Merge pull request #7755 from jmchilton/job_error_reporting

Report a couple common errors in dataset/job report.

client/galaxy/scripts/mvc/dataset/dataset-error.js

@@ -32,6 +32,7 @@ var View = Backbone.View.extend({
                     url: job_url,
                     success: job => {
                         this.render_error_page(dataset, job);
+                        this.find_common_problems(job);
                     },
                     error: response => {
                         var error_response = {
@@ -56,15 +57,53 @@ var View = Backbone.View.extend({
         });
     },
 
+    find_common_problems: function(job) {
+        var job_url = `${getAppRoot()}api/jobs/${job.id}/common_problems`;
+        Utils.get({
+            url: job_url,
+            success: common_problems => {
+                this.render_common_problems(job, common_problems);
+            },
+            error: response => {
+                console.log("error");
+                console.log(response);
+            }
+        });
+        return;
+    },
+
+    render_common_problems: function(job, common_problems) {
+        const has_duplicate_inputs = common_problems.has_duplicate_inputs;
+        const has_empty_inputs = common_problems.has_empty_inputs;
+        if (has_duplicate_inputs || has_empty_inputs) {
+            const reportEl = this.$el.find(".common_problems");
+            reportEl.text("Detected Common Potential Problems");
+            if (has_empty_inputs) {
+                reportEl.after(`
+                    <p>
+                        The tool was executed with one or more empty input datasets, this isn't
+                        always a problem and may not have been but frequently this is a source
+                        of error.
+                    <p>`);
+            }
+            if (has_duplicate_inputs) {
+                reportEl.after(`
+                    <p>
+                        The tool was executed with one or more duplicate input datasets, this isn't
+                        always a problem and may not have been but frequently this is a source
+                        of error.
+                    <p>`);
+            }
+        }
+    },
+
     /** Render the view */
     render_error_page: function(dataset, job) {
         this.$el.empty().append(`
             ${this._templateHeader()}
             <h2>Dataset Error</h2>
             <p>An error occurred while running the tool <b>${job.tool_id}</b>.</p>
-            <p>Tool execution generated the following messages:</p>
-            <pre class="code">${_.escape(job.stderr)}</pre>
-
+            ${this.job_summary(job)}
             <h3>Troubleshoot This Error</h3>
             <p>
                 There are a number of help resources to self diagnose and
@@ -85,6 +124,32 @@ var View = Backbone.View.extend({
         this.$el.append(this._getBugFormTemplate(dataset, job));
     },
 
+    job_summary: function(job) {
+        const tool_stderr = job.tool_stderr;
+        const job_stderr = job.job_stderr;
+        const job_messages = job.job_messages;
+        if (!tool_stderr && !job_stderr && !job_messages) {
+            return '<h3 class="common_problems"></h3>';
+        }
+        var message = "<h3>Error Details</h3>";
+        if (job_messages) {
+            message += "<p>Execution resulted in the following messages:</p>";
+            for (let job_message of job_messages) {
+                message += `<p><pre>${_.escape(job_message["desc"])}</pre></p>`;
+            }
+        }
+        if (tool_stderr) {
+            message += "<p>Tool generated the following standard error:</p>";
+            message += `<pre class="code">${_.escape(tool_stderr)}</pre>`;
+        }
+        if (job_stderr) {
+            message += "<p>Galaxy job runner generated the following standard error:</p>";
+            message += `<pre class="code">${_.escape(job_stderr)}</pre>`;
+        }
+        message += `<h3 class="common_problems"></h3>`;
+        return message;
+    },
+
     /** Display actions messages */
     display_message: function(response, $el, doNotClear, safe) {
         if (!safe) {

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

@@ -169,6 +169,30 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
                 job_dict['job_metrics'] = [metric_to_dict(metric) for metric in job.metrics]
         return job_dict
 
+    @expose_api
+    def common_problems(self, trans, id, **kwd):
+        """
+        * GET /api/jobs/{id}/common_problems
+            check inputs and job for common potential problems to aid in error reporting
+        """
+        job = self.__get_job(trans, id)
+        seen_ids = set()
+        has_empty_inputs = False
+        has_duplicate_inputs = False
+        for job_input_assoc in job.input_datasets:
+            input_dataset_instance = job_input_assoc.dataset
+            if input_dataset_instance.get_total_size() == 0:
+                has_empty_inputs = True
+            input_instance_id = input_dataset_instance.id
+            if input_instance_id in seen_ids:
+                has_duplicate_inputs = True
+            else:
+                seen_ids.add(input_instance_id)
+        # TODO: check percent of failing jobs around a window on job.update_time for handler - report if high.
+        # TODO: check percent of failing jobs around a window on job.update_time for destination_id - report if high.
+        # TODO: sniff inputs (add flag to allow checking files?)
+        return {"has_empty_inputs": has_empty_inputs, "has_duplicate_inputs": has_duplicate_inputs}
+
     @expose_api
     def inputs(self, trans, id, **kwd):
         """

lib/galaxy/webapps/galaxy/buildapp.py

@@ -888,6 +888,7 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('build_for_rerun', '/api/jobs/{id}/build_for_rerun', controller='jobs', action='build_for_rerun', conditions=dict(method=['GET']))
     webapp.mapper.connect('resume', '/api/jobs/{id}/resume', controller='jobs', action='resume', conditions=dict(method=['PUT']))
     webapp.mapper.connect('job_error', '/api/jobs/{id}/error', controller='jobs', action='error', conditions=dict(method=['POST']))
+    webapp.mapper.connect('common_problems', '/api/jobs/{id}/common_problems', controller='jobs', action='common_problems', conditions=dict(method=['GET']))
 
     # Job files controllers. Only for consumption by remote job runners.
     webapp.mapper.resource('file',

test/api/test_jobs.py

@@ -190,6 +190,34 @@ class JobsApiTestCase(api.ApiTestCase):
                                                                          assert_ok=False)
             assert not dataset['visible']
 
+    @skip_without_tool('empty_output')
+    def test_common_problems(self):
+        with self.dataset_populator.test_history() as history_id:
+            empty_run_response = self.dataset_populator.run_tool(
+                tool_id='empty_output',
+                inputs={},
+                history_id=history_id,
+            )
+            empty_hda = empty_run_response["outputs"][0]
+            cat_empty_twice_run_response = self.dataset_populator.run_tool(
+                tool_id='cat1',
+                inputs={
+                    'input1': {'src': 'hda', 'id': empty_hda['id']},
+                    'queries_0|input2': {'src': 'hda', 'id': empty_hda['id']}
+                },
+                history_id=history_id,
+            )
+            empty_output_job = empty_run_response["jobs"][0]
+            cat_empty_job = cat_empty_twice_run_response["jobs"][0]
+            empty_output_common_problems_response = self._get('jobs/%s/common_problems' % empty_output_job["id"]).json()
+            cat_empty_common_problems_response = self._get('jobs/%s/common_problems' % cat_empty_job["id"]).json()
+            self._assert_has_keys(empty_output_common_problems_response, "has_empty_inputs", "has_duplicate_inputs")
+            self._assert_has_keys(cat_empty_common_problems_response, "has_empty_inputs", "has_duplicate_inputs")
+            assert not empty_output_common_problems_response["has_empty_inputs"]
+            assert cat_empty_common_problems_response["has_empty_inputs"]
+            assert not empty_output_common_problems_response["has_duplicate_inputs"]
+            assert cat_empty_common_problems_response["has_duplicate_inputs"]
+
     @skip_without_tool('detect_errors_aggressive')
     def test_report_error(self):
         with self.dataset_populator.test_history() as history_id: