Merge branch 'dev' of https://github.com/biocore/qiita into dev

Author: antgonza

qiita_db/processing_job.py

@@ -1636,6 +1636,9 @@ def _update_and_launch_children(self, mapping):
         # Submit all the children that already have all the input parameters
         for c in ready:
             c.submit()
+            # some jobs create several children jobs/validators and this can
+            # clog the submission process; giving it a second to avoid this
+            sleep(1)
 
     @property
     def outputs(self):

qiita_db/study.py

@@ -57,6 +57,7 @@ class Study(qdb.base.QiitaObject):
     title
     owner
     specimen_id_column
+    autoloaded
 
     Methods
     -------
@@ -77,7 +78,8 @@ class Study(qdb.base.QiitaObject):
     _table = "study"
     _portal_table = "study_portal"
     # The following columns are considered not part of the study info
-    _non_info = frozenset(["email", "study_title", "ebi_study_accession"])
+    _non_info = frozenset(["email", "study_title", "ebi_study_accession",
+                           "autoloaded"])
 
     def _lock_non_sandbox(self):
         """Raises QiitaDBStatusError if study is non-sandboxed"""
@@ -481,6 +483,34 @@ def insert_tags(cls, user, tags):
             qdb.sql_connection.TRN.execute()
 
 # --- Attributes ---
+    @property
+    def autoloaded(self):
+        """Returns if the study was autoloaded
+
+        Returns
+        -------
+        bool
+            If the study was autoloaded or not
+        """
+        with qdb.sql_connection.TRN:
+            sql = """SELECT autoloaded FROM qiita.{0}
+                     WHERE study_id = %s""".format(self._table)
+            qdb.sql_connection.TRN.add(sql, [self._id])
+            return qdb.sql_connection.TRN.execute_fetchlast()
+
+    @autoloaded.setter
+    def autoloaded(self, value):
+        """Sets the autoloaded status of the study
+
+        Parameters
+        ----------
+        value : bool
+            Whether the study was autoloaded
+        """
+        sql = """UPDATE qiita.{0} SET autoloaded = %s
+                 WHERE study_id = %s""".format(self._table)
+        qdb.sql_connection.perform_as_transaction(sql, [value, self._id])
+
     @property
     def title(self):
         """Returns the title of the study

qiita_db/support_files/patches/80.sql

@@ -0,0 +1,4 @@
+-- Nov 10, 2020
+-- Add a flag to the studies to see if the study was submitted by Qiita or downloaded by EBI
+
+ALTER TABLE qiita.study ADD autoloaded BOOL NOT NULL DEFAULT false;