Merge branch 'dev' into remove_samples_000

.ci/flake8_lint_include_list.txt

@@ -1,4 +1,5 @@
 client/galaxy/style/source_material/circle.py
+config/
 contrib/
 cron/
 doc/parse_gx_xsd.py
@@ -21,22 +22,13 @@ lib/galaxy/jobs/command_factory.py
 lib/galaxy/jobs/datasets.py
 lib/galaxy/jobs/deferred/
 lib/galaxy/jobs/error_level.py
+lib/galaxy/jobs/handler.py
 lib/galaxy/jobs/__init__.py
 lib/galaxy/jobs/manager.py
 lib/galaxy/jobs/metrics/
+lib/galaxy/jobs/output_checker.py
 lib/galaxy/jobs/rules/
-lib/galaxy/jobs/runners/cli.py
-lib/galaxy/jobs/runners/condor.py
-lib/galaxy/jobs/runners/drmaa.py
-lib/galaxy/jobs/runners/godocker.py
-lib/galaxy/jobs/runners/kubernetes.py
-lib/galaxy/jobs/runners/local.py
-lib/galaxy/jobs/runners/pbs.py
-lib/galaxy/jobs/runners/pulsar.py
-lib/galaxy/jobs/runners/slurm.py
-lib/galaxy/jobs/runners/state_handlers/
-lib/galaxy/jobs/runners/tasks.py
-lib/galaxy/jobs/runners/util/
+lib/galaxy/jobs/runners/
 lib/galaxy/jobs/splitters/basic.py
 lib/galaxy/jobs/splitters/__init__.py
 lib/galaxy/jobs/stock_rules.py
@@ -61,16 +53,15 @@ lib/galaxy/objectstore/s3_multipart_upload.py
 lib/galaxy/objectstore/s3.py
 lib/galaxy/openid/__init__.py
 lib/galaxy/quota/
-lib/galaxy/sample_tracking/data_transfer.py
-lib/galaxy/sample_tracking/__init__.py
-lib/galaxy/sample_tracking/sample.py
+lib/galaxy/sample_tracking/
 lib/galaxy/security/
 lib/galaxy/tags/
 lib/galaxy/tools/
 lib/galaxy/util/
 lib/galaxy/version.py
 lib/galaxy/visualization/data_providers/basic.py
 lib/galaxy/visualization/data_providers/cigar.py
+lib/galaxy/visualization/data_providers/genome.py
 lib/galaxy/visualization/data_providers/__init__.py
 lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
 lib/galaxy/visualization/genome/
@@ -99,14 +90,23 @@ lib/galaxy/web/framework/middleware/xforwardedhost.py
 lib/galaxy/web/framework/webapp.py
 lib/galaxy/web/__init__.py
 lib/galaxy/web/params.py
+lib/galaxy/web/stack/
+lib/galaxy/webapps/galaxy/api/authenticate.py
+lib/galaxy/webapps/galaxy/api/forms.py
 lib/galaxy/webapps/galaxy/api/genomes.py
+lib/galaxy/webapps/galaxy/api/group_roles.py
+lib/galaxy/webapps/galaxy/api/group_users.py
+lib/galaxy/webapps/galaxy/api/groups.py
 lib/galaxy/webapps/galaxy/api/histories.py
 lib/galaxy/webapps/galaxy/api/__init__.py
 lib/galaxy/webapps/galaxy/api/jobs.py
+lib/galaxy/webapps/galaxy/api/library_contents.py
 lib/galaxy/webapps/galaxy/api/library_datasets.py
 lib/galaxy/webapps/galaxy/api/requests.py
+lib/galaxy/webapps/galaxy/api/request_types.py
 lib/galaxy/webapps/galaxy/api/roles.py
 lib/galaxy/webapps/galaxy/api/samples.py
+lib/galaxy/webapps/galaxy/api/tool_data.py
 lib/galaxy/webapps/galaxy/api/tools.py
 lib/galaxy/webapps/galaxy/api/tours.py
 lib/galaxy/webapps/galaxy/api/users.py
@@ -116,6 +116,7 @@ lib/galaxy/webapps/galaxy/config_watchers.py
 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
 lib/galaxy/webapps/galaxy/controllers/async.py
 lib/galaxy/webapps/galaxy/controllers/data_manager.py
+lib/galaxy/webapps/galaxy/controllers/dataset.py
 lib/galaxy/webapps/galaxy/controllers/error.py
 lib/galaxy/webapps/galaxy/controllers/external_services.py
 lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -124,21 +125,29 @@ lib/galaxy/webapps/galaxy/controllers/__init__.py
 lib/galaxy/webapps/galaxy/controllers/library_common.py
 lib/galaxy/webapps/galaxy/controllers/mobile.py
 lib/galaxy/webapps/galaxy/controllers/page.py
+lib/galaxy/webapps/galaxy/controllers/requests_admin.py
+lib/galaxy/webapps/galaxy/controllers/requests_common.py
 lib/galaxy/webapps/galaxy/controllers/requests.py
+lib/galaxy/webapps/galaxy/controllers/request_type.py
+lib/galaxy/webapps/galaxy/controllers/root.py
 lib/galaxy/webapps/galaxy/controllers/search.py
 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
 lib/galaxy/webapps/galaxy/controllers/userskeys.py
 lib/galaxy/webapps/galaxy/__init__.py
 lib/galaxy/webapps/__init__.py
+lib/galaxy/webapps/reports/buildapp.py
 lib/galaxy/webapps/reports/config.py
 lib/galaxy/webapps/reports/controllers/__init__.py
 lib/galaxy/webapps/reports/controllers/query.py
+lib/galaxy/webapps/reports/controllers/system.py
 lib/galaxy/webapps/reports/controllers/tools.py
 lib/galaxy/webapps/reports/__init__.py
 lib/galaxy/webapps/tool_shed/api/__init__.py
+lib/galaxy/webapps/tool_shed/buildapp.py
 lib/galaxy/webapps/tool_shed/config.py
 lib/galaxy/webapps/tool_shed/controllers/groups.py
 lib/galaxy/webapps/tool_shed/controllers/__init__.py
+lib/galaxy/webapps/tool_shed/controllers/repository.py
 lib/galaxy/webapps/tool_shed/controllers/user.py
 lib/galaxy/webapps/tool_shed/framework/__init__.py
 lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py

