Merge pull request #1034 from antgonza/delete-process-data

Delete process data

Author: squirrelo

qiita_db/data.py

@@ -1257,6 +1257,61 @@ def create(cls, processed_params_table, processed_params_id, filepaths,
         pd.add_filepaths(filepaths, conn_handler)
         return cls(pd_id)
 
+    @classmethod
+    def delete(cls, processed_data_id):
+        """Removes the processed data with id processed_data_id
+
+        Parameters
+        ----------
+        processed_data_id : int
+            The processed data id
+
+        Raises
+        ------
+        QiitaDBStatusError
+            If the processed data status is not sandbox
+        QiitaDBError
+            If the processed data has (meta)analyses
+        """
+        if cls(processed_data_id).status != 'sandbox':
+            raise QiitaDBStatusError(
+                "Illegal operation on non sandbox processed data")
+
+        conn_handler = SQLConnectionHandler()
+
+        analyses = [str(n[0]) for n in conn_handler.execute_fetchall(
+            "SELECT DISTINCT name FROM qiita.analysis JOIN "
+            "qiita.analysis_sample USING (analysis_id) WHERE "
+            "processed_data_id = {0} ORDER BY name".format(processed_data_id))]
+
+        if analyses:
+            raise QiitaDBError(
+                "Processed data %d cannot be removed because it is linked to "
+                "the following (meta)analysis: %s" % (processed_data_id,
+                                                      ', '.join(analyses)))
+
+        # delete
+        queue = "delete_processed_data_%d" % processed_data_id
+        conn_handler.create_queue(queue)
+
+        sql = ("DELETE FROM qiita.preprocessed_processed_data WHERE "
+               "processed_data_id = {0}".format(processed_data_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.processed_filepath WHERE "
+               "processed_data_id = {0}".format(processed_data_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.study_processed_data WHERE "
+               "processed_data_id = {0}".format(processed_data_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.processed_data WHERE "
+               "processed_data_id = {0}".format(processed_data_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        conn_handler.execute_queue(queue)
+
     @property
     def preprocessed_data(self):
         r"""The preprocessed data id used to generate the processed data"""

qiita_db/test/test_data.py

@@ -785,6 +785,29 @@ def test_create(self):
         # preprocessed_data_id, processed_Data_id
         self.assertEqual(obs, [[1, 2]])
 
+    def test_delete(self):
+        """Correctly deletes a processed data"""
+        # testing regular delete
+        pd = ProcessedData.create(self.params_table, self.params_id,
+                                  self.filepaths,
+                                  preprocessed_data=self.preprocessed_data,
+                                  processed_date=self.date)
+        ProcessedData.delete(pd.id)
+
+        # testing that it raises an error if ID doesn't exist
+        with self.assertRaises(QiitaDBUnknownIDError):
+            ProcessedData.delete(pd.id)
+
+        # testing that we can not remove cause the processed data != sandbox
+        with self.assertRaises(QiitaDBStatusError):
+            ProcessedData.delete(1)
+
+        # testing that we can not remove cause processed data has analyses
+        pd = ProcessedData(1)
+        pd.status = 'sandbox'
+        with self.assertRaises(QiitaDBError):
+            ProcessedData.delete(1)
+
     def test_create_no_date(self):
         """Correctly adds a processed data with no date on it"""
         # All the other settings have been already tested on test_create

qiita_pet/handlers/study_handlers/description_handlers.py

@@ -697,6 +697,33 @@ def delete_prep_template(self, study, user, callback):
 
         callback((msg, msg_level, 'raw_data_tab', prep_id, None))
 
+    def delete_processed_data(self, study, user, callback):
+        """Delete the selected processed data
+
+        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
+        """
+        pd_id = int(self.get_argument('processed_data_id'))
+
+        try:
+            ProcessedData.delete(pd_id)
+            msg = ("Processed data %d has been deleted" % pd_id)
+            msg_level = "success"
+            pd_id = None
+        except Exception as e:
+            msg = ("Couldn't remove processed data %d: %s" %
+                   (pd_id, str(e)))
+            msg_level = "danger"
+
+        callback((msg, msg_level, 'processed_data_tab', pd_id, None))
+
     @authenticated
     def get(self, study_id):
         study, user, full_access = self._get_study_and_check_access(study_id)
@@ -728,7 +755,8 @@ def post(self, study_id):
             make_sandbox=self.make_sandbox,
             update_investigation_type=self.update_investigation_type,
             delete_raw_data=self.delete_raw_data,
-            delete_prep_template=self.delete_prep_template)
+            delete_prep_template=self.delete_prep_template,
+            delete_processed_data=self.delete_processed_data)
 
         # Get the action that we need to perform
         action = self.get_argument("action", None)

qiita_pet/templates/study_description.html

@@ -222,6 +222,26 @@
   }
 }
 
+function delete_processed_data(processed_data_id) {
+  if (confirm('Are you sure you want to delete processed data ID: ' + processed_data_id + '?')) {
+    var form = $("<form>")
+    .attr("action", window.location.href)
+    .attr("method", "post")
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "processed_data_id")
+    .attr("value", processed_data_id))
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "action")
+    .attr("value", "delete_processed_data"));
+    $("body").append(form);
+    form.submit();
+  } else {
+    return false;
+  }
+}
+
 function make_public(pd_id) {
   if (confirm("Are you sure you want to make this study public?")) {
     var form = $("<form>")

qiita_pet/templates/study_description_templates/processed_data_tab.html

@@ -6,10 +6,13 @@
       <li class="active"><a href="#add_processed_data_tab" role="tab" data-toggle="tab">Add processed data</a></li>
       <!-- Create the tabs for each processed data -->
       {% for pd_id, pd, (class_icon1, class_icon2, color) in available_processed_data %}
-        <li><a href="#processed_data_info_{{pd_id}}" role="tab" data-toggle="tab">ID: {{pd_id}}&nbsp;
-          <div class="{{class_icon1}}" style="color: {{color}};"></div>
-          <div class="{{class_icon2}}" style="color: {{color}};"></div>
-        </a></li>
+        <li>
+          <a href="#processed_data_info_{{pd_id}}" role="tab" data-toggle="tab">ID: {{pd_id}}&nbsp;
+            <div class="{{class_icon1}}" style="color: {{color}};"></div>
+            <div class="{{class_icon2}}" style="color: {{color}};"></div>
+            <button class="close" title="Remove this processed data" type="button" onclick="delete_processed_data({{pd_id}})">&nbsp; ×</button>
+          </a>
+        </li>
       {% end %}
     </ul>
     <!-- Create the tab panes -->