Merge pull request #5747 from nsoranzo/typos_refactors

Typo fixes and small refactors

config/job_conf.xml.sample_advanced

@@ -121,7 +121,7 @@
             <!-- The Kubernetes (k8s) plugin allows to send jobs to a k8s cluster which shares filesystem with Galaxy.
 
                  This requires installing pykube. Install pykube by activating Galaxy's virtual
-                 and then executing the following pip command:
+                 environment and then executing the following pip command:
 
                  pip install pykube==0.15.0
 

doc/source/admin/nginx.md

@@ -69,10 +69,9 @@ http {
     gzip on;
     gzip_http_version 1.1;
     gzip_vary on;
-    gzip_comp_level 4;
+    gzip_comp_level 6;
     gzip_proxied any;
     gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
-    gzip_comp_level 6;
     gzip_buffers 16 8k;
 
     # allow up to 3 minutes for Galaxy to respond to slow requests before timing out

doc/source/admin/scaling.md

@@ -193,7 +193,7 @@ uwsgi:
     # fix up signal handling
     die-on-term: true
     hook-master-start: unix_signal:2 gracefully_kill_them_all
-    hook-master-start: unix_signal:5 gracefully_kill_them_all
+    hook-master-start: unix_signal:15 gracefully_kill_them_all
 
     # listening options
 
@@ -398,7 +398,7 @@ $ ./scripts/galaxy-main -c config/galaxy.yml --server-name handler2 --daemonize
 However, a better option to managing processes by hand is to use a process manager as documented in the [Starting and
 Stopping](#starting-and-stopping) section.
 
-#### uWSGI Minutiea
+#### uWSGI Minutiae
 
 **Threads**
 

lib/galaxy/datatypes/sniff.py

@@ -97,21 +97,6 @@ def stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd):
     return stream_to_open_named_file(stream, fd, temp_name, **kwd)
 
 
-def check_newlines(fname, bytes_to_read=52428800):
-    """
-    Determines if there are any non-POSIX newlines in the first
-    number_of_bytes (by default, 50MB) of the file.
-    """
-    CHUNK_SIZE = 2 ** 20
-    with open(fname, 'r') as f:
-        for chunk in f.read(CHUNK_SIZE):
-            if f.tell() > bytes_to_read:
-                break
-            if chunk.count('\r'):
-                return True
-    return False
-
-
 def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
     """
     Converts in place a file from universal line endings

lib/galaxy/webapps/config_manage.py

@@ -1,7 +1,6 @@
 from __future__ import absolute_import, print_function
 
 import argparse
-import copy
 import os
 import shutil
 import string
@@ -56,12 +55,12 @@
     }),
     ('buffer-size', {
         'desc': """By default uWSGI allocates a very small buffer (4096 bytes) for the headers of each request. If you start receiving "invalid request block size" in your logs, it could mean you need a bigger buffer. Increase it up to 65535.""",
-        'default': '4096',
+        'default': 4096,
         'type': 'int',
     }),
     ('processes', {
         'desc': """Number of web server (worker) processes to fork after the application has loaded.""",
-        'default': '1',
+        'default': 1,
         'type': 'int',
     }),
     ('threads', {
@@ -71,7 +70,7 @@
     }),
     ('offload-threads', {
         'desc': """Number of threads for serving static content and handling internal routing requests.""",
-        'default': '2',
+        'default': 2,
         'type': 'int',
     }),
     ('static-map.1', {
@@ -88,8 +87,8 @@
     }),
     ('master', {
         'desc': """Enable the master process manager. Disabled by default for maximum compatibility with CTRL+C, but should be enabled for use with --daemon and/or production deployments.""",
-        'default': 'false',
-        'type': 'str',
+        'default': False,
+        'type': 'bool',
     }),
     ('virtualenv', {
         'desc': """Path to the application's Python virtual environment.""",
@@ -108,8 +107,8 @@
     }),
     ('die-on-term', {
         'desc': """Cause uWSGI to respect the traditional behavior of dying on SIGTERM (its default is to brutally reload workers)""",
-        'default': 'true',
-        'type': 'str',
+        'default': True,
+        'type': 'bool',
     }),
     ('hook-master-start.1', {
         'key': 'hook-master-start',
@@ -125,13 +124,13 @@
     }),
     ('py-call-osafterfork', {
         'desc': """Feature necessary for proper mule signal handling""",
-        'default': 'true',
-        'type': 'str',
+        'default': True,
+        'type': 'bool',
     }),
     ('enable-threads', {
         'desc': """Ensure application threads will run if `threads` is unset.""",
-        'default': 'true',
-        'type': 'str',
+        'default': True,
+        'type': 'bool',
     }),
     # ('route-uri', {
     #     'default': '^/proxy/ goto:proxy'
@@ -149,7 +148,7 @@
     #     'default': "['log:Proxy ${HTTP_HOST} to ${TARGET_HOST}', 'httpdumb:${TARGET_HOST}']",
     # }),
     # ('http-raw-body', {
-    #     'default': 'True'
+    #     'default': True
     # }),
 ])
 