client/galaxy/scripts/apps/admin.js

@@ -22,6 +22,7 @@ window.app = function app(options, bootstrapped) {
             "(/)admin(/)groups": "show_groups",
             "(/)admin(/)tool_versions": "show_tool_versions",
             "(/)admin(/)quotas": "show_quotas",
+            "(/)admin(/)repositories": "show_repositories",
             "(/)admin(/)forms": "show_forms",
             "(/)admin(/)form(/)(:form_id)": "show_form"
         },
@@ -60,6 +61,17 @@ window.app = function app(options, bootstrapped) {
             );
         },
 
+        show_repositories: function() {
+            this.page.display(
+                new GridView({
+                    url_base:
+                        Galaxy.root + "admin_toolshed/browse_repositories",
+                    url_data: Galaxy.params,
+                    dict_format: true
+                })
+            );
+        },
+
         show_tool_versions: function() {
             this.page.display(
                 new GridView({

client/galaxy/scripts/apps/panels/admin-panel.js

@@ -77,8 +77,9 @@ var AdminPanel = Backbone.View.extend({
                 enabled : self.settings.installing_repository_ids
             },{
                 title   : "Manage installed tools",
-                url     : "admin_toolshed/browse_repositories",
-                enabled : self.settings.is_repo_installed
+                url     : "admin/repositories",
+                enabled : self.settings.is_repo_installed,
+                target  : "__use_router__"
             },{
                 title   : "Reset metadata",
                 url     : "admin_toolshed/reset_metadata_on_selected_installed_repositories",

client/galaxy/scripts/layout/page.js

@@ -142,7 +142,7 @@ define(
                     '<div id="messagebox"/>',
                     '<div id="inactivebox" class="panel-warning-message" />',
                     '<div id="left" />',
-                    '<div id="center" class="inbound" />',
+                    '<div id="center" />',
                     '<div id="right" />',
                     "</div>",
                     '<div id="dd-helper" />'

client/galaxy/scripts/mvc/grid/grid-view.js

@@ -671,13 +671,8 @@ define(
                     async: async
                 });
                 switch (target) {
-                    case "inbound":
-                        // this currently assumes that there is only a single grid shown at a time
-                        var $div = $(".grid-header").closest(".inbound");
-                        if ($div.length !== 0) {
-                            $div.load(href);
-                            return;
-                        }
+                    case "center":
+                        $("#galaxy_main").attr("src", href);
                         break;
                     case "top":
                         window.top.location = href;

client/galaxy/scripts/utils/utils.js

@@ -312,7 +312,7 @@ define(["utils/localization"], function(_l) {
         var d = new Date();
         var hours = (d.getHours() < 10 ? "0" : "") + d.getHours();
         var minutes = (d.getMinutes() < 10 ? "0" : "") + d.getMinutes();
-        return (datetime =
+        return (
             d.getDate() +
             "/" +
             (d.getMonth() + 1) +
@@ -321,7 +321,8 @@ define(["utils/localization"], function(_l) {
             ", " +
             hours +
             ":" +
-            minutes);
+            minutes
+        );
     }
 
