From 604dfb27ce0acba176c059f08642aae7a390ddf0 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Fri, 7 Oct 2016 11:02:35 -0400 Subject: [PATCH 01/32] Fix for reruning tool with workflow resume that is part of a collection. The special casing of "__identifier__" that occurs here and elsewhere in the code is less than ideal. --- lib/galaxy/tools/parameters/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index cbb58e107f0..32086f18f22 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -201,7 +201,7 @@ def update_param( prefixed_name, input_values, new_value ): """ for key in input_values: match = re.match( '^' + key + '_(\d+)\|(.+)', prefixed_name ) - if match: + if match and not key.endswith( "|__identifier__" ): index = int( match.group( 1 ) ) if isinstance( input_values[ key ], list ) and len( input_values[ key ] ) > index: update_param( match.group( 2 ), input_values[ key ][ index ], new_value ) From 415c7fa67be28885fa92246fb63efdf5bfd777bf Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Fri, 7 Oct 2016 20:37:07 +0200 Subject: [PATCH 02/32] Verify tools coming from cache have correct id. --- lib/galaxy/tools/toolbox/base.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index 2ac9b8e7221..23145efca45 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -520,8 +520,13 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ): tool = self.load_tool_from_cache(os.path.join(tool_path, path)) from_cache = tool if from_cache: - log.debug("Loading tool %s from cache", str(tool.id)) - elif guid: # tool was not in cache and is a tool shed tool + if guid and tool.id != guid: + # In rare cases a tool shed tool is loaded into the cache without guid. + # In that case recreating the tool will correct the cached version. + from_cache = False + else: + log.debug("Loading tool %s from cache", str(tool.id)) + if guid and not from_cache: # tool was not in cache and is a tool shed tool tool_shed_repository = self.get_tool_repository_from_xml_item(item, path) if tool_shed_repository: # Only load tools if the repository is not deactivated or uninstalled. From 89278b0ec70b7a8f1cf42bda87335cf4f98f175b Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 7 Oct 2016 15:11:00 -0400 Subject: [PATCH 03/32] Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. --- config/galaxy.ini.sample | 2 +- doc/source/admin/dependency_resolvers.rst | 2 +- lib/galaxy/tools/deps/__init__.py | 2 +- lib/galaxy/tools/deps/resolvers/conda.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index b590b8a589c..5e1b6cb50ab 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -198,7 +198,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Pass debug flag to conda commands. #conda_debug = False # conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html) -#conda_ensure_channels = r,bioconda,iuc +#conda_ensure_channels = conda-forge,r,bioconda,iuc # Set to True to instruct Galaxy to look for and install missing tool # dependencies before each job runs. #conda_auto_install = False diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index 3c140d5d987..6ec8e9f6804 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -182,7 +182,7 @@ debug ensure_channels conda channels to enable by default. See http://conda.pydata.org/docs/custom-channels.html for more - information about channels. (default: r,bioconda). + information about channels. (default: conda-forge,r,bioconda,iuc). auto_install Set to True to instruct Galaxy to look for and install missing tool diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py index d683afb364f..aecab6c8b29 100644 --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -20,7 +20,7 @@ EXTRA_CONFIG_KWDS = { 'conda_prefix': None, 'conda_exec': None, 'conda_debug': None, - 'conda_ensure_channels': 'r,bioconda,iuc', + 'conda_ensure_channels': 'conda-forge,r,bioconda,iuc', 'conda_auto_install': False, 'conda_auto_init': False, 'conda_copy_dependencies': False, diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index d2ff051477e..f94cc015692 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -32,7 +32,7 @@ from ..conda_util import ( DEFAULT_BASE_PATH_DIRECTORY = "_conda" DEFAULT_CONDARC_OVERRIDE = "_condarc" -DEFAULT_ENSURE_CHANNELS = "r,bioconda,iuc" +DEFAULT_ENSURE_CHANNELS = "conda-forge,r,bioconda,iuc" import logging log = logging.getLogger(__name__) From 56dfaf003f3239d2475715b478e319ff359e08d4 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sat, 8 Oct 2016 08:48:47 +0200 Subject: [PATCH 04/32] Fix tool reload in 415c7fa67be28885fa92246fb63efdf5bfd777bf Previous commit changed the if/elif/else logic. The else was now applying also to cached tools, which it should not. Instead, explicitly check that we still don't have a tool object. --- lib/galaxy/tools/toolbox/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index 23145efca45..a26ef0b5d86 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -533,7 +533,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ): can_load_into_panel_dict = not tool_shed_repository.deleted repository_id = self.app.security.encode_id(tool_shed_repository.id) tool = self.load_tool(os.path.join( tool_path, path ), guid=guid, repository_id=repository_id, use_cached=False) - else: # tool was not in cache and is not a tool shed tool. + if not tool: # tool was not in cache and is not a tool shed tool. tool = self.load_tool(os.path.join(tool_path, path), use_cached=False) if string_as_bool(item.get( 'hidden', False )): tool.hidden = True From 5a72449246be6f0f2fe3955bebf6f42ae89966bc Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 29 Sep 2016 14:28:56 -0400 Subject: [PATCH 05/32] Implement beta support for dynamically discovering mulled containers for dependencies. Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening. --- config/galaxy.ini.sample | 31 ++ lib/galaxy/config.py | 20 +- lib/galaxy/tools/deps/__init__.py | 4 +- lib/galaxy/tools/deps/conda_compat.py | 112 +++++++ lib/galaxy/tools/deps/conda_util.py | 84 +++++- .../deps/container_resolvers/__init__.py | 50 +++ .../deps/container_resolvers/explicit.py | 26 ++ .../tools/deps/container_resolvers/mulled.py | 207 +++++++++++++ lib/galaxy/tools/deps/containers.py | 106 +++++-- lib/galaxy/tools/deps/installable.py | 77 +++++ lib/galaxy/tools/deps/mulled/__init__.py | 0 lib/galaxy/tools/deps/mulled/_cli.py | 19 ++ lib/galaxy/tools/deps/mulled/invfile.lua | 67 +++++ lib/galaxy/tools/deps/mulled/mulled_build.py | 284 ++++++++++++++++++ .../tools/deps/mulled/mulled_build_channel.py | 109 +++++++ .../tools/deps/mulled/mulled_build_files.py | 80 +++++ .../tools/deps/mulled/mulled_build_tool.py | 52 ++++ lib/galaxy/tools/deps/mulled/mulled_search.py | 131 ++++++++ lib/galaxy/tools/deps/mulled/util.py | 116 +++++++ lib/galaxy/tools/deps/resolvers/__init__.py | 19 +- lib/galaxy/tools/deps/resolvers/conda.py | 43 +-- .../tools/mulled_example_multi_1.xml | 18 ++ test/functional/tools/samples_tool_conf.xml | 2 + 23 files changed, 1569 insertions(+), 88 deletions(-) create mode 100644 lib/galaxy/tools/deps/conda_compat.py create mode 100644 lib/galaxy/tools/deps/container_resolvers/__init__.py create mode 100644 lib/galaxy/tools/deps/container_resolvers/explicit.py create mode 100644 lib/galaxy/tools/deps/container_resolvers/mulled.py create mode 100644 lib/galaxy/tools/deps/installable.py create mode 100644 lib/galaxy/tools/deps/mulled/__init__.py create mode 100644 lib/galaxy/tools/deps/mulled/_cli.py create mode 100644 lib/galaxy/tools/deps/mulled/invfile.lua create mode 100644 lib/galaxy/tools/deps/mulled/mulled_build.py create mode 100644 lib/galaxy/tools/deps/mulled/mulled_build_channel.py create mode 100644 lib/galaxy/tools/deps/mulled/mulled_build_files.py create mode 100644 lib/galaxy/tools/deps/mulled/mulled_build_tool.py create mode 100644 lib/galaxy/tools/deps/mulled/mulled_search.py create mode 100644 lib/galaxy/tools/deps/mulled/util.py create mode 100644 test/functional/tools/mulled_example_multi_1.xml diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 72876dfc65c..f60ce30d917 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -228,6 +228,37 @@ paste.app_factory = galaxy.web.buildapp:app_factory # than the watchdog default. #watch_tools = False +# Enable Galaxy to fetch Docker containers registered with quay.io generated +# from tool requirements resolved through conda. These containers (when +# available) have been generated using mulled - https://github.com/mulled. +# These containers are highly beta and availablity will vary by tool. +# This option will additionally only be used for job destinations with +# Docker enabled. +#enable_beta_mulled_containers = False + +# Container resolvers configuration (beta). Setup a file describing container +# resolvers to use when discovering containers for Galaxy. If this is set to +# None, the default containers loaded is determined by +# enable_beta_mulled_containers. +#containers_resolvers_config_file = None + +# Container resolvers configuration (beta). Setup a file describing container +# resolvers to use when discovering containers for Galaxy. If this is set to +# None, the default containers loaded is determined by +# enable_beta_mulled_containers. +#containers_resolvers_config_file = None + +# involucro is a tool used to build Docker containers for tools from Conda +# dependencies referenced in tools as `requirement`s. The following path is +# the location of involucro on the Galaxy host. This is ignored if the relevant +# container resolver isn't enabled, and will install on demand unless +# involucro_auto_init is set to False. +#involucro_path = database/dependencies/involucro + +# Install involucro as needed to build Docker containers for tools. Ignored if +# relevant container resolver is not used. +#involucro_auto_init = True + # Enable automatic polling of relative tool sheds to see if any updates # are available for installed repositories. Ideally only one Galaxy # server process should be able to check for repository updates. The diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 9c590c4c747..86b9cc82785 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -226,6 +226,7 @@ class Configuration( object ): self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2)) self.tool_submission_burst_threads = int( kwargs.get( 'tool_submission_burst_threads', '1' ) ) self.tool_submission_burst_at = int( kwargs.get( 'tool_submission_burst_at', '10' ) ) + # Enable new interface for API installations from TS. # Admin menu will list both if enabled. self.enable_beta_ts_api_install = string_as_bool( kwargs.get( 'enable_beta_ts_api_install', 'False' ) ) @@ -323,6 +324,19 @@ class Configuration( object ): else: self.tool_dependency_dir = None self.use_tool_dependencies = os.path.exists(self.dependency_resolvers_config_file) + + self.enable_beta_mulled_containers = string_as_bool( kwargs.get( 'enable_beta_mulled_containers', 'False' ) ) + containers_resolvers_config_file = kwargs.get( 'containers_resolvers_config_file', None ) + if containers_resolvers_config_file: + containers_resolvers_config_file = resolve_path(containers_resolvers_config_file, self.root) + self.containers_resolvers_config_file = containers_resolvers_config_file + + involucro_path = kwargs.get('involucro_path', None) + if involucro_path is None: + involucro_path = os.path.join(tool_dependency_dir, "involucro") + self.involucro_path = resolve_path(involucro_path, self.root) + self.involucro_auto_init = string_as_bool(kwargs.get( 'involucro_auto_init', True)) + # Configuration options for taking advantage of nginx features self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) ) self.apache_xsendfile = string_as_bool( kwargs.get( 'apache_xsendfile', False ) ) @@ -846,7 +860,11 @@ class ConfiguresGalaxyMixin: default_file_path=file_path, outputs_to_working_directory=self.config.outputs_to_working_directory, container_image_cache_path=self.config.container_image_cache_path, - library_import_dir=self.config.library_import_dir + library_import_dir=self.config.library_import_dir, + enable_beta_mulled_containers=self.config.enable_beta_mulled_containers, + containers_resolvers_config_file=self.config.containers_resolvers_config_file, + involucro_path=self.config.involucro_path, + involucro_auto_init=self.config.involucro_auto_init, ) self.container_finder = containers.ContainerFinder(app_info) diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py index 763732e4dc7..ccf5bb25753 100644 --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -8,7 +8,7 @@ import os.path from galaxy.util import plugin_config from .resolvers import NullDependency -from .resolvers.conda import CondaDependencyResolver +from .resolvers.conda import CondaDependencyResolver, DEFAULT_ENSURE_CHANNELS from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver @@ -21,7 +21,7 @@ EXTRA_CONFIG_KWDS = { 'conda_prefix': None, 'conda_exec': None, 'conda_debug': None, - 'conda_ensure_channels': 'r,bioconda,iuc', + 'conda_ensure_channels': DEFAULT_ENSURE_CHANNELS, 'conda_auto_install': False, 'conda_auto_init': False, 'conda_copy_dependencies': False, diff --git a/lib/galaxy/tools/deps/conda_compat.py b/lib/galaxy/tools/deps/conda_compat.py new file mode 100644 index 00000000000..1443378f9f5 --- /dev/null +++ b/lib/galaxy/tools/deps/conda_compat.py @@ -0,0 +1,112 @@ +"""Compat. layer with conda_build/verify if Galaxy/galaxy-lib not installed through conda. + +In general there are utilities available for Conda building and parsing that are high-quality +and should be utilized when available but that are only available in conda channels and not in +PyPI. This module serves as a PyPI capable interface to these utilities. +""" +import collections +import os +import yaml + + +try: + from conda_build.metadata import MetaData +except ImportError: + MetaData = None + +try: + from anaconda_verify.recipe import render_jinja2, parse +except ImportError: + render_jinja2 = None + parse = None + + +class _Memoized(object): + + def __init__(self, func): + self.func = func + self.cache = {} + + def __call__(self, *args): + if not isinstance(args, collections.Hashable): + # uncacheable. a list, for instance. + # better to not cache than blow up. + return self.func(*args) + if args in self.cache: + return self.cache[args] + else: + value = self.func(*args) + self.cache[args] = value + return value + + +def _parse(data, cfg): + """Parse metadata YAML.""" + assert cfg is None, "Conda utilities for evaluating cfg are not available." + return dict(yamlize(data)) + + +def _render_jinja2(recipe_dir): + """Evaluate Conda recipe as a jinja template.""" + try: + import jinja2 + except ImportError: + raise Exception("Failed to import jinja2 for evaluating Conda recipe templates.") + + loaders = [jinja2.FileSystemLoader(recipe_dir)] + env = jinja2.Environment(loader=jinja2.ChoiceLoader(loaders)) + template = env.get_or_select_template('meta.yaml') + return template.render(environment=env) + + +@_Memoized +def yamlize(data): + res = yaml.load(data) + # ensure the result is a dict + if res is None: + res = {} + return res + + +if render_jinja2 is None: + render_jinja2 = _render_jinja2 + +if parse is None: + parse = _parse + + +def raw_metadata(recipe_dir): + """Evaluate Conda template if needed and return raw metadata for supplied recipe directory.""" + meta_path = os.path.join(recipe_dir, 'meta.yaml') + with open(meta_path, 'rb') as fi: + data = fi.read() + if b'{{' in data: + data = render_jinja2(recipe_dir) + meta = parse(data, None) + return meta + + +class _MetaData(object): + + def __init__(self, input_dir): + self.meta = raw_metadata(input_dir) + + def get_value(self, field, default=None): + """Get nested field value or supplied default is not present.""" + section, key = field.split('/') + submeta = self.meta.get(section) + if submeta is None: + submeta = {} + res = submeta.get(key) + if res is None: + res = default + return res + + +if MetaData is None: + MetaData = _MetaData + +__all__ = [ + "MetaData", + "raw_metadata", +] diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py index dc91f9f967a..117acca4389 100644 --- a/lib/galaxy/tools/deps/conda_util.py +++ b/lib/galaxy/tools/deps/conda_util.py @@ -7,12 +7,14 @@ import re import shutil import tempfile +from distutils.version import LooseVersion from sys import platform as _platform import six import yaml from ..deps import commands +from ..deps import installable log = logging.getLogger(__name__) @@ -47,7 +49,8 @@ def find_conda_prefix(conda_prefix=None): return conda_prefix -class CondaContext(object): +class CondaContext(installable.InstallableContext): + installable_description = "Conda" def __init__(self, conda_prefix=None, conda_exec=None, shell_exec=None, debug=False, ensure_channels='', @@ -230,6 +233,16 @@ class CondaContext(object): def activate(self): return self._bin("activate") + def is_installed(self): + return self.is_conda_installed() + + def can_install(self): + return self.can_install_conda() + + @property + def parent_path(self): + return os.path.dirname(os.path.abspath(self.conda_prefix)) + def _bin(self, name): return os.path.join(self.conda_prefix, "bin", name) @@ -273,6 +286,8 @@ class CondaTarget(object): return "CondaTarget[%s]" % attributes + __repr__ = __str__ + @property def package_specifier(self): """ Return a package specifier as consumed by conda install/create. @@ -293,6 +308,17 @@ class CondaTarget(object): else: return "__%s@_uv_" % (self.package) + def __hash__(self): + return hash((self.package, self.version, self.channel)) + + def __eq__(self, other): + if isinstance(other, self.__class__): + return (self.package, self.version, self.channel) == (other.package, other.version, other.channel) + return False + + def __ne__(self, other): + return not(self == other) + def hash_conda_packages(conda_packages, conda_target=None): """ Produce a unique hash on supplied packages. @@ -339,23 +365,55 @@ def cleanup_failed_install(conda_target, conda_context=None): conda_context.exec_remove([conda_target.install_environment]) -def is_target_available(conda_target, conda_context=None): - """ Checks if a specified target is available for installation. - If the package name exists return "True". If in addition the version matches exactly return "exact". - Otherwise return False. +def best_search_result(conda_target, conda_context=None, channels_override=None): + """Find best "conda search" result for specified target. + + Return ``None`` if no results match. """ conda_context = _ensure_conda_context(conda_context) - conda_context.ensure_channels_configured() - search_cmd = [conda_context.conda_exec, "search", "--full-name", "--json", conda_target.package] + if not channels_override: + conda_context.ensure_channels_configured() + + search_cmd = [conda_context.conda_exec, "search", "--full-name", "--json"] + if channels_override: + search_cmd.append("--override-channels") + for channel in channels_override: + search_cmd.extend(["--channel", channel]) + search_cmd.append(conda_target.package) res = commands.execute(search_cmd) hits = json.loads(res).get(conda_target.package, []) + hits = sorted(hits, key=lambda hit: LooseVersion(hit['version']), reverse=True) - if len(hits) > 0: - if conda_target.version: - for hit in hits: - if hit['version'] == conda_target.version: - return 'exact' - return True + if len(hits) == 0: + return (None, None) + + best_result = (hits[0], False) + + for hit in hits: + if is_search_hit_exact(conda_target, hit): + best_result = (hit, True) + break + + return best_result + + +def is_search_hit_exact(conda_target, search_hit): + target_version = conda_target.version + # It'd be nice to make request verson of 1.0 match available + # version of 1.0.3 or something like that. + return not target_version or search_hit['version'] == target_version + + +def is_target_available(conda_target, conda_context=None, channels_override=None): + """Check if a specified target is available for installation. + + If the package name exists return ``True`` (the ``bool``). If in addition + the version matches exactly return "exact" (a string). Otherwise return + ``False``. + """ + (best_hit, exact) = best_search_result(conda_target, conda_context, channels_override) + if best_hit: + return 'exact' if exact else True else: return False diff --git a/lib/galaxy/tools/deps/container_resolvers/__init__.py b/lib/galaxy/tools/deps/container_resolvers/__init__.py new file mode 100644 index 00000000000..c478bcce3a2 --- /dev/null +++ b/lib/galaxy/tools/deps/container_resolvers/__init__.py @@ -0,0 +1,50 @@ +"""The module defines the abstract interface for resolving container images for tool execution.""" +from abc import ( + ABCMeta, + abstractmethod, + abstractproperty, +) + +from galaxy.util.dictifiable import Dictifiable + + +class ContainerResolver(Dictifiable, object): + """Description of a technique for resolving container images for tool execution.""" + + # Keys for dictification. + dict_collection_visible_keys = ['resolver_type'] + + __metaclass__ = ABCMeta + + def __init__(self, app_info=None, **kwds): + """Default initializer for ``ContainerResolver`` subclasses.""" + self.app_info = app_info + self.resolver_kwds = kwds + + def _get_config_option(self, key, default=None, config_prefix=None, **kwds): + """Look in resolver-specific settings for option and then fallback to + global settings. + """ + global_key = "%s_%s" % (config_prefix, key) + if key in kwds: + return kwds.get(key) + elif self.app_info and hasattr(self.app_info, global_key): + return getattr(self.app_info, global_key) + else: + return default + + @abstractmethod + def resolve(self, tool_info): + """Find a container matching all supplied requirements for tool. + + The supplied argument is a :class:`galaxy.tools.deps.containers.ToolInfo` description + of the tool and its requirements. + """ + + @abstractproperty + def resolver_type(self): + """Short label for the type of container resolution.""" + + def _container_type_enabled(self, container_description, enabled_container_types): + """Return a boolean indicating if the specified container type is enabled.""" + return container_description.type in enabled_container_types diff --git a/lib/galaxy/tools/deps/container_resolvers/explicit.py b/lib/galaxy/tools/deps/container_resolvers/explicit.py new file mode 100644 index 00000000000..851f0c1f99c --- /dev/null +++ b/lib/galaxy/tools/deps/container_resolvers/explicit.py @@ -0,0 +1,26 @@ +"""This module describes the :class:`ExplicitContainerResolver` ContainerResolver plugin.""" +import logging + +from ..container_resolvers import ( + ContainerResolver, +) + +log = logging.getLogger(__name__) + + +class ExplicitContainerResolver(ContainerResolver): + """Find explicit containers referenced in the tool description (e.g. tool XML file) if present.""" + + resolver_type = "explicit" + + def resolve(self, enabled_container_types, tool_info): + """Find a container explicitly mentioned in tool description. + + This ignores the tool requirements and assumes the tool author crafted + a correct container. + """ + for container_description in tool_info.container_descriptions: + if self._container_type_enabled(container_description): + return True + + return False diff --git a/lib/galaxy/tools/deps/container_resolvers/mulled.py b/lib/galaxy/tools/deps/container_resolvers/mulled.py new file mode 100644 index 00000000000..2b2701270ef --- /dev/null +++ b/lib/galaxy/tools/deps/container_resolvers/mulled.py @@ -0,0 +1,207 @@ +"""This module describes the :class:`MulledContainerResolver` ContainerResolver plugin.""" + +import collections +import logging + +from ..container_resolvers import ( + ContainerResolver, +) +from ..docker_util import build_docker_images_command +from ..mulled.mulled_build import ( + check_output, + DEFAULT_CHANNELS, + ensure_installed, + InvolucroContext, + mull_targets, +) +from ..mulled.mulled_build_tool import requirements_to_mulled_targets +from ..mulled.util import ( + image_name, + mulled_tags_for, + split_tag, +) +from ..requirements import ContainerDescription + +log = logging.getLogger(__name__) + + +CachedMulledImageSingleTarget = collections.namedtuple("CachedMulledImageSingleTarget", ["package_name", "version", "build", "image_identifier"]) +CachedMulledImageMultiTarget = collections.namedtuple("CachedMulledImageMultiTarget", ["hash", "image_identifier"]) + +CachedMulledImageSingleTarget.multi_target = False +CachedMulledImageMultiTarget.multi_target = True + + +def list_cached_mulled_images(namespace=None): + command = build_docker_images_command(truncate=True, sudo_docker=False) + command = "%s | tail -n +2 | tr -s ' ' | cut -d' ' -f1,2" % command + images_and_versions = check_output(command) + name_filter = get_filter(namespace) + + def output_line_to_image(line): + image_name, version = line.split(" ", 1) + identifier = "%s:%s" % (image_name, version) + url, namespace, package_description = image_name.split("/") + + if package_description.startswith("mulled-v1-"): + hash = package_description + image = CachedMulledImageMultiTarget(hash, identifier) + else: + build = None + if not version or version == "latest": + version = None + + if version and "--" in version: + version, build = split_tag(version) + + image = CachedMulledImageSingleTarget(image_name, version, build, identifier) + + return image + + return map(output_line_to_image, filter(name_filter, images_and_versions.splitlines())) + + +def get_filter(namespace): + prefix = "quay.io/" if namespace is None else "quay.io/%s" % namespace + return lambda name: name.startswith(prefix) and name.count("/") == 2 + + +def cached_container_description(targets, namespace): + if len(targets) == 0: + return None + + cached_images = list_cached_mulled_images(namespace) + image = None + if len(targets) == 1: + target = targets[0] + for cached_image in cached_images: + if cached_image.multi_target: + continue + if not cached_image.package_name == target.package_name: + continue + if not target.version or target.version == cached_image.version: + image = cached_image + break + else: + name = image_name(targets) + for cached_image in cached_images: + if not cached_image.multi_target: + continue + + if name == cached_image.hash: + image = cached_image + break + + container = None + if image: + container = ContainerDescription( + image.image_identifier, + type="docker", + ) + + return container + + +class CachedMulledContainerResolver(ContainerResolver): + + resolver_type = "cached_mulled" + + def __init__(self, app_info=None, namespace=None): + super(CachedMulledContainerResolver, self).