@@ -664,8 +663,7 @@ def _replace_file(args, f, app_desc, from_path, to_path):
 def _build_sample_yaml(args, app_desc):
     schema = app_desc.schema
     f = StringIO()
-    options = copy.deepcopy(UWSGI_OPTIONS)
-    for key, value in options.items():
+    for key, value in UWSGI_OPTIONS.items():
         for field in ["desc", "default"]:
             if field not in value:
                 continue
@@ -684,7 +682,7 @@ def _build_sample_yaml(args, app_desc):
         description = description.lstrip()
         as_comment = "\n".join(["# %s" % l for l in description.split("\n")]) + "\n"
         f.write(as_comment)
-    _write_sample_section(args, f, 'uwsgi', Schema(options), as_comment=False, uwsgi_hack=True)
+    _write_sample_section(args, f, 'uwsgi', Schema(UWSGI_OPTIONS), as_comment=False, uwsgi_hack=True)
     _write_sample_section(args, f, app_desc.app_name, schema)
     destination = os.path.join(args.galaxy_root, app_desc.sample_destination)
     _write_to_file(args, f, destination)
@@ -744,6 +742,8 @@ def _write_option(args, f, key, option_value, as_comment=False, uwsgi_hack=False
         comment += "\n"
     as_comment_str = "#" if as_comment else ""
     if uwsgi_hack:
+        if option.get("type", "str") == "bool":
+            value = str(value).lower()
         key_val_str = "%s: %s" % (key, value)
     else:
         key_val_str = yaml.dump({key: value}, width=float("inf")).lstrip("{").rstrip("\n}")

lib/galaxy/webapps/galaxy/api/remote_files.py

@@ -8,8 +8,14 @@
 from operator import itemgetter
 
 from galaxy import exceptions
-from galaxy.util import jstree, unicodify
-from galaxy.util.path import safe_path, safe_walk
+from galaxy.util import (
+    jstree,
+    smart_str
+)
+from galaxy.util.path import (
+    safe_path,
+    safe_walk
+)
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web.base.controller import BaseAPIController
 
@@ -135,13 +141,13 @@ def __create_jstree(self, directory, disable='folders', whitelist=None):
             for (dirpath, dirnames, filenames) in safe_walk(directory, whitelist=whitelist):
                 for dirname in dirnames:
                     dir_path = os.path.relpath(os.path.join(dirpath, dirname), directory)
-                    dir_path_hash = hashlib.sha1(unicodify(dir_path).encode('utf-8')).hexdigest()
+                    dir_path_hash = hashlib.sha1(smart_str(dir_path)).hexdigest()
                     disabled = True if disable == 'folders' else False
                     jstree_paths.append(jstree.Path(dir_path, dir_path_hash, {'type': 'folder', 'state': {'disabled': disabled}, 'li_attr': {'full_path': dir_path}}))
 
                 for filename in filenames:
                     file_path = os.path.relpath(os.path.join(dirpath, filename), directory)
-                    file_path_hash = hashlib.sha1(unicodify(file_path).encode('utf-8')).hexdigest()
+                    file_path_hash = hashlib.sha1(smart_str(file_path)).hexdigest()
                     disabled = True if disable == 'files' else False
                     jstree_paths.append(jstree.Path(file_path, file_path_hash, {'type': 'file', 'state': {'disabled': disabled}, 'li_attr': {'full_path': file_path}}))
         else:

test/api/test_workflows.py

@@ -1845,7 +1845,7 @@ def test_workflow_rerun_with_use_cached_job(self):
                 first_wf_output = self._get("datasets/%s" % run_workflow_response['outputs'][0]).json()
                 second_wf_output = self._get("datasets/%s" % new_workflow_response['outputs'][0]).json()
                 assert first_wf_output['file_name'] == second_wf_output['file_name'], \
-                    "first output :\n%s\nsecond output: %s" % (first_wf_output, second_wf_output)
+                    "first output:\n%s\nsecond output:\n%s" % (first_wf_output, second_wf_output)
 
     @skip_without_tool('cat1')
     def test_nested_workflow_rerun_with_use_cached_job(self):
@@ -1860,7 +1860,7 @@ def test_nested_workflow_rerun_with_use_cached_job(self):
             run_jobs_summary = self._run_jobs(workflow_run_description, history_id=history_id_one)
             self.dataset_populator.wait_for_history(history_id_one, assert_ok=True)
             workflow_request = run_jobs_summary.workflow_request
-            # We copy the inputs to a new history and re-reun the workflow
+            # We copy the inputs to a new history and re-run the workflow
             inputs = json.loads(workflow_request['inputs'])
             dataset_type = inputs['outer_input']['src']
             dataset_id = inputs['outer_input']['id']