fixing errors and gui

qiita_pet/handlers/study_handlers/base.py

@@ -21,11 +21,17 @@ class StudyIndexHandler(BaseHandler):
     @authenticated
     def get(self, study_id):
         study = to_int(study_id)
+        level = self.get_argument('level', '')
+        message = self.get_argument('message', '')
 
         study_info = study_get_req(study, self.current_user.id)
         if study_info['status'] != 'success':
             raise HTTPError(404, study_info['message'])
 
+        if message != '':
+            study_info['level'] = level
+            study_info['message'] = message
+
         self.render("study_base.html", **study_info)
 
 

qiita_pet/handlers/study_handlers/ebi_handlers.py

@@ -8,11 +8,12 @@
 from __future__ import division
 
 from tornado.web import authenticated, HTTPError
+from tornado.escape import url_escape
 from json import dumps
 
 from qiita_files.demux import stats as demux_stats
 
-from qiita_core.qiita_settings import r_client
+from qiita_core.qiita_settings import r_client, qiita_config
 from qiita_core.util import execute_as_transaction
 from qiita_db.metadata_template.constants import (SAMPLE_TEMPLATE_COLUMNS,
                                                   PREP_TEMPLATE_COLUMNS)
@@ -109,9 +110,6 @@ def get(self, preprocessed_data_id):
     @authenticated
     @execute_as_transaction
     def post(self, preprocessed_data_id):
-        status = 'success'
-        message = ''
-
         user = self.current_user
         # make sure user is admin and can therefore actually submit to EBI
         if user.level != 'admin':
@@ -123,10 +121,11 @@ def post(self, preprocessed_data_id):
             raise HTTPError(403, "User: %s, %s is not a recognized submission "
                             "type" % (user.id, submission_type))
 
-        state = Artifact(preprocessed_data_id).study.ebi_submission_status
+        study = Artifact(preprocessed_data_id).study
+        state = study.ebi_submission_status
         if state == 'submitting':
+            level = 'danger'
             message = "Cannot resubmit! Current state is: %s" % state
-            status = 'danger'
         else:
             qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
             cmd = qiita_plugin.get_command('submit_to_EBI')
@@ -137,5 +136,10 @@ def post(self, preprocessed_data_id):
 
             r_client.set('ebi_submission_%s' % preprocessed_data_id,
                          dumps({'job_id': job.id, 'is_qiita_job': True}))
+            job.submit()
+
+            level = 'success'
+            message = 'EBI submission started. Job id: %s' % job.id
 
-        return {'status': status, 'message': message}
+            self.redirect("%s/study/description/%d?level=%s&message=%s" % (
+                qiita_config.portal_dir, study.id, level, url_escape(message)))

qiita_ware/private_plugin.py

@@ -100,9 +100,20 @@ def copy_artifact(job):
         job._set_status('success')
 
 
-def submit_to_ebi(preprocessed_data_id, submission_type):
-    """Submit a study to EBI"""
-    submit_EBI(preprocessed_data_id, submission_type, True)
+def submit_to_EBI(job):
+    """Submit a study to EBI
+
+    Parameters
+    ----------
+    job : qiita_db.processing_job.ProcessingJob
+        The processing job performing the task
+    """
+    with qdb.sql_connection.TRN:
+        param_vals = job.parameters.values
+        artifact_id = int(param_vals['artifact'])
+        submission_type = param_vals['submission_type']
+        submit_EBI(artifact_id, submission_type, False)
+        job._set_status('success')
 
 
 def delete_artifact(job):
@@ -126,7 +137,6 @@ def create_sample_template(job):
     ----------
     job : qiita_db.processing_job.ProcessingJob
         The processing job performing the task
-
     """
     with qdb.sql_connection.TRN:
         params = job.parameters.values
@@ -151,7 +161,7 @@ def create_sample_template(job):
     'release_validators': release_validators,
     'submit_to_VAMPS': submit_to_VAMPS,
     'copy_artifact': copy_artifact,
-    'submit_to_ebi': submit_to_ebi,
+    'submit_to_EBI': submit_to_EBI,
     'delete_artifact': delete_artifact,
     'create_sample_template': create_sample_template,
 }

qiita_ware/test/test_private_plugin.py

@@ -21,8 +21,7 @@
 from qiita_db.artifact import Artifact
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.exceptions import QiitaDBUnknownIDError
-from qiita_ware.private_plugin import (
-    private_task, create_sample_template, delete_artifact)
+from qiita_ware.private_plugin import private_task
 
 
 @qiita_test_checker()
@@ -44,7 +43,7 @@ def tearDown(self):
     def _create_job(self, cmd, values_dict):
         user = User('test@foo.bar')
         qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
-        cmd = qiita_plugin.get_command('copy_artifact')
+        cmd = qiita_plugin.get_command(cmd)
         params = Parameters.load(cmd, values_dict=values_dict)
         job = ProcessingJob.create(user, params)
         job._set_status('queued')
@@ -79,37 +78,41 @@ def test_copy_artifact(self):
         self.assertEqual(job.status, 'success')
 
     def test_delete_artifact(self):
-        obs = delete_artifact(1)
-        exp = {'status': 'danger',
-               'message': 'Cannot delete artifact 1: it has children: 2, 3'}
-        self.assertEqual(obs, exp)
-
-        obs = delete_artifact(3)
-        exp = {'status': 'success',
-               'message': ''}
-        self.assertEqual(obs, exp)
+        job = self._create_job('delete_artifact', {'artifact': 1})
+        private_task(job.id)
+        self.assertEqual(job.status, 'error')
+        self.assertIn(
+            'Cannot delete artifact 1: it has children: 2, 3', job.log.msg)
 
+        job = self._create_job('delete_artifact', {'artifact': 3})
+        private_task(job.id)
+        self.assertEqual(job.status, 'success')
         with self.assertRaises(QiitaDBUnknownIDError):
             Artifact(3)
 
     def test_create_sample_template(self):
-        obs = create_sample_template(self.fp, Study(1), False)
-        exp = {'status': 'danger',
-               'message': "The 'SampleTemplate' object with attributes "
-                          "(id: 1) already exists."}
-        self.assertEqual(obs, exp)
+        job = self._create_job('create_sample_template', {
+            'fp': self.fp, 'study_id': 1, 'is_mapping_file': False,
+            'data_type': None})
+        private_task(job.id)
+        self.assertEqual(job.status, 'error')
+        self.assertIn("The 'SampleTemplate' object with attributes (id: 1) "
+                      "already exists.", job.log.msg)
 
     def test_create_sample_template_nonutf8(self):
         fp = join(dirname(abspath(__file__)), 'test_data',
                   'sample_info_utf8_error.txt')
-        obs = create_sample_template(fp, Study(1), False)
-        exp = {'status': 'danger',
-               'message': 'There are invalid (non UTF-8) characters in your '
-                          'information file. The offending fields and their '
-                          'location (row, column) are listed below, invalid '
-                          'characters are represented using 🐾: '
-                          '"🐾collection_timestamp" = (0, 13)'}
-        self.assertEqual(obs, exp)
+        job = self._create_job('create_sample_template', {
+            'fp': fp, 'study_id': 1, 'is_mapping_file': False,
+            'data_type': None})
+        private_task(job.id)
+        self.assertEqual(job.status, 'error')
+        self.assertIn(
+            'There are invalid (non UTF-8) characters in your information '
+            'file. The offending fields and their location (row, column) are '
+            'listed below, invalid characters are represented using '
+            '🐾: "🐾collection_timestamp" = (0, 13)',
+            job.log.msg)
 
 
 if __name__ == '__main__':