__init__(app_info) + self.namespace = namespace + + def resolve(self, enabled_container_types, tool_info): + targets = mulled_targets(tool_info) + return cached_container_description(targets, self.namespace) + + +class MulledContainerResolver(ContainerResolver): + """Look for mulled images matching tool dependencies.""" + + resolver_type = "mulled" + + def __init__(self, app_info=None, namespace="mulled"): + super(MulledContainerResolver, self).__init__(app_info) + self.namespace = namespace + + def resolve(self, enabled_container_types, tool_info): + targets = mulled_targets(tool_info) + if len(targets) == 0: + return None + + name = None + + if len(targets) == 1: + target = targets[0] + target_version = target.version + tags = mulled_tags_for(self.namespace, target.package_name) + + if not tags: + return None + + if target_version: + for tag in tags: + version, build = split_tag(tag) + if version == target_version: + name = "%s:%s--%s" % (target.package_name, version, build) + break + else: + version, build = split_tag(tags[0]) + name = "%s:%s--%s" % (target.package_name, version, build) + else: + base_image_name = image_name(targets) + tags = mulled_tags_for(self.namespace, base_image_name) + if tags: + name = "%s:%s" % (base_image_name, tags[0]) + + if name: + return ContainerDescription( + "quay.io/%s/%s" % (self.namespace, name), + type="docker", + ) + + +class BuildMulledContainerResolver(ContainerResolver): + """Look for mulled images matching tool dependencies.""" + + resolver_type = "build_mulled" + + def __init__(self, app_info=None, namespace="local", **kwds): + super(BuildMulledContainerResolver, self).__init__(app_info) + self._involucro_context_kwds = { + 'involucro_bin': self._get_config_option("involucro_path", None) + } + self.namespace = namespace + self._mulled_kwds = { + 'namespace': namespace, + 'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"), + } + self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro") + + def resolve(self, enabled_container_types, tool_info): + targets = mulled_targets(tool_info) + if len(targets) == 0: + return None + + mull_targets( + targets, + involucro_context=self._get_involucro_context(), + **self._mulled_kwds + ) + return cached_container_description(targets, self.namespace) + + def _get_involucro_context(self): + involucro_context = InvolucroContext(**self._involucro_context_kwds) + self.enabled = ensure_installed(involucro_context, self.auto_init) + return involucro_context + + +def mulled_targets(tool_info): + return requirements_to_mulled_targets(tool_info.requirements) + + +__all__ = [ + "CachedMulledContainerResolver", + "MulledContainerResolver", + "BuildMulledContainerResolver", +] diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py index aadf73ef482..fff1989986b 100644 --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -10,14 +10,23 @@ from abc import ( import six from galaxy.util import asbool +from galaxy.util import plugin_config +from .container_resolvers.explicit import ExplicitContainerResolver +from .container_resolvers.mulled import ( + BuildMulledContainerResolver, + CachedMulledContainerResolver, + MulledContainerResolver, +) from .requirements import ContainerDescription from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL from ..deps import docker_util log = logging.getLogger(__name__) -DEFAULT_CONTAINER_TYPE = "docker" +DOCKER_CONTAINER_TYPE = "docker" +DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE +ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE] LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = ''' python << EOF @@ -47,9 +56,18 @@ class ContainerFinder(object): def __init__(self, app_info): self.app_info = app_info - self.container_registry = ContainerRegistry() + self.container_registry = ContainerRegistry(app_info) + + def __enabled_container_types(self, destination_info): + return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)] def find_container(self, tool_info, destination_info, job_info): + enabled_container_types = self.__enabled_container_types(destination_info) + + # Short-cut everything else and just skip checks if no container type is enabled. + if not enabled_container_types: + return NULL_CONTAINER + def __destination_container(container_description=None, container_id=None, container_type=None): if container_description: container_id = container_description.identifier @@ -82,23 +100,10 @@ class ContainerFinder(object): return container # Otherwise lets see if we can find container for the tool. - - # Exact matches first from explicitly listed containers in tools... - for container_description in tool_info.container_descriptions: - container = __destination_container(container_description) - if container: - return container - - # Implement vague concept of looping through all containers - # matching requirements. Exact details need to be worked through - # but hopefully the idea that it sits below find_container somewhere - # external components to this module don't need to worry about it - # is good enough. - container_descriptions = self.container_registry.container_descriptions_for_requirements(tool_info.requirements) - for container_description in container_descriptions: - container = __destination_container(container_description) - if container: - return container + container_description = self.container_registry.find_best_container_description(enabled_container_types, tool_info) + container = __destination_container(container_description) + if container: + return container # If we still don't have a container, check to see if any container # types define a default container id and use that. @@ -175,14 +180,55 @@ class NullContainerFinder(object): return [] -class ContainerRegistry(): +class ContainerRegistry(object): + """Loop through enabled ContainerResolver plugins and find first match.""" - def __init__(self): - pass + def __init__(self, app_info): + self.resolver_classes = self.__resolvers_dict() + self.enable_beta_mulled_containers = app_info.enable_beta_mulled_containers + self.app_info = app_info + self.container_resolvers = self.__build_container_resolvers(app_info) - def container_descriptions_for_requirements(self, requirements): - # Return lists of containers that would match requirements... - return [] + def __build_container_resolvers( self, app_info ): + conf_file = getattr(app_info, 'containers_resolvers_config_file', None) + if not conf_file: + return self.__default_containers_resolvers() + if not os.path.exists( conf_file ): + log.debug( "Unable to find config file '%s'", conf_file) + return self.__default_containers_resolvers() + plugin_source = plugin_config.plugin_source_from_path( conf_file ) + return self.__parse_resolver_conf_xml( plugin_source ) + + def __parse_resolver_conf_xml(self, plugin_source): + extra_kwds = {} + return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds) + + def __default_containers_resolvers(self): + default_resolvers = [ + ExplicitContainerResolver(self.app_info), + ] + if self.enable_beta_mulled_containers: + default_resolvers.extend([ + CachedMulledContainerResolver(self.app_info), + MulledContainerResolver(self.app_info, namespace="mulled"), + BuildMulledContainerResolver(self.app_info), + ]) + return default_resolvers + + def __resolvers_dict( self ): + import galaxy.tools.deps.container_resolvers + return plugin_config.plugins_dict( galaxy.tools.deps.container_resolvers, 'resolver_type' ) + + def find_best_container_description(self, enabled_container_types, tool_info): + """Yield best container description of supplied types matching tool info.""" + for container_resolver in self.container_resolvers: + container_description = container_resolver.resolve(enabled_container_types, tool_info) + log.info("Checking with container resolver [%s] found description [%s]" % (container_resolver, container_description)) + if container_description: + assert container_description.type in enabled_container_types + return container_description + + return None class AppInfo(object): @@ -193,7 +239,11 @@ class AppInfo(object): default_file_path=None, outputs_to_working_directory=False, container_image_cache_path=None, - library_import_dir=None + library_import_dir=None, + enable_beta_mulled_containers=False, + containers_resolvers_config_file=None, + involucro_path=None, + involucro_auto_init=True, ): self.galaxy_root_dir = galaxy_root_dir self.default_file_path = default_file_path @@ -201,6 +251,10 @@ class AppInfo(object): self.outputs_to_working_directory = outputs_to_working_directory self.container_image_cache_path = container_image_cache_path self.library_import_dir = library_import_dir + self.enable_beta_mulled_containers = enable_beta_mulled_containers + self.containers_resolvers_config_file = containers_resolvers_config_file + self.involucro_path = involucro_path + self.involucro_auto_init = involucro_auto_init class ToolInfo(object): diff --git a/lib/galaxy/tools/deps/installable.py b/lib/galaxy/tools/deps/installable.py new file mode 100644 index 00000000000..cacc069fe65 --- /dev/null +++ b/lib/galaxy/tools/deps/installable.py @@ -0,0 +1,77 @@ +"""Abstractions for installing local software managed and required by Galaxy/galaxy-lib.""" + +import logging +import os + +from abc import ( + ABCMeta, + abstractmethod, + abstractproperty, +) + +from galaxy.util.filelock import ( + FileLock, + FileLockException +) + +log = logging.getLogger(__name__) + + +class InstallableContext(object): + """Represent a directory/configuration of something that can be installed.""" + + __metaclass__ = ABCMeta + + @abstractmethod + def is_installed(self): + """Return bool indicating if the configured software is installed.""" + + @abstractmethod + def can_install(self): + """Check preconditions for installation.""" + + @abstractproperty + def installable_description(self): + """Short description of thing being installed for log statements.""" + + @abstractproperty + def parent_path(self): + """Return parent path of the location the installable will be created within.""" + + +def ensure_installed(installable_context, install_func, auto_init): + """Make sure target is installed - handle multiple processes potentially attempting installation.""" + parent_path = installable_context.parent_path + desc = installable_context.installable_description + + def _check(): + if not installable_context.is_installed(): + if auto_init: + if installable_context.can_install(): + if install_func(installable_context): + installed = False + log.warning("%s installation requested and failed." % desc) + else: + installed = installable_context.is_installed() + if not installed: + log.warning("%s installation requested, seemed to succeed, but not found." % desc) + else: + installed = False + else: + installed = False + log.warning("%s not installed and auto-installation disabled.", desc) + else: + installed = True + return installed + + if not os.path.exists(parent_path): + os.mkdir(parent_path) + + try: + if auto_init and os.access(parent_path, os.W_OK): + with FileLock(os.path.join(parent_path, desc.lower())): + return _check() + else: + return _check() + except FileLockException: + return ensure_installed(installable_context, auto_init) diff --git a/lib/galaxy/tools/deps/mulled/__init__.py b/lib/galaxy/tools/deps/mulled/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/galaxy/tools/deps/mulled/_cli.py b/lib/galaxy/tools/deps/mulled/_cli.py new file mode 100644 index 00000000000..3cf32bad5de --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/_cli.py @@ -0,0 +1,19 @@ +"""CLI helpers for mulled command-line tools.""" + +import argparse + + +def arg_parser(argv, globals): + """Build an argparser for this CLI tool.""" + doc = globals["__doc__"] + description, epilog = doc.split("\n", 1) + parser = argparse.ArgumentParser( + description=description, + epilog=epilog, + formatter_class=argparse.RawTextHelpFormatter, + ) + return parser + +__all__ = [ + "arg_parser" +] diff --git a/lib/galaxy/tools/deps/mulled/invfile.lua b/lib/galaxy/tools/deps/mulled/invfile.lua new file mode 100644 index 00000000000..629c15f7b67 --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/invfile.lua @@ -0,0 +1,67 @@ +-- http://stackoverflow.com/questions/19262761/lua-need-to-split-at-comma/19263313#19263313 +function string:split( inSplitPattern, outResults ) + if not outResults then + outResults = { } + end + local theStart = 1 + local theSplitStart, theSplitEnd = string.find( self, inSplitPattern, theStart ) + while theSplitStart do + table.insert( outResults, string.sub( self, theStart, theSplitStart-1 ) ) + theStart = theSplitEnd + 1 + theSplitStart, theSplitEnd = string.find( self, inSplitPattern, theStart ) + end + table.insert( outResults, string.sub( self, theStart ) ) + return outResults +end + +local repo = VAR.REPO + +local channel_args = '' +local channels = VAR.CHANNELS:split(",") +for i = 1, #channels do + channel_args = channel_args .. " -c " .. channels[i] +end + +local target_args = '' +local targets = VAR.TARGETS:split(",") +for i = 1, #targets do + target_args = target_args .. " " .. targets[i] +end + +local bind_args = {} +local binds_table = VAR.BINDS:split(",") +for i = 1, #binds_table do + table.insert(bind_args, binds_table[i]) +end + +inv.task('build') + .using('continuumio/miniconda:latest') + .withHostConfig({binds = {"build:/data"}}) + .run('rm', '-rf', '/data/dist') + .using('continuumio/miniconda:latest') + .withHostConfig({binds = bind_args}) + .run('/bin/sh', '-c', 'conda install ' + .. channel_args .. ' ' + .. target_args + .. ' -p /usr/local --copy --yes') + .wrap('build/dist') + .at('/usr/local') + .inImage('bgruening/busybox-bash:0.1') + .as(repo) + +inv.task('test') + .using(repo) + .withConfig({entrypoint = {'/bin/sh', '-c'}}) + .run(VAR.TEST) + +inv.task('push') + .push(repo) + +inv.task('build-and-test') + .runTask('build') + .runTask('test') + +inv.task('all') + .runTask('build') + .runTask('test') + .runTask('push') diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py new file mode 100644 index 00000000000..b359c540cbf --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/mulled_build.py @@ -0,0 +1,284 @@ +#!/usr/bin/env python +"""Build a mulled image for specified conda targets. + +Examples + +Build a mulled image with: + + mulled-build build 'samtools=1.3.1,bedtools=2.22' + +""" +from __future__ import print_function + +import json +import os +import string +import subprocess + +from sys import platform as _platform + +from galaxy.tools.deps import commands +from galaxy.tools.deps import installable + +try: + import yaml +except ImportError: + yaml = None + +from ._cli import arg_parser +from .util import build_target, conda_build_target_str, image_name +from ..conda_compat import MetaData + +DIRNAME = os.path.dirname(__file__) +DEFAULT_CHANNEL = "bioconda" +DEFAULT_EXTRA_CHANNELS = ["conda-forge", "r"] +DEFAULT_CHANNELS = [DEFAULT_CHANNEL] + DEFAULT_EXTRA_CHANNELS +DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}" +DEFAULT_BINDS = ["build/dist:/usr/local/"] +IS_OS_X = _platform == "darwin" +INVOLUCRO_VERSION = "1.1.2" + + +def involucro_link(): + if IS_OS_X: + url = "https://github.com/involucro/involucro/releases/download/v%s/involucro.darwin" % INVOLUCRO_VERSION + else: + url = "https://github.com/involucro/involucro/releases/download/v%s/involucro" % INVOLUCRO_VERSION + return url + + +def get_tests(args, pkg_path): + """Extract test cases given a recipe's meta.yaml file.""" + recipes_dir = args.recipes_dir + + tests = "" + input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path)) + recipe_meta = MetaData(input_dir) + + tests_commands = recipe_meta.get_value('test/commands') + tests_imports = recipe_meta.get_value('test/imports') + requirements = recipe_meta.get_value('requirements/run') + + if tests_imports or tests_commands: + if tests_commands: + tests = ' && '.join(tests_commands) + elif tests_imports and 'python' in requirements: + tests = ' && '.join('python -c "import %s"' % imp for imp in tests_imports) + elif tests_imports and ('perl' in requirements or 'perl-threaded' in requirements): + tests = ' && '.join('''perl -e "use %s;"''' % imp for imp in tests_imports) + tests = tests.replace('$R ', 'Rscript ') + else: + pass + return tests + + +def get_pkg_name(args, pkg_path): + """Extract the package name from a given meta.yaml file.""" + recipes_dir = args.recipes_dir + + input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path)) + recipe_meta = MetaData(input_dir) + return recipe_meta.get_value('package/name') + + +def get_affected_packages(args): + """Return a list of all meta.yaml file that where modified/created recently. + + Length of time to check for indicated by the ``hours`` parameter. + """ + recipes_dir = args.recipes_dir + hours = args.diff_hours + cmd = """cd '%s' && git log --diff-filter=ACMRTUXB --name-only --pretty="" --since="%s hours ago" | grep -E '^recipes/.