Fix 1293 (#2291)

* fix #1293

* flake8

* fix errors

* addressing @ElDeveloper comments

Author: antgonza

qiita_db/study.py

@@ -998,6 +998,28 @@ def prep_templates(self, data_type=None):
             return [qdb.metadata_template.prep_template.PrepTemplate(ptid)
                     for ptid in qdb.sql_connection.TRN.execute_fetchflatten()]
 
+    def analyses(self):
+        """Get all analyses where samples from this study have been used
+
+        Returns
+        -------
+        list of qiita_db.analysis.Analysis
+        """
+        with qdb.sql_connection.TRN:
+            if self.sample_template is not None:
+                sids = self.sample_template.keys()
+                if sids:
+                    sql = """SELECT DISTINCT analysis_id
+                             FROM qiita.analysis_sample
+                             WHERE sample_id IN %s
+                             ORDER BY analysis_id"""
+                    qdb.sql_connection.TRN.add(
+                        sql, [tuple(self.sample_template.keys())])
+
+                    return [qdb.analysis.Analysis(_id) for _id in
+                            qdb.sql_connection.TRN.execute_fetchflatten()]
+            return []
+
     def has_access(self, user, no_public=False):
         """Returns whether the given user has access to the study
 

qiita_db/support_files/patches/python_patches/58.py

@@ -120,6 +120,11 @@ def correct_redis_data(key, cmd, values_dict, user):
     st_cmd = Command.create(qiita_plugin, "update_sample_template",
                             "Updates the sample template", parameters)
 
+    # Create the delete study command
+    parameters = {'study': ['integer', None]}
+    Command.create(qiita_plugin, "delete_study",
+                   "Deletes a full study", parameters)
+
     # Create the delete sample template command
     parameters = {'study': ['integer', None]}
     Command.create(qiita_plugin, "delete_sample_template",

qiita_db/test/test_study.py

@@ -766,6 +766,20 @@ def test_retrieve_prep_templates_none(self):
         self.assertEqual(new.prep_templates(), [])
         qdb.study.Study.delete(new.id)
 
+    def test_analyses(self):
+        new = qdb.study.Study.create(
+            qdb.user.User('[email protected]'),
+            'NOT Identification of the Microbiomes for Cannabis Soils 13',
+            self.info)
+
+        self.assertEqual(qdb.study.Study(1).analyses(), [
+            qdb.analysis.Analysis(1), qdb.analysis.Analysis(2),
+            qdb.analysis.Analysis(3)])
+
+        self.assertEqual(qdb.study.Study(2).analyses(), [])
+
+        qdb.study.Study.delete(new.id)
+
     def test_environmental_packages(self):
         obs = self.study.environmental_packages
         exp = ['soil', 'plant-associated']

qiita_pet/handlers/api_proxy/studies.py

@@ -7,16 +7,24 @@
 # -----------------------------------------------------------------------------
 from __future__ import division
 from collections import defaultdict
+from json import dumps, loads
 
 from future.utils import viewitems
 
+from qiita_core.exceptions import IncompetentQiitaDeveloperError
+from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import r_client
 from qiita_db.user import User
 from qiita_db.study import Study
 from qiita_db.metadata_template.prep_template import PrepTemplate
+from qiita_db.processing_job import ProcessingJob
+from qiita_db.software import Software, Parameters
 from qiita_db.util import (supported_filepath_types,
                            get_files_from_uploads_folders)
 from qiita_pet.handlers.api_proxy.util import check_access
-from qiita_core.exceptions import IncompetentQiitaDeveloperError
+
+
+STUDY_KEY_FORMAT = 'study_%s'
 
 
 def data_types_get_req():
@@ -35,8 +43,7 @@ def data_types_get_req():
     """
     return {'status': 'success',
             'message': '',
-            'data_types': Study.all_data_types()
-            }
+            'data_types': Study.all_data_types()}
 
 
 def study_get_req(study_id, user_id):
@@ -110,12 +117,35 @@ def study_get_req(study_id, user_id):
     study_info['show_raw_download_button'] = any([
         True for pt in study.prep_templates() if pt.artifact is not None])
 
