Merge pull request #1175 from antgonza/delete-analysis

Delete analysis

Author: adamrp

qiita_db/analysis.py

@@ -32,7 +32,7 @@
 from .base import QiitaStatusObject
 from .data import ProcessedData
 from .study import Study
-from .exceptions import QiitaDBStatusError, QiitaDBError
+from .exceptions import QiitaDBStatusError, QiitaDBError, QiitaDBUnknownIDError
 from .util import (convert_to_id, get_work_base_dir,
                    get_mountpoint, insert_filepaths)
 
@@ -66,9 +66,13 @@ class Analysis(QiitaStatusObject):
     unshare
     build_files
     summary_data
+    exists
+    create
+    delete
     """
 
     _table = "analysis"
+    _analysis_id_column = 'analysis_id'
 
     def _lock_check(self, conn_handler):
         """Raises QiitaDBStatusError if analysis is not in_progress"""
@@ -165,6 +169,73 @@ def create(cls, owner, name, description, parent=None, from_default=False):
         a_id = conn_handler.execute_queue(queue)[0]
         return cls(a_id)
 
+    @classmethod
+    def delete(cls, _id):
+        """Deletes an analysis
+
+        Parameters
+        ----------
+        _id : int
+            The analysis id
+
+        Raises
+        ------
+        QiitaDBUnknownIDError
+            If the analysis id doesn't exist
+        """
+        # check if the analysis exist
+        if not cls.exists(_id):
+            raise QiitaDBUnknownIDError(_id, "analysis")
+
+        queue = "delete_analysis_%d" % _id
+        conn_handler = SQLConnectionHandler()
+        conn_handler.create_queue(queue)
+
+        sql = ("DELETE FROM qiita.analysis_filepath WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.analysis_workflow WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.analysis_sample WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        sql = ("DELETE FROM qiita.collection_analysis WHERE "
+               "{0} = {1}".format(cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        # TODO: issue #1176
+
+        sql = ("DELETE FROM qiita.{0} WHERE "
+               "{1} = {2}".format(cls._table, cls._analysis_id_column, _id))
+        conn_handler.add_to_queue(queue, sql)
+
+        conn_handler.execute_queue(queue)
+
+    @classmethod
+    def exists(cls, analysis_id):
+        r"""Checks if the given analysis _id exists
+
+        Parameters
+        ----------
+        analysis_id : int
+            The id of the analysis we are searching for
+
+        Returns
+        -------
+        bool
+            True if exists, false otherwise.
+        """
+        conn_handler = SQLConnectionHandler()
+
+        return conn_handler.execute_fetchone(
+            "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE "
+            "{1}=%s)".format(cls._table, cls._analysis_id_column),
+            (analysis_id, ))[0]
+
     # ---- Properties ----
     @property
     def owner(self):

qiita_db/test/test_analysis.py

@@ -12,7 +12,8 @@
 from qiita_db.analysis import Analysis, Collection
 from qiita_db.job import Job
 from qiita_db.user import User
-from qiita_db.exceptions import QiitaDBStatusError, QiitaDBError
+from qiita_db.exceptions import (QiitaDBStatusError, QiitaDBError,
+                                 QiitaDBUnknownIDError)
 from qiita_db.util import get_mountpoint, get_count
 from qiita_db.study import Study, StudyPerson
 from qiita_db.data import ProcessedData
@@ -145,6 +146,21 @@ def test_create_from_default(self):
                [new_id, 1, '1.SKM4.640180']]
         self.assertEqual(obs, exp)
 
+    def test_exists(self):
+        self.assertTrue(Analysis.exists(1))
+        new_id = get_count("qiita.analysis") + 1
+        self.assertFalse(Analysis.exists(new_id))
+
+    def test_delete(self):
+        # successful delete
+        total_analyses = get_count("qiita.analysis")
+        Analysis.delete(1)
+        self.assertEqual(total_analyses - 1, get_count("qiita.analysis"))
+
+        # no possible to delete
+        with self.assertRaises(QiitaDBUnknownIDError):
+            Analysis.delete(total_analyses + 1)
+
     def test_retrieve_owner(self):
         self.assertEqual(self.analysis.owner, "test@foo.bar")
 

qiita_pet/handlers/analysis_handlers.py

@@ -31,6 +31,7 @@
                            filepath_ids_to_rel_paths)
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.study import Study
+from qiita_db.logger import LogEntry
 
