Merge pull request #1068 from antgonza/delete-study

Delete study

Author: josenavas

qiita_db/study.py

@@ -107,6 +107,7 @@
 from .util import (check_required_columns, check_table_cols, convert_to_id,
                    get_environmental_packages, get_table_cols, infer_status)
 from .sql_connection import SQLConnectionHandler
+from .util import exists_table
 
 
 class Study(QiitaObject):
@@ -347,6 +348,68 @@ def create(cls, owner, title, efo, info, investigation=None):
 
         return cls(study_id)
 
+    @classmethod
+    def delete(cls, id_):
+        r"""Deletes the study from the database
+
+        Parameters
+        ----------
+        id_ : integer
+            The object identifier
+
+        Raises
+        ------
+        QiitaDBError
+            If the sample_(id_) table exists means a sample template exists
+        """
+        cls._check_subclass()
+
+        # checking that the id_ exists
+        cls(id_)
+
+        conn_handler = SQLConnectionHandler()
+        if exists_table('sample_%d' % id_, conn_handler):
+            raise QiitaDBError('Study "%s" cannot be erased because it has a '
+                               'sample template' % cls(id_).title)
+
+        queue = "delete_study_%d" % id_
+        conn_handler.create_queue(queue)
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study_sample_columns WHERE study_id = %s",
+            (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study_experimental_factor WHERE study_id = %s",
+            (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study_pmid WHERE study_id = %s", (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study_environmental_package WHERE study_id = "
+            "%s", (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study_users WHERE study_id = %s", (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.investigation_study WHERE study_id = "
+            "%s", (id_, ))
+
+        conn_handler.add_to_queue(
+            queue,
+            "DELETE FROM qiita.study WHERE study_id = %s", (id_, ))
+
+        conn_handler.execute_queue(queue)
+
+
 # --- Attributes ---
     @property
     def title(self):

qiita_db/test/test_study.py

@@ -11,7 +11,9 @@
 from qiita_db.user import User
 from qiita_db.data import RawData
 from qiita_db.util import convert_to_id
-from qiita_db.exceptions import QiitaDBColumnError, QiitaDBStatusError
+from qiita_db.exceptions import (
+    QiitaDBColumnError, QiitaDBStatusError, QiitaDBError,
+    QiitaDBUnknownIDError)
 
 # -----------------------------------------------------------------------------
 # Copyright (c) 2014--, The Qiita Development Team.
@@ -438,6 +440,18 @@ def test_create_unknown_db_col(self):
             Study.create(User('test@foo.bar'), "Fried Chicken Microbiome",
                          [1], self.info)
 
+    def test_delete(self):
+        title = "Fried chicken microbiome"
+        study = Study.create(User('test@foo.bar'), title, [1], self.info)
+        study.delete(study.id)
+        self.assertFalse(study.exists(title))
+
+        with self.assertRaises(QiitaDBError):
+            Study.delete(1)
+
+        with self.assertRaises(QiitaDBUnknownIDError):
+            Study.delete(41)
+
     def test_retrieve_title(self):
         self.assertEqual(self.study.title, 'Identification of the Microbiomes'
                          ' for Cannabis Soils')

qiita_pet/handlers/study_handlers/description_handlers.py

@@ -29,6 +29,8 @@
                                  QiitaDBDuplicateHeaderError, QiitaDBError)
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import check_access
+from qiita_pet.handlers.study_handlers.listing_handlers import (
+    ListStudiesHandler)
 
 html_error_message = "<b>An error occurred %s %s</b></br>%s"
 
@@ -640,6 +642,38 @@ def display_template(self, study, user, msg, msg_level, full_access,
                     sub_tab=sub_tab,
                     prep_tab=prep_tab)
 
+    def delete_study(self, study, user, callback):
+        """Delete study
+
+        Parameters
+        ----------
+        study : Study
+            The current study object
+        user : User
+            The current user object
+        callback : function
+            The callback function to call with the results once the processing
+            is done and it fails
+        """
+        study_id = study.id
+        study_title = study.title
+
+        try:
+            Study.delete(study_id)
+
+            # redirecting to list but also passing messages
+            # we need to change the request.method to GET
+            self.request.method = 'GET'
+            ListStudiesHandler(self.application, self.request)._execute(
+                [t(self.request) for t in self.application.transforms],
+                message=('Study "%s" has been deleted' % study_title),
+                msg_level='success')
+        except Exception as e:
+            msg = "Couldn't remove study %d: %s" % (study_id, str(e))
+            msg_level = "danger"
+
+            callback((msg, msg_level, 'study_information_tab', None, None))
+
     def delete_sample_template(self, study, user, callback):
         """Delete sample template
 