+    # getting study processing status from redis
+    processing = False
+    study_info['level'] = ''
+    study_info['message'] = ''
+    job_info = r_client.get(STUDY_KEY_FORMAT % study_id)
+    if job_info:
+        job_info = defaultdict(lambda: '', loads(job_info))
+        job_id = job_info['job_id']
+        job = ProcessingJob(job_id)
+        job_status = job.status
+        processing = job_status not in ('success', 'error')
+        if processing:
+            study_info['level'] = 'info'
+            study_info['message'] = 'This study is currently being processed'
+        elif job_status == 'error':
+            study_info['level'] = 'danger'
+            study_info['message'] = job.log.msg.replace('\n', '</br>')
+        else:
+            study_info['level'] = job_info['alert_type']
+            study_info['message'] = job_info['alert_msg'].replace(
+                '\n', '</br>')
+
     return {'status': 'success',
             'message': '',
             'study_info': study_info,
             'editable': study.can_edit(User(user_id))}
 
 
+@execute_as_transaction
 def study_delete_req(study_id, user_id):
     """Delete a given study
 
@@ -137,17 +167,17 @@ def study_delete_req(study_id, user_id):
     if access_error:
         return access_error
 
-    status = 'success'
-    try:
-        Study.delete(int(study_id))
-        msg = ''
-    except Exception as e:
-        status = 'error'
-        msg = 'Unable to delete study: %s' % str(e)
-    return {
-        'status': status,
-        'message': msg
-    }
+    qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
+    cmd = qiita_plugin.get_command('delete_study')
+    params = Parameters.load(cmd, values_dict={'study': study_id})
+    job = ProcessingJob.create(User(user_id), params)
+    # Store the job id attaching it to the sample template id
+    r_client.set(STUDY_KEY_FORMAT % study_id,
+                 dumps({'job_id': job.id}))
+
+    job.submit()
+
+    return {'status': 'success', 'message': ''}
 
 
 def study_prep_get_req(study_id, user_id):

qiita_pet/handlers/api_proxy/tests/test_studies.py

@@ -51,8 +51,8 @@ def test_study_get_req(self):
         exp = {
             'status': 'success',
             'study_info': {
-                'mixs_compliant': True, 'metadata_complete': True,
-                'reprocess': False, 'owner': '[email protected]',
+                'mixs_compliant': True, 'metadata_complete': True, 'level': '',
+                'reprocess': False, 'owner': '[email protected]', 'message': '',
                 'emp_person_id': 2, 'number_samples_promised': 27,
                 'funding': None, 'show_biom_download_button': True,
                 'publication_pid': ['123456', '7891011'], 'vamps_id': None,
@@ -341,37 +341,6 @@ def test_study_prep_get_req_no_access(self):
                'message': 'User does not have access to study'}
         self.assertEqual(obs, exp)
 
-    def test_study_delete_req(self):
-        info = {
-            "timeseries_type_id": 1,
-            "metadata_complete": True,
-            "mixs_compliant": True,
-            "number_samples_collected": 25,
-            "number_samples_promised": 28,
-            "study_alias": "FCM",
-            "study_description": "DESC",
-            "study_abstract": "ABS",
-            "emp_person_id": qdb.study.StudyPerson(2),
-            "principal_investigator_id": qdb.study.StudyPerson(3),
-            "lab_person_id": qdb.study.StudyPerson(1)
-        }
-
-        new_study = qdb.study.Study.create(
-            qdb.user.User('[email protected]'), "Some New Study to delete", info)
-
-        study_delete_req(new_study.id, '[email protected]')
-
-        with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
-            qdb.study.Study(new_study.id)
-
-    def test_study_delete_req_error(self):
-        obs = study_delete_req(1, '[email protected]')
-        exp = {'status': 'error',
-               'message': 'Unable to delete study: Study "Identification of '
-                          'the Microbiomes for Cannabis Soils" cannot be '
-                          'erased because it has a sample template'}
-        self.assertEqual(obs, exp)
-
     def test_study_delete_req_no_access(self):
         obs = study_delete_req(1, '[email protected]')
         exp = {'status': 'error',
@@ -525,7 +494,7 @@ def test_study_get_tags_request(self):
         self.assertEqual(obs, exp)
 
