classified["code"],
+            "message": classified["message"],
+            "hint": classified["hint"],
+            "details": redact_sensitive_values(str(exc)),
+            "technical_details": {
+                "terminal_output": redact_sensitive_values(terminal_output),
+                "traceback": redact_sensitive_values(traceback.format_exc()),
+            },
+        },
+    }), classified["status"]
 
 #routes
 #check if the app is running
@@ -129,26 +212,26 @@
             os.remove(data_filename)
 
     # instantiate the XDC class using the params_from_request dictionary
+    stdout_buffer = io.StringIO()
+    stderr_buffer = io.StringIO()
     try:
-        xdc = tricahue.XDC(input_excel_path = metadata_path, attachments=attachments)
-        # print(params_from_request['sbh_url'], params_from_request['collection_url'], params_from_request['sbh_overwrite'], params_from_request['sbh_user'],params_from_request['sbh_pass'], params_from_request['sbh_pass'],params_from_request['fj_url'], params_from_request['fj_overwrite'], params_from_request['fj_user'], params_from_request['fj_pass'],params_from_request['fj_token'])
-        sbh_url, fj_url = xdc.upload_to_existing_collection(sbh_url = params_from_request['sbh_url'],
-                                      collection_url = params_from_request['collection_url'], 
-                                      sbh_overwrite = params_from_request['sbh_overwrite'], 
-                                      sbh_user = params_from_request['sbh_user'],
-                                      sbh_pass = params_from_request['sbh_pass'], 
-                                      sbh_token = params_from_request['sbh_token'],
-                                      fj_url = fj_url,
-                                      fj_overwrite = fj_overwrite, 
-                                      fj_user = fj_user, 
-                                      fj_pass = fj_pass,
-                                      fj_token = fj_token)
-    except AttributeError as e:
-        os.remove(metadata_path)
-        return jsonify({"error": str(e)}), 400
+        with contextlib.redirect_stdout(stdout_buffer), contextlib.redirect_stderr(stderr_buffer):
+            xdc = tricahue.XDC(input_excel_path = metadata_path, attachments=attachments)
+            # print(params_from_request['sbh_url'], params_from_request['collection_url'], params_from_request['sbh_overwrite'], params_from_request['sbh_user'],params_from_request['sbh_pass'], params_from_request['sbh_pass'],params_from_request['fj_url'], params_from_request['fj_overwrite'], params_from_request['fj_user'], params_from_request['fj_pass'],params_from_request['fj_token'])
+            sbh_url, fj_url = xdc.upload_to_existing_collection(sbh_url = params_from_request['sbh_url'],
+                                          collection_url = params_from_request['collection_url'], 
+                                          sbh_overwrite = params_from_request['sbh_overwrite'], 
+                                          sbh_user = params_from_request['sbh_user'],
+                                          sbh_pass = params_from_request['sbh_pass'], 
+                                          sbh_token = params_from_request['sbh_token'],
+                                          fj_url = fj_url,
+                                          fj_overwrite = fj_overwrite, 
+                                          fj_user = fj_user, 
+                                          fj_pass = fj_pass,
+                                          fj_token = fj_token)
     except Exception as e:
         os.remove(metadata_path)
-        return jsonify({"error": str(e)}), 500
+        return excel2sbol_error_response(e, stdout_buffer, stderr_buffer)
 
     sbs_upload_response_dict ={
         "sbh_url": sbh_url,

backend/tests/test_excel2sbol_errors.py

@@ -0,0 +1,84 @@
+import json
+import sys
+import types
+from io import BytesIO
+from pathlib import Path
+
+
+ROOT = Path(__file__).resolve().parents[1] / "sbs_server"
+if str(ROOT) not in sys.path:
+    sys.path.insert(0, str(ROOT))
+
+
+class _FakePartShop:
+    pass
+
+
+def _install_optional_dependency_stubs():
+    sys.modules.setdefault("tricahue", types.SimpleNamespace())
+    sys.modules.setdefault("pudu", types.SimpleNamespace())
+    sys.modules.setdefault("sbol2", types.SimpleNamespace(Document=object, PartShop=_FakePartShop))
+
+    if "flask_swagger_ui" not in sys.modules:
+        def get_swaggerui_blueprint(*args, **kwargs):
+            from flask import Blueprint
+            return Blueprint("swagger_ui_stub", __name__)
+
+        sys.modules["flask_swagger_ui"] = types.SimpleNamespace(
+            get_swaggerui_blueprint=get_swaggerui_blueprint,
+        )
+
+
+_install_optional_dependency_stubs()
+from app.main import app  # noqa: E402
+from app import views  # noqa: E402
+
+
+def test_excel2sbol_value_error_returns_friendly_error_with_technical_details(monkeypatch, tmp_path):
+    monkeypatch.chdir(tmp_path)
+    monkeypatch.setenv("SYNBIOHUB_PASSWORD", "super-secret")
+
+    class FailingXDC:
+        def __init__(self, *args, **kwargs):
+            print("started conversion with super-secret")
+            raise ValueError("bad value contains super-secret")
+
+    monkeypatch.setattr(views.tricahue, "XDC", FailingXDC, raising=False)
+
+    params = {
+        "sbh_url": "https://synbiohub.example",
+        "sbh_token": "token",
+        "sbh_user": None,
+        "sbh_pass": None,
+        "fj_url": None,
+        "fj_token": None,
+        "fj_user": None,
+        "fj_pass": None,
+        "collection_url": "https://synbiohub.example/user/collection/1",
+        "sbh_overwrite": 0,
+        "fj_overwrite": 1,
+        "attachments": {},
+    }
+
+    response = app.test_client().post(
+        "/api/uploadResource",
+        data={
+            "Metadata": (BytesIO(b"excel bytes"), "metadata.xlsx"),
+            "Params": (BytesIO(json.dumps(params).encode("utf-8")), "params.json"),
+        },
+        content_type="multipart/form-data",
+    )
+
+    assert response.status_code == 400
+    payload = response.get_json()
+    assert payload["status"] == "error"
+    assert payload["error"]["code"] == "E_WORKBOOK_VALUE"
+    assert payload["error"]["message"] == "A value in the Excel file could not be converted to SBOL."
+    assert payload["error"]["hint"] == "Check the reported sheet, column, row, or pattern requirement."
+    assert payload["error"]["details"] == "bad value contains [REDACTED]"
+    assert "started conversion with [REDACTED]" in payload["error"]["technical_details"]["terminal_output"]
+    assert "Traceback" in payload["error"]["technical_details"]["traceback"]
+    assert "ValueError" in payload["error"]["technical_details"]["traceback"]
+    assert "super-secret" not in payload["error"]["details"]
+    assert "super-secret" not in payload["error"]["technical_details"]["terminal_output"]
+    assert "super-secret" not in payload["error"]["technical_details"]["traceback"]

