Merge pull request #3299 from antgonza/2023.06-fixes-rc

2023.06-fixes-rc

Author: charles-cowart

qiita_db/handlers/artifact.py

@@ -320,5 +320,4 @@ def post(self):
         r_client.set('prep_template_%d' % prep_id,
                      dumps({'job_id': new_job.id, 'is_qiita_job': True}))
 
-        self.write(new_job.id)
-        self.finish()
+        self.finish({'job_id': new_job.id})

qiita_db/handlers/tests/test_artifact.py

@@ -368,7 +368,7 @@ def test_post(self):
         # send the new data
         del data['prep_id']
         obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
-        jid = obs.body.decode("utf-8")
+        jid = loads(obs.body)['job_id']
 
         job = qdb.processing_job.ProcessingJob(jid)
         while job.status not in ('error', 'success'):
@@ -404,7 +404,7 @@ def test_post(self):
                 'files': dumps({'biom': [fp]})}
 
         obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
-        jid = obs.body.decode("utf-8")
+        jid = loads(obs.body)['job_id']
 
         job = qdb.processing_job.ProcessingJob(jid)
         while job.status not in ('error', 'success'):

qiita_db/handlers/tests/test_prep_template.py

@@ -172,6 +172,11 @@ def test_post(self):
         self.assertEqual(pt.name, data['name'])
         self.assertEqual(pt.creation_job_id, data['job-id'])
 
+        # testing setter
+        jid = 'aaaaaaaa-aaaa-bbbb-aaaa-aaaaaaaaaaaa'
+        pt.creation_job_id = jid
+        self.assertEqual(pt.creation_job_id, jid)
+
 
 if __name__ == '__main__':
     main()

qiita_db/metadata_template/prep_template.py

@@ -970,3 +970,12 @@ def creation_job_id(self):
                      WHERE prep_template_id = %s"""
             qdb.sql_connection.TRN.add(sql, [self.id])
             return qdb.sql_connection.TRN.execute_fetchlast()
+
+    @creation_job_id.setter
+    def creation_job_id(self, creation_job_id):
+        with qdb.sql_connection.TRN:
+            sql = """UPDATE qiita.prep_template
+                     SET creation_job_id = %s
+                     WHERE prep_template_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [creation_job_id, self.id])
+            qdb.sql_connection.TRN.execute()

qiita_pet/handlers/admin_processing_job.py

@@ -15,6 +15,8 @@
 from qiita_db.software import Software
 from qiita_db.study import Study
 from qiita_db.exceptions import QiitaDBUnknownIDError
+from qiita_db.sql_connection import TRN
+from qiita_db.processing_job import ProcessingJob as PJ
 
 from json import dumps
 from collections import Counter
@@ -57,35 +59,44 @@ def get(self):
         echo = self.get_argument('sEcho')
         command_id = int(self.get_argument('commandId'))
 
-        jobs = []
-        for ps in self._get_private_software():
-            for cmd in ps.commands:
-                if cmd.id != command_id:
-                    continue
+        with TRN:
+            # different versions of the same plugin will have different
+            # command_id, this will make sure to get them all (commands)
+            sql = """SELECT processing_job_id FROM qiita.processing_job
+                     WHERE hidden = false and command_id in (
+                        SELECT command_id FROM qiita.software_command
+                        WHERE
+                            name in (
+                                SELECT name FROM qiita.software_command
+                                WHERE command_id = %s)) AND
+                            (heartbeat > current_date - interval '14' day OR
+                             heartbeat is NULL)"""
+            TRN.add(sql, [command_id])
+            jids = TRN.execute_fetchflatten()
 
