Added backend API endpoint when there is no Job ID (Tool Form Page): …

…passes newly included Error-Transcript JSON and User object to the email report methods

client/src/components/Common/UserReportingError.vue

@@ -79,6 +79,7 @@ import { useMarkdown } from "@/composables/markdown";
 import { useUserStore } from "@/stores/userStore";
 
 import { sendErrorReport } from "../DatasetInformation/services";
+import { sendErrorReportTool } from "../ToolInformation/services";
 
 export default {
     components: {
@@ -141,14 +142,25 @@ export default {
         submit(dataset, userEmailJob) {
             const email = userEmailJob || this.currentUserEmail;
             const message = this.message;
-            sendErrorReport(dataset, message, email, this.transcript).then(
-                (resultMessages) => {
-                    this.resultMessages = resultMessages;
-                },
-                (errorMessage) => {
-                    this.errorMessage = errorMessage;
-                }
-            );
+            if (this.transcript) {
+                sendErrorReportTool(dataset, message, email, this.transcript).then(
+                    (resultMessages) => {
+                        this.resultMessages = resultMessages;
+                    },
+                    (errorMessage) => {
+                        this.errorMessage = errorMessage;
+                    }
+                );
+            } else {
+                sendErrorReport(dataset, message, email, this.transcript).then(
+                    (resultMessages) => {
+                        this.resultMessages = resultMessages;
+                    },
+                    (errorMessage) => {
+                        this.errorMessage = errorMessage;
+                    }
+                );
+            }
         },
         hasDetails(outputs) {
             return (

client/src/components/ToolInformation/services.js

@@ -0,0 +1,19 @@
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import { rethrowSimple } from "utils/simple-error";
+
+export async function sendErrorReportTool(dataset, message, email, transcript) {
+    const payload = {
+        dataset_id: dataset.id,
+        message,
+        email,
+        transcript,
+    };
+    const url = `${getAppRoot()}api/user-reporting/error`;
+    try {
+        const { data } = await axios.post(url, payload);
+        return data.messages;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

lib/galaxy/schema/schema.py

@@ -3657,3 +3657,34 @@ class DatasetSummary(Model):
     file_size: int
     total_size: int
     uuid: UuidField
+
+
+class UserReportingErrorPayload(Model):
+    dataset_id: DecodedDatabaseIdField = Field(
+        default=...,
+        title="History Dataset Association ID",
+        description="The History Dataset Association ID related to the error.",
+    )
+    message: Optional[str] = Field(
+        default=None,
+        title="Message",
+        description="The optional message sent with the error report.",
+    )
+    email: Optional[str] = Field(
+        default=None,
+        title="Email",
+        description="Email address for communication with the user. Only required for anonymous users.",
+    )
+    transcript: Optional[str] = Field(
+        default=None,
+        title="Transcript",
+        description="The optional tool transcript sent with the error report.",
+    )
+
+
+class UserReportingErrorSummary(Model):
+    messages: List[List[str]] = Field(
+        default=...,
+        title="Error messages",
+        description="The error messages for the specified job.",
+    )

lib/galaxy/tools/error_reports/__init__.py

@@ -57,7 +57,8 @@ def _can_access_dataset(self, dataset, user):
             roles = []
         return self.app.security_agent.can_access_dataset(roles, dataset.dataset)
 
-    def submit_report(self, dataset, job, tool, user=None, user_submission=False, **kwargs):
+    def submit_report(self, dataset, job, tool, user_submission=False, **kwargs):
+        user = kwargs.get("user")
         if user_submission:
             assert self._can_access_dataset(dataset, user), Exception("You are not allowed to access this dataset.")
 

lib/galaxy/tools/error_reports/plugins/email.py

@@ -25,12 +25,25 @@ def __init__(self, **kwargs):
 
     def submit_report(self, dataset, job, tool, **kwargs):
         """Send report as an email"""
+        data_uid = None
         try:
-            error_reporter = EmailErrorReporter(dataset.id, self.app)
+            report_type = kwargs.get("report_type")
+            transcript = kwargs.get("transcript")
+            if report_type == "dataset":
+                data_uid = dataset.id
+                user = job.get_user()
+            elif report_type == "tool":
+                data_uid = dataset
+                user = kwargs.get("user")
+
+            error_reporter = EmailErrorReporter(data_uid, self.app, report_type)
             error_reporter.send_report(
-                user=job.get_user(),
+                user=user,
                 email=kwargs.get("email", None),
                 message=kwargs.get("message", None),
+                report_type=report_type,
+                tool=tool,
+                transcript=transcript,
                 redact_user_details_in_bugreport=self.redact_user_details_in_bugreport,
             )
             return ("Your error report has been sent", "success")

lib/galaxy/tools/errors.py

@@ -57,6 +57,9 @@
 job traceback:
 ${job_traceback}
 -----------------------------------------------------------------------------
+tool transcript:
+${tool_transcript}
+-----------------------------------------------------------------------------
 (This is an automated message).
 """
 
