Merge pull request #3205 from antgonza/allow-summary-update

allow artifact summary update

Author: charles-cowart

qiita_db/artifact.py

@@ -1131,10 +1131,12 @@ def set_html_summary(self, html_fp, support_dir=None):
             the HTML file
         """
         with qdb.sql_connection.TRN:
-            if self.html_summary_fp:
-                # Delete the current HTML summary
+            old_summs = self.html_summary_fp
+            to_delete_fps = []
+            if old_summs:
+                # Delete from the DB current HTML summary; below we will remove
+                # files, if necessary
                 to_delete_ids = []
-                to_delete_fps = []
                 for x in self.filepaths:
                     if x['fp_type'] in ('html_summary', 'html_summary_dir'):
                         to_delete_ids.append([x['fp_id']])
@@ -1146,17 +1148,6 @@ def set_html_summary(self, html_fp, support_dir=None):
                 # From the filepath table
                 sql = "DELETE FROM qiita.filepath WHERE filepath_id=%s"
                 qdb.sql_connection.TRN.add(sql, to_delete_ids, many=True)
-                # And from the filesystem only after the transaction is
-                # successfully completed (after commit)
-
-                def path_cleaner(fps):
-                    for fp in fps:
-                        if isfile(fp):
-                            remove(fp)
-                        else:
-                            rmtree(fp)
-                qdb.sql_connection.TRN.add_post_commit_func(
-                    path_cleaner, to_delete_fps)
 
             # Add the new HTML summary
             filepaths = [(html_fp, 'html_summary')]
@@ -1171,6 +1162,19 @@ def path_cleaner(fps):
             qdb.sql_connection.TRN.add(sql, sql_args, many=True)
             qdb.sql_connection.TRN.execute()
 
+        # to avoid deleting potentially necessary files, we are going to add
+        # that check after the previous transaction is commited
+        if to_delete_fps:
+            for x in self.filepaths:
+                if x['fp'] in to_delete_fps:
+                    to_delete_fps.remove(x['fp'])
+
+            for fp in to_delete_fps:
+                if isfile(fp):
+                    remove(fp)
+                else:
+                    rmtree(fp)
+
     @property
     def parents(self):
         """Returns the parents of the artifact

qiita_db/test/test_artifact.py

@@ -1352,6 +1352,10 @@ def test_html_summary_setter(self):
                        if x['fp_type'] == 'html_summary_dir']
         self.assertEqual(summary_dir, [])
 
+        # let's check if we update, we do _not_ remove the files
+        a.set_html_summary(exp3)
+        self.assertTrue(exists(a.html_summary_fp[1]))
+
     def test_descendants_with_jobs_one_element(self):
         artifact = qdb.artifact.Artifact.create(
             self.filepaths_root, 'FASTQ', prep_template=self.prep_template)

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -242,7 +242,7 @@ def artifact_summary_get_request(user, artifact_id):
             'errored_summary_jobs': errored_summary_jobs}
 
 
-def artifact_summary_post_request(user, artifact_id):
+def artifact_summary_post_request(user, artifact_id, force_creation=False):
     """Launches the HTML summary generation and returns the job information
 
     Parameters
@@ -251,6 +251,8 @@ def artifact_summary_post_request(user, artifact_id):
         The user making the request
     artifact_id : int or str
         The artifact id
+    force_creation : bool
+        If all jobs should be ignored and it should force creation
 
     Returns
     -------
@@ -267,7 +269,7 @@ def artifact_summary_post_request(user, artifact_id):
     command = Command.get_html_generator(artifact.artifact_type)
     jobs = artifact.jobs(cmd=command)
     jobs = [j for j in jobs if j.status in ['queued', 'running', 'success']]
-    if jobs:
+    if not force_creation and jobs:
         # The HTML summary is either being generated or already generated.
         # Return the information of that job so we only generate the HTML
         # once - Magic number 0 -> we are ensuring that there is only one