         # check error
-        obs = study_get_tags_request('[email protected]', 2)
+        obs = study_get_tags_request('[email protected]', 2000)
         exp = {'message': 'Study does not exist', 'status': 'error'}
         self.assertEqual(obs, exp)
 
@@ -560,7 +529,7 @@ def test_study_tags_patch_request(self):
         self.assertEqual(obs, exp)
 
         obs = study_tags_patch_request(
-            '[email protected]', 2, 'replace', '/tags', ['testA', 'testB'])
+            '[email protected]', 2000, 'replace', '/tags', ['testA', 'testB'])
         exp = {'message': 'Study does not exist', 'status': 'error'}
         self.assertEqual(obs, exp)
 

qiita_pet/handlers/study_handlers/base.py

@@ -28,7 +28,7 @@ def get(self, study_id):
         if study_info['status'] != 'success':
             raise HTTPError(404, study_info['message'])
 
-        if message != '':
+        if message != '' and level != '':
             study_info['level'] = level
             study_info['message'] = message
 

qiita_pet/handlers/study_handlers/tests/test_base.py

@@ -6,7 +6,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from unittest import main
-from json import loads
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 from qiita_db.handlers.tests.oauthbase import OauthTestingBase
@@ -27,17 +26,6 @@ class StudyBaseInfoAJAX(TestHandlerBase):
     pass
 
 
-class StudyDeleteAjaxTests(TestHandlerBase):
-    def test_delete_study(self):
-        response = self.post('/study/delete/', {'study_id': 1})
-        self.assertEqual(response.code, 200)
-        exp = {'status': 'error',
-               'message': 'Unable to delete study: Study "Identification of '
-                          'the Microbiomes for Cannabis Soils" cannot be '
-                          'erased because it has a sample template'}
-        self.assertEqual(loads(response.body), exp)
-
-
 class DataTypesMenuAJAXTests(TestHandlerBase):
     def test_get(self):
         response = self.get('/study/description/data_type_menu/',

