Merge branch 'release_20.01' into dev

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -66,12 +66,13 @@ def get_keys_from_dict(dl, keys_list):
     """
     This function builds a list using the keys from nest dictionaries
     """
-    assert isinstance(keys_list, list)
     if isinstance(dl, dict):
-        keys_list += list(dl.keys())
-        list(map(lambda x: get_keys_from_dict(x, keys_list), dl.values()))
+        keys_list.extend(dl.keys())
+        for x in dl.values():
+            get_keys_from_dict(x, keys_list)
     elif isinstance(dl, list):
-        list(map(lambda x: get_keys_from_dict(x, keys_list), dl))
+        for x in dl:
+            get_keys_from_dict(x, keys_list)
 
 
 class RuleValidator(object):

lib/galaxy/managers/sharable.py

@@ -152,7 +152,7 @@ def share_with(self, item, user, flush=True):
         # precondition: user has been validated
         # allow user to be a list and call recursivly
         if isinstance(user, list):
-            return list(map(lambda user: self.share_with(item, user, flush=False), user))
+            return [self.share_with(item, _, flush=False) for _ in user]
         # get or create
         existing = self.get_share_assocs(item, user=user)
         if existing:
@@ -181,7 +181,7 @@ def unshare_with(self, item, user, flush=True):
         Delete a user share (or list of shares) from the database.
         """
         if isinstance(user, list):
-            return list(map(lambda user: self.unshare_with(item, user, flush=False), user))
+            return [self.unshare_with(item, _, flush=False) for _ in user]
         # Look for and delete sharing relation for user.
         user_share_assoc = self.get_share_assocs(item, user=user)[0]
         self.session().delete(user_share_assoc)

lib/galaxy/tool_util/verify/interactor.py

@@ -1092,7 +1092,7 @@ def to_dict(self):
         return {
             "inputs": inputs_dict,
             "outputs": self.outputs,
-            "output_collections": list(map(lambda o: o.to_dict(), self.output_collections)),
+            "output_collections": [_.to_dict() for _ in self.output_collections],
             "num_outputs": self.num_outputs,
             "command_line": self.command_line,
             "command_version": self.command_version,

lib/galaxy/tools/__init__.py

@@ -2638,7 +2638,8 @@ def check_dataset_instance(input_dataset):
                 if not input_dataset_collection.collection.populated:
                     raise ToolInputsNotReadyException("An input collection is not populated.")
 
-            list(map(check_dataset_instance, input_dataset_collection.dataset_instances))
+            for dataset_instance in input_dataset_collection.dataset_instances:
+                check_dataset_instance(dataset_instance)
 
     def _add_datasets_to_history(self, history, elements, datasets_visible=False):
         datasets = []

lib/galaxy/util/__init__.py

@@ -26,6 +26,7 @@
 from datetime import datetime
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
+from functools import partial
 from hashlib import md5
 from os.path import relpath
 from xml.etree import ElementInclude, ElementTree
@@ -191,6 +192,14 @@ def caller(*params, **kparams):
     return caller
 
 
+def iter_start_of_line(fh, chunk_size=None):
+    """
+    Iterate over fh and call readline(chunk_size)
+    """
+    for line in iter(partial(fh.readline, chunk_size), ""):
+        yield line
+
+
 def file_iter(fname, sep=None):
     """
     This generator iterates over a file and yields its lines
@@ -201,9 +210,10 @@ def file_iter(fname, sep=None):
     >>> len(lines) !=  0
     True
     """
-    for line in open(fname):
-        if line and line[0] != '#':
-            yield line.split(sep)
+    with open(fname) as fh:
+        for line in fh:
+            if line and line[0] != '#':
+                yield line.split(sep)
 
 
 def file_reader(fp, chunk_size=CHUNK_SIZE):

lib/galaxy/webapps/reports/controllers/jobs.py

@@ -164,11 +164,11 @@ def filter(self, trans, user, query, column_filter):
             # We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:  # We are filtering on a date like YYYY-MM-DD
-                year, month, day = list(map(int, column_filter.split("-")))
+                year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
             if column_filter.count('-') == 1:  # We are filtering on a month like YYYY-MM
-                year, month = list(map(int, column_filter.split("-")))
+                year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
 
@@ -371,7 +371,7 @@ def specified_month_all(self, trans, **kwd):
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
 
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -472,7 +472,7 @@ def specified_month_in_error(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")

lib/galaxy/webapps/reports/controllers/users.py

@@ -61,7 +61,7 @@ def specified_month(self, trans, **kwd):
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
         specified_month = specified_date[:7]
-        year, month = list(map(int, specified_month.split("-")))
+        year, month = map(int, specified_month.split("-"))
         start_date = date(year, month, 1)
         end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
         month_label = start_date.strftime("%B")
@@ -91,7 +91,7 @@ def specified_date(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
-        year, month, day = list(map(int, specified_date.split("-")))
+        year, month, day = map(int, specified_date.split("-"))
         start_date = date(year, month, day)
         end_date = start_date + timedelta(days=1)
         day_of_month = start_date.strftime("%d")

lib/galaxy/webapps/reports/controllers/workflows.py

@@ -64,14 +64,14 @@ def filter(self, trans, user, query, column_filter):
             # so we need to figure out which type of date we have
             if column_filter.count('-') == 2:
                 # We are filtering on a date like YYYY-MM-DD
-                year, month, day = list(map(int, column_filter.split("-")))
+                year, month, day = map(int, column_filter.split("-"))
                 start_date = date(year, month, day)
                 end_date = start_date + timedelta(days=1)
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,
                                          self.model_class.table.c.create_time < end_date))
             if column_filter.count('-') == 1:
                 # We are filtering on a month like YYYY-MM
-                year, month = list(map(int, column_filter.split("-")))
+                year, month = map(int, column_filter.split("-"))
                 start_date = date(year, month, 1)
                 end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
                 return query.filter(and_(self.model_class.table.c.create_time >= start_date,