@@ -808,6 +842,7 @@ def post(self, study_id):
             request_approval=self.request_approval,
             make_sandbox=self.make_sandbox,
             update_investigation_type=self.update_investigation_type,
+            delete_study=self.delete_study,
             delete_sample_template=self.delete_sample_template,
             delete_raw_data=self.delete_raw_data,
             delete_prep_template=self.delete_prep_template,

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -123,13 +123,16 @@ def _check_owner(user, study):
 class ListStudiesHandler(BaseHandler):
     @authenticated
     @coroutine
-    def get(self):
+    def get(self, message="", msg_level=None):
         all_emails_except_current = yield Task(self._get_all_emails)
         all_emails_except_current.remove(self.current_user.id)
         avail_meta = SampleTemplate.metadata_headers() +\
             get_table_cols("study")
-        self.render('list_studies.html', availmeta=avail_meta,
-                    all_emails_except_current=all_emails_except_current)
+        self.render('list_studies.html',
+                    availmeta=avail_meta,
+                    all_emails_except_current=all_emails_except_current,
+                    message=message,
+                    msg_level=msg_level)
 
     def _get_all_emails(self, callback):
         callback(list(User.iter()))

qiita_pet/templates/study_description.html

@@ -184,6 +184,36 @@
   form.submit();
 }
 
+function validate_delete_study_text() {
+  if ($("#study-alias").val() == "{{study_alias}}") {
+    $('#delete-study-button').prop('disabled', false);
+  } else {
+    $('#delete-study-button').prop('disabled', true);
+  }
+}
+
+function delete_study() {
+  if ($("#study-alias").val() != "{{study_alias}}") {
+    alert("The added name doesn't match the study alias");
+    return false;
+  }
+  if (confirm('Are you sure you want to delete "{{study_title}}"?')) {
+    var form = $("<form>")
+    .attr("action", window.location.href)
+    .attr("method", "post")
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "study_id")
+    .attr("value", {{study.id}}))
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "action")
+    .attr("value", "delete_study"));
+    $("body").append(form);
+    form.submit();
+  }
+}
+
 function delete_sample_template() {
   sample_template_id = {{study.sample_template}};
   if (confirm('Are you sure you want to delete sample template ID: ' + sample_template_id + '?')) {
@@ -548,6 +578,7 @@ <h2><i>{{study_alias}}</i></h2>
         <a class="btn btn-default glyphicon glyphicon-edit" href="/study/edit/{{study.id}}" title="Edit the study information" style="margin:5px; word-spacing: -10px;"> Edit</a>
       {% end %}
       <a href="/study/upload/{{study.id}}" class="btn btn-default glyphicon glyphicon-upload" title="Upload study files" style="margin:5px; word-spacing: -10px;"> Upload</a>
+      <a class="btn btn-danger glyphicon glyphicon-trash" style="display: inline-block;" data-toggle="modal" data-target="#delete-study"> Delete-study</a>
     </td>
   </tr>
 </table>
@@ -580,4 +611,24 @@ <h2><i>{{study_alias}}</i></h2>
   {% end %}
 </div>
 
+
+<div class="modal fade delete-study" tabindex="-1" role="dialog" id="delete-study">
+  <div class="modal-dialog modal-sm">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
+        <h3>Deleting:<br/></h3><h4>{{study_title}}</h4>
+      </div>
+      <div class="modal-body">
+        You will only be able to delete a study that has no data associated with it.
+      </div>
+      <div class="modal-footer">
+        To continue you need to write the alias name of the study:
+        <input type="text" name="study-alias" id="study-alias" onkeyup="validate_delete_study_text();">
+        <button class="btn btn-danger glyphicon glyphicon-trash" onclick="delete_study();" id="delete-study-button" disabled></button>
+      </div>
+    </div>
+  </div>
+</div>
+
 {% end %}

qiita_pet/test/test_study_handlers.py

@@ -385,6 +385,15 @@ class TestEBISubmitHandler(TestHandlerBase):
 class TestDelete(TestHandlerBase):
     database = True
 
+    def test_delete_study(self):
+        response = self.post('/study/description/1',
+                             {'study_id': 1,
+                              'action': 'delete_study'})
+        self.assertEqual(response.code, 200)
+
+        # checking that the action was sent
+        self.assertIn("Couldn't remove study", response.body)
+
     def test_delete_sample_template(self):
         response = self.post('/study/description/1',
                              {'sample_template_id': 1,