*/meta.yaml' | sort | uniq""" % (recipes_dir, hours) + pkg_list = check_output(cmd, shell=True) + ret = list() + for pkg in pkg_list.strip().split('\n'): + if pkg and os.path.exists(os.path.join( recipes_dir, pkg )): + ret.append( (get_pkg_name(args, pkg), get_tests(args, pkg)) ) + return ret + + +def check_output(cmd, shell=True): + return subprocess.check_output(cmd, shell=shell) + + +def conda_versions(pkg_name, file_name): + """Return all conda version strings for a specified package name.""" + j = json.load(open(file_name)) + ret = list() + for pkg in j['packages'].values(): + if pkg['name'] == pkg_name: + ret.append('%s--%s' % (pkg['version'], pkg['build'])) + return ret + + +def mull_targets( + targets, involucro_context=None, + command="build", channels=DEFAULT_CHANNELS, namespace="mulled", + test='true', image_build=None, name_override=None, + repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False, + binds=DEFAULT_BINDS +): + if involucro_context is None: + involucro_context = InvolucroContext() + + repo_template_kwds = { + "namespace": namespace, + "image": image_name(targets, image_build=image_build, name_override=name_override) + } + repo = string.Template(repository_template).safe_substitute(repo_template_kwds) + + for channel in channels: + if channel.startswith('file://'): + bind_path = channel.lstrip('file://') + binds.append('/%s:/%s' % (bind_path, bind_path)) + + channels = ",".join(channels) + target_str = ",".join(map(conda_build_target_str, targets)) + bind_str = ",".join(binds) + involucro_args = [ + '-f', '%s/invfile.lua' % DIRNAME, + '-set', "CHANNELS='%s'" % channels, + '-set', "TEST='%s'" % test, + '-set', "TARGETS='%s'" % target_str, + '-set', "REPO='%s'" % repo, + '-set', "BINDS='%s'" % bind_str, + command, + ] + print(" ".join(involucro_context.build_command(involucro_args))) + if not dry_run: + ensure_installed(involucro_context, True) + involucro_context.exec_command(involucro_args) + + +def context_from_args(args): + return InvolucroContext(involucro_bin=args.involucro_path) + + +class InvolucroContext(installable.InstallableContext): + + installable_description = "Involucro" + + def __init__(self, involucro_bin=None, shell_exec=None, verbose="3"): + if involucro_bin is None: + if os.path.exists("./involucro"): + self.involucro_bin = "./involucro" + else: + self.involucro_bin = "involucro" + else: + self.involucro_bin = involucro_bin + self.shell_exec = shell_exec or commands.shell + self.verbose = verbose + + def build_command(self, involucro_args): + return [self.involucro_bin, "-v=%s" % self.verbose] + involucro_args + + def exec_command(self, involucro_args): + cmd = self.build_command(involucro_args) + return self.shell_exec(" ".join(cmd)) + + def is_installed(self): + return os.path.exists(self.involucro_bin) + + def can_install(self): + return True + + @property + def parent_path(self): + return os.path.dirname(os.path.abspath(self.involucro_bin)) + + +def ensure_installed(involucro_context, auto_init): + return installable.ensure_installed(involucro_context, install_involucro, auto_init) + + +def install_involucro(involucro_context=None, to_path=None): + to_path = involucro_context.involucro_bin + download_cmd = " ".join(commands.download_command(involucro_link(), to=to_path, quote_url=True)) + full_cmd = "%s && chmod +x %s" % (download_cmd, to_path) + return involucro_context.shell_exec(full_cmd) + + +def add_build_arguments(parser): + """Base arguments describing how to 'mull'.""" + parser.add_argument('--involucro-path', dest="involucro_path", default=None, + help="Path to involucro (if not set will look in working directory and on PATH).") + parser.add_argument('--force-rebuild', dest="force_rebuild", action="store_true", + help="Rebuild package even if already published.") + parser.add_argument('--dry-run', dest='dry_run', action="store_true", + help='Just print commands instead of executing them.') + parser.add_argument('-n', '--namespace', dest='namespace', default="mulled", + help='quay.io namespace.') + parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE, + help='Docker repository target for publication (only quay.io or compat. API is currently supported).') + parser.add_argument('-c', '--channel', dest='channel', default=DEFAULT_CHANNEL, + help='Target conda channel') + parser.add_argument('--extra-channels', dest='extra_channels', default=",".join(DEFAULT_EXTRA_CHANNELS), + help='Dependent conda channels.') + + +def add_single_image_arguments(parser): + parser.add_argument("--name-override", dest="name_override", default=None, + help="Override mulled image name - this is not recommended since metadata will not be detectable from the name of resulting images") + parser.add_argument("--image-build", dest="image_build", default=None, + help="Build a versioned variant of this image.") + + +def target_str_to_targets(targets_raw): + def parse_target(target_str): + if "=" in target_str: + package_name, version = target_str.split("=", 1) + target = build_target(package_name, version) + else: + target = build_target(target_str) + return target + + targets = map(parse_target, targets_raw.split(",")) + return targets + + +def args_to_mull_targets_kwds(args): + kwds = {} + if hasattr(args, "image_build"): + kwds["image_build"] = args.image_build + if hasattr(args, "name_override"): + kwds["name_override"] = args.name_override + if hasattr(args, "namespace"): + kwds["namespace"] = args.namespace + if hasattr(args, "dry_run"): + kwds["dry_run"] = args.dry_run + if hasattr(args, "test"): + kwds["test"] = args.test + if hasattr(args, "channel"): + channels = [args.channel] + if hasattr(args, "extra_channels"): + channels += args.extra_channels.split(",") + kwds["channels"] = channels + if hasattr(args, "command"): + kwds["command"] = args.command + if hasattr(args, "repository_template"): + kwds["repository_template"] = args.repository_template + + kwds["involucro_context"] = context_from_args(args) + + return kwds + + +def main(argv=None): + """Main entry-point for the CLI tool.""" + parser = arg_parser(argv, globals()) + add_build_arguments(parser) + add_single_image_arguments(parser) + parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)') + parser.add_argument('targets', metavar="TARGETS", default=None, help="Build a single container with specific package(s).") + parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of mulled container (leave blank to auto-generate based on packages - recommended).") + parser.add_argument('--test', help='Provide a test command for the container.') + args = parser.parse_args() + targets = target_str_to_targets(args.targets) + mull_targets(targets, **args_to_mull_targets_kwds(args)) + + +__all__ = ["main"] + + +if __name__ == '__main__': + main() diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py new file mode 100644 index 00000000000..b5082224649 --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py @@ -0,0 +1,109 @@ +#!/usr/bin/env python +"""Build a mulled images for all recent conda recipe updates that don't have existing images. + +Examples: + +Build mulled images for recent bioconda changes with: + + mulled-build-channel build + +Build, test, and publish images with the follow command: + + mulled-build-channel all + +See recent changes that would be built with: + + mulled-build-channel list + +""" + + +import os +import time + +from ._cli import arg_parser +from .mulled_build import ( + add_build_arguments, + args_to_mull_targets_kwds, + build_target, + check_output, + conda_versions, + get_affected_packages, + mull_targets, +) +from .util import quay_versions, version_sorted + + +def _fetch_repo_data(args): + repo_data = args.repo_data + channel = args.channel + if repo_data is None: + repo_data = "%s-repodata.json" % channel + if not os.path.exists(repo_data): + check_output("wget --quiet https://conda.anaconda.org/%s/linux-64/repodata.json.bz2 -O '%s.bz2' && bzip2 -d '%s.bz2'" % (channel, repo_data, repo_data)) + return repo_data + + +def _new_versions(quay, conda): + """Calculate the versions that are in conda but not on quay.io.""" + sconda = set(conda) + squay = set(quay) if quay else set() + return sconda - squay # sconda.symmetric_difference(squay) + + +def run_channel(args, build_last_n_versions=1): + """Build list of involucro commands (as shell snippet) to run.""" + pkgs = get_affected_packages(args) + for pkg_name, pkg_tests in pkgs: + repo_data = _fetch_repo_data(args) + c = conda_versions(pkg_name, repo_data) + # only package the most recent N versions + c = version_sorted(c)[:build_last_n_versions] + + if not args.force_rebuild: + time.sleep(1) + q = quay_versions(args.namespace, pkg_name) + versions = _new_versions(q, c) + else: + versions = c + + for tag in versions: + target = build_target(pkg_name, tag=tag) + targets = [target] + mull_targets(targets, test=pkg_tests, **args_to_mull_targets_kwds(args)) + + +def get_pkg_names(args): + """Print package names that would be affected.""" + print('\n'.join([pkg_name for pkg_name, pkg_tests in get_affected_packages(args)])) + + +def add_channel_arguments(parser): + """Add arguments only used if running mulled over a whole conda channel.""" + parser.add_argument('--repo-data', dest='repo_data', default=None, + help='Published repository data (will be fetched from --channel if not available and written). Defaults to [channel_name]-repodata.json.') + parser.add_argument('--diff-hours', dest='diff_hours', default="25", + help='If finding all recently changed recipes, use this number of hours.') + parser.add_argument('--recipes-dir', dest="recipes_dir", default="./bioconda-recipes") + + +def main(argv=None): + """Main entry-point for the CLI tool.""" + parser = arg_parser(argv, globals()) + add_channel_arguments(parser) + add_build_arguments(parser) + parser.add_argument('command', metavar='COMMAND', help='Command (list, build-and-test, build, all)') + parser.add_argument('--targets', dest="targets", default=None, help="Build a single container with specific package(s).") + parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of a single container (leave blank to auto-generate based on packages).") + args = parser.parse_args() + if args.command == "list": + get_pkg_names(args) + else: + run_channel(args) + + +__all__ = ["main"] + + +if __name__ == '__main__': + main() diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_files.py b/lib/galaxy/tools/deps/mulled/mulled_build_files.py new file mode 100644 index 00000000000..0fd065c504d --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/mulled_build_files.py @@ -0,0 +1,80 @@ +"""Build all composite mulled recipes discovered in TSV files. + +Use mulled-build-channel to build images for single recipes for a whole conda +channel. This script instead builds images for combinations of recipes. This +script can be given a single TSV file or a directory of TSV files to process. + +Examples: + +Build all recipes discovered in tsv files in a single directory. + + mulled-build-files build + +""" + +import collections +import glob +import os + +from ._cli import arg_parser + +from .mulled_build import ( + add_build_arguments, + args_to_mull_targets_kwds, + mull_targets, + target_str_to_targets, +) + + +def main(argv=None): + """Main entry-point for the CLI tool.""" + parser = arg_parser(argv, globals()) + add_build_arguments(parser) + parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)') + parser.add_argument('files', metavar="FILES", default=".", + help="Path to directory (or single file) of TSV files describing composite recipes.") + args = parser.parse_args() + for targets in generate_targets(args.files): + mull_targets(targets, **args_to_mull_targets_kwds(args)) + + +def generate_targets(target_source): + """Generate all targets from TSV files in specified file or directory.""" + target_source = os.path.abspath(target_source) + if os.path.isdir(target_source): + target_source_files = glob.glob(target_source + "/*.tsv") + else: + target_source_files = [target_source] + + for target_source_file in target_source_files: + with open(target_source_file, "r") as f: + for line in f.readlines(): + if line: + line = line.strip() + + if not line or line.startswith("#"): + continue + + yield line_to_targets(line) + + +def line_to_targets(line_str): + line = _parse_line(line_str) + return target_str_to_targets(line) + + +_Line = collections.namedtuple("_Line", ["targets", "image_build", "name_override"]) + + +def _parse_line(line_str): + line_parts = line_str.split(" ") + assert len(line_parts) < 3, "Too many fields in line [%s], expect at most 3 - targets, image build number, and name override." % line_str + line_parts += [None] * (3 - len(line_parts)) + return _Line(*line_parts) + + +__all__ = ["main"] + + +if __name__ == '__main__': + main() diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py new file mode 100644 index 00000000000..7281c7940ae --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python +"""Build a mulled images for a tool source (Galaxy or CWL tool). + +Examples: + +Build mulled images for requirements defined in a tool: + + mulled-build-tool build path/to/tool_file.xml + +""" + +from galaxy.tools.parser import get_tool_source + +from ._cli import arg_parser +from .mulled_build import ( + add_build_arguments, + add_single_image_arguments, + args_to_mull_targets_kwds, + build_target, + mull_targets, +) + + +def main(argv=None): + """Main entry-point for the CLI tool.""" + parser = arg_parser(argv, globals()) + add_build_arguments(parser) + add_single_image_arguments(parser) + parser.add_argument('command', metavar='COMMAND', help='Command (build-and-test, build, all)') + parser.add_argument('tool', metavar="TOOL", default=None, help="Path to tool to build mulled image for.") + args = parser.parse_args() + tool_source = get_tool_source(args.tool) + requirements, _ = tool_source.parse_requirements_and_containers() + targets = requirements_to_mulled_targets(requirements) + mull_targets(targets, **args_to_mull_targets_kwds(args)) + + +def requirements_to_mulled_targets(requirements): + """Convert Galaxy's representation of requirements into mulled Target objects. + + Only package requirements are retained. + """ + package_requirements = filter(lambda r: r.type == "package", requirements) + targets = map(lambda r: build_target(r.name, r.version), package_requirements) + return targets + + +__all__ = ["main", "requirements_to_mulled_targets"] + + +if __name__ == '__main__': + main() diff --git a/lib/galaxy/tools/deps/mulled/mulled_search.py b/lib/galaxy/tools/deps/mulled/mulled_search.py new file mode 100644 index 00000000000..724956a1335 --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/mulled_search.py @@ -0,0 +1,131 @@ +#!/usr/bin/env python + +import argparse +import json +import sys +import tempfile + +try: + import requests +except ImportError: + requests = None + +try: + from whoosh.fields import Schema + from whoosh.fields import TEXT + from whoosh.fields import STORED + from whoosh.index import create_in + from whoosh.qparser import QueryParser +except ImportError: + Schema = TEXT = STORED = create_in = QueryParser = None + +QUAY_API_URL = 'https://quay.io/api/v1/repository' + + +class QuaySearch(): + """ + Tool to search within a quay organization for a given software name. + """ + def __init__(self, organization): + self.index = None + self.organization = organization + + def build_index(self): + """ + Create an index to quickly examine the repositories of a given quay.io organization. + """ + # download all information about the repositories from the + # given organization in self.organization + + parameters = {'public': 'true', 'namespace': self.organization} + r = requests.get(QUAY_API_URL, headers={'Accept-encoding': 'gzip'}, params=parameters, + timeout=12) + + tmp_dir = tempfile.mkdtemp() + schema = Schema(title=TEXT(stored=True), content=STORED) + self.index = create_in(tmp_dir, schema) + + json_decoder = json.JSONDecoder() + decoded_request = json_decoder.decode(r.text) + writer = self.index.writer() + for repository in decoded_request['repositories']: + writer.add_document(title=repository['name'], content=repository['description']) + writer.commit() + + def search_repository(self, search_string, non_strict): + """ + Search Docker containers on quay.io. + Results are displayed with all available versions, + including the complete image name. + """ + # with statement closes searcher after usage. + with self.index.searcher() as searcher: + search_string = "*%s*" % search_string + query = QueryParser("title", self.index.schema).parse(search_string) + results = searcher.search(query) + if non_strict: + # look for spelling errors and use suggestions as a search term too + corrector = searcher.corrector("title") + suggestions = corrector.suggest(search_string, limit=2) + + # get all repositories with suggested keywords + for suggestion in suggestions: + search_string = "*%s*" % suggestion + query = QueryParser("title", self.index.schema).parse(search_string) + results_tmp = searcher.search(query) + results.extend(results_tmp) + + sys.stdout.write("The query \033[1m %s \033[0m resulted in %s result(s).\n" % (search_string, len(results))) + + if non_strict: + sys.stdout.write('The search was relaxed and the following search terms were searched: ') + sys.stdout.write('\033[1m %s \033[0m\n' % ', '.join(suggestions)) + + out = list() + for result in results: + title = result['title'] + for version in self.get_additional_repository_information(title): + row = [title] + row.append(version) + out.append(row) + if out: + col_width = max(len(word) for row in out for word in row) + 2 # padding + for row in out: + name = row[0] + version = row[1] + sys.stdout.write("".join(word.ljust(col_width) for word in row) + "docker pull quay.io/%s/%s:%s\n" % (self.organization, name, version)) + else: + sys.stdout.write("No results found for %s in quay.io/%s.\n" % (search_string, self.organization)) + + def get_additional_repository_information(self, repository_string): + """ + Function downloads additional information from quay.io to + get the tag-field which includes the version number. + """ + url = "%s/%s/%s" % (QUAY_API_URL, self.organization, repository_string) + r = requests.get(url, headers={'Accept-encoding': 'gzip'}, timeout=12) + + json_decoder = json.JSONDecoder() + decoded_request = json_decoder.decode(r.text) + return decoded_request['tags'] + + +def main(argv=None): + parser = argparse.ArgumentParser(description='Searches in a given quay organization for a repository') + parser.add_argument('-o', '--organization', dest='organization_string', default="mulled", + help='Change organization. Default is mulled.') + parser.add_argument('--non-strict', dest='non_strict', action="store_true", + help='Autocorrection of typos activated. Lists more results but can be confusing.\ + For too many queries quay.io blocks the request and the results can be incomplete.') + parser.add_argument('-s', '--search', required=True, + help='The name of the tool you want to search for.') + args = parser.parse_args() + + quay = QuaySearch(args.organization_string) + quay.build_index() + + quay.search_repository(args.search, args.non_strict) + + +if __name__ == "__main__": + main() diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tools/deps/mulled/util.py new file mode 100644 index 00000000000..4fc5312afbe --- /dev/null +++ b/lib/galaxy/tools/deps/mulled/util.py @@ -0,0 +1,116 @@ +"""Utilities for working with mulled abstractions outside the mulled package.""" +from __future__ import print_function + +import collections +import hashlib + +from distutils.version import LooseVersion + +try: + import requests +except ImportError: + requests = None + + +def quay_versions(namespace, pkg_name): + """Get all version tags for a Docker image stored on quay.io for supplied package name.""" + if requests is None: + raise Exception("requets library is unavailable, functionality not available.") + + assert namespace is not None + assert pkg_name is not None + url = 'https://quay.io/api/v1/repository/%s/%s' % (namespace, pkg_name) + response = requests.get(url, timeout=None) + data = response.json() + if 'error_type' in data and data['error_type'] == "invalid_token": + return [] + + if 'tags' not in data: + raise Exception("Unexpected response from quay.io - not tags description found [%s]" % data) + + return [tag for tag in data['tags'] if tag != 'latest'] + + +def mulled_tags_for(namespace, image): + """Fetch remote tags available for supplied image name. + + The result will be sorted so newest tags are first. + """ + tags = quay_versions(namespace, image) + tags = version_sorted(tags) + return tags + + +def split_tag(tag): + """Split mulled image name into conda version and conda build.""" + version = tag.split('--', 1)[0] + build = tag.split('--', 1)[1] + return version, build + + +def version_sorted(elements): + """Sort iterable based on loose description of "version" from newest to oldest.""" + return sorted(elements, key=LooseVersion, reverse=True) + + +Target = collections.namedtuple("Target", ["package_name", "version", "build"]) + + +def build_target(package_name, version=None, build=None, tag=None): + """Use supplied arguments to build a :class:`Target` object.""" + if tag is not None: + assert version is None + assert build is None + version, build = split_tag(tag) + + return Target(package_name, version, build) + + +def conda_build_target_str(target): + rval = target.package_name + if target.version: + rval += "=%s" % target.version + + if target.build: + rval += "=%s" % target.build + + return rval + + +def image_name(targets, image_build=None, name_override=None): + if name_override is not None: + print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.") + return name_override + + if len(targets) == 1: + target = targets[0] + suffix = "" + if target.version is not None: + if image_build is not None: + print("WARNING: Hard-coding image build instead of using Conda build - this is not recommended.") + suffix = image_build + else: + suffix += ":%s" % target.version + build = target.build + if build is not None: + suffix += "--%s" % build + return "%s%s" % (target.package_name, suffix) + else: + targets_order = sorted(targets, key=lambda t: t.package_name) + requirements_buffer = "\n".join(map(conda_build_target_str, targets_order)) + m = hashlib.sha1() + m.update(requirements_buffer) + suffix = "" if not image_build else ":%s" % image_build + return "mulled-v1-%s%s" % (m.hexdigest(), suffix) + + +__all__ = [ + "build_target", + "conda_build_target_str", + "image_name", + "mulled_tags_for", + "quay_versions", + "split_tag", + "Target", + "version_sorted", +] diff --git a/lib/galaxy/tools/deps/resolvers/__init__.py b/lib/galaxy/tools/deps/resolvers/__init__.py index 2ea5abeaa4f..6165fdb6af8 100644 --- a/lib/galaxy/tools/deps/resolvers/__init__.py +++ b/lib/galaxy/tools/deps/resolvers/__init__.py @@ -1,3 +1,4 @@ +"""The module defines the abstract interface for dealing tool dependency resolution plugins.""" from abc import ( ABCMeta, abstractmethod, @@ -10,6 +11,8 @@ from ..requirements import ToolRequirement class DependencyResolver(Dictifiable, object): + """Abstract description of a technique for resolving container images for tool execution.""" + # Keys for dictification. dict_collection_visible_keys = ['resolver_type', 'resolves_simple_dependencies'] # A "simple" dependency is one that does not depend on the the tool @@ -23,13 +26,15 @@ class DependencyResolver(Dictifiable, object): @abstractmethod def resolve( self, name, version, type, **kwds ): - """ - Given inputs describing dependency in the abstract, yield tuple of - (script, bin, version). Here script is the env.sh file to source - before running a job, if that is not found the bin directory will be - appended to the path (if it is not None). Finally, version is the - resolved tool dependency version (which may differ from requested - version for instance if the request version is 'default'.) + """Given inputs describing dependency in the abstract yield a Dependency object. + + The Dependency object describes various attributes (script, bin, + version) used to build scripts with the dependency availble. Here + script is the env.sh file to source before running a job, if that is + not found the bin directory will be appended to the path (if it is + not ``None``). Finally, version is the resolved tool dependency + version (which may differ from requested version for instance if the + request version is 'default'.) """ def _get_config_option(self, key, dependency_resolver, default=None, config_prefix=None, **kwds): diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index 3b3d85d16f9..f16734a268e 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -6,10 +6,8 @@ incompatible changes coming. import logging import os -from galaxy.util.filelock import ( - FileLock, - FileLockException -) +import galaxy.tools.deps.installable + from ..conda_util import ( build_isolated_environment, cleanup_failed_install, @@ -32,7 +30,7 @@ from ..resolvers import ( DEFAULT_BASE_PATH_DIRECTORY = "_conda" DEFAULT_CONDARC_OVERRIDE = "_condarc" -DEFAULT_ENSURE_CHANNELS = "r,bioconda,iuc" +DEFAULT_ENSURE_CHANNELS = "conda-forge,r,bioconda,iuc" log = logging.getLogger(__name__) @@ -95,44 +93,11 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In copy_dependencies = _string_as_bool(get_option("copy_dependencies")) self.auto_init = _string_as_bool(get_option("auto_init")) self.conda_context = conda_context - self.ensure_conda_installed() + self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init) self.auto_install = auto_install self.copy_dependencies = copy_dependencies self.verbose_install_check = verbose_install_check - def ensure_conda_installed(self): - """ - Make sure that conda is installed, and if conda can't be installed, mark resolver as disabled. - We acquire a lock, so that multiple handlers do not attempt to install conda simultaneously. - """ - target_path = self.conda_prefix_parent - - def _check(): - if not self.conda_context.is_conda_installed(): - if self.auto_init: - if self.conda_context.can_install_conda(): - if install_conda(self.conda_context): - self.disabled = True - log.warning("Conda installation requested and failed.") - else: - self.disabled = True - else: - self.disabled = True - log.warning("Conda not installed