@@ -125,28 +128,37 @@
 ${job_traceback}
 </pre>
 
+<h4>Tool Transcript</h4>
+<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
+${tool_transcript}
+</pre>
+
 This is an automated message. Do not reply to this address.
 </body></html>
 """
 
 
 class ErrorReporter:
-    def __init__(self, hda, app):
-        # Get the dataset
-        sa_session = app.model.context
-        if not isinstance(hda, model.HistoryDatasetAssociation):
-            hda_id = hda
-            try:
-                hda = sa_session.get(model.HistoryDatasetAssociation, hda_id)
-                assert hda is not None, ValueError("No HDA yet")
-            except Exception:
-                hda = sa_session.get(model.HistoryDatasetAssociation, app.security.decode_id(hda_id))
-        assert isinstance(hda, model.HistoryDatasetAssociation), ValueError(f"Bad value provided for HDA ({hda}).")
-        self.hda = hda
-        # Get the associated job
-        self.job = hda.creating_job
+    def __init__(self, hda, app, report_type="dataset"):
+        if report_type == "dataset":
+            # Get the dataset
+            sa_session = app.model.context
+            if not isinstance(hda, model.HistoryDatasetAssociation):
+                hda_id = hda
+                try:
+                    hda = sa_session.get(model.HistoryDatasetAssociation, hda_id)
+                    assert hda is not None, ValueError("No HDA yet")
+                except Exception:
+                    hda = sa_session.get(model.HistoryDatasetAssociation, app.security.decode_id(hda_id))
+            assert isinstance(hda, model.HistoryDatasetAssociation), ValueError(f"Bad value provided for HDA ({hda}).")
+            self.hda = hda
+            # Get the associated job
+            self.job = hda.creating_job
+            self.tool_id = self.job.tool_id
+        elif report_type == "tool":
+            self.hda = None
+            self.tool_id = hda
         self.app = app
-        self.tool_id = self.job.tool_id
         self.report = None
 
     def _can_access_dataset(self, user):
@@ -157,15 +169,65 @@ def _can_access_dataset(self, user):
         return self.app.security_agent.can_access_dataset(roles, self.hda.dataset)
 
     def create_report(self, user, email="", message="", redact_user_details_in_bugreport=False, **kwd):
-        hda = self.hda
-        job = self.job
-        host = self.app.url_for("/", qualified=True)
-        history_id_encoded = self.app.security.encode_id(hda.history_id)
-        history_view_link = self.app.url_for("/histories/view", id=history_id_encoded, qualified=True)
-        hda_id_encoded = self.app.security.encode_id(hda.id)
-        hda_show_params_link = self.app.url_for(
-            controller="dataset", action="details", dataset_id=hda_id_encoded, qualified=True
-        )
+        report_type = kwd.get("report_type")
+        tool = kwd.get("tool")
+        hda = ""
+        job = ""
+        history_id_encoded = ""
+        history_view_link = ""
+        hda_id_encoded = ""
+        hda_show_params_link = ""
+        dataset_id_encoded=""
+        dataset_id=""
+        history_id=""
+        hid=""
+        history_item_name=""
+        history_id_encoded = ""
+        history_view_link = ""
+        hda_id_encoded = ""
+        hda_show_params_link = ""
+        job_id_encoded = ""
+        job_id=""
+        tool_version=""
+        job_tool_id=""
+        job_tool_version=""
+        tool_transcript=""
+        job_runner_external_id=""
+        job_command_line=""
+        job_stderr=""
+        job_stdout=""
+        job_info=""
+        job_traceback=""
+
+        if report_type == "dataset":
+            hda = self.hda
+            job = self.job
+            dataset_id_encoded=self.app.security.encode_id(hda.dataset_id)
+            dataset_id=hda.dataset_id
+            history_id=hda.history_id
+            hid=hda.hid
+            history_item_name=hda.get_display_name()
+            history_id_encoded = self.app.security.encode_id(hda.history_id)
+            history_view_link = self.app.url_for("/histories/view", id=history_id_encoded, qualified=True)
+            hda_id_encoded = self.app.security.encode_id(hda.id)
+            hda_show_params_link = self.app.url_for(
+                controller="dataset", action="details", dataset_id=hda_id_encoded, qualified=True
+            )
+            job_id_encoded=self.app.security.encode_id(job.id)
+            job_id=job.id
+            tool_version=job.tool_version
+            job_tool_id=job.tool_id
+            job_tool_version=hda.tool_version
+            job_runner_external_id=job.job_runner_external_id
+            job_command_line=job.command_line
+            job_stderr=util.unicodify(job.stderr)
+            job_stdout=util.unicodify(job.stdout)
+            job_info=util.unicodify(job.info)
+            job_traceback=util.unicodify(job.traceback)
+        elif report_type == "tool":
+            job_tool_id=tool.id
+            job_tool_version=tool.version
+            tool_transcript = kwd.get("transcript")
         # Build the email message
         if redact_user_details_in_bugreport:
             # This is sub-optimal but it is hard to solve fully. This affects
@@ -193,27 +255,28 @@ def create_report(self, user, email="", message="", redact_user_details_in_bugre
                 email_str = "'%s'" % (email or "anonymous")
 
