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[WIP] Fix for Dataset Email Reports #18057

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[WIP] Fix for Dataset Email Reports #18057

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d2c0190
Added front-end email template files (removed back-end email templati…
hujambo-dunia Apr 25, 2024
5d77c98
Fix for clarification of output stream sources
hujambo-dunia Apr 29, 2024
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109 changes: 109 additions & 0 deletions lib/galaxy/tools/email_templates/errors_dataset.html
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Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
<html>
<body>
<h1>Galaxy Tool Error Report</h1>
<span class="sub">
<i>from</i>
<span style="font-family: monospace;">
<a href="${host}">${host}</a>
</span>
</span>

<h3>Error Localization</h3>
<table style="margin:1em">
<tbody>
<tr>
<td>Dataset</td>
<td>
<a href="${hda_show_params_link}">${dataset_id} (${dataset_id_encoded})</a>
</td>
</tr>
<tr style="background-color: #f2f2f2">
<td>History</td>
<td>
<a href="${history_view_link}">${history_id} (${history_id_encoded})</a>
</td>
</tr>
<tr>
<td>Failed Job</td>
<td>${hid}: ${history_item_name} (${hda_id_encoded})</td>
</tr>
</tbody>
</table>

<h3>User Provided Information</h3>
The user
<span style="font-family: monospace;">${email_str}</span>
provided the following information:
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${message}
</pre>

<h3>Detailed Job Information</h3>
Job environment and execution information is available at the job
<a href="${hda_show_params_link}">info page</a>.

<table style="margin:1em">
<tbody>
<tr>
<td>Job ID</td>
<td>${job_id} (${job_id_encoded})</td>
</tr>
<tr style="background-color: #f2f2f2">
<td>Tool ID</td>
<td>${job_tool_id}</td>
</tr>
<tr>
<td>Tool Version</td>
<td>${tool_version}</td>
</tr>
<tr style="background-color: #f2f2f2">
<td>Job PID or DRM id</td>
<td>${job_runner_external_id}</td>
</tr>
<tr>
<td>Job Tool Version</td>
<td>${job_tool_version}</td>
</tr>
</tbody>
</table>

<h3>Job Execution and Failure Information</h3>
<h4>Command Line</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_command_line}
</pre>

<h4>Job stderr</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_stderr}
</pre>

<h4>Job stdout</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_stdout}
</pre>

<h4>Job Information</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_info}
</pre>

<h4>Job Traceback</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_traceback}
</pre>

<h3>Tool Execution and Failure Information</h3>
<h4>Tool stderr</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${tool_stderr}
</pre>

<h4>Tool stdout</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${tool_stdout}
</pre>

This is an automated message. Do not reply to this address.
</body>
</html>
50 changes: 50 additions & 0 deletions lib/galaxy/tools/email_templates/errors_dataset.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
GALAXY TOOL ERROR REPORT
------------------------

This error report was sent from the Galaxy instance hosted on the server
"${host}"
-----------------------------------------------------------------------------
This is in reference to dataset id ${dataset_id} (${dataset_id_encoded}) from history id ${history_id} (${history_id_encoded})
-----------------------------------------------------------------------------
You should be able to view the history containing the related history item (${hda_id_encoded})

${hid}: ${history_item_name}

by logging in as a Galaxy admin user to the Galaxy instance referenced above
and pointing your browser to the following link.

${history_view_link}
-----------------------------------------------------------------------------
The user ${email_str} provided the following information:

${message}
-----------------------------------------------------------------------------
info url: ${hda_show_params_link}
job id: ${job_id} (${job_id_encoded})
tool id: ${job_tool_id}
tool version: ${tool_version}
job pid or drm id: ${job_runner_external_id}
job tool version: ${job_tool_version}
-----------------------------------------------------------------------------
job command line:
${job_command_line}
-----------------------------------------------------------------------------
job stderr:
${job_stderr}
-----------------------------------------------------------------------------
job stdout:
${job_stdout}
-----------------------------------------------------------------------------
job info:
${job_info}
-----------------------------------------------------------------------------
job traceback:
${job_traceback}
-----------------------------------------------------------------------------
tool stderr:
${tool_stderr}
-----------------------------------------------------------------------------
tool stdout:
${tool_stdout}
-----------------------------------------------------------------------------
(This is an automated message).
138 changes: 18 additions & 120 deletions lib/galaxy/tools/errors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,10 @@
Functionality for dealing with tool errors.
"""

import os
import string

import jinja2
import markupsafe

from galaxy import (
Expand All @@ -13,122 +15,6 @@
from galaxy.security.validate_user_input import validate_email_str
from galaxy.util import unicodify

error_report_template = """
GALAXY TOOL ERROR REPORT
------------------------

This error report was sent from the Galaxy instance hosted on the server
"${host}"
-----------------------------------------------------------------------------
This is in reference to dataset id ${dataset_id} (${dataset_id_encoded}) from history id ${history_id} (${history_id_encoded})
-----------------------------------------------------------------------------
You should be able to view the history containing the related history item (${hda_id_encoded})

${hid}: ${history_item_name}

by logging in as a Galaxy admin user to the Galaxy instance referenced above
and pointing your browser to the following link.