and auto-installation disabled.") - else: - self.disabled = False - - if not os.path.exists(target_path): - os.mkdir(target_path) - try: - if self.auto_init and os.access(target_path, os.W_OK): - with FileLock(os.path.join(target_path, 'conda')): - _check() - else: - _check() - except FileLockException: - self.ensure_conda_installed() - def resolve(self, name, version, type, **kwds): # Check for conda just not being there, this way we can enable # conda by default and just do nothing in not configured. diff --git a/test/functional/tools/mulled_example_multi_1.xml b/test/functional/tools/mulled_example_multi_1.xml new file mode 100644 index 00000000000..1f025598c04 --- /dev/null +++ b/test/functional/tools/mulled_example_multi_1.xml @@ -0,0 +1,18 @@ + + $out_file1 ; + echo "Moo" >> $out_file1 ; + samtools >> $out_file1 2>&1 ; + echo "Cow" >> $out_file1 ; + ]]> + + samtools + bedtools + + + + + + + + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index d57356e25d9..90d64f86c37 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -111,6 +111,8 @@ + + + + diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 0ab674dc7c8..9ca65ee0bec 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -803,6 +803,10 @@ class JobWrapper( object ): """ return self.get_destination_configuration("cleanup_job", DEFAULT_CLEANUP_JOB) + @property + def requires_containerization(self): + return util.asbool(self.get_destination_configuration("require_container", "False")) + def can_split( self ): # Should the job handler split this job up? return self.app.config.use_tasked_jobs and self.tool.parallelism diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index afed2069f1f..17ac05ee726 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -198,6 +198,8 @@ class BaseJobRunner( object ): def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True, modify_command_for_container=True ): container = self._find_container( job_wrapper ) + if not container and job_wrapper.requires_containerization: + raise Exception("Failed to find a container when required, contact Galaxy admin.") return build_command( self, job_wrapper, diff --git a/test/unit/jobs/test_runner_local.py b/test/unit/jobs/test_runner_local.py index 22012258951..840c4eb6b3d 100644 --- a/test/unit/jobs/test_runner_local.py +++ b/test/unit/jobs/test_runner_local.py @@ -105,6 +105,7 @@ class MockJobWrapper( object ): os.makedirs( tool_working_directory ) self.app = app self.tool = tool + self.requires_containerization = False self.state = model.Job.states.QUEUED self.command_line = "echo HelloWorld" self.environment_variables = [] From 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 9 Oct 2016 12:40:50 +0200 Subject: [PATCH 07/32] Add initial documentation about the new mulled features. --- doc/source/admin/mulled_containers.rst | 128 +++++++++++++++++++++++++ 1 file changed, 128 insertions(+) create mode 100644 doc/source/admin/mulled_containers.rst diff --git a/doc/source/admin/mulled_containers.rst b/doc/source/admin/mulled_containers.rst new file mode 100644 index 00000000000..7c16ba72353 --- /dev/null +++ b/doc/source/admin/mulled_containers.rst @@ -0,0 +1,128 @@ +================================= +Containers for Tool Dependencies +================================= + +Galaxy tools (also called wrappers) are able to use Conda packages +(see more information in our `Galaxy Conda documentation`_) and Docker containers as dependency resolvers. +The IUC_ recommends to use Conda packages as primary dependency resolver, mainly because Docker is not +available on every (HPC-) system. Conda on the other hand can be installed by Galaxy and maintained +entirely in user-space. Nevertheless, Docker (Containers in general) has some uniq features and +there are a bunch of use-cases in the Galaxy community that makes containerized systems very appealing. + +Since 2014 Galaxy supports running tools in Docker containers via a special `container annotation`_ inside of the +requirement field. + +.. code-block:: xml + + + + busybox:ubuntu-14.04 + + gnu_coreutils + + + +This approach has shown two limitations that slowed down the adoption by Tool developers. +First, every tool needs to be annotated with a container name (as shown above) and this container needs +to be created beforehand, usually manually. The second reason is that a Galaxy tool aims to be deployed everywhere, +independet of the underlying system, meaning if Docker is not availble Galaxy should use Conda packages. +This puts an additionl burden to tool developers that needs to take care of two dependency resolvers and can yield to +different results of your tool depending on the resolver, because both the Conda package and the Docker container is +usually not created out of the same recipe and maybe was compiled in a different way, uses different sources etc ... + +Not an ideal solution and something we wanted to solve. + +Here we demonstrate a solution that can create Containers out of Conda packages automatically. +This can be either used to support communities like BioContainers_ to create Containers +before deploying a Galaxy tool, or this can be used by Galaxy to create Containers on-demand and on-the-fly if no one +is available already. + + +Automatic build of linux containers +----------------------------------- + +We utilize [mulled](https://github.com/mulled/mulled) and with this [involucro](https://github.com/involucro/involucro) +in an automatic way. This is for example used to convert all packages in bioconda_ into Linux Containers +(Docker and rkt at the moment) and made available at the `BioContainers Quay.io account`_. + +We have developed small utilities around this technology stack which is currently included in galaxy-lib_. +Here is a short introduction: + +Search for containers +^^^^^^^^^^^^^^^^^^^^^ + +This will search for containers in the biocontainers organisation. + +.. code-block:: bash + + $ mulled-search -s vsearch -o biocontainers + + +Build all packages from bioconda from the last 24h +^^^^^^^^^^^^^^^^^^^^^ + +The BioConda community is building a container for every package they create with a command similar to this. + +.. code-block:: bash + + $ mulled-build-channel --channel bioconda --namespace biocontainers \ + --involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build + + +Building Docker containers for local Conda packages +^^^^^^^^^^^^^^^^^^^^^ + +Conda packages can be tested with creating a busybox based container for this particular package in the following way. +This also demonstrates how you can build a container locally and on-the-fly. + + > we modified the samtools package to version 3.0 to make clear we are using a local version + +1) build your recipe + +.. code-block:: bash + + $ conda build recipes/samtools + +2) index your local builds + +.. code-block:: bash + + $ conda index /home/bag/miniconda2/conda-bld/linux-64/ + + +3) build a container for your local package + +.. code-block:: bash + + $ mulled-build build-and-test 'samtools=3.0--0' \ + --extra-channel file://home/bag/miniconda2/conda-bld/ --test 'samtools --help' + +The ``--0`` indicates the build version of the conda package. It is recommended to specify this number otherwise +you will override already exsisting images. For python conda packages this extension might look like this ``--py35_1``. + +Build, test and push a conda-forge package to biocontainers +^^^^^^^^^^^^^^^^^^^^^ + + > You need to have write access to the biocontainers repository + +You can build packages from other Conda channels as well, not only from BioConda. ``pandoc`` is available from the +conda-forge channel and conda-forge is also enabled by default in Galaxy. To build ``pandoc`` and push it to biocontainrs +you could do something along these lines. + + +.. code-block:: bash + + $ mulled-build build-and-test 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers + +.. code-block:: bash + + $ mulled-build push 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers + + +.. _Galaxy Conda documentation: ./conda_faq.rst +.. _IUC: https://wiki.galaxyproject.org/IUC +.. _container annotation: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4 +.. _BioContainers: https://github.com/biocontainers +.. _bioconda: https://github.com/bioconda/bioconda-recipes +.. _BioContainers Quay.io account: https://quay.io/organization/biocontainers +.. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib From ad0d0bc7cec7c281052610b9453db42cfce8dcea Mon Sep 17 00:00:00 2001 From: ramezrawas Date: Mon, 10 Oct 2016 09:52:02 +0200 Subject: [PATCH 08/32] Missing double quotation line 3664: name="output_vcf> --- lib/galaxy/tools/xsd/galaxy.xsd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd index e9c62893ee2..b9c7d00fd3c 100644 --- a/lib/galaxy/tools/xsd/galaxy.xsd +++ b/lib/galaxy/tools/xsd/galaxy.xsd @@ -3661,7 +3661,7 @@ conditionals are accessed using a hash named after the conditional. - options['selection_mode'] == 'advanced' and options['vcf_output'] From fad562876f886e3384fec1a9782685251d12e2c1 Mon Sep 17 00:00:00 2001 From: carlfeberhard Date: Mon, 10 Oct 2016 10:31:29 -0400 Subject: [PATCH 09/32] Datatypes: include base classes in search by name Fixes #2982 Adds the base class 'images.Image' to the list of classes returnable by 'datatypes_registry.get_datatype_class_by_name'. Normally that method searches the registry's list of datatypes and those are instantiable classes only. The images.Image can be considered an abstract base class and you'd never create a dataset of that datatype. The method is used for getting classes for 'isinstance' tests, however, so including base classes like 'images.Image' allow testing for all its image subclasses. This change makes that possible and allows the method (and its consumers) to behave in a much more predictable and useful manner. --- lib/galaxy/datatypes/registry.py | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py index 5bde4a1ecc2..099c2bccf35 100644 --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -434,27 +434,18 @@ class Registry( object ): Return the datatype class where the datatype's `type` attribute (as defined in the datatype_conf.xml file) contains `name`. """ - # TODO: too roundabout - would be better to generate this once as a map and store in this object + # TODO: obviously not ideal but some of these base classes that are useful for testing datatypes + # aren't loaded into the datatypes registry, so we'd need to test for them here + if name == 'images.Image': + return images.Image + + # TODO: too inefficient - would be better to generate this once as a map and store in this object for ext, datatype_obj in self.datatypes_by_extension.items(): datatype_obj_class = datatype_obj.__class__ datatype_obj_class_str = str( datatype_obj_class ) if name in datatype_obj_class_str: return datatype_obj_class return None - # these seem to be connected to the dynamic classes being generated in this file, lines 157-158 - # they appear when a one of the three are used in inheritance with subclass="True" - # TODO: a possible solution is to def a fn in datatypes __init__ for creating the dynamic classes - - # remap = { - # 'galaxy.datatypes.registry.Tabular' : galaxy.datatypes.tabular.Tabular, - # 'galaxy.datatypes.registry.Text' : galaxy.datatypes.data.Text, - # 'galaxy.datatypes.registry.Binary' : galaxy.datatypes.binary.Binary - # } - # datatype_str = str( datatype ) - # if datatype_str in remap: - # datatype = remap[ datatype_str ] - # - # return datatype def get_available_tracks( self ): return self.available_tracks From 91bfecea67b78f7e459a250a7844c6344154367f Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 7 Oct 2016 15:56:02 -0400 Subject: [PATCH 10/32] Add documentation on optional ``multiple="true"`` data parameters. Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility). Rebased with indention requested by @nsoranzo and fixes for the test case tool. --- lib/galaxy/tools/xsd/galaxy.xsd | 27 +++++++++++++++++++ test/functional/tools/multi_data_optional.xml | 27 +++++++++++++++++++ test/functional/tools/samples_tool_conf.xml | 1 + 3 files changed, 55 insertions(+) create mode 100644 test/functional/tools/multi_data_optional.xml diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd index 8d0cecc92c1..978fc769716 100644 --- a/lib/galaxy/tools/xsd/galaxy.xsd +++ b/lib/galaxy/tools/xsd/galaxy.xsd @@ -1990,6 +1990,33 @@ multiple formats. help="The set of aligned reads." /> ``` +Perhaps counter-intuitively, a ``multiple="true"`` data parameter requires at least one +data input. If ``optional="true"`` is specified, this condition is relaxed and the user +is allowed to select 0 datasets. Unfortunately, if 0 datasets are selected the resulting +value for the parameter during Cheetah templating (such as in a ``command`` block) will +effectively be a list with one ``None``-like entity in it. + +The following idiom can be used to iterate over such a list and build a hypothetical ``-B`` +parameter for each file - the ``if`` block is used to handle the case where a ``None``-like +entity appears in the list because no files were selected: + +``` +#for $input in $input1 + #if $input + -B "$input" + #end if +#end for +``` + +Some example tools using ``multiple="true"`` data parameters include: + +- [multi_data_param.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_data_param.xml) +- [multi_data_optional.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_data_optional.xml) + +Additionally, a detailed discussion of handling multiple homogenous files can be found in the +the [Planemo Documentation](http://planemo.readthedocs.io/en/latest/writing_advanced.html#consuming-collections) +on this topic. + $attribute_list:format,multiple #### ``select`` diff --git a/test/functional/tools/multi_data_optional.xml b/test/functional/tools/multi_data_optional.xml new file mode 100644 index 00000000000..5f914259f8a --- /dev/null +++ b/test/functional/tools/multi_data_optional.xml @@ -0,0 +1,27 @@ + + + touch $out1; + #for $input in $input1 + #if $input + cat $input >> $out1; + #end if + #end for + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index d57356e25d9..6286cbcb9c0 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -57,6 +57,7 @@ + From f0b988da78f081bf6845ce2d280d153e221f3633 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 10 Oct 2016 11:07:05 -0400 Subject: [PATCH 11/32] Bring in latest galaxy-lib fixes. --- lib/galaxy/tools/deps/mulled/mulled_build.py | 8 ++++++-- lib/galaxy/tools/deps/mulled/util.py | 3 ++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py index b359c540cbf..e110969b203 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build.py @@ -5,7 +5,7 @@ Examples Build a mulled image with: - mulled-build build 'samtools=1.3.1,bedtools=2.22' + mulled-build build 'samtools=1.3.1--4,bedtools=2.22' """ from __future__ import print_function @@ -118,6 +118,7 @@ def mull_targets( repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False, binds=DEFAULT_BINDS ): + targets = list(targets) if involucro_context is None: involucro_context = InvolucroContext() @@ -227,7 +228,10 @@ def target_str_to_targets(targets_raw): def parse_target(target_str): if "=" in target_str: package_name, version = target_str.split("=", 1) - target = build_target(package_name, version) + build = None + if "--" in version: + version, build = version.split('--') + target = build_target(package_name, version, build) else: target = build_target(target_str) return target diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tools/deps/mulled/util.py index 4fc5312afbe..a190d0e2192 100644 --- a/lib/galaxy/tools/deps/mulled/util.py +++ b/lib/galaxy/tools/deps/mulled/util.py @@ -82,6 +82,7 @@ def image_name(targets, image_build=None, name_override=None): print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.") return name_override + targets = list(targets) if len(targets) == 1: target = targets[0] suffix = "" @@ -99,7 +100,7 @@ def image_name(targets, image_build=None, name_override=None): targets_order = sorted(targets, key=lambda t: t.package_name) requirements_buffer = "\n".join(map(conda_build_target_str, targets_order)) m = hashlib.sha1() - m.update(requirements_buffer) + m.update(requirements_buffer.encode()) suffix = "" if not image_build else ":%s" % image_build return "mulled-v1-%s%s" % (m.hexdigest(), suffix) From 1e32c0926ca3fcee79f355577c5525c4bf73c8e4 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 10 Oct 2016 18:13:33 +0100 Subject: [PATCH 12/32] Fix import order and Python3 compatibility for most of test/ --- .ci/flake8_blacklist.txt | 4 +-- .ci/flake8_lint_include_list.txt | 23 +++++++++++++--- .ci/py3_sources.txt | 2 ++ client/galaxy/style/source_material/circle.py | 5 ++-- doc/parse_gx_xsd.py | 6 ++--- test/api/helpers.py | 9 ++++--- test/api/test_api_batch.py | 4 ++- test/api/test_authenticate.py | 2 +- test/api/test_dataset_collections.py | 7 ++--- test/api/test_history_contents.py | 11 ++++---- test/api/test_page_revisions.py | 3 ++- test/api/test_pages.py | 7 +++-- test/api/test_tool_data.py | 4 ++- test/api/test_tools.py | 21 +++++++-------- test/api/test_users.py | 2 ++ test/api/test_workflow_extraction.py | 5 ++-- test/api/test_workflows.py | 26 +++++++++---------- test/api/workflows_format_2/__init__.py | 2 +- test/api/workflows_format_2/converter.py | 12 ++++----- test/base/api.py | 24 +++++++---------- test/base/driver_util.py | 19 ++++++-------- test/base/integration_util.py | 2 +- test/base/interactor.py | 7 +++-- test/base/test_logging.py | 3 +-- test/base/twilltestcase.py | 11 +++----- test/functional/test_data_managers.py | 16 +++++++----- test/functional/test_library_templates.py | 16 ++++++------ test/functional/test_toolbox.py | 21 ++++++++------- test/functional/workflow.py | 25 +++++++++--------- test/integration/test_resolvers.py | 4 +-- test/manual/workflows_scaling.py | 9 +++---- test/shed_functional/base/test_db_util.py | 5 ++-- .../test_0300_reset_all_metadata.py | 2 +- .../test_1300_reset_all_metadata.py | 2 +- test/shed_functional/functional_tests.py | 4 +-- 35 files changed, 168 insertions(+), 157 deletions(-) diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt index bac2e110b7f..bfef6f7adeb 100644 --- a/.ci/flake8_blacklist.txt +++ b/.ci/flake8_blacklist.txt @@ -1,8 +1,8 @@ .venv/ .tox/ -eggs/ -client/ +client/node_modules/ database/ doc/patch.py doc/source/conf.py +eggs/ lib/galaxy/util/jstree.py diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt index 735434e27ce..eb2ab916d61 100644 --- a/.ci/flake8_lint_include_list.txt +++ b/.ci/flake8_lint_include_list.txt @@ -1,8 +1,10 @@ +client/galaxy/style/source_material/circle.py contrib/ cron/add_manual_builds.py cron/cleanup_datasets.py cron/parse_builds_3_sites.py cron/parse_builds.py +doc/parse_gx_xsd.py lib/galaxy/actions/ lib/galaxy/auth/__init__.py lib/galaxy/auth/providers/__init__.py @@ -440,6 +442,7 @@ scripts/tool_shed/migrate_tools_to_repositories.py scripts/tool_shed/show_tool_dependency_installation_dir_contents.py scripts/tools/re_escape_output.py test/api/__init__.py +test/api/test_dataset_collections.py test/api/test_datasets.py test/api/test_datatypes.py test/api/test_framework.py @@ -447,27 +450,39 @@ test/api/test_histories.py test/api/test_history_contents_provenance.py test/api/test_jobs.py test/api/test_libraries.py +test/api/test_page_revisions.py test/api/test_search.py +test/api/test_tool_data.py +test/api/test_tools.py test/api/test_tours.py +test/api/test_workflow_extraction.py test/api/test_workflows_from_yaml.py -test/api/workflows_format_2/interface.py -test/api/workflows_format_2/main.py +test/api/workflows_format_2/ test/base/api_asserts.py +test/base/api.py test/base/api_util.py test/base/__init__.py test/base/instrument.py +test/base/integration_util.py +test/base/interactor.py test/base/nose_util.py +test/base/test_logging.py test/base/tool_shed_util.py +test/base/twilltestcase.py test/casperjs/ test/functional/database_contexts.py test/functional/__init__.py +test/functional/test_data_managers.py +test/functional/test_toolbox.py +test/functional/tool-data/ test/functional/tools/ -test/integration/__init__.py -test/integration/test_pulsar_embedded.py +test/functional/workflow.py +test/integration/ test/manual/__init__.py test/shed_functional/base/common.py test/shed_functional/base/__init__.py test/shed_functional/functional/ +test/shed_functional/functional_tests.py test/shed_functional/__init__.py test/unit/dataset_collections/__init__.py test/unit/datatypes/dataproviders/__init__.py diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt index d9f47f7b999..ecd7f79c9d4 100644 --- a/.ci/py3_sources.txt +++ b/.ci/py3_sources.txt @@ -1,5 +1,7 @@ +client/galaxy/style/source_material/circle.py contrib/ cron/ +doc/parse_gx_xsd.py lib/galaxy/actions/ lib/galaxy/auth/ lib/galaxy/config.py diff --git a/client/galaxy/style/source_material/circle.py b/client/galaxy/style/source_material/circle.py index 5331a0e0cc4..f1f014b9565 100755 --- a/client/galaxy/style/source_material/circle.py +++ b/client/galaxy/style/source_material/circle.py @@ -1,15 +1,14 @@ #!