         report_variables = dict(
-            host=host,
-            dataset_id_encoded=self.app.security.encode_id(hda.dataset_id),
-            dataset_id=hda.dataset_id,
+            host=self.app.url_for("/", qualified=True),
+            dataset_id_encoded=dataset_id_encoded,
+            dataset_id=dataset_id,
             history_id_encoded=history_id_encoded,
-            history_id=hda.history_id,
+            history_id=history_id,
             hda_id_encoded=hda_id_encoded,
-            hid=hda.hid,
-            history_item_name=hda.get_display_name(),
+            hid=hid,
+            history_item_name=history_item_name,
             history_view_link=history_view_link,
             hda_show_params_link=hda_show_params_link,
-            job_id_encoded=self.app.security.encode_id(job.id),
-            job_id=job.id,
-            tool_version=job.tool_version,
-            job_tool_id=job.tool_id,
-            job_tool_version=hda.tool_version,
-            job_runner_external_id=job.job_runner_external_id,
-            job_command_line=job.command_line,
-            job_stderr=util.unicodify(job.stderr),
-            job_stdout=util.unicodify(job.stdout),
-            job_info=util.unicodify(job.info),
-            job_traceback=util.unicodify(job.traceback),
+            job_id_encoded=job_id_encoded,
+            job_id=job_id,
+            tool_version=tool_version,
+            job_tool_id=job_tool_id,
+            job_tool_version=job_tool_version,
+            tool_transcript=tool_transcript,
+            job_runner_external_id=job_runner_external_id,
+            job_command_line=job_command_line,
+            job_stderr=job_stderr,
+            job_stdout=job_stdout,
+            job_info=job_info,
+            job_traceback=job_traceback,
             email_str=email_str,
             message=util.unicodify(message),
         )
@@ -235,9 +298,16 @@ def send_report(self, user, email=None, message=None, **kwd):
             self.create_report(user, email=email, message=message, **kwd)
         return self._send_report(user, email=email, message=message, **kwd)
 
+    def email_report(self, user, email=None, message=None, **kwd):
+        if self.report is None:
+            self.create_report(user, email=email, message=message, **kwd)
+        return self._send_report(user, email=email, message=message, **kwd)
+
 
 class EmailErrorReporter(ErrorReporter):
     def _send_report(self, user, email=None, message=None, **kwd):
+        report_type = kwd.get("report_type")
+        tool = kwd.get("tool")
         smtp_server = self.app.config.smtp_server
         assert smtp_server, ValueError("Mail is not configured for this Galaxy instance")
         to = self.app.config.error_email_to
@@ -248,9 +318,12 @@ def _send_report(self, user, email=None, message=None, **kwd):
             to += f", {email.strip()}"
         subject = f"Galaxy tool error report from {email}"
         try:
-            subject = "{} ({})".format(
-                subject, self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id
-            )
+            if report_type == "dataset":
+                subject = "{} ({})".format(
+                    subject, self.app.toolbox.get_tool(self.job.tool_id, self.job.tool_version).old_id
+                )
+            elif report_type == "tool":
+                subject = "{} ({})".format(subject, tool.old_id)
         except Exception:
             pass
 

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -328,6 +328,7 @@ def error(
             job=job,
             tool=tool,
             user_submission=True,
+            report_type="dataset",
             user=trans.user,
             email=email,
             message=payload.message,