     /** Append script and style tags to Galaxy main application */

config/plugins/webhooks/demo/tour_generator/helper/__init__.py

@@ -1,5 +1,5 @@
-import os
 import logging
+import os
 from cgi import FieldStorage
 
 from galaxy.util import Params

cron/add_manual_builds.py

@@ -19,7 +19,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
             if line.startswith("#"):
                 continue
             existing_builds.append(line.replace("\n", "").replace("\r", "").split("\t")[0])
-        except:
+        except Exception:
             continue
     build_file_out = open(build_file, 'a')
     for line in open(input_file):
@@ -31,15 +31,15 @@ def add_manual_builds(input_file, build_file, chr_dir):
             name = fields.pop(0)
             try:  # get chrom lens if included in file, otherwise still add build
                 chrs = fields.pop(0).split(",")
-            except:
+            except Exception:
                 chrs = []
             print>>build_file_out, build + "\t" + name + " (" + build + ")"
             if chrs:  # create len file if provided chrom lens
                 chr_len_out = open(os.path.join(chr_dir, build + ".len"), 'w')
                 for chr in chrs:
                     print>>chr_len_out, chr.replace("=", "\t")
                 chr_len_out.close()
-        except:
+        except Exception:
             continue
     build_file_out.close()
 

cron/build_chrom_db.py

@@ -60,13 +60,13 @@ def getchrominfo(url, db):
                 if line.startswith("#"):
                     continue
                 builds.append(line.split("\t")[0])
-        except:
+        except Exception:
             sys.exit("Bad input file.")
     else:
         try:
             for build in parse_builds.getbuilds("http://genome.cse.ucsc.edu/cgi-bin/das/dsn"):
                 builds.append(build[0])
-        except:
+        except Exception:
             sys.exit("Unable to retrieve builds.")
     for build in builds:
         if build == "?":

cron/parse_builds.py

@@ -15,14 +15,14 @@
 def getbuilds(url):
     try:
         text = requests.get(url).text
-    except:
+    except Exception:
         print("#Unable to open " + url)
         print("?\tunspecified (?)")
         sys.exit(1)
 
     try:
         tree = ElementTree.fromstring(text)
-    except:
+    except Exception:
         print("#Invalid xml passed back from " + url)
         print("?\tunspecified (?)")
         sys.exit(1)

cron/parse_builds_3_sites.py

@@ -21,13 +21,13 @@ def main():
         builds = []
         try:
             text = requests.get(site).text
-        except:
+        except Exception:
             print("#Unable to connect to " + site)
             continue
 
         try:
             tree = ElementTree.fromstring(text)
-        except:
+        except Exception:
             print("#Invalid xml passed back from " + site)
             continue
         print("#Harvested from", site)

lib/galaxy/auth/providers/ldap_ad.py

@@ -95,7 +95,7 @@ def authenticate(self, email, username, password, options):
 
         try:
             import ldap
-        except:
+        except ImportError:
             log.debug('LDAP authenticate: could not load ldap module')
             return (failure_mode, '', '')
 

lib/galaxy/config.py

@@ -212,7 +212,7 @@ def __init__(self, **kwargs):
                         self.hours_between_check = 12.0
             else:
                 self.hours_between_check = 12
-        except:
+        except Exception:
             self.hours_between_check = 12
         self.update_integrated_tool_panel = kwargs.get("update_integrated_tool_panel", True)
         self.enable_data_manager_user_view = string_as_bool(kwargs.get("enable_data_manager_user_view", "False"))
@@ -797,7 +797,7 @@ def guess_galaxy_port(self):
 
         try:
             port = config.getint('server:%s' % self.server_name, 'port')
-        except:
+        except Exception:
             # uWSGI galaxy installations don't use paster and only speak uWSGI not http
             port = None
         return port

lib/galaxy/datatypes/annotation.py

@@ -23,7 +23,7 @@ def set_peek(self, dataset, is_multi_byte=False):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "SNAP HMM model (%s)" % (nice_size(dataset.get_size()))
 
     def sniff(self, filename):
@@ -54,7 +54,7 @@ def set_peek(self, dataset, is_multi_byte=False):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Augustus model (%s)" % (nice_size(dataset.get_size()))
 
     def sniff(self, filename):

lib/galaxy/datatypes/assembly.py

@@ -63,7 +63,7 @@ def sniff(self, filename):
                         if re.match(r'{(RED|CTG|TLE)$', line):
                             isAmos = True
             fh.close()
-        except:
+        except Exception:
             pass
         return isAmos
 
@@ -102,7 +102,7 @@ def sniff(self, filename):
                     else:
                         break  # we found a non-empty line, but it's not a fasta header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -138,7 +138,7 @@ def sniff(self, filename):
                 else:
                     break  # we found a non-empty line, but it's not a fasta header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -202,7 +202,7 @@ def regenerate_primary_file(self, dataset):
                 gen_msg = gen_msg + ' Long Reads'
             if len(gen_msg) > 0:
                 gen_msg = 'Uses: ' + gen_msg
-        except:
+        except Exception:
             log.debug("Velveth could not read Log file in %s" % efp)
         log.debug("Velveth log info  %s" % gen_msg)
         rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']