/usr/bin/env python - """ usage: %prog width height bg_color hatch_color [color alpha stop_pos] + """ - from __future__ import division import sys -import cairo from math import pi +import cairo + assert sys.version_info[:2] >= ( 2, 4 ) diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py index 7263ae358fd..452b7f4e43b 100644 --- a/doc/parse_gx_xsd.py +++ b/doc/parse_gx_xsd.py @@ -2,14 +2,12 @@ # TODO: Add examples, tables and best practice links to command # TODO: Examples of truevalue, falsevalue # TODO: Test param extra_file -from __future__ import print_function - # Things dropped from TOC (still documented inside schema). # - request_parameter_translation +from __future__ import print_function from lxml import etree -from StringIO import StringIO - +from six import StringIO with open("doc/schema_template.md", "r") as f: MARKDOWN_TEMPLATE = f.read() diff --git a/test/api/helpers.py b/test/api/helpers.py index 2a6b0c2537c..a4276a010cf 100644 --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -1,10 +1,11 @@ -from base import api_asserts +import json +import time from operator import itemgetter -import time -import json -from six import StringIO from pkg_resources import resource_string +from six import StringIO + +from base import api_asserts # Simple workflow that takes an input and call cat wrapper on it. workflow_str = resource_string( __name__, "test_workflow_1.ga" ) diff --git a/test/api/test_api_batch.py b/test/api/test_api_batch.py index 186e0964d6a..d85f0c890c4 100644 --- a/test/api/test_api_batch.py +++ b/test/api/test_api_batch.py @@ -1,7 +1,9 @@ import json -import pprint import logging +import pprint + from requests import post + from base import api log = logging.getLogger( "functional_tests.py" ) diff --git a/test/api/test_authenticate.py b/test/api/test_authenticate.py index 6e58693e2d3..d713e27066e 100644 --- a/test/api/test_authenticate.py +++ b/test/api/test_authenticate.py @@ -1,8 +1,8 @@ import base64 from requests import get -from base import api +from base import api TEST_USER_EMAIL = "auth_user_test@bx.psu.edu" TEST_USER_PASSWORD = "testpassword1" diff --git a/test/api/test_dataset_collections.py b/test/api/test_dataset_collections.py index 2e298fe7698..7e38350956f 100644 --- a/test/api/test_dataset_collections.py +++ b/test/api/test_dataset_collections.py @@ -1,7 +1,8 @@ -from base import api import json -from .helpers import DatasetPopulator -from .helpers import DatasetCollectionPopulator + +from base import api + +from .helpers import DatasetCollectionPopulator, DatasetPopulator class DatasetCollectionApiTestCase( api.ApiTestCase ): diff --git a/test/api/test_history_contents.py b/test/api/test_history_contents.py index 3a35515a92c..8f58bb321c7 100644 --- a/test/api/test_history_contents.py +++ b/test/api/test_history_contents.py @@ -1,11 +1,10 @@ -from base import api import json -from .helpers import TestsDatasets -from .helpers import LibraryPopulator -from .helpers import DatasetCollectionPopulator -from requests import delete -from requests import put +from requests import delete, put + +from base import api + +from .helpers import DatasetCollectionPopulator, LibraryPopulator, TestsDatasets # TODO: Test anonymous access. diff --git a/test/api/test_page_revisions.py b/test/api/test_page_revisions.py index 674ee5805ae..8f6013c1312 100644 --- a/test/api/test_page_revisions.py +++ b/test/api/test_page_revisions.py @@ -1,5 +1,6 @@ from galaxy.exceptions import error_codes -from api.test_pages import BasePageApiTestCase + +from .test_pages import BasePageApiTestCase class PageRevisionsApiTestCase( BasePageApiTestCase ): diff --git a/test/api/test_pages.py b/test/api/test_pages.py index f0195cdb0a5..1e72de9f3b5 100644 --- a/test/api/test_pages.py +++ b/test/api/test_pages.py @@ -1,8 +1,7 @@ -from galaxy.exceptions import error_codes -from base import api from requests import delete -from operator import itemgetter +from base import api +from galaxy.exceptions import error_codes class BasePageApiTestCase( api.ApiTestCase ): @@ -102,4 +101,4 @@ class PageApiTestCase( BasePageApiTestCase ): index_response = self._get( "pages" ) self._assert_status_code_is( index_response, 200 ) pages = index_response.json() - return id in map( itemgetter( "id" ), pages ) + return id in ( _["id"] for _ in pages ) diff --git a/test/api/test_tool_data.py b/test/api/test_tool_data.py index 0a2408e6f8d..0a0f3b14d9c 100644 --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -1,9 +1,11 @@ """ Tests for the tool data API. """ from __future__ import print_function -from base import api + import operator +from base import api + class ToolDataApiTestCase( api.ApiTestCase ): diff --git a/test/api/test_tools.py b/test/api/test_tools.py index 82e310b06a9..2db9ed5e2c8 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -1,13 +1,12 @@ # Test tools API. -from base import api import json -from operator import itemgetter -from .helpers import DatasetPopulator -from .helpers import DatasetCollectionPopulator -from .helpers import LibraryPopulator -from .helpers import skip_without_tool + +from base import api from galaxy.tools.verify.test_data import TestDataResolver +from .helpers import (DatasetCollectionPopulator, DatasetPopulator, + LibraryPopulator, skip_without_tool) + class ToolsTestCase( api.ApiTestCase ): @@ -25,7 +24,7 @@ class ToolsTestCase( api.ApiTestCase ): tools_index = index.json() # No need to flatten out sections, with in_panel=False, only tools are # returned. - tool_ids = map( itemgetter( "id" ), tools_index ) + tool_ids = [_["id"] for _ in tools_index] assert "upload1" in tool_ids @skip_without_tool( "cat1" ) @@ -195,7 +194,7 @@ class ToolsTestCase( api.ApiTestCase ): def get_state(dce): return dce["object"]["state"] - mixed_states = map(get_state, mixed_hdca["elements"]) + mixed_states = [get_state(_) for _ in mixed_hdca["elements"]] assert mixed_states == [u"ok", u"error", u"ok", u"error"], mixed_states inputs = { "input": { "src": "hdca", "id": mixed_hdca["id"] }, @@ -206,7 +205,7 @@ class ToolsTestCase( api.ApiTestCase ): self.assertEquals( len(filter_output_collections), 1 ) filtered_hid = filter_output_collections[0]["hid"] filtered_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=filtered_hid, wait=False) - filtered_states = map(get_state, filtered_hdca["elements"]) + filtered_states = [get_state(_) for _ in filtered_hdca["elements"]] assert filtered_states == [u"ok", u"ok"], filtered_states @skip_without_tool( "multi_select" ) @@ -525,7 +524,7 @@ class ToolsTestCase( api.ApiTestCase ): # Assert we have three outputs with 1, 2, and 3 lines respectively. assert len( outputs ) == 3 outputs_contents = [ self.dataset_populator.get_history_dataset_content( history_id, dataset=o ).strip() for o in outputs ] - assert sorted( map( lambda c: len( c.split( "\n" ) ), outputs_contents ) ) == [ 1, 2, 3 ] + assert sorted( len( c.split( "\n" ) ) for c in outputs_contents ) == [ 1, 2, 3 ] @skip_without_tool( "cat1" ) def test_multirun_in_repeat( self ): @@ -1230,7 +1229,7 @@ class ToolsTestCase( api.ApiTestCase ): else: tools.append( tool_or_section ) - tool_ids = map( itemgetter( "id" ), tools ) + tool_ids = [_["id"] for _ in tools] return tool_ids def __build_nested_list( self, history_id ): diff --git a/test/api/test_users.py b/test/api/test_users.py index 897c3499d89..9a7a14291c4 100644 --- a/test/api/test_users.py +++ b/test/api/test_users.py @@ -1,5 +1,7 @@ import json + from requests import put + from base import api TEST_USER_EMAIL = "user_for_users_index_test@bx.psu.edu" diff --git a/test/api/test_workflow_extraction.py b/test/api/test_workflow_extraction.py index 47f0ab009eb..41545bbe3e4 100644 --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -1,8 +1,9 @@ from __future__ import print_function -from collections import namedtuple + import functools -from json import dumps, loads import operator +from collections import namedtuple +from json import dumps, loads from .helpers import skip_without_tool from .test_workflows import BaseWorkflowsApiTestCase diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py index a6e1c94d2c2..a98f87cc1f8 100644 --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -1,26 +1,24 @@ from __future__ import print_function import time -import yaml -from json import dumps from collections import namedtuple +from json import dumps from uuid import uuid4 +import yaml +from requests import delete, put + from base import api -from galaxy.tools.verify.test_data import TestDataResolver from galaxy.exceptions import error_codes -from .helpers import WorkflowPopulator -from .helpers import DatasetPopulator -from .helpers import DatasetCollectionPopulator -from .helpers import skip_without_tool +from galaxy.tools.verify.test_data import TestDataResolver + +from .helpers import (DatasetCollectionPopulator, DatasetPopulator, + skip_without_tool, WorkflowPopulator) from .workflows_format_2 import ( convert_and_import_workflow, ImporterGalaxyInterface, ) -from requests import delete -from requests import put - SIMPLE_NESTED_WORKFLOW_YAML = """ class: GalaxyWorkflow inputs: @@ -277,7 +275,7 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ): workflow = show_response.json() self._assert_looks_like_instance_workflow_representation( workflow ) assert len(workflow["steps"]) == 3 - self.assertEqual(sorted([step["id"] for step in workflow["steps"].values()]), [0, 1, 2]) + self.assertEqual(sorted(step["id"] for step in workflow["steps"].values()), [0, 1, 2]) show_response = self._get( "workflows/%s" % workflow_id, {"legacy": True} ) workflow = show_response.json() @@ -285,7 +283,7 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ): assert len(workflow["steps"]) == 3 # Can't reay say what the legacy IDs are but must be greater than 3 because dummy # workflow was created first in this instance. - self.assertNotEqual(sorted([step["id"] for step in workflow["steps"].values()]), [0, 1, 2]) + self.assertNotEqual(sorted(step["id"] for step in workflow["steps"].values()), [0, 1, 2]) def test_show_invalid_key_is_400( self ): show_response = self._get( "workflows/%s" % self._random_key() ) @@ -457,7 +455,7 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ): def get_subworkflow_content_id(workflow_id): workflow_contents = self._download_workflow(workflow_id, style="editor") steps = workflow_contents['steps'] - subworkflow_step = filter(lambda s: s["type"] == "subworkflow", steps.values())[0] + subworkflow_step = next(s for s in steps.values() if s["type"] == "subworkflow") return subworkflow_step['content_id'] workflow_id = self._upload_yaml_workflow(SIMPLE_NESTED_WORKFLOW_YAML, publish=True) @@ -1636,7 +1634,7 @@ steps: contents_url = "histories/%s/contents" % history history_contents_response = self._get( contents_url ) self._assert_status_code_is( history_contents_response, 200 ) - hda_summary = filter( lambda hc: hc[ "hid" ] == hid, history_contents_response.json() )[ 0 ] + hda_summary = next(hc for hc in history_contents_response.json() if hc[ "hid" ] == hid) hda_info_response = self._get( "%s/%s" % ( contents_url, hda_summary[ "id" ] ) ) self._assert_status_code_is( hda_info_response, 200 ) self.assertEqual( hda_info_response.json()[ "metadata_data_lines" ], lines ) diff --git a/test/api/workflows_format_2/__init__.py b/test/api/workflows_format_2/__init__.py index 96461e5e62f..e680a3db612 100644 --- a/test/api/workflows_format_2/__init__.py +++ b/test/api/workflows_format_2/__init__.py @@ -1,8 +1,8 @@ """ This module defines the public interface or entry point for the Format 2 workflow code. """ -from .main import convert_and_import_workflow from .interface import ImporterGalaxyInterface +from .main import convert_and_import_workflow __all__ = [ diff --git a/test/api/workflows_format_2/converter.py b/test/api/workflows_format_2/converter.py index 2795982914d..61ef54e6685 100644 --- a/test/api/workflows_format_2/converter.py +++ b/test/api/workflows_format_2/converter.py @@ -1,11 +1,11 @@ """Functionality for converting a Format 2 workflow into a standard Galaxy workflow.""" from __future__ import print_function -from collections import OrderedDict import json import os import sys import uuid +from collections import OrderedDict import yaml @@ -96,7 +96,7 @@ def _python_to_workflow(as_python, conversion_context): as_python["steps"] = steps_as_dict steps = steps_as_dict - for step in steps.itervalues(): + for step in steps.values(): step_type = step.get("type", None) if "run" in step: if step_type is not None: @@ -118,7 +118,7 @@ def _python_to_workflow(as_python, conversion_context): run_to_step_function(conversion_context, step, run_action) del step["run"] - for step in steps.itervalues(): + for step in steps.values(): step_type = step.get("type", "tool") step_type = STEP_TYPE_ALIASES.get(step_type, step_type) if step_type not in STEP_TYPES: @@ -326,7 +326,7 @@ def transform_tool(context, step): return {"__class__": "RuntimeValue"} if isinstance(value, dict): new_values = {} - for k, v in value.iteritems(): + for k, v in value.items(): new_key = _join_prefix(key, k) new_values[k] = replace_links(v, new_key) return new_values @@ -349,7 +349,7 @@ def transform_tool(context, step): step_state = step["state"] step_state = replace_links(step_state) - for key, value in step_state.iteritems(): + for key, value in step_state.items(): tool_state[key] = json.dumps(value) del step["state"] @@ -470,7 +470,7 @@ def _populate_input_connections(context, step, connect): input_connections = step["input_connections"] is_subworkflow_step = step.get("type") == "subworkflow" - for key, values in connect.iteritems(): + for key, values in connect.items(): input_connection_value = [] if not isinstance(values, list): values = [values] diff --git a/test/base/api.py b/test/base/api.py index d366f792193..3cd31428296 100644 --- a/test/base/api.py +++ b/test/base/api.py @@ -1,23 +1,19 @@ from contextlib import contextmanager +from six.moves.urllib.parse import urlencode + +from .api_asserts import ( + assert_error_code_is, + assert_has_keys, + assert_not_has_keys, + assert_status_code_is, +) +from .api_util import get_master_api_key, get_user_api_key +from .interactor import GalaxyInteractorApi as BaseInteractor # TODO: We don't need all of TwillTestCase, strip down to a common super class # shared by API and Twill test cases. from .twilltestcase import TwillTestCase -from base.interactor import GalaxyInteractorApi as BaseInteractor - -from .api_util import get_master_api_key -from .api_util import get_user_api_key -from .api_asserts import ( - assert_status_code_is, - assert_has_keys, - assert_not_has_keys, - assert_error_code_is, -) - -from urllib import urlencode - - TEST_USER = "user@bx.psu.edu" DEFAULT_OTHER_USER = "otheruser@bx.psu.edu" # A second user for API testing. diff --git a/test/base/driver_util.py b/test/base/driver_util.py index 3536efe9ae5..977a88a3d0a 100644 --- a/test/base/driver_util.py +++ b/test/base/driver_util.py @@ -17,24 +17,21 @@ import nose.config import nose.core import nose.loader import nose.plugins.manager - -from paste import httpserver import requests - -from .api_util import get_master_api_key, get_user_api_key -from .tool_shed_util import parse_tool_panel_config -from .nose_util import run -from .instrument import StructuredTestDataPlugin +from paste import httpserver from functional import database_contexts - from galaxy.app import UniverseApplication as GalaxyUniverseApplication -from galaxy.web import buildapp -from galaxy.webapps.tool_shed.app import UniverseApplication as ToolshedUniverseApplication from galaxy.util import asbool from galaxy.util.properties import load_app_properties +from galaxy.web import buildapp +from galaxy.webapps.tool_shed.app import UniverseApplication as ToolshedUniverseApplication -from base.test_logging import logging_config_file +from .api_util import get_master_api_key, get_user_api_key +from .instrument import StructuredTestDataPlugin +from .nose_util import run +from .test_logging import logging_config_file +from .tool_shed_util import parse_tool_panel_config galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir)) DEFAULT_WEB_HOST = "localhost" diff --git a/test/base/integration_util.py b/test/base/integration_util.py index ca603ade4a4..76db3cfeb8f 100644 --- a/test/base/integration_util.py +++ b/test/base/integration_util.py @@ -4,9 +4,9 @@ Tests that start an actual Galaxy server with a particular configuration in order to test something that cannot be tested with the default functional/api tessting configuration. """ +from unittest import TestCase from .driver_util import GalaxyTestDriver -from unittest import TestCase NO_APP_MESSAGE = "test_case._app called though no Galaxy has been configured." diff --git a/test/base/interactor.py b/test/base/interactor.py index 0ede58b30b1..feac086410e 100644 --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -2,12 +2,12 @@ from __future__ import print_function import os import re +import time from json import dumps from logging import getLogger -from requests import get, post, delete, patch -from six import StringIO -from six import text_type +from requests import delete, get, patch, post +from six import StringIO, text_type from galaxy import util from galaxy.tools.parser.interface import TestCollectionDef @@ -118,7 +118,6 @@ class GalaxyInteractorApi( object ): metadata[ "file_ext" ] = expected_file_type if metadata: - import time time.sleep(5) dataset = self._get( "histories/%s/contents/%s" % ( history_id, hid ) ).json() for key, value in metadata.items(): diff --git a/test/base/test_logging.py b/test/base/test_logging.py index 295f278220a..de11008ca4c 100644 --- a/test/base/test_logging.py +++ b/test/base/test_logging.py @@ -1,9 +1,8 @@ from __future__ import absolute_import -import os - import logging import logging.config +import os # This is done in paster or galaxy.main for server app, provide # an entry point testing as well. diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 84c300887cd..d077448fe27 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -15,7 +15,6 @@ from xml.etree import ElementTree # Be sure to use Galaxy's vanilla pyparsing instead of the older version # imported by twill. import pyparsing # noqa: F401 - import twill import twill.commands as tc from markupsafe import escape @@ -23,17 +22,15 @@ from six import string_types, StringIO from six.moves.urllib.parse import unquote, urlencode, urlparse from twill.other_packages._mechanize_dist import ClientForm -from galaxy.web import security -from galaxy.web.framework.helpers import iff - -from galaxy.tools.verify.test_data import TestDataResolver from galaxy.tools.verify import ( - verify, check_command, files_diff, make_temp_fname, + verify, ) - +from galaxy.tools.verify.test_data import TestDataResolver +from galaxy.web import security +from galaxy.web.framework.helpers import iff # Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose? buffer = StringIO() diff --git a/test/functional/test_data_managers.py b/test/functional/test_data_managers.py index 2843ad070c3..b75925ed13b 100644 --- a/test/functional/test_data_managers.py +++ b/test/functional/test_data_managers.py @@ -1,12 +1,14 @@ +import logging import new -import tempfile import os.path import shutil -from test_toolbox import ToolTestCase -from base.interactor import stage_data_in_history -import logging -log = logging.getLogger( __name__ ) +import tempfile +from base.interactor import stage_data_in_history + +from .test_toolbox import ToolTestCase + +log = logging.getLogger( __name__ ) data_managers = None @@ -68,7 +70,7 @@ def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, us del G[ key ] # first we will loop through data table loc files and copy them to temporary location, then swap out filenames: - for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().iteritems(): + for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().items(): for filename, value in list( data_table.filenames.items() ): new_filename = tempfile.NamedTemporaryFile( prefix=os.path.basename( filename ), dir=tmp_dir ).name try: @@ -81,7 +83,7 @@ def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, us del data_table.filenames[ filename ] # remove filename:value pair data_table.filenames[ new_filename ] = value # add new value by - for i, ( data_manager_id, data_manager ) in enumerate( data_managers.data_managers.iteritems() ): + for i, ( data_manager_id, data_manager ) in enumerate( data_managers.data_managers.items() ): tool = data_manager.tool if not tool: log.warning( "No Tool has been specified for Data Manager: %s", data_manager_id ) diff --git a/test/functional/test_library_templates.py b/test/functional/test_library_templates.py index d1abfc8fe2b..7986fcf4fa6 100644 --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -1,17 +1,17 @@ -from base.twilltestcase import TwillTestCase +import galaxy.model from base.test_db_util import ( - get_user, - get_private_role, - get_form, - get_library, get_folder, - get_user_address, - get_latest_ldda_by_name, + get_form, get_latest_hda, + get_latest_ldda_by_name, + get_library, + get_private_role, + get_user, + get_user_address, mark_obj_deleted, refresh ) -import galaxy.model +from base.twilltestcase import TwillTestCase AddressField_form = None CheckboxField_form = None diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index 2069c543f9f..99d5f97b998 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -1,12 +1,8 @@ +from __future__ import print_function + import logging import new import sys -from base.twilltestcase import TwillTestCase -from base.interactor import build_interactor, stage_data_in_history, RunToolException -from base.instrument import register_job_data -from galaxy.tools import DataManagerTool -from galaxy.tools.verify.asserts import verify_assertions -from galaxy.util import bunch try: from nose.tools import nottest @@ -14,6 +10,13 @@ except ImportError: def nottest(x): return x +from base.instrument import register_job_data +from base.interactor import build_interactor, RunToolException, stage_data_in_history +from base.twilltestcase import TwillTestCase +from galaxy.tools import DataManagerTool +from galaxy.tools.verify.asserts import verify_assertions +from galaxy.util import bunch + log = logging.getLogger( __name__ ) toolbox = None @@ -83,7 +86,7 @@ class ToolTestCase( TwillTestCase ): if job_stdio is not None: job_data["job"] = job_stdio if job_output_exceptions: - job_data["output_problems"] = map(str, job_output_exceptions) + job_data["output_problems"] = [str(_) for _ in job_output_exceptions] if tool_execution_exception: job_data["execution_problem"] = str(tool_execution_exception) register_job_data(job_data) @@ -120,7 +123,7 @@ class ToolTestCase( TwillTestCase ): # Only print this stuff out once. for stream in ['stdout', 'stderr']: if stream in job_stdio: - print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) + print(self._format_stream( job_stdio[ stream ], stream=stream, format=True ), file=sys.stderr) found_exceptions.append(e) if testdef.expect_failure: @@ -161,7 +164,7 @@ class ToolTestCase( TwillTestCase ): # just a list (case with twill variant or if output changes its # name). if hasattr(data_list, "values"): - output_data = data_list.values()[ output_index ] + output_data = list(data_list.values())[ output_index ] else: output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ] self.assertTrue( output_data is not None ) diff --git a/test/functional/workflow.py b/test/functional/workflow.py index 9dbba1fbe7e..2d8e466bd06 100644 --- a/test/functional/workflow.py +++ b/test/functional/workflow.py @@ -1,14 +1,15 @@ +from __future__ import print_function + import os import sys -from base.twilltestcase import TwillTestCase -from base.interactor import GalaxyInteractorApi, stage_data_in_history - -from galaxy.util import parse_xml -from galaxy.util import bunch -from galaxy.tools.test import parse_param_elem, require_file, test_data_iter, parse_output_elems -from json import load, dumps - +from json import dumps, load from logging import getLogger + +from base.interactor import GalaxyInteractorApi, stage_data_in_history +from base.twilltestcase import TwillTestCase +from galaxy.tools.test import parse_output_elems, parse_param_elem, require_file, test_data_iter +from galaxy.util import bunch, parse_xml + log = getLogger( __name__ ) @@ -75,7 +76,7 @@ class WorkflowTestCase( TwillTestCase ): except Exception: for stream in ['stdout', 'stderr']: stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream ) - print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) + print(self._format_stream( stream_output, stream=stream, format=True ), file=sys.stderr) raise def __import_workflow( self, galaxy_interactor, workflow ): @@ -94,8 +95,8 @@ class WorkflowTestCase( TwillTestCase ): imported_workflow = galaxy_interactor.read_workflow( workflow_id ) step_id_map = {} - local_steps_ids = sorted( [ int( step_id ) for step_id in workflow[ 'steps' ].keys() ] ) - imported_steps_ids = sorted( [ int( step_id ) for step_id in imported_workflow[ 'steps' ].keys() ] ) + local_steps_ids = sorted( int( step_id ) for step_id in workflow[ 'steps' ].keys() ) + imported_steps_ids = sorted( int( step_id ) for step_id in imported_workflow[ 'steps' ].keys() ) for local_step_id, imported_step_id in zip( local_steps_ids, imported_steps_ids ): step_id_map[ local_step_id ] = imported_step_id @@ -152,7 +153,7 @@ class WorkflowTest( object ): def input_datasets( self ): steps = self.workflow[ "steps" ] log.info("in input_datasets with steps %s" % steps) - for step_index, step_dict in steps.iteritems(): + for step_index, step_dict in steps.items(): if step_dict.get( "name", None ) == "Input dataset": yield int( step_index ), step_dict[ "inputs" ][0][ "name" ] diff --git a/test/integration/test_resolvers.py b/test/integration/test_resolvers.py index 74fa377f032..f1ee7d9b8eb 100644 --- a/test/integration/test_resolvers.py +++ b/test/integration/test_resolvers.py @@ -1,10 +1,10 @@ """Integration tests for conda dependency resolution.""" - import os import shutil +from tempfile import mkdtemp + from base import integration_util from base.api import ApiTestCase -from tempfile import mkdtemp GNUPLOT = {u'version': u'4.6', u'type': u'package', u'name': u'gnuplot'} diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py index f9d47396a02..f81467d6c43 100644 --- a/test/manual/workflows_scaling.py +++ b/test/manual/workflows_scaling.py @@ -10,17 +10,16 @@ import json import os import random import sys +from argparse import ArgumentParser from threading import Thread from uuid import uuid4 -galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir)) -sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ] - -from argparse import ArgumentParser - import requests from bioblend import galaxy +galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, os.path.pardir)) +sys.path[1:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ] + from api import helpers, yaml_to_workflow LONG_TIMEOUT = 1000000000 diff --git a/test/shed_functional/base/test_db_util.py b/test/shed_functional/base/test_db_util.py index a2f4240fad3..d4750023c15 100644 --- a/test/shed_functional/base/test_db_util.py +++ b/test/shed_functional/base/test_db_util.py @@ -6,9 +6,8 @@ import galaxy.model import galaxy.model.tool_shed_install import galaxy.webapps.tool_shed.model as model -from functional.database_contexts import tool_shed_context as sa_session -from functional.database_contexts import galaxy_context as ga_session -from functional.database_contexts import install_context as install_session +from functional.database_contexts import (galaxy_context as ga_session, + install_context as install_session, tool_shed_context as sa_session) log = logging.getLogger( 'test.tool_shed.test_db_util' ) diff --git a/test/shed_functional/functional/test_0300_reset_all_metadata.py b/test/shed_functional/functional/test_0300_reset_all_metadata.py index c5f6b7cb900..a8a8e10e915 100644 --- a/test/shed_functional/functional/test_0300_reset_all_metadata.py +++ b/test/shed_functional/functional/test_0300_reset_all_metadata.py @@ -594,7 +594,7 @@ class TestResetAllRepositoryMetadata( ShedTwillTestCase ): old_metadata[ self.security.encode_id( repository.id ) ] = dict() for metadata in self.get_repository_metadata( repository ): old_metadata[ self.security.encode_id( repository.id ) ][ metadata.changeset_revision ] = metadata.metadata - self.reset_metadata_on_selected_repositories( old_metadata.keys() ) + self.reset_metadata_on_selected_repositories( list(old_metadata.keys()) ) for repository in repositories: new_metadata[ self.security.encode_id( repository.id ) ] = dict() for metadata in self.get_repository_metadata( repository ): diff --git a/test/shed_functional/functional/test_1300_reset_all_metadata.py b/test/shed_functional/functional/test_1300_reset_all_metadata.py index a7d16dceac8..25bf7b7a1eb 100644 --- a/test/shed_functional/functional/test_1300_reset_all_metadata.py +++ b/test/shed_functional/functional/test_1300_reset_all_metadata.py @@ -443,7 +443,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ): repositories = self.test_db_util.get_all_installed_repositories( actually_installed=True ) for repository in repositories: repository_metadata[ self.security.encode_id( repository.id ) ] = repository.metadata - self.reset_metadata_on_selected_installed_repositories( repository_metadata.keys() ) + self.reset_metadata_on_selected_installed_repositories( list(repository_metadata.keys()) ) for repository in repositories: self.test_db_util.ga_refresh( repository ) old_metadata = repository_metadata[ self.security.encode_id( repository.id ) ] diff --git a/test/shed_functional/functional_tests.py b/test/shed_functional/functional_tests.py index 8a2511f4bd1..1fba4d9b4b7 100644 --- a/test/shed_functional/functional_tests.py +++ b/test/shed_functional/functional_tests.py @@ -15,12 +15,12 @@ galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pa sys.path[0:1] = [ os.path.join( galaxy_root, "lib" ), os.path.join( galaxy_root, "test" ) ] from base import driver_util -log = driver_util.build_logger() # This is for the tool shed application. -from galaxy.webapps.tool_shed import buildapp as toolshedbuildapp from galaxy.web import buildapp as galaxybuildapp +from galaxy.webapps.tool_shed import buildapp as toolshedbuildapp +log = driver_util.build_logger() tool_sheds_conf_xml_template = ''' From 20dcc4d693ae8fa7e846eb32e65292c3c4a38863 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 10 Oct 2016 19:19:51 -0400 Subject: [PATCH 13/32] remove duplicated option from config sample --- config/galaxy.ini.sample | 6 ------ 1 file changed, 6 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index f60ce30d917..cc5f3b37943 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -242,12 +242,6 @@ paste.app_factory = galaxy.web.buildapp:app_factory # enable_beta_mulled_containers. #containers_resolvers_config_file = None -# Container resolvers configuration (beta). Setup a file describing container -# resolvers to use when discovering containers for Galaxy. If this is set to -# None, the default containers loaded is determined by -# enable_beta_mulled_containers. -#containers_resolvers_config_file = None - # involucro is a tool used to build Docker containers for tools from Conda # dependencies referenced in tools as `requirement`s. The following path is # the location of involucro on the Galaxy host. This is ignored if the relevant From bcabbd8707e0064e041e730e5abd1d8dfc0a692c Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 10 Oct 2016 19:26:36 -0400 Subject: [PATCH 14/32] minor changes to mulled admin docs --- doc/source/admin/mulled_containers.rst | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/doc/source/admin/mulled_containers.rst b/doc/source/admin/mulled_containers.rst index 7c16ba72353..792a47f94ad 100644 --- a/doc/source/admin/mulled_containers.rst +++ b/doc/source/admin/mulled_containers.rst @@ -6,8 +6,8 @@ Galaxy tools (also called wrappers) are able to use Conda packages (see more information in our `Galaxy Conda documentation`_) and Docker containers as dependency resolvers. The IUC_ recommends to use Conda packages as primary dependency resolver, mainly because Docker is not available on every (HPC-) system. Conda on the other hand can be installed by Galaxy and maintained -entirely in user-space. Nevertheless, Docker (Containers in general) has some uniq features and -there are a bunch of use-cases in the Galaxy community that makes containerized systems very appealing. +entirely in user-space. Nevertheless, Docker (Containers in general) has some unique features and +there are many use-cases in the Galaxy community which makes containerized systems very appealing. Since 2014 Galaxy supports running tools in Docker containers via a special `container annotation`_ inside of the requirement field. @@ -22,26 +22,26 @@ requirement field. -This approach has shown two limitations that slowed down the adoption by Tool developers. +This approach has shown two limitations that slowed down the adoption by tool developers. First, every tool needs to be annotated with a container name (as shown above) and this container needs to be created beforehand, usually manually. The second reason is that a Galaxy tool aims to be deployed everywhere, -independet of the underlying system, meaning if Docker is not availble Galaxy should use Conda packages. -This puts an additionl burden to tool developers that needs to take care of two dependency resolvers and can yield to -different results of your tool depending on the resolver, because both the Conda package and the Docker container is -usually not created out of the same recipe and maybe was compiled in a different way, uses different sources etc ... +independet of the underlying system, meaning if Docker is not available Galaxy should use Conda packages. +This puts an additional burden on tool developers who need to take care of two dependency resolvers. This setup can cause +different tool results depending on the resolver, because both the Conda package and the Docker container are +usually not created out of the same recipe and maybe were compiled in a different way, use different sources etc. Not an ideal solution and something we wanted to solve. Here we demonstrate a solution that can create Containers out of Conda packages automatically. This can be either used to support communities like BioContainers_ to create Containers -before deploying a Galaxy tool, or this can be used by Galaxy to create Containers on-demand and on-the-fly if no one -is available already. +before deploying a Galaxy tool, or this can be used by Galaxy to create Containers on-demand and on-the-fly if one +is not available already. -Automatic build of linux containers +Automatic build of Linux containers ----------------------------------- -We utilize [mulled](https://github.com/mulled/mulled) and with this [involucro](https://github.com/involucro/involucro) +We utilize [mulled](https://github.com/mulled/mulled) with [involucro](https://github.com/involucro/involucro) in an automatic way. This is for example used to convert all packages in bioconda_ into Linux Containers (Docker and rkt at the moment) and made available at the `BioContainers Quay.io account`_. @@ -98,7 +98,7 @@ This also demonstrates how you can build a container locally and on-the-fly. --extra-channel file://home/bag/miniconda2/conda-bld/ --test 'samtools --help' The ``--0`` indicates the build version of the conda package. It is recommended to specify this number otherwise -you will override already exsisting images. For python conda packages this extension might look like this ``--py35_1``. +you will override already existing images. For Python Conda packages this extension might look like this ``--py35_1``. Build, test and push a conda-forge package to biocontainers ^^^^^^^^^^^^^^^^^^^^^ From 1a2d75fade1077359b2a9b1072feab793022b7f4 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 10 Oct 2016 20:54:26 -0400 Subject: [PATCH 15/32] add muled docs to admin index --- doc/source/admin/index.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst index 50bf0a90cd0..64ba2986d04 100644 --- a/doc/source/admin/index.rst +++ b/doc/source/admin/index.rst @@ -11,6 +11,8 @@ documentation. These resources should be used together. dependency_resolvers.rst conda_faq.rst + + mulled_containers.rst interactive_environments.rst From 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 11 Oct 2016 17:07:23 +0200 Subject: [PATCH 16/32] Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now --- .travis.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 83463757ea4..c968701ad6d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,9 +17,6 @@ matrix: env: TOX_ENV=py27-unit language: generic -before_install: - - if [ `uname` == "Darwin" ]; then bash -c "brew update && brew install python"; fi - install: - pip install tox - if [ "$TOX_ENV" == "qunit" ]; then bash -c 'cd test/qunit && npm install'; fi From 2b9281a37832346b0a3e5aed1b13ee84270ffe44 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Tue, 11 Oct 2016 13:10:50 -0400 Subject: [PATCH 17/32] Fix dependency ordering broken in #2917. We will store dependencies in an OrderedDict, matching the order of ``. Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting. --- lib/galaxy/tools/deps/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py index ccf5bb25753..4ec3e42a1a4 100644 --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -5,6 +5,8 @@ Dependency management for tools. import logging import os.path +from collections import OrderedDict + from galaxy.util import plugin_config from .resolvers import NullDependency @@ -97,7 +99,7 @@ class DependencyManager( object ): Takes a list of requirements and returns a dictionary with requirements as key and dependencies as value. """ - requirement_to_dependency = dict() + requirement_to_dependency = OrderedDict() for requirement in requirements: if requirement.type in [ 'package', 'set_environment' ]: dependency = self.find_dep( name=requirement.name, From dcde64ce407b332072525c66885adf03a26eeb5e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 12 Oct 2016 11:07:01 +0100 Subject: [PATCH 18/32] Fix import order. Fix typos and improve readability --- .ci/flake8_lint_include_list.txt | 1 + lib/galaxy/workflow/extract.py | 87 ++++++++++++++-------------- test/api/test_workflow_extraction.py | 4 +- 3 files changed, 45 insertions(+), 47 deletions(-) diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt index eb2ab916d61..343e3818220 100644 --- a/.ci/flake8_lint_include_list.txt +++ b/.ci/flake8_lint_include_list.txt @@ -347,6 +347,7 @@ lib/galaxy/web/framework/middleware/statsd.py lib/galaxy/web/framework/middleware/translogger.py lib/galaxy/web/framework/middleware/xforwardedhost.py lib/galaxy/web/params.py +lib/galaxy/workflow/extract.py lib/galaxy/workflow/__init__.py lib/galaxy/workflow/render.py lib/galaxy/workflow/schedulers/__init__.py diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index e9469a02767..adc61d0e1c9 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -1,25 +1,26 @@ """ This module contains functionality to aid in extracting workflows from histories. """ -from galaxy.util.odict import odict -from galaxy import exceptions -from galaxy import model +import logging + +from galaxy import exceptions, model from galaxy.tools.parameters.basic import ( - DataToolParameter, - DataCollectionToolParameter + DataCollectionToolParameter, + DataToolParameter ) -from galaxy.tools.parser import ToolOutputCollectionPart from galaxy.tools.parameters.grouping import ( Conditional, Repeat, Section ) +from galaxy.tools.parser import ToolOutputCollectionPart +from galaxy.util.odict import odict + from .steps import ( attach_ordered_steps, order_workflow_steps_with_levels ) -import logging log = logging.getLogger( __name__ ) WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored" @@ -67,16 +68,14 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_ elif type( dataset_collection_ids) is not list: dataset_collection_ids = [ dataset_collection_ids ] # Convert both sets of ids to integers - job_ids = [ int( id ) for id in job_ids ] - dataset_ids = [ int( id ) for id in dataset_ids ] - dataset_collection_ids = [ int( id ) for id in dataset_collection_ids ] - # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. + job_ids = [ int( _ ) for _ in job_ids ] + dataset_ids = [ int( _ ) for _ in dataset_ids ] + dataset_collection_ids = [ int( _ ) for _ in dataset_collection_ids ] + # Find each job, for security we (implicitly) check that they are + # associated with a job in the current history. summary = WorkflowSummary( trans, history ) jobs = summary.jobs - jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) steps = [] - steps_by_job_id = {} hid_to_output_pair = {} # Input dataset steps for i, hid in enumerate( dataset_ids ): @@ -103,6 +102,7 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_ hid_to_output_pair[ hid ] = ( step, 'output' ) steps.append( step ) # Tool steps + jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) for job_id in job_ids: if job_id not in jobs_by_id: log.warning( "job_id %s not found in jobs_by_id %s" % ( job_id, jobs_by_id ) ) @@ -134,7 +134,6 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_ conn.output_step = other_step conn.output_name = other_name steps.append( step ) - steps_by_job_id[ job_id ] = step # Store created dataset hids for assoc in (job.output_datasets + job.output_dataset_collection_instances): assoc_name = assoc.name @@ -147,8 +146,8 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_ if query_assoc_name == assoc_name: hid = dataset_collection.hid if hid is None: - template = "Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s." - message = template % ( job.id, jobs, assoc.name ) + template = "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s." + message = template % ( job.id, jobs[job], assoc_name ) log.warning( message ) raise Exception( "Failed to extract job." ) else: @@ -223,25 +222,24 @@ class WorkflowSummary( object ): else: self.__summarize_dataset( content ) - def __summarize_dataset_collection( self, content ): - content = self.__original_hdca( content ) - dataset_collection = content - hid = content.hid - self.collection_types[ hid ] = content.collection.collection_type - cja = content.creating_job_associations + def __summarize_dataset_collection( self, dataset_collection ): + dataset_collection = self.__original_hdca( dataset_collection ) + hid = dataset_collection.hid + self.collection_types[ hid ] = dataset_collection.collection.collection_type + cja = dataset_collection.creating_job_associations if cja: - # Use the first job to represent all mapped jobs. - representive_job_assoc = content.creating_job_associations[0] - job = representive_job_assoc.job - if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": - self.jobs[ job ] = [ ( representive_job_assoc.name, dataset_collection ) ] - if content.implicit_output_name: - self.implicit_map_jobs.append( job ) + # Use the "first" job to represent all mapped jobs. + representative_assoc = cja[0] + representative_job = representative_assoc.job + if representative_job not in self.jobs or self.jobs[ representative_job ][ 0 ][ 1 ].history_content_type == "dataset": + self.jobs[ representative_job ] = [ ( representative_assoc.name, dataset_collection ) ] + if dataset_collection.implicit_output_name: + self.implicit_map_jobs.append( representative_job ) else: - self.jobs[ job ].append( ( representive_job_assoc.name, dataset_collection ) ) + self.jobs[ representative_job ].append( ( representative_assoc.name, dataset_collection ) ) # This whole elif condition may no longer be needed do to additional # tracking with creating_job_associations. Will delete at some point. - elif content.implicit_output_name: + elif dataset_collection.implicit_output_name: # TODO: Optimize db call dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] if not self.__check_state( dataset_instance ): @@ -249,13 +247,13 @@ class WorkflowSummary( object ): # makes me wonder if even need this check at all? return - job_hda = self.__original_hda( dataset_instance ) - if not job_hda.creating_job_associations: + original_hda = self.__original_hda( dataset_instance ) + if not original_hda.creating_job_associations: log.warning( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" ) job = DatasetCollectionCreationJob( dataset_collection ) self.jobs[ job ] = [ ( None, dataset_collection ) ] - for assoc in job_hda.creating_job_associations: + for assoc in original_hda.creating_job_associations: job = assoc.job if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] @@ -263,19 +261,19 @@ class WorkflowSummary( object ): else: self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) else: - job = DatasetCollectionCreationJob( content ) - self.jobs[ job ] = [ ( None, content ) ] + job = DatasetCollectionCreationJob( dataset_collection ) + self.jobs[ job ] = [ ( None, dataset_collection ) ] def __summarize_dataset( self, dataset ): if not self.__check_state( dataset ): return - job_hda = self.__original_hda( dataset ) + original_hda = self.__original_hda( dataset ) - if not job_hda.creating_job_associations: + if not original_hda.creating_job_associations: self.jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - for assoc in job_hda.creating_job_associations: + for assoc in original_hda.creating_job_associations: job = assoc.job if job in self.jobs: self.jobs[ job ].append( ( assoc.name, dataset ) ) @@ -288,11 +286,10 @@ class WorkflowSummary( object ): return hdca def __original_hda( self, hda ): - # if this hda was copied from another, we need to find the job that created the origial hda - job_hda = hda - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - return job_hda + # if this hda was copied from another, we need to find the job that created the original hda + while hda.copied_from_history_dataset_association: + hda = hda.copied_from_history_dataset_association + return hda def __check_state( self, hda ): # FIXME: Create "Dataset.is_finished" diff --git a/test/api/test_workflow_extraction.py b/test/api/test_workflow_extraction.py index 41545bbe3e4..53864393edd 100644 --- a/test/api/test_workflow_extraction.py +++ b/test/api/test_workflow_extraction.py @@ -216,7 +216,7 @@ test_data: text_input2: "samp1\t30.0\nsamp2\t40.0\n" """) tool_ids = [ "cat1", "collection_split_on_column", "cat_list" ] - job_ids = list(map( functools.partial(self._job_id_for_tool, jobs_summary.jobs ), tool_ids )) + job_ids = [ functools.partial(self._job_id_for_tool, jobs_summary.jobs )(_) for _ in tool_ids ] downloaded_workflow = self._extract_and_download_workflow( dataset_ids=[ "1", "2" ], job_ids=job_ids, @@ -266,7 +266,7 @@ test_data: content: "samp1\t30.0\nsamp2\t40.0\n" """) tool_ids = [ "cat1", "collection_creates_pair", "cat_collection", "cat_list" ] - job_ids = list(map( functools.partial(self._job_id_for_tool, jobs_summary.jobs ), tool_ids )) + job_ids = [ functools.partial(self._job_id_for_tool, jobs_summary.jobs )(_) for _ in tool_ids ] downloaded_workflow = self._extract_and_download_workflow( dataset_collection_ids=[ "3" ], job_ids=job_ids, From 04bf2153b8f61c60288cb180d448e7c20352f6e7 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 12 Oct 2016 14:01:29 +0100 Subject: [PATCH 19/32] WorkflowSummary: add dict to map a job id to its representative job Fix #2742 introduced in commit 9ede8e556be1f6038361b579c1457068e50e951a . The representative job is the first in the returned query, so substantially random and not necessarily the one with the lowest job id. Mapping a job id to its representative job in extract_steps() makes it robust also against API requests with manually chosen collection job ids. --- lib/galaxy/workflow/extract.