Merge branch 'master' of https://github.com/biocore/qiita into unify-update-category

Author: josenavas

qiita_db/data.py

@@ -103,7 +103,7 @@ class BaseData(QiitaObject):
     --------
     RawData
     PreprocessedData
-    PreprocessedData
+    ProcessedData
     """
     _filepath_table = "filepath"
 
@@ -807,6 +807,73 @@ def create(cls, study, preprocessed_params_table, preprocessed_params_id,
         ppd.add_filepaths(filepaths, conn_handler)
         return ppd
 
+    @classmethod
+    def delete(cls, ppd_id):
+        """Removes the preprocessed data with id ppd_id
+
+        Parameters
+        ----------
+        ppd_id : int
+            The preprocessed data id
+
+        Raises
+        ------
+        QiitaDBStatusError
+            If the preprocessed data status is not sandbox or if the
+            preprocessed data EBI and VAMPS submission is not in a valid state
+            ['not submitted', 'failed']
+        QiitaDBError
+            If the preprocessed data has been processed
+        """
+        valid_submission_states = ['not submitted', 'failed']
+        ppd = cls(ppd_id)
+        if ppd.status != 'sandbox':
+            raise QiitaDBStatusError(
+                "Illegal operation on non sandboxed preprocessed data")
+        elif ppd.submitted_to_vamps_status() not in valid_submission_states:
+            raise QiitaDBStatusError(
+                "Illegal operation. This preprocessed data has or is being "
+                "added to VAMPS.")
+        elif ppd.submitted_to_insdc_status() not in valid_submission_states:
+            raise QiitaDBStatusError(
+                "Illegal operation. This preprocessed data has or is being "
+                "added to EBI.")
+
+        conn_handler = SQLConnectionHandler()
+
+        processed_data = [str(n[0]) for n in conn_handler.execute_fetchall(
+            "SELECT processed_data_id FROM qiita.preprocessed_processed_data "
+            "WHERE preprocessed_data_id = {0} ORDER BY "
+            "processed_data_id".format(ppd_id))]
+
+        if processed_data:
+            raise QiitaDBError(
+                "Preprocessed data %d cannot be removed because it was used "
+                "to generate the following processed data: %s" % (
+                    ppd_id, ', '.join(processed_data)))
+
+        # delete
+        queue = "delete_preprocessed_data_%d" % ppd_id
+        conn_handler.create_queue(queue)
+
+        sql = ("DELETE FROM qiita.prep_template_preprocessed_data WHERE "
+               "preprocessed_data_id = {0}".format(ppd_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.preprocessed_filepath WHERE "
+               "preprocessed_data_id = {0}".format(ppd_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.study_preprocessed_data WHERE "
+               "preprocessed_data_id = {0}".format(ppd_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.preprocessed_data WHERE "
+               "preprocessed_data_id = {0}".format(ppd_id))
+        conn_handler.add_to_queue(queue, sql)
+
+        conn_handler.execute_queue(queue)
+
     @property
     def processed_data(self):
         r"""The processed data list generated from this preprocessed data"""
@@ -1275,7 +1342,7 @@ def delete(cls, processed_data_id):
         """
         if cls(processed_data_id).status != 'sandbox':
             raise QiitaDBStatusError(
-                "Illegal operation on non sandbox processed data")
+                "Illegal operation on non sandboxed processed data")
 
         conn_handler = SQLConnectionHandler()
 

qiita_db/test/test_data.py

@@ -478,6 +478,48 @@ def test_create_data_type_only(self):
         # preprocessed_data_id, filepath_id
         self.assertEqual(obs, [[3, obs_id - 1], [3, obs_id]])
 
+    def test_delete_basic(self):
+        """Correctly deletes a preprocessed data"""
+        # testing regular delete
+        ppd = PreprocessedData.create(
+            self.study, self.params_table,
+            self.params_id, self.filepaths, prep_template=self.prep_template,
+            ebi_submission_accession=self.ebi_submission_accession,
+            ebi_study_accession=self.ebi_study_accession)
+        PreprocessedData.delete(ppd.id)
+
+        # testing that the deleted preprocessed data can't be instantiated
+        with self.assertRaises(QiitaDBUnknownIDError):
+            PreprocessedData(ppd.id)
+        # and for completeness testing that it raises an error if ID
+        # doesn't exist
+        with self.assertRaises(QiitaDBUnknownIDError):
+            PreprocessedData.delete(ppd.id)
+
+        # testing that we can not remove cause the preprocessed data != sandbox
+        with self.assertRaises(QiitaDBStatusError):
+            PreprocessedData.delete(1)
+
+    def test_delete_advanced(self):
+        # testing that we can not remove cause preprocessed data has been
+        # submitted to EBI or VAMPS
+        ppd = PreprocessedData.create(
+            self.study, self.params_table,
+            self.params_id, self.filepaths, prep_template=self.prep_template,
+            ebi_submission_accession=self.ebi_submission_accession,
+            ebi_study_accession=self.ebi_study_accession)
+
+        # fails due to VAMPS submission
+        ppd.update_vamps_status('success')
+        with self.assertRaises(QiitaDBStatusError):
+            PreprocessedData.delete(ppd.id)
+        ppd.update_vamps_status('failed')
+
+        # fails due to EBI submission
+        ppd.update_insdc_status('success', 'AAAA', 'AAAA')
+        with self.assertRaises(QiitaDBStatusError):
+            PreprocessedData.delete(ppd.id)
+
     def test_create_error_dynamic_table(self):
         """Raises an error if the preprocessed_params_table does not exist"""
         with self.assertRaises(IncompetentQiitaDeveloperError):

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_preprocessed_data(self, study, user, callback):
+        """Delete the selected preprocessed 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
+        """
+        ppd_id = int(self.get_argument('preprocessed_data_id'))
+
+        try:
+            PreprocessedData.delete(ppd_id)
+            msg = ("Preprocessed data %d has been deleted" % ppd_id)
+            msg_level = "success"
+            ppd_id = None
+        except Exception as e:
+            msg = ("Couldn't remove preprocessed data %d: %s" %
+                   (ppd_id, str(e)))
+            msg_level = "danger"
+
+        callback((msg, msg_level, 'preprocessed_data_tab', ppd_id, None))
+
     def delete_processed_data(self, study, user, callback):
         """Delete the selected processed data
 
@@ -756,6 +783,7 @@ def post(self, study_id):
             update_investigation_type=self.update_investigation_type,
             delete_raw_data=self.delete_raw_data,
             delete_prep_template=self.delete_prep_template,
+            delete_preprocessed_data=self.delete_preprocessed_data,
             delete_processed_data=self.delete_processed_data)
 
         # Get the action that we need to perform

qiita_pet/templates/study_description.html

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

qiita_pet/templates/study_description_templates/preprocessed_data_tab.html

@@ -9,6 +9,7 @@
         <li><a href="#preprocessed_data_info_{{ppd_id}}" role="tab" data-toggle="tab">ID: {{ppd_id}}&nbsp;
           <div class="{{class_icon1}}" style="color: {{color}};"></div>
           <div class="{{class_icon2}}" style="color: {{color}};"></div>
+          <button class="close" title="Remove this preprocessed data" type="button" onclick="delete_preprocessed_data({{ppd_id}})">&nbsp; ×</button>
         </a></li>
       {% end %}
     </ul>