frontend/src/components/activities/explorer/ImportFile.jsx

@@ -9,7 +9,7 @@ import { writeToFileHandle } from "../../../redux/hooks/workingDirectoryHooks";
 import { useOpenPanel } from "../../../redux/hooks/panelsHooks";
 import { workingDirectorySlice } from "../../../redux/store";
 import { useLocalStorage } from "@mantine/hooks";
-import { showErrorNotification } from "../../../modules/util";
+import { showErrorNotification, showUploadErrorNotification } from "../../../modules/util";
 import { upload_resource } from "../../../API";
 import { useUnifiedModal } from "../../../redux/hooks/useUnifiedModal";
 import { loadOverlay, closeOverlay } from "../../../redux/slices/loadingOverlay";
@@ -206,6 +206,9 @@ export default function ImportFile({ onSelect, text, useSubdirectory = false })
             onSelect?.(fileMetadata)
         } catch (err) {
             console.warn("File selection canceled or failed", err)
+            if (err?.response) {
+                showUploadErrorNotification("Upload failed", err, "Unable to upload the collection metadata.")
+            }
         }
     }
 

frontend/src/components/panels/xdc/CollectionWizard.jsx

@@ -6,7 +6,7 @@ import { useLocalStorage } from '@mantine/hooks'
 import { PanelContext } from './CollectionPanel'
 import { ObjectTypes } from '../../../objectTypes'
 import { uploadExperiment } from '../../../API'
-import { showErrorNotification } from '../../../modules/util'
+import { showErrorNotification, showUploadErrorNotification } from '../../../modules/util'
 import Dropzone from '../../Dropzone'
 
 export default function CollectionWizard() {
@@ -73,7 +73,7 @@ export default function CollectionWizard() {
 
             setUploads((currentUploads) => [...(currentUploads || []), uploadEntry])
         } catch (error) {
-            showErrorNotification('Upload failed', error?.response?.data?.error || error.message || 'Unable to upload the collection metadata.')
+            showUploadErrorNotification('Upload failed', error, 'Unable to upload the collection metadata.')
         } finally {
             setIsSubmitting(false)
         }

frontend/src/modules/util.js

@@ -1,3 +1,4 @@
+import React, { useState } from "react"
 import { showNotification } from "@mantine/notifications"
 
 export function titleFromRunFileName(fileName) {
@@ -16,11 +17,87 @@ export function betterMax(arr) {
         return arr.reduce((accum, current) => current > accum ? current : accum, arr[0])
 }
 
+function ConversionError({ error }) {
+    const [showDetails, setShowDetails] = useState(false)
+
+    if (!error) {
+        return null
+    }
+
+    const technicalDetails = [
+        `Error code: ${error.code || ""}`,
+        "",
+        "Details:",
+        error.details || "",
+        "",
+        "Terminal output:",
+        error.technical_details?.terminal_output || "",
+        "",
+        "Python traceback:",
+        error.technical_details?.traceback || "",
+    ].join("\n")
+
+    return React.createElement(
+        "div",
+        null,
+        React.createElement("strong", null, error.message || "Conversion failed"),
+        error.hint ? React.createElement("p", null, error.hint) : null,
+        React.createElement(
+            "button",
+            {
+                type: "button",
+                onClick: () => setShowDetails(!showDetails),
+                style: {
+                    background: "transparent",
+                    border: "none",
+                    color: "inherit",
+                    cursor: "pointer",
+                    padding: 0,
+                    textDecoration: "underline",
+                },
+            },
+            showDetails ? "Hide details" : "More"
+        ),
+        showDetails ? React.createElement(
+            "pre",
+            {
+                style: {
+                    marginTop: 8,
+                    maxHeight: 240,
+                    overflow: "auto",
+                    whiteSpace: "pre-wrap",
+                },
+            },
+            technicalDetails
+        ) : null
+    )
+}
+
 export function showErrorNotification(title, message) {
     showNotification({
         title,
         color: "red",
         message,
         autoClose: false,
     });
-}
+}
+
+export function showConversionErrorNotification(title, error) {
+    showNotification({
+        title,
+        color: "red",
+        message: React.createElement(ConversionError, { error }),
+        autoClose: false,
+    });
+}
+
+export function showUploadErrorNotification(title, error, fallbackMessage) {
+    const responseError = error?.response?.data?.error
+
+    if (responseError && typeof responseError === "object") {
+        showConversionErrorNotification(title, responseError)
+        return
+    }
+
+    showErrorNotification(title, responseError || error.message || fallbackMessage)
+}