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index adc61d0e1c9..4b3a3bc9289 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -102,12 +102,11 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_ hid_to_output_pair[ hid ] = ( step, 'output' ) steps.append( step ) # Tool steps - jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) for job_id in job_ids: - if job_id not in jobs_by_id: - log.warning( "job_id %s not found in jobs_by_id %s" % ( job_id, jobs_by_id ) ) + if job_id not in summary.job_id2representative_job: + log.warning( "job_id %s not found in job_id2representative_job %s" % ( job_id, summary.job_id2representative_job ) ) raise AssertionError( "Attempt to create workflow with job not connected to current history" ) - job = jobs_by_id[ job_id ] + job = summary.job_id2representative_job[job_id] tool_inputs, associations = step_inputs( trans, job ) step = model.WorkflowStep() step.type = 'tool' @@ -201,6 +200,7 @@ class WorkflowSummary( object ): self.history = history self.warnings = set() self.jobs = odict() + self.job_id2representative_job = {} # map a non-fake job id to its representative job self.implicit_map_jobs = [] self.collection_types = {} @@ -237,6 +237,9 @@ class WorkflowSummary( object ): self.implicit_map_jobs.append( representative_job ) else: self.jobs[ representative_job ].append( ( representative_assoc.name, dataset_collection ) ) + for assoc in cja: + job = assoc.job + self.job_id2representative_job[job.id] = representative_job # This whole elif condition may no longer be needed do to additional # tracking with creating_job_associations. Will delete at some point. elif dataset_collection.implicit_output_name: @@ -257,6 +260,7 @@ class WorkflowSummary( object ): job = assoc.job if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] + self.job_id2representative_job[job.id] = job self.implicit_map_jobs.append( job ) else: self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) @@ -279,6 +283,7 @@ class WorkflowSummary( object ): self.jobs[ job ].append( ( assoc.name, dataset ) ) else: self.jobs[ job ] = [ ( assoc.name, dataset ) ] + self.job_id2representative_job[job.id] = job def __original_hdca( self, hdca ): while hdca.copied_from_history_dataset_collection_association: From 77f78cfbc79ddc345bc22277afc335f11e189491 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 13 Oct 2016 12:51:36 +0100 Subject: [PATCH 20/32] Change __all__ from list to tuple Also fix import order and Python3 compatibility. --- .ci/flake8_lint_include_list.txt | 17 +++++++++++--- .ci/py3_sources.txt | 12 ++++++++++ lib/galaxy/managers/collections_util.py | 13 +++++------ lib/galaxy/model/item_attrs.py | 8 ++++--- lib/galaxy/model/metadata.py | 23 ++++++++++--------- lib/galaxy/model/orm/now.py | 2 +- lib/galaxy/tools/cwl/__init__.py | 7 +++--- lib/galaxy/tools/cwl/cwltool_deps.py | 7 +++--- lib/galaxy/tools/cwl/parser.py | 16 +++++++------ lib/galaxy/tools/cwl/runtime_actions.py | 6 ++--- lib/galaxy/tools/deps/commands.py | 16 +++++-------- lib/galaxy/tools/deps/conda_compat.py | 8 +++---- lib/galaxy/tools/deps/conda_util.py | 8 +++---- .../tools/deps/container_resolvers/mulled.py | 6 ++--- lib/galaxy/tools/deps/docker_util.py | 23 +++++++++++-------- lib/galaxy/tools/deps/mulled/_cli.py | 6 ++--- lib/galaxy/tools/deps/mulled/mulled_build.py | 10 ++++---- .../tools/deps/mulled/mulled_build_channel.py | 6 ++--- .../tools/deps/mulled/mulled_build_files.py | 3 +-- .../tools/deps/mulled/mulled_build_tool.py | 6 ++--- lib/galaxy/tools/deps/mulled/util.py | 4 ++-- .../resolvers/brewed_tool_shed_packages.py | 3 +-- lib/galaxy/tools/deps/resolvers/conda.py | 2 +- .../tools/deps/resolvers/galaxy_packages.py | 6 ++++- lib/galaxy/tools/deps/resolvers/homebrew.py | 2 +- lib/galaxy/tools/deps/resolvers/modules.py | 3 +-- .../deps/resolvers/tool_shed_packages.py | 3 +-- .../resolvers/unlinked_tool_shed_packages.py | 3 +-- lib/galaxy/tools/exception_handling.py | 4 ++-- lib/galaxy/tools/execute.py | 19 +++++++-------- lib/galaxy/tools/loader.py | 2 +- lib/galaxy/tools/loader_directory.py | 8 +++---- lib/galaxy/tools/parameters/__init__.py | 15 ++++++------ .../tools/parameters/dataset_matcher.py | 5 ++-- lib/galaxy/tools/parameters/wrapped.py | 23 ++++++++++--------- lib/galaxy/tools/parameters/wrapped_json.py | 8 +++---- lib/galaxy/tools/parser/__init__.py | 7 +++--- lib/galaxy/tools/parser/factory.py | 5 ++-- lib/galaxy/tools/toolbox/__init__.py | 11 ++++----- lib/galaxy/tools/toolbox/lineages/__init__.py | 2 +- lib/galaxy/tools/toolbox/lineages/factory.py | 2 +- .../tools/toolbox/lineages/tool_shed.py | 9 ++++---- lib/galaxy/tools/toolbox/parser.py | 21 ++++++++--------- lib/galaxy/workflow/extract.py | 2 +- lib/galaxy/workflow/run.py | 16 ++++++------- lib/galaxy/workflow/schedulers/core.py | 9 ++++---- test/api/workflows_format_2/__init__.py | 4 ++-- test/api/workflows_format_2/converter.py | 4 ++-- test/api/workflows_format_2/main.py | 4 ++-- test/base/driver_util.py | 4 ++-- test/unit/tools_support.py | 18 +++++++-------- test/unit/unittest_utils/utility.py | 11 +++------ 52 files changed, 226 insertions(+), 216 deletions(-) diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt index 343e3818220..0d9cbbba508 100644 --- a/.ci/flake8_lint_include_list.txt +++ b/.ci/flake8_lint_include_list.txt @@ -95,6 +95,7 @@ lib/galaxy/main.py lib/galaxy/managers/annotatable.py lib/galaxy/managers/api_keys.py lib/galaxy/managers/base.py +lib/galaxy/managers/collections_util.py lib/galaxy/managers/context.py lib/galaxy/managers/deletable.py lib/galaxy/managers/__init__.py @@ -103,7 +104,9 @@ lib/galaxy/managers/libraries.py lib/galaxy/managers/secured.py lib/galaxy/managers/taggable.py lib/galaxy/model/__init__.py +lib/galaxy/model/item_attrs.py lib/galaxy/model/mapping.py +lib/galaxy/model/metadata.py lib/galaxy/model/migrate/__init__.py lib/galaxy/model/migrate/versions/0001_initial_tables.py lib/galaxy/model/migrate/versions/0002_metadata_file_table.py @@ -246,9 +249,11 @@ lib/galaxy/sample_tracking/sample.py lib/galaxy/security/validate_user_input.py lib/galaxy/tags/ lib/galaxy/tools/actions/metadata.py -lib/galaxy/tools/cwl +lib/galaxy/tools/cwl/ lib/galaxy/tools/data_manager/__init__.py -lib/galaxy/tools/deps +lib/galaxy/tools/deps/ +lib/galaxy/tools/exception_handling.py +lib/galaxy/tools/execute.py lib/galaxy/tools/filters/ lib/galaxy/tools/imp_exp/export_history.py lib/galaxy/tools/imp_exp/__init__.py @@ -256,11 +261,15 @@ lib/galaxy/tools/linters/ lib/galaxy/tools/lint.py lib/galaxy/tools/lint_util.py lib/galaxy/tools/loader_directory.py +lib/galaxy/tools/loader.py +lib/galaxy/tools/parameters/dataset_matcher.py lib/galaxy/tools/parameters/history_query.py +lib/galaxy/tools/parameters/__init__.py lib/galaxy/tools/parameters/input_translation.py lib/galaxy/tools/parameters/sanitize.py lib/galaxy/tools/parameters/validation.py lib/galaxy/tools/parameters/wrapped_json.py +lib/galaxy/tools/parameters/wrapped.py lib/galaxy/tools/parser/ lib/galaxy/tools/special_tools.py lib/galaxy/tools/test.py @@ -350,7 +359,8 @@ lib/galaxy/web/params.py lib/galaxy/workflow/extract.py lib/galaxy/workflow/__init__.py lib/galaxy/workflow/render.py -lib/galaxy/workflow/schedulers/__init__.py +lib/galaxy/workflow/run.py +lib/galaxy/workflow/schedulers/ lib/galaxy/workflow/steps.py lib/galaxy/work/__init__.py lib/mimeparse.py @@ -518,6 +528,7 @@ test/unit/tools/test_tool_deps.py test/unit/tools/test_tool_loader.py test/unit/tools/test_toolbox_filters.py test/unit/tools/test_watcher.py +test/unit/tools_support.py test/unit/unittest_utils/__init__.py test/unit/unittest_utils/utility.py test/unit/visualizations/__init__.py diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt index ecd7f79c9d4..6ff2e8cd0a9 100644 --- a/.ci/py3_sources.txt +++ b/.ci/py3_sources.txt @@ -28,8 +28,11 @@ lib/galaxy/forms/ lib/galaxy/jobs/ lib/galaxy/managers/ lib/galaxy/model/__init__.py +lib/galaxy/model/item_attrs.py lib/galaxy/model/mapping.py +lib/galaxy/model/metadata.py lib/galaxy/model/migrate/ +lib/galaxy/model/orm/now.py lib/galaxy/objectstore/ lib/galaxy/openid/ lib/galaxy/quota/ @@ -38,17 +41,26 @@ lib/galaxy/security/ lib/galaxy/tags/ lib/galaxy/tools/cwl/ lib/galaxy/tools/deps/ +lib/galaxy/tools/exception_handling.py +lib/galaxy/tools/execute.py lib/galaxy/tools/lint.py lib/galaxy/tools/lint_util.py lib/galaxy/tools/linters/ lib/galaxy/tools/loader.py lib/galaxy/tools/loader_directory.py +lib/galaxy/tools/parameters/dataset_matcher.py +lib/galaxy/tools/parameters/__init__.py +lib/galaxy/tools/parameters/wrapped_json.py +lib/galaxy/tools/parameters/wrapped.py lib/galaxy/tools/parser/ lib/galaxy/tools/toolbox/ lib/galaxy/tours/ lib/galaxy/util/ lib/galaxy/visualization/ lib/galaxy/work/ +lib/galaxy/workflow/extract.py +lib/galaxy/workflow/run.py +lib/galaxy/workflow/schedulers/core.py lib/galaxy_ext/ lib/galaxy_utils/ lib/log_tempfile.py diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py index d6938071274..21725877075 100644 --- a/lib/galaxy/managers/collections_util.py +++ b/lib/galaxy/managers/collections_util.py @@ -1,8 +1,7 @@ -from galaxy import exceptions -from galaxy import web -from galaxy import model - import logging + +from galaxy import exceptions, model, web + log = logging.getLogger( __name__ ) ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." @@ -77,7 +76,7 @@ def dictify_dataset_collection_instance( dataset_collection_instance, parent, se dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) if view == "element": collection = dataset_collection_instance.collection - dict_value[ 'elements' ] = map( dictify_element, collection.elements ) + dict_value[ 'elements' ] = [ dictify_element(_) for _ in collection.elements ] dict_value[ 'populated' ] = collection.populated security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recursive formulation of this. return dict_value @@ -89,10 +88,10 @@ def dictify_element( element ): if element.child_collection: # Recursively yield elements for each nested collection... child_collection = element.child_collection - object_detials[ "elements" ] = map( dictify_element, child_collection.elements ) + object_detials[ "elements" ] = [ dictify_element(_) for _ in child_collection.elements ] object_detials[ "populated" ] = child_collection.populated dictified[ "object" ] = object_detials return dictified -__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ] +__all__ = ( 'api_payload_to_create_params', 'dictify_dataset_collection_instance' ) diff --git a/lib/galaxy/model/item_attrs.py b/lib/galaxy/model/item_attrs.py index dc9666a13af..b4dd1f305d9 100644 --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -1,7 +1,9 @@ +import logging + from sqlalchemy.sql.expression import func + # Cannot import galaxy.model b/c it creates a circular import graph. import galaxy -import logging log = logging.getLogger( __name__ ) @@ -162,8 +164,8 @@ class UsesAnnotations: return getattr( galaxy.model, class_name, None ) -__all__ = [ +__all__ = ( 'UsesAnnotations', 'UsesItemRatings', 'RuntimeException', -] +) diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py index 2b869213c33..52c459d2503 100644 --- a/lib/galaxy/model/metadata.py +++ b/lib/galaxy/model/metadata.py @@ -4,7 +4,6 @@ Galaxy Metadata """ import copy -import cPickle import json import logging import os @@ -15,6 +14,7 @@ import weakref from os.path import abspath from six import string_types +from six.moves import cPickle from sqlalchemy.orm import object_session import galaxy.model @@ -93,13 +93,14 @@ class MetadataCollection( object ): return default def items(self): - return iter( [ ( k, self.get( k ) ) for k in self.spec.iterkeys() ] ) + return iter( [ ( k, self.get( k ) ) for k in self.spec.keys() ] ) def __str__(self): return dict( self.items() ).__str__() - def __nonzero__( self ): + def __bool__( self ): return bool( self.parent._metadata ) + __nonzero__ = __bool__ def __getattr__( self, name ): if name in self.spec: @@ -205,7 +206,7 @@ class MetadataSpecCollection( odict ): self[item.name] = item def iter( self ): - return self.itervalues() + return iter(self.values()) def __getattr__( self, name ): return self.get( name ) @@ -452,7 +453,7 @@ class RangeParameter( SelectParameter ): other_values = other_values or {} if values is None: - values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) + values = list(zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step ) )) return SelectParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context=None, other_values=None, values=None, **kwd ): @@ -460,7 +461,7 @@ class RangeParameter( SelectParameter ): other_values = other_values or {} if values is None: - values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) + values = list(zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step ) )) return SelectParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) @classmethod @@ -478,7 +479,7 @@ class ColumnParameter( RangeParameter ): if values is None and context: column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) - values = zip( column_range, column_range ) + values = list(zip( column_range, column_range )) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context=None, other_values=None, values=None, **kwd ): @@ -487,7 +488,7 @@ class ColumnParameter( RangeParameter ): if values is None and context: column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) - values = zip( column_range, column_range ) + values = list(zip( column_range, column_range )) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) @@ -815,7 +816,7 @@ class JobExternalOutputMetadataWrapper( object ): metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="metadata_override_%s_" % key ).name ) open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) override_metadata = [] - for meta_key, spec_value in dataset.metadata.spec.iteritems(): + for meta_key, spec_value in dataset.metadata.spec.items(): if isinstance( spec_value.param, FileParameter ) and dataset.metadata.get( meta_key, None ) is not None: metadata_temp = MetadataTempFile() shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) @@ -871,7 +872,7 @@ class JobExternalOutputMetadataWrapper( object ): sa_session.add( metadata_files ) sa_session.flush() -__all__ = [ +__all__ = ( "Statement", "MetadataElement", "MetadataCollection", @@ -889,4 +890,4 @@ __all__ = [ "FileParameter", "MetadataTempFile", "JobExternalOutputMetadataWrapper", -] +) diff --git a/lib/galaxy/model/orm/now.py b/lib/galaxy/model/orm/now.py index b6b4de8fa0d..1b90b5bff9a 100644 --- a/lib/galaxy/model/orm/now.py +++ b/lib/galaxy/model/orm/now.py @@ -10,4 +10,4 @@ from datetime import datetime # Return the current time in UTC without any timezone information now = datetime.utcnow -__all__ = [now] +__all__ = ('now', ) diff --git a/lib/galaxy/tools/cwl/__init__.py b/lib/galaxy/tools/cwl/__init__.py index b51eddbfcb8..fe28381120d 100644 --- a/lib/galaxy/tools/cwl/__init__.py +++ b/lib/galaxy/tools/cwl/__init__.py @@ -2,13 +2,12 @@ from .cwltool_deps import ( needs_shell_quoting, shellescape, ) -from .parser import tool_proxy -from .parser import workflow_proxy +from .parser import tool_proxy, workflow_proxy from .representation import to_cwl_job, to_galaxy_parameters from .runtime_actions import handle_outputs -__all__ = [ +__all__ = ( 'tool_proxy', 'workflow_proxy', 'handle_outputs', @@ -16,4 +15,4 @@ __all__ = [ 'to_galaxy_parameters', 'needs_shell_quoting', 'shellescape', -] +) diff --git a/lib/galaxy/tools/cwl/cwltool_deps.py b/lib/galaxy/tools/cwl/cwltool_deps.py index 376fd30f5ca..a2a946c91a1 100644 --- a/lib/galaxy/tools/cwl/cwltool_deps.py +++ b/lib/galaxy/tools/cwl/cwltool_deps.py @@ -4,6 +4,7 @@ Use this as the import interface for cwltool and just call :func:`ensure_cwltool_available` before using any of the imported functionality at runtime. """ +import re try: import requests @@ -40,8 +41,6 @@ except (ImportError, SyntaxError): # Drop SyntaxError once schema_salad supports Python 3 schema_salad = None -import re - needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search @@ -65,7 +64,7 @@ def ensure_cwltool_available(): raise ImportError(message) -__all__ = [ +__all__ = ( 'main', 'load_tool', 'workflow', @@ -74,4 +73,4 @@ __all__ = [ 'schema_salad', 'shellescape', 'needs_shell_quoting', -] +) diff --git a/lib/galaxy/tools/cwl/parser.py b/lib/galaxy/tools/cwl/parser.py index ff4a56691a6..3e106440933 100644 --- a/lib/galaxy/tools/cwl/parser.py +++ b/lib/galaxy/tools/cwl/parser.py @@ -10,6 +10,8 @@ import logging import os from abc import ABCMeta, abstractmethod +import six + from galaxy.util import safe_makedirs from galaxy.util.bunch import Bunch from galaxy.util.odict import odict @@ -119,8 +121,8 @@ def check_requirements(rec, tool=True): check_requirements(d, tool=tool) +@six.add_metaclass(ABCMeta) class ToolProxy( object ): - __metaclass__ = ABCMeta def __init__(self, tool, tool_path): self._tool = tool @@ -176,7 +178,7 @@ class CommandLineToolProxy(ToolProxy): schema = self._tool.schemaDefs[schema_type] if schema["type"] == "record": - return map(_simple_field_to_input, schema["fields"]) + return [_simple_field_to_input(_) for _ in schema["fields"]] def output_instances(self): outputs_schema = self._tool.outputs_record_schema @@ -235,12 +237,12 @@ class JobProxy(object): def _ensure_cwl_job_initialized(self): if self._cwl_job is None: - self._cwl_job = self._tool_proxy._tool.job( + self._cwl_job = next(self._tool_proxy._tool.job( self._input_dict, self._output_callback, basedir=self._job_directory, use_container=False - ).next() + )) self._is_command_line_job = hasattr(self._cwl_job, "command_line") @property @@ -536,7 +538,7 @@ class ConditionalInstance(object): when=odict(), ) for value, block in self.whens: - as_dict["when"][value] = map(lambda i: i.to_dict(), block) + as_dict["when"][value] = [i.to_dict() for i in block] return as_dict @@ -616,7 +618,7 @@ class OutputInstance(object): self.path = path -__all__ = [ +__all__ = ( 'tool_proxy', 'load_job_proxy', -] +) diff --git a/lib/galaxy/tools/cwl/runtime_actions.py b/lib/galaxy/tools/cwl/runtime_actions.py index 7b596b4ca1b..84fe2c6f339 100644 --- a/lib/galaxy/tools/cwl/runtime_actions.py +++ b/lib/galaxy/tools/cwl/runtime_actions.py @@ -20,7 +20,7 @@ def handle_outputs(job_directory=None): job_proxy = load_job_proxy(job_directory) tool_working_directory = os.path.join(job_directory, "working") outputs = job_proxy.collect_outputs(tool_working_directory) - for output_name, output in outputs.iteritems(): + for output_name, output in outputs.items(): target_path = job_proxy.output_path( output_name ) if isinstance(output, dict) and "path" in output: output_path = output["path"] @@ -48,6 +48,6 @@ def handle_outputs(job_directory=None): with open(target_path, "w") as f: f.write(json.dumps(output)) -__all__ = [ +__all__ = ( 'handle_outputs', -] +) diff --git a/lib/galaxy/tools/deps/commands.py b/lib/galaxy/tools/deps/commands.py index 0a2046c4d9e..3b131f8552d 100644 --- a/lib/galaxy/tools/deps/commands.py +++ b/lib/galaxy/tools/deps/commands.py @@ -3,15 +3,12 @@ import os import subprocess import sys as _sys +from six.moves import shlex_quote + from galaxy.util import which STDOUT_INDICATOR = "-" -try: - from shlex import quote as shell_quote -except ImportError: - from pipes import quote as shell_quote - def redirecting_io(sys=_sys): """Predicate to determine if we are redicting I/O in process.""" @@ -83,11 +80,11 @@ def argv_to_str(command_argv, quote=True): If None appears in the command list it is simply excluded. - Arguments are quoted with shlex.quote. That said, this method is not meant to be + Arguments are quoted with shlex_quote. That said, this method is not meant to be used in security critical paths of code and should not be used to sanitize code. """ - map_func = shell_quote if quote else lambda x: x + map_func = shlex_quote if quote else lambda x: x return " ".join([map_func(c) for c in command_argv if c is not None]) @@ -144,7 +141,7 @@ class CommandLineException(Exception): return self.message -__all__ = [ +__all__ = ( 'argv_to_str', 'CommandLineException', 'download_command', @@ -153,6 +150,5 @@ __all__ = [ 'redirecting_io', 'shell', 'shell_process', - 'shell_quote', 'which', -] +) diff --git a/lib/galaxy/tools/deps/conda_compat.py b/lib/galaxy/tools/deps/conda_compat.py index 1443378f9f5..c45573ef49d 100644 --- a/lib/galaxy/tools/deps/conda_compat.py +++ b/lib/galaxy/tools/deps/conda_compat.py @@ -6,8 +6,8 @@ PyPI. This module serves as a PyPI capable interface to these utilities. """ import collections import os -import yaml +import yaml try: from conda_build.metadata import MetaData @@ -15,7 +15,7 @@ except ImportError: MetaData = None try: - from anaconda_verify.recipe import render_jinja2, parse + from anaconda_verify.recipe import parse, render_jinja2 except ImportError: render_jinja2 = None parse = None @@ -106,7 +106,7 @@ class _MetaData(object): if MetaData is None: MetaData = _MetaData -__all__ = [ +__all__ = ( "MetaData", "raw_metadata", -] +) diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py index 117acca4389..d63dd02055f 100644 --- a/lib/galaxy/tools/deps/conda_util.py +++ b/lib/galaxy/tools/deps/conda_util.py @@ -445,7 +445,7 @@ def filter_installed_targets(conda_targets, conda_context=None, verbose_install_ installed = functools.partial(is_conda_target_installed, conda_context=conda_context, verbose_install_check=verbose_install_check) - return filter(installed, conda_targets) + return list(filter(installed, conda_targets)) def build_isolated_environment( @@ -510,7 +510,7 @@ def requirement_to_conda_targets(requirement, conda_context=None): def requirements_to_conda_targets(requirements, conda_context=None): r_to_ct = functools.partial(requirement_to_conda_targets, conda_context=conda_context) - conda_targets = map(r_to_ct, requirements) + conda_targets = (r_to_ct(_) for _ in requirements) return [c for c in conda_targets if c is not None] @@ -520,10 +520,10 @@ def _ensure_conda_context(conda_context): return conda_context -__all__ = [ +__all__ = ( 'CondaContext', 'CondaTarget', 'install_conda', 'install_conda_target', 'requirements_to_conda_targets', -] +) diff --git a/lib/galaxy/tools/deps/container_resolvers/mulled.py b/lib/galaxy/tools/deps/container_resolvers/mulled.py index 2b2701270ef..3ada6fa08e2 100644 --- a/lib/galaxy/tools/deps/container_resolvers/mulled.py +++ b/lib/galaxy/tools/deps/container_resolvers/mulled.py @@ -58,7 +58,7 @@ def list_cached_mulled_images(namespace=None): return image - return map(output_line_to_image, filter(name_filter, images_and_versions.splitlines())) + return [output_line_to_image(_) for _ in filter(name_filter, images_and_versions.splitlines())] def get_filter(namespace): @@ -200,8 +200,8 @@ def mulled_targets(tool_info): return requirements_to_mulled_targets(tool_info.requirements) -__all__ = [ +__all__ = ( "CachedMulledContainerResolver", "MulledContainerResolver", "BuildMulledContainerResolver", -] +) diff --git a/lib/galaxy/tools/deps/docker_util.py b/lib/galaxy/tools/deps/docker_util.py index c25c2def80b..5d27d2b353a 100644 --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -3,7 +3,10 @@ ...using common defaults and configuration mechanisms. """ import os -from .commands import argv_to_str, shell_quote + +from six.moves import shlex_quote + +from .commands import argv_to_str DEFAULT_DOCKER_COMMAND = "docker" DEFAULT_SUDO = True @@ -33,7 +36,7 @@ class DockerVolume(object): if not volumes_as_str: return [] volume_strs = [v.strip() for v in volumes_as_str.split(",")] - return map(DockerVolume.volume_from_str, volume_strs) + return [DockerVolume.volume_from_str(_) for _ in volume_strs] @staticmethod def volume_from_str(as_str): @@ -152,19 +155,19 @@ def build_docker_run_command( if terminal: command_parts.append("-t") for env_directive in env_directives: - command_parts.extend(["-e", shell_quote(env_directive)]) + command_parts.extend(["-e", shlex_quote(env_directive)]) for volume in volumes: - command_parts.extend(["-v", shell_quote(str(volume))]) + command_parts.extend(["-v", shlex_quote(str(volume))]) if volumes_from: - command_parts.extend(["--volumes-from", shell_quote(str(volumes_from))]) + command_parts.extend(["--volumes-from", shlex_quote(str(volumes_from))]) if memory: - command_parts.extend(["-m", shell_quote(memory)]) + command_parts.extend(["-m", shlex_quote(memory)]) if name: - command_parts.extend(["--name", shell_quote(name)]) + command_parts.extend(["--name", shlex_quote(name)]) if working_directory: - command_parts.extend(["-w", shell_quote(working_directory)]) + command_parts.extend(["-w", shlex_quote(working_directory)]) if net: - command_parts.extend(["--net", shell_quote(net)]) + command_parts.extend(["--net", shlex_quote(net)]) if auto_rm: command_parts.append("--rm") if run_extra_arguments: @@ -177,7 +180,7 @@ def build_docker_run_command( full_image = image if tag: full_image = "%s:%s" % (full_image, tag) - command_parts.append(shell_quote(full_image)) + command_parts.append(shlex_quote(full_image)) command_parts.append(container_command) return " ".join(command_parts) diff --git a/lib/galaxy/tools/deps/mulled/_cli.py b/lib/galaxy/tools/deps/mulled/_cli.py index 3cf32bad5de..8cf4e6fc1e3 100644 --- a/lib/galaxy/tools/deps/mulled/_cli.py +++ b/lib/galaxy/tools/deps/mulled/_cli.py @@ -14,6 +14,6 @@ def arg_parser(argv, globals): ) return parser -__all__ = [ - "arg_parser" -] +__all__ = ( + "arg_parser", +) diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py index e110969b203..cf55e4e46d1 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build.py @@ -14,17 +14,15 @@ import json import os import string import subprocess - from sys import platform as _platform -from galaxy.tools.deps import commands -from galaxy.tools.deps import installable - try: import yaml except ImportError: yaml = None +from galaxy.tools.deps import commands, installable + from ._cli import arg_parser from .util import build_target, conda_build_target_str, image_name from ..conda_compat import MetaData @@ -236,7 +234,7 @@ def target_str_to_targets(targets_raw): target = build_target(target_str) return target - targets = map(parse_target, targets_raw.split(",")) + targets = [parse_target(_) for _ in targets_raw.split(",")] return targets @@ -281,7 +279,7 @@ def main(argv=None): mull_targets(targets, **args_to_mull_targets_kwds(args)) -__all__ = ["main"] +__all__ = ("main", ) if __name__ == '__main__': diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py index b5082224649..272940eed7a 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py @@ -16,7 +16,7 @@ See recent changes that would be built with: mulled-build-channel list """ - +from __future__ import print_function import os import time @@ -75,7 +75,7 @@ def run_channel(args, build_last_n_versions=1): def get_pkg_names(args): """Print package names that would be affected.""" - print('\n'.join([pkg_name for pkg_name, pkg_tests in get_affected_packages(args)])) + print('\n'.join(pkg_name for pkg_name, pkg_tests in get_affected_packages(args))) def add_channel_arguments(parser): @@ -102,7 +102,7 @@ def main(argv=None): run_channel(args) -__all__ = ["main"] +__all__ = ("main", ) if __name__ == '__main__': diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_files.py b/lib/galaxy/tools/deps/mulled/mulled_build_files.py index 0fd065c504d..931da7647c1 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build_files.