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Source code for galaxy.tools.errors

"""
Functionality for dealing with tool errors.
"""
import cgi
import string

from galaxy import (
    model,
    util,
    web
)
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>${dataset_id} (${dataset_id_encoded})</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 <a href="mailto:${email_str}"><span style="font-family: monospace;">${email_str}</span></a> 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>
"""


[docs]class ErrorReporter( object ):
[docs] 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.query( model.HistoryDatasetAssociation ).get( hda_id ) assert hda is not None, ValueError( "No HDA yet" ) except Exception: hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda_id ) ) assert isinstance( hda, model.HistoryDatasetAssociation ), ValueError( "Bad value provided for HDA (%s)." % ( hda ) ) self.hda = hda # Get the associated job self.job = hda.creating_job self.app = app self.tool_id = self.job.tool_id self.report = None
def _can_access_dataset( self, user ): if user: roles = user.all_roles() else: roles = [] return self.app.security_agent.can_access_dataset( roles, self.hda.dataset )
[docs] def create_report( self, user, email='', message='', **kwd ): hda = self.hda job = self.job host = web.url_for( '/', qualified=True ) history_id_encoded = self.app.security.encode_id( hda.history_id ) history_view_link = web.url_for( controller="history", action="view", id=history_id_encoded, qualified=True ) hda_id_encoded = self.app.security.encode_id( hda.id ) hda_show_params_link = web.url_for( controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True ) # Build the email message if user and user.email != email: email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email) else: email_str = "'%s'" % (email or 'anonymously') report_variables = dict( host=host, dataset_id_encoded=self.app.security.encode_id( hda.dataset_id ), dataset_id=hda.dataset_id, history_id_encoded=history_id_encoded, history_id=hda.history_id, hda_id_encoded=hda_id_encoded, hid=hda.hid, history_item_name=hda.get_display_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 ), email_str=email_str, message=util.unicodify( message ) ) self.report = string.Template( error_report_template ).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] = cgi.escape(unicodify(report_variables[parameter])) self.html_report = string.Template( error_report_template_html ).safe_substitute( report_variables )
def _send_report( self, user, email=None, message=None, **kwd ): return self.report
[docs] def send_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 )
[docs]class EmailErrorReporter( ErrorReporter ): def _send_report( self, user, email=None, message=None, **kwd ): smtp_server = self.app.config.smtp_server assert smtp_server, ValueError( "Mail is not configured for this galaxy instance" ) to_address = self.app.config.error_email_to assert to_address, ValueError( "Error reporting has been disabled for this galaxy instance" ) frm = to_address # Check email a bit email = email or '' email = email.strip() parts = email.split() if len( parts ) == 1 and len( email ) > 0 and self._can_access_dataset( user ): to = to_address + ", " + email else: to = to_address subject = "Galaxy tool error report from %s" % email try: subject = "%s (%s)" % ( subject, self.app.toolbox.get_tool( self.job.tool_id, self.job.tool_version ).old_id ) except Exception: pass # Send it return util.send_mail( frm, to, subject, self.report, self.app.config, html=self.html_report )