qiita_pet/templates/study_base.html

@@ -152,12 +152,7 @@
     else if(confirm("Are you sure you want to delete {% raw study_title_msg %}?")) {
       $.post('{% raw qiita_config.portal_dir %}/study/delete/', { study_id: {{study_info['study_id']}} })
         .done(function ( data ) {
-          if(data.status == "error") {
-            bootstrapAlert(data.message.replace("\n", "<br/>"), "danger");
-            $("#delete-study").modal('hide');
-          } else {
-            window.location.replace('{% raw qiita_config.portal_dir %}/study/list/');
-          }
+          location.reload();
         });
     }
   }
@@ -211,6 +206,9 @@
       $("#sample-summary-btn").hide();
       $("#add-new-preparation-btn").hide();
     {% end %}
+    {% if study_info['message'] != '' %}
+      bootstrapAlert("{{study_info['message']}}", "{{study_info['level']}}");
+    {% end %}
   });
 </script>
 <style>
@@ -223,24 +221,26 @@
 {% end %}
 {% block content %}
 <div class="row">
-  <div class="col-md-3">
-    <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/baseinfo/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Study Information</button>
-    <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/sample_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Sample Information</button>
-    <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/sample_summary/', { study_id: {{study_info['study_id']}} })" id="sample-summary-btn"><span class="glyphicon glyphicon-th-list"></span> Sample Summary</button>
-    {% if editable %}
-      <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/study/upload/{{study_info['study_id']}}"><span class="glyphicon glyphicon-upload"></span> Upload Files</a>
-      <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/new_prep_template/', { study_id: {{study_info['study_id']}} })" id="add-new-preparation-btn"><span class="glyphicon glyphicon-plus-sign"></span> Add New Preparation</button>
-    {% end %}
-    {% if study_info['show_biom_download_button'] %}
-      <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/download_study_bioms/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> All QIIME maps and BIOMs</a>
-    {% end %}
-    {% if study_info['has_access_to_raw_data'] and study_info['show_raw_download_button'] %}
-      <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/download_raw_data/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> All raw data</a>
-    {% end %}
-    <div style="text-align: center;"><small><a href="{% raw qiita_config.portal_dir %}/static/doc/html/faq.html#how-to-solve-unzip-errors">Issues opening the downloaded zip?</a></small></div>
+  {% if study_info['level'] != 'info' %}
+    <div class="col-md-3">
+      <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/baseinfo/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Study Information</button>
+      <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/sample_template/', { study_id: {{study_info['study_id']}} })"><span class="glyphicon glyphicon-info-sign"></span> Sample Information</button>
+      <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/description/sample_summary/', { study_id: {{study_info['study_id']}} })" id="sample-summary-btn"><span class="glyphicon glyphicon-th-list"></span> Sample Summary</button>
+      {% if editable %}
+        <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/study/upload/{{study_info['study_id']}}"><span class="glyphicon glyphicon-upload"></span> Upload Files</a>
+        <button class="btn btn-default btn-block" onclick="populate_main_div('{% raw qiita_config.portal_dir %}/study/new_prep_template/', { study_id: {{study_info['study_id']}} })" id="add-new-preparation-btn"><span class="glyphicon glyphicon-plus-sign"></span> Add New Preparation</button>
+      {% end %}
+      {% if study_info['show_biom_download_button'] %}
+        <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/download_study_bioms/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> All QIIME maps and BIOMs</a>
+      {% end %}
+      {% if study_info['has_access_to_raw_data'] and study_info['show_raw_download_button'] %}
+        <a class="btn btn-default btn-block" href="{% raw qiita_config.portal_dir %}/download_raw_data/{{study_info['study_id']}}"><span class="glyphicon glyphicon-download-alt"></span> All raw data</a>
+      {% end %}
+      <div style="text-align: center;"><small><a href="{% raw qiita_config.portal_dir %}/static/doc/html/faq.html#how-to-solve-unzip-errors">Issues opening the downloaded zip?</a></small></div>
 
-    <div id="data-types-menu"></div>
-  </div>
+      <div id="data-types-menu"></div>
+    </div>
+  {% end %}
 
   <div class="col-md-9">
     <!-- Study ID and study alias always on top -->

qiita_ware/private_plugin.py

@@ -273,6 +273,40 @@ def delete_sample_or_column(job):
         job._set_status('success')
 
 
+def delete_study(job):
+    """Deletes a full study
+
+    Parameters
+    ----------
+    job : qiita_db.processing_job.ProcessingJob
+        The processing job performing the task
+    """
+    with qdb.sql_connection.TRN:
+        study_id = job.parameters.values['study']
+        study = qdb.study.Study(study_id)
+
+        for a in study.analyses():
+            artifacts = sorted(
+                a.artifacts, key=lambda a: a.id, reverse=True)
+            for artifact in artifacts:
+                qdb.artifact.Artifact.delete(artifact.id)
+            qdb.analysis.Analysis.delete(a.id)
+
+        artifacts = sorted(
+            study.artifacts(), key=lambda a: a.id, reverse=True)
+        for a in artifacts:
+            qdb.artifact.Artifact.delete(a.id)
+
+        for pt in study.prep_templates():
+            qdb.metadata_template.prep_template.PrepTemplate.delete(pt.id)
+
+        qdb.metadata_template.sample_template.SampleTemplate.delete(study_id)
+
+        qdb.study.Study.delete(study_id)
+
+        job._set_status('success')
+
+
 def complete_job(job):
     """Deletes a sample or a column from the metadata
 
@@ -310,6 +344,7 @@ def complete_job(job):
              'delete_sample_template': delete_sample_template,
              'update_prep_template': update_prep_template,
              'delete_sample_or_column': delete_sample_or_column,
+             'delete_study': delete_study,
              'complete_job': complete_job}