 SELECT_SAMPLES = 2
 SELECT_COMMANDS = 3
@@ -153,21 +154,54 @@ def get(self, analysis_id):
             dropped[data_type].append((Study(study).title, len(samples),
                                        ', '.join(samples)))
 
-        self.render("analysis_results.html",
+        self.render("analysis_results.html", analysis_id=analysis_id,
                     jobres=jobres, aname=analysis.name, dropped=dropped,
                     basefolder=get_db_files_base_dir())
 
+    @authenticated
+    def post(self, analysis_id):
+        analysis_id = int(analysis_id.split("/")[0])
+        analysis_id_sent = int(self.get_argument('analysis_id'))
+        action = self.get_argument('action')
+
+        if analysis_id != analysis_id_sent or action != 'delete_analysis':
+            raise QiitaPetAuthorizationError(
+                self.current_user.id,
+                'analysis/results/%d-delete' % analysis_id)
+
+        analysis = Analysis(analysis_id)
+        analysis_name = analysis.name
+        check_analysis_access(self.current_user, analysis)
+
+        try:
+            Analysis.delete(analysis_id)
+            msg = ("Analysis <b><i>%s</i></b> has been deleted." % (
+                analysis_name))
+            level = "success"
+        except Exception as e:
+            e = str(e)
+            msg = ("Couldn't remove <b><i>%s</i></b> analysis: %s" % (
+                analysis_name, e))
+            level = "danger"
+            LogEntry.create('Runtime', "Couldn't remove analysis ID %d: %s" %
+                            (analysis_id, e))
+
+        self.redirect(u"/analysis/show/?level=%s&message=%s" % (level, msg))
+
 
 class ShowAnalysesHandler(BaseHandler):
     """Shows the user's analyses"""
     @authenticated
     def get(self):
+        message = self.get_argument('message', '')
+        level = self.get_argument('level', '')
         user = self.current_user
 
         analyses = [Analysis(a) for a in
                     user.shared_analyses | user.private_analyses]
 
-        self.render("show_analyses.html", analyses=analyses)
+        self.render("show_analyses.html", analyses=analyses, message=message,
+                    level=level)
 
 
 class ResultsHandler(StaticFileHandler, BaseHandler):

qiita_pet/templates/analysis_results.html

@@ -11,7 +11,16 @@
 
 
 <div class="row">
-  <h1>&nbsp;Analysis: <u>{{aname}}</u></h1>
+    <table border="0">
+      <tr>
+        <td><h1>&nbsp;Analysis: <u>{{aname}}</u></h1></td>
+        <td width="20px"></td>
+        <td>
+          <h1><a class="btn btn-danger glyphicon glyphicon-trash" onclick="delete_analysis();"></a></h1>
+        </td>
+      </tr>
+    </table>
+  </h1>
 </div>
 
 
@@ -74,4 +83,27 @@ <h3 style="color:red">ERROR</h3>
       <iframe id="resframe" name="resframe" width="100%" height="900" frameBorder=0></iframe>
   </div>
 </div>
+
+
+<script>
+
+function delete_analysis() {
+  if (confirm('Are you sure you want to delete analysis: {{aname}}?')) {
+    var form = $("<form>")
+    .attr("action", window.location.href)
+    .attr("method", "post")
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "analysis_id")
+    .attr("value", {{analysis_id}}))
+    .append($("<input>")
+    .attr("type", "hidden")
+    .attr("name", "action")
+    .attr("value", "delete_analysis"));
+    $("body").append(form);
+    form.submit();
+  }
+}
+
+</script>
 {%end%}