-                for job in cmd.processing_jobs:
-                    if job.hidden:
-                        continue
-                    msg = ''
-                    if job.status == 'error':
-                        msg = job.log.msg
-                    elif job.status == 'running':
-                        msg = job.step
-                    msg = msg.replace('\n', '</br>')
-                    outputs = []
-                    if job.status == 'success':
-                        outputs = [[k, v.id] for k, v in job.outputs.items()]
-                    validator_jobs = [v.id for v in job.validator_jobs]
-
-                    if job.heartbeat is not None:
-                        heartbeat = job.heartbeat.strftime('%Y-%m-%d %H:%M:%S')
-                    else:
-                        heartbeat = 'N/A'
-
-                    jobs.append([job.id, job.command.name, job.status, msg,
-                                 outputs, validator_jobs, heartbeat,
-                                 job.parameters.values, job.external_id,
-                                 job.user.email])
+        jobs = []
+        for jid in jids:
+            job = PJ(jid)
+            msg = ''
+            if job.status == 'error':
+                msg = job.log.msg
+            elif job.status == 'running':
+                msg = job.step
+            msg = msg.replace('\n', '</br>')
+            outputs = []
+            if job.status == 'success':
+                outputs = [[k, v.id] for k, v in job.outputs.items()]
+            validator_jobs = [v.id for v in job.validator_jobs]
+
+            if job.heartbeat is not None:
+                heartbeat = job.heartbeat.strftime('%Y-%m-%d %H:%M:%S')
+            else:
+                heartbeat = 'N/A'
+
+            jobs.append([job.id, job.command.name, job.status, msg,
+                         outputs, validator_jobs, heartbeat,
+                         job.parameters.values, job.external_id,
+                         job.user.email])
         results = {
             "sEcho": echo,
             "recordsTotal": len(jobs),

qiita_pet/handlers/study_handlers/prep_template.py

@@ -76,9 +76,9 @@ def get(self):
         res['alert_message'] = url_escape(res['alert_message'])
         res['user_level'] = current_user.level
         if res['creation_job'] is not None:
-            vals = res['creation_job'].values
-            res['creation_job_filename'] = vals['filename']
-            res['creation_job_filename_body'] = vals['body']
+            fp = res['creation_job'].parameters.values['sample_sheet']
+            res['creation_job_filename'] = fp['filename']
+            res['creation_job_filename_body'] = fp['body']
 
         self.render('study_ajax/prep_summary.html', **res)
 

qiita_pet/templates/admin_processing_job.html

@@ -71,12 +71,12 @@
       };
 
       out.push('<b class="' + statusToClass[status] + '">' + status + ' ' +
-                row[0] + ' </b> [ ' + row[9] + ' ]</br>');
+                row[0] + ' (' + row[8] + ') </b> [ ' + row[9] + ' ]</br>');
 
       if (status === 'running' || status === 'queued') {
         // row[0] is qiita job-id
         // row[3] is status 'Step n of 6' and other messages
-        out.push('[' + row[8] + ']</br> <i>' + row[3] + '</i>')
+        out.push('<i>' + row[3] + '</i>')
       }
       else {
         // We write a callback attribute on the link to be able to display a

qiita_pet/templates/study_ajax/prep_summary.html

@@ -431,7 +431,7 @@ <h4>
 
       <span id="prep-name-span">{{name}}</span> - ID {{prep_id}} ({{data_type}})
       {% if user_level in ('admin', 'wet-lab admin') and creation_job is not None %}
-          <a class="btn btn-default" download="{{creation_job_filename}}" href="data:text/plain;charset=utf-8,encodeURIComponent({{creation_job_filename_body}})"><span class="glyphicon glyphicon-download-alt"></span> SampleSheet</a>
+          <a class="btn btn-default" download="{{creation_job_filename}}" href="data:text/plain;charset=utf-8,{{creation_job_filename_body}}"><span class="glyphicon glyphicon-download-alt"></span> SampleSheet</a>
       {% end %}
       <a class="btn btn-default" data-toggle="modal" data-target="#update-prep-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
       <a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download/{{download_prep_id}}"><span class="glyphicon glyphicon-download-alt"></span> Prep info</a>

qiita_pet/test/test_admin_processing_job_handlers.py

@@ -32,7 +32,7 @@ def test_get(self):
 
 class TestAJAXAdminProcessingJobListing(BaseAdminTests):
     def test_get(self):
-        response = self.get('/admin/processing_jobs/list?sEcho=3&commandId=1')
+        response = self.get('/admin/processing_jobs/list?sEcho=3&commandId=2')
         self.assertEqual(response.code, 200)
 
         exp = {'sEcho': '3', 'recordsTotal': 0, 'recordsFiltered': 0,