${history_view_link}
-----------------------------------------------------------------------------
The user ${email_str} provided the following information:

${message}
-----------------------------------------------------------------------------
info url: ${hda_show_params_link}
job id: ${job_id} (${job_id_encoded})
tool id: ${job_tool_id}
tool version: ${tool_version}
job pid or drm id: ${job_runner_external_id}
job tool version: ${job_tool_version}
-----------------------------------------------------------------------------
job command line:
${job_command_line}
-----------------------------------------------------------------------------
job stderr:
${job_stderr}
-----------------------------------------------------------------------------
job stdout:
${job_stdout}
-----------------------------------------------------------------------------
job info:
${job_info}
-----------------------------------------------------------------------------
job traceback:
${job_traceback}
-----------------------------------------------------------------------------
(This is an automated message).
"""

error_report_template_html = """
<html>
<body>
<h1>Galaxy Tool Error Report</h1>
<span class="sub"><i>from</i> <span style="font-family: monospace;"><a href="${host}">${host}</a></span>

<h3>Error Localization</h3>
<table style="margin:1em">
<tbody>
<tr><td>Dataset</td><td><a href="${hda_show_params_link}">${dataset_id} (${dataset_id_encoded})</a></td></tr>
<tr style="background-color: #f2f2f2"><td>History</td><td><a href="${history_view_link}">${history_id} (${history_id_encoded})</a></td></tr>
<tr><td>Failed Job</td><td>${hid}: ${history_item_name} (${hda_id_encoded})</td></tr>
</tbody>
</table>

<h3>User Provided Information</h3>

The user <span style="font-family: monospace;">${email_str}</span> provided the following information:

<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${message}
</pre>


<h3>Detailed Job Information</h3>

Job environment and execution information is available at the job <a href="${hda_show_params_link}">info page</a>.

<table style="margin:1em">
<tbody>
<tr><td>Job ID</td><td>${job_id} (${job_id_encoded})</td></tr>
<tr style="background-color: #f2f2f2"><td>Tool ID</td><td>${job_tool_id}</td></tr>
<tr><td>Tool Version</td><td>${tool_version}</td></tr>
<tr style="background-color: #f2f2f2"><td>Job PID or DRM id</td><td>${job_runner_external_id}</td></tr>
<tr><td>Job Tool Version</td><td>${job_tool_version}</td></tr>
</tbody>
</table>

<h3>Job Execution and Failure Information</h3>

<h4>Command Line</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_command_line}
</pre>

<h4>stderr</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_stderr}
</pre>

<h4>stdout</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_stdout}
</pre>

<h4>Job Information</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_info}
</pre>

<h4>Job Traceback</h4>
<pre style="white-space: pre-wrap;background: #eeeeee;border:1px solid black;padding:1em;">
${job_traceback}
</pre>

This is an automated message. Do not reply to this address.
</body></html>
"""


class ErrorReporter:
def __init__(self, hda, app):
Expand Down Expand Up @@ -210,22 +96,28 @@ def create_report(self, user, email="", message="", redact_user_details_in_bugre
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_stderr=util.unicodify(job.job_stderr),
job_stdout=util.unicodify(job.job_stdout),
job_info=util.unicodify(job.info),
job_traceback=util.unicodify(job.traceback),
tool_stderr=util.unicodify(job.tool_stderr),
tool_stdout=util.unicodify(job.tool_stdout),
email_str=email_str,
message=util.unicodify(message),
)

self.report = string.Template(error_report_template).safe_substitute(report_variables)
self.report = string.Template(self.get_report_template("errors_dataset", "txt")).safe_substitute(
report_variables
)

# Escape all of the content for use in the HTML report
for parameter in report_variables.keys():
if report_variables[parameter] is not None:
report_variables[parameter] = markupsafe.escape(unicodify(report_variables[parameter]))

self.html_report = string.Template(error_report_template_html).safe_substitute(report_variables)
self.html_report = string.Template(self.get_report_template("errors_dataset", "html")).safe_substitute(
report_variables
)

def _send_report(self, user, email=None, message=None, **kwd):
return self.report
Expand All @@ -235,6 +127,12 @@ 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 get_report_template(self, report_type, report_format):
path = os.path.abspath(os.path.join(os.path.dirname(__file__), "email_templates"))
env = jinja2.Environment(loader=jinja2.FileSystemLoader(path))
template = env.get_template(report_type + "." + report_format)
return template.render()


class EmailErrorReporter(ErrorReporter):
def _send_report(self, user, email=None, message=None, **kwd):
Expand Down
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