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build_files.py @@ -17,7 +17,6 @@ import glob import os from ._cli import arg_parser - from .mulled_build import ( add_build_arguments, args_to_mull_targets_kwds, @@ -73,7 +72,7 @@ def _parse_line(line_str): return _Line(*line_parts) -__all__ = ["main"] +__all__ = ("main", ) if __name__ == '__main__': diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py index 7281c7940ae..fbe353d38c7 100644 --- a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py +++ b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py @@ -40,12 +40,12 @@ def requirements_to_mulled_targets(requirements): Only package requirements are retained. """ - package_requirements = filter(lambda r: r.type == "package", requirements) - targets = map(lambda r: build_target(r.name, r.version), package_requirements) + package_requirements = [r for r in requirements if r.type == "package"] + targets = [build_target(r.name, r.version) for r in package_requirements] return targets -__all__ = ["main", "requirements_to_mulled_targets"] +__all__ = ("main", "requirements_to_mulled_targets") if __name__ == '__main__': diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tools/deps/mulled/util.py index a190d0e2192..6ea62f241c9 100644 --- a/lib/galaxy/tools/deps/mulled/util.py +++ b/lib/galaxy/tools/deps/mulled/util.py @@ -105,7 +105,7 @@ def image_name(targets, image_build=None, name_override=None): return "mulled-v1-%s%s" % (m.hexdigest(), suffix) -__all__ = [ +__all__ = ( "build_target", "conda_build_target_str", "image_name", @@ -114,4 +114,4 @@ __all__ = [ "split_tag", "Target", "version_sorted", -] +) diff --git a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py index 79464e23a46..5585de56c42 100644 --- a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py @@ -5,7 +5,6 @@ via shed2tap (e.g. https://github.com/jmchilton/homebrew-toolshed). """ import logging import os - from xml.etree import ElementTree as ET from .resolver_mixins import ( @@ -147,4 +146,4 @@ def build_recipe_name(package_name, package_version, repository_owner, repositor return base -__all__ = ['HomebrewToolShedDependencyResolver'] +__all__ = ('HomebrewToolShedDependencyResolver', ) diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index f16734a268e..1ffe821527f 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -244,4 +244,4 @@ def _string_as_bool( value ): return str( value ).lower() == "true" -__all__ = ['CondaDependencyResolver'] +__all__ = ('CondaDependencyResolver', ) diff --git a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py index 755c8849330..858ff0faf98 100644 --- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py +++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py @@ -122,4 +122,8 @@ def _is_dependency_directory(directory): return exists(join(directory, 'env.sh')) or exists(join(directory, 'bin')) -__all__ = ['GalaxyPackageDependencyResolver', 'GalaxyPackageDependency', 'ToolShedDependency'] +__all__ = ( + 'GalaxyPackageDependency', + 'GalaxyPackageDependencyResolver', + 'ToolShedDependency' +) diff --git a/lib/galaxy/tools/deps/resolvers/homebrew.py b/lib/galaxy/tools/deps/resolvers/homebrew.py index 3d4a741e7b0..395eb1eb518 100644 --- a/lib/galaxy/tools/deps/resolvers/homebrew.py +++ b/lib/galaxy/tools/deps/resolvers/homebrew.py @@ -53,4 +53,4 @@ def _string_as_bool( value ): return str( value ).lower() == "true" -__all__ = ['HomebrewDependencyResolver'] +__all__ = ('HomebrewDependencyResolver', ) diff --git a/lib/galaxy/tools/deps/resolvers/modules.py b/lib/galaxy/tools/deps/resolvers/modules.py index 9ac9c38a8a6..be64e6b7489 100644 --- a/lib/galaxy/tools/deps/resolvers/modules.py +++ b/lib/galaxy/tools/deps/resolvers/modules.py @@ -7,7 +7,6 @@ it, hence support for it will be minimal. The Galaxy team eagerly welcomes community contribution and maintenance however. """ import logging - from os import environ, pathsep from os.path import exists, isdir, join from subprocess import PIPE, Popen @@ -180,4 +179,4 @@ class ModuleDependency(Dependency): def _string_as_bool( value ): return str( value ).lower() == "true" -__all__ = ['ModuleDependencyResolver'] +__all__ = ('ModuleDependencyResolver', ) diff --git a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py index f60de4ad805..8b6ddac682f 100644 --- a/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/tool_shed_packages.py @@ -2,7 +2,6 @@ from os.path import abspath, exists, join from .galaxy_packages import BaseGalaxyPackageDependencyResolver, ToolShedDependency from .resolver_mixins import UsesInstalledRepositoriesMixin - from ..resolvers import NullDependency @@ -64,4 +63,4 @@ class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, Use return NullDependency(version=None, name=name) -__all__ = ['ToolShedPackageDependencyResolver'] +__all__ = ('ToolShedPackageDependencyResolver', ) diff --git a/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py index dfa7380a48f..c02bcd4a314 100644 --- a/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py +++ b/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py @@ -19,7 +19,6 @@ See bottom for instructions on how to add this resolver. """ import logging - from os import listdir from os.path import exists, getmtime, join @@ -153,7 +152,7 @@ class CandidateDependency(Dependency): return self.dependency.shell_commands( requirement ) -__all__ = ['UnlinkedToolShedPackageDependencyResolver'] +__all__ = ('UnlinkedToolShedPackageDependencyResolver', ) """ At the time of writing July 3 2015 this resolver has to be plugged in. diff --git a/lib/galaxy/tools/exception_handling.py b/lib/galaxy/tools/exception_handling.py index a9017ad3d3d..0c161622e8c 100644 --- a/lib/galaxy/tools/exception_handling.py +++ b/lib/galaxy/tools/exception_handling.py @@ -1,6 +1,6 @@ # We put a tool that references this package into the tool shed # so we have to provide this legacy location for import indefinitely # it seems. -from galaxy.util.ucsc import UCSCOutWrapper, UCSCLimitException +from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper -__all__ = ['UCSCOutWrapper', 'UCSCLimitException'] +__all__ = ('UCSCOutWrapper', 'UCSCLimitException') diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index 39cec6b346a..0a15dc80079 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -4,13 +4,15 @@ from various states, tracking results, and building implicit dataset collections from matched collections. """ import collections +import logging +from threading import Thread + +from six.moves.queue import Queue + +from galaxy.tools.actions import on_text_for_names, ToolExecutionCache from galaxy.tools.parser import ToolOutputCollectionPart from galaxy.util import ExecutionTimer -from galaxy.tools.actions import on_text_for_names, ToolExecutionCache -from threading import Thread -from Queue import Queue -import logging log = logging.getLogger( __name__ ) EXECUTION_SUCCESS_MESSAGE = "Tool [%s] created job [%s] %s" @@ -135,7 +137,6 @@ class ToolExecutionTracker( object ): return [] structure = self.collection_info.structure - collections = self.collection_info.collections.values() # params is just one sample tool param execution with parallelized # collection replaced with a specific dataset. Need to replace this @@ -143,13 +144,13 @@ class ToolExecutionTracker( object ): # label. params.update( self.collection_info.collections ) # Replace datasets with source collections for labelling outputs. - collection_names = map( lambda c: "collection %d" % c.hid, collections ) + collection_names = ["collection %d" % c.hid for c in self.collection_info.collections.values()] on_text = on_text_for_names( collection_names ) collections = {} - implicit_inputs = list(self.collection_info.collections.iteritems()) - for output_name, outputs in self.outputs_by_output_name.iteritems(): + implicit_inputs = list(self.collection_info.collections.items()) + for output_name, outputs in self.outputs_by_output_name.items(): if not len( structure ) == len( outputs ): # Output does not have the same structure, if all jobs were # successfully submitted this shouldn't have happened. @@ -202,4 +203,4 @@ class ToolExecutionTracker( object ): trans.sa_session.flush() self.implicit_collections = collections -__all__ = [ execute ] +__all__ = ( 'execute', ) diff --git a/lib/galaxy/tools/loader.py b/lib/galaxy/tools/loader.py index 123e9ef409f..0a8629321f1 100644 --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -7,4 +7,4 @@ from galaxy.util.xml_macros import ( load_tool = load -__all__ = ["load_tool", "raw_tool_xml_tree", "imported_macro_paths", "template_macro_params"] +__all__ = ("load_tool", "raw_tool_xml_tree", "imported_macro_paths", "template_macro_params") diff --git a/lib/galaxy/tools/loader_directory.py b/lib/galaxy/tools/loader_directory.py index 74b3a3404b7..bf78802d480 100644 --- a/lib/galaxy/tools/loader_directory.py +++ b/lib/galaxy/tools/loader_directory.py @@ -241,11 +241,11 @@ def _find_tool_files(path, recursive, enable_beta_formats): files = glob.glob(path + "/*.xml") else: files = _find_files(path, "*.xml") - return map(os.path.abspath, files) + return [os.path.abspath(_) for _ in files] def _has_extension(path, extensions): - return any(map(lambda e: path.endswith(e), extensions)) + return any(path.endswith(e) for e in extensions) def _find_files(directory, pattern='*'): @@ -266,7 +266,7 @@ BETA_TOOL_CHECKERS = { 'cwl': looks_like_a_tool_cwl, } -__all__ = [ +__all__ = ( "find_possible_tools_from_path", "is_a_yaml_with_class", "is_tool_load_error", @@ -276,4 +276,4 @@ __all__ = [ "looks_like_a_tool_cwl", "looks_like_a_tool_xml", "looks_like_a_tool_yaml", -] +) diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index cbb58e107f0..2652bf7ca3b 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -4,15 +4,16 @@ Classes encapsulating Galaxy tool parameters. import re from json import dumps, loads -from basic import RuntimeValue, DataCollectionToolParameter, DataToolParameter, SelectToolParameter -from grouping import Conditional, Repeat, Section, UploadDataset from galaxy.util.expressions import ExpressionContext from galaxy.util.json import json_fix +from .basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue, SelectToolParameter +from .grouping import Conditional, Repeat, Section, UploadDataset + REPLACE_ON_TRUTHY = object() # Some tools use the code tag and access the code base, expecting certain tool parameters to be available here. -__all__ = [ DataCollectionToolParameter, DataToolParameter, SelectToolParameter ] +__all__ = ( 'DataCollectionToolParameter', 'DataToolParameter', 'SelectToolParameter' ) def visit_input_values( inputs, input_values, callback, name_prefix='', label_prefix='', parent_prefix='', context=None, no_replacement_value=REPLACE_ON_TRUTHY ): @@ -82,7 +83,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr context = ExpressionContext( input_values, context ) payload = { 'context': context, 'no_replacement_value': no_replacement_value } - for input in inputs.itervalues(): + for input in inputs.values(): if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): values = input_values[ input.name ] = input_values.get( input.name, [] ) for i, d in enumerate( values ): @@ -143,7 +144,7 @@ def params_to_strings( params, param_values, app ): such). """ rval = dict() - for key, value in param_values.iteritems(): + for key, value in param_values.items(): if key in params: value = params[ key ].value_to_basic( value, app ) rval[ key ] = str( dumps( value ) ) @@ -158,7 +159,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ): preferred form). """ rval = dict() - for key, value in param_values.iteritems(): + for key, value in param_values.items(): value = json_fix( loads( value ) ) if key in params: value = params[ key ].value_from_basic( value, app, ignore_errors ) @@ -173,7 +174,7 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): Useful for e.g. the rerun function. """ - for input in inputs.itervalues(): + for input in inputs.values(): if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): for d in input_values[ input.name ]: index = d[ '__index__' ] diff --git a/lib/galaxy/tools/parameters/dataset_matcher.py b/lib/galaxy/tools/parameters/dataset_matcher.py index ca06e1e5d61..6ff696e6880 100644 --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -1,6 +1,7 @@ +from logging import getLogger + import galaxy.model -from logging import getLogger log = getLogger( __name__ ) ROLES_UNSET = object() @@ -179,4 +180,4 @@ class DatasetCollectionMatcher( object ): break return valid -__all__ = [ DatasetMatcher, DatasetCollectionMatcher ] +__all__ = ( 'DatasetMatcher', 'DatasetCollectionMatcher' ) diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py index a193088b2f5..b6dbebdedd8 100644 --- a/lib/galaxy/tools/parameters/wrapped.py +++ b/lib/galaxy/tools/parameters/wrapped.py @@ -1,20 +1,21 @@ from galaxy.tools.parameters.basic import ( - DataToolParameter, DataCollectionToolParameter, + DataToolParameter, SelectToolParameter ) -from galaxy.tools.wrappers import ( - InputValueWrapper, - SelectToolParameterWrapper, - DatasetFilenameWrapper, - DatasetListWrapper, - DatasetCollectionWrapper -) from galaxy.tools.parameters.grouping import ( - Repeat, Conditional, + Repeat, Section ) +from galaxy.tools.wrappers import ( + DatasetCollectionWrapper, + DatasetFilenameWrapper, + DatasetListWrapper, + InputValueWrapper, + SelectToolParameterWrapper +) + PARAMS_UNWRAPPED = object() @@ -40,7 +41,7 @@ class WrappedParameters( object ): incoming = self.incoming # Wrap tool inputs as necessary - for input in inputs.itervalues(): + for input in inputs.values(): if input.name not in input_values and skip_missing_values: continue value = input_values[ input.name ] @@ -112,4 +113,4 @@ def make_list_copy( from_list ): return new_list -__all__ = [ 'WrappedParameters', 'make_dict_copy' ] +__all__ = ( 'WrappedParameters', 'make_dict_copy' ) diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py index d5d8a5afdf0..b5b4989776a 100644 --- a/lib/galaxy/tools/parameters/wrapped_json.py +++ b/lib/galaxy/tools/parameters/wrapped_json.py @@ -1,6 +1,6 @@ import logging -log = logging.getLogger(__name__) +log = logging.getLogger(__name__) SKIP_INPUT = object() @@ -9,7 +9,7 @@ def json_wrap(inputs, input_values, as_dict=None, handle_files="SKIP"): if as_dict is None: as_dict = {} - for input in inputs.itervalues(): + for input in inputs.values(): input_name = input.name value = input_values[input_name] json_value = _json_wrap_input(input, value, handle_files=handle_files) @@ -65,7 +65,7 @@ def _json_wrap_input(input, value, handle_files="SKIP"): json_value = _cast_if_not_none(value, bool) elif input_type == "data_column": # value is a SelectToolParameterWrapper() - json_value = map(int, _cast_if_not_none(value.value, list)) + json_value = [int(_) for _ in _cast_if_not_none(value.value, list)] else: raise NotImplementedError("input_type [%s] not implemented" % input_type) @@ -80,4 +80,4 @@ def _cast_if_not_none(value, cast_to, empty_to_none=False): return cast_to(value) -__all__ = ['json_wrap'] +__all__ = ('json_wrap', ) diff --git a/lib/galaxy/tools/parser/__init__.py b/lib/galaxy/tools/parser/__init__.py index 7ef870ceec0..7f7fdf15579 100644 --- a/lib/galaxy/tools/parser/__init__.py +++ b/lib/galaxy/tools/parser/__init__.py @@ -1,15 +1,14 @@ """ Package responsible for parsing tools from files/abstract tool sources. """ -from .factory import get_input_source -from .factory import get_tool_source +from .factory import get_input_source, get_tool_source from .interface import ToolSource from .output_objects import ( ToolOutputCollectionPart, ) -__all__ = [ +__all__ = ( "get_input_source", "get_tool_source", "ToolOutputCollectionPart", "ToolSource", -] +) diff --git a/lib/galaxy/tools/parser/factory.py b/lib/galaxy/tools/parser/factory.py index e72e4ec1f1b..d38949f8498 100644 --- a/lib/galaxy/tools/parser/factory.py +++ b/lib/galaxy/tools/parser/factory.py @@ -10,8 +10,7 @@ from galaxy.util.odict import odict from .cwl import CwlToolSource from .interface import InputSource -from .xml import XmlInputSource -from .xml import XmlToolSource +from .xml import XmlInputSource, XmlToolSource from .yaml import YamlToolSource log = logging.getLogger(__name__) @@ -72,4 +71,4 @@ def get_input_source(content): return content -__all__ = ["get_tool_source", "get_input_source"] +__all__ = ("get_tool_source", "get_input_source") diff --git a/lib/galaxy/tools/toolbox/__init__.py b/lib/galaxy/tools/toolbox/__init__.py index 4983a5331fa..604c4e49231 100644 --- a/lib/galaxy/tools/toolbox/__init__.py +++ b/lib/galaxy/tools/toolbox/__init__.py @@ -1,16 +1,13 @@ """API for this module containing functionality related to the toolbox.""" -from .base import AbstractToolBox -from .base import BaseGalaxyToolBox +from .base import AbstractToolBox, BaseGalaxyToolBox -from .panel import panel_item_types -from .panel import ToolSection -from .panel import ToolSectionLabel +from .panel import panel_item_types, ToolSection, ToolSectionLabel -__all__ = [ +__all__ = ( "AbstractToolBox", "BaseGalaxyToolBox", "panel_item_types", "ToolSection", "ToolSectionLabel", -] +) diff --git a/lib/galaxy/tools/toolbox/lineages/__init__.py b/lib/galaxy/tools/toolbox/lineages/__init__.py index d178d4f96ab..f79c808b79b 100644 --- a/lib/galaxy/tools/toolbox/lineages/__init__.py +++ b/lib/galaxy/tools/toolbox/lineages/__init__.py @@ -3,4 +3,4 @@ from .interface import ToolLineage from .tool_shed import ToolVersionCache -__all__ = ["LineageMap", "ToolLineage", "ToolVersionCache"] +__all__ = ("LineageMap", "ToolLineage", "ToolVersionCache") diff --git a/lib/galaxy/tools/toolbox/lineages/factory.py b/lib/galaxy/tools/toolbox/lineages/factory.py index bd1f049e0d0..2da533471c6 100644 --- a/lib/galaxy/tools/toolbox/lineages/factory.py +++ b/lib/galaxy/tools/toolbox/lineages/factory.py @@ -46,4 +46,4 @@ class LineageMap(object): return self.lineage_map.get(versionless_tool_id, None) -__all__ = ["LineageMap"] +__all__ = ("LineageMap", ) diff --git a/lib/galaxy/tools/toolbox/lineages/tool_shed.py b/lib/galaxy/tools/toolbox/lineages/tool_shed.py index 347b35591c5..a2412d12ad3 100644 --- a/lib/galaxy/tools/toolbox/lineages/tool_shed.py +++ b/lib/galaxy/tools/toolbox/lineages/tool_shed.py @@ -1,5 +1,4 @@ -from .interface import ToolLineage -from .interface import ToolLineageVersion +from .interface import ToolLineage, ToolLineageVersion try: from galaxy.model.tool_shed_install import ToolVersion @@ -78,13 +77,13 @@ class ToolShedLineage(ToolLineage): return result def get_versions( self, reverse=False ): - return map( ToolLineageVersion.from_guid, self.get_version_ids( reverse=reverse ) ) + return [ ToolLineageVersion.from_guid(_) for _ in self.get_version_ids( reverse=reverse ) ] def to_dict(self): tool_shed_repository = self._tool_shed_repository rval = dict( tool_version_id=self.tool_version_id, - tool_versions=map(lambda v: v.to_dict(), self.get_versions()), + tool_versions=[v.to_dict() for v in self.get_versions()], tool_shed_repository=tool_shed_repository if tool_shed_repository is not None else None, lineage_type='tool_shed', ) @@ -94,4 +93,4 @@ class ToolShedLineage(ToolLineage): def get_installed_tool_version( app, tool_id ): return app.tool_version_cache.tool_version_by_tool_id.get(tool_id, None) -__all__ = [ "ToolShedLineage" ] +__all__ = ( "ToolShedLineage", ) diff --git a/lib/galaxy/tools/toolbox/parser.py b/lib/galaxy/tools/toolbox/parser.py index 834ebdd450b..8023988d9ba 100644 --- a/lib/galaxy/tools/toolbox/parser.py +++ b/lib/galaxy/tools/toolbox/parser.py @@ -3,9 +3,9 @@ These files define tool lists, sections, labels, etc... the elements of the Galaxy tool panel. """ -from abc import ABCMeta -from abc import abstractmethod +from abc import ABCMeta, abstractmethod +import six import yaml from galaxy.util import parse_xml, string_as_bool @@ -13,11 +13,10 @@ from galaxy.util import parse_xml, string_as_bool DEFAULT_MONITOR = False +@six.add_metaclass(ABCMeta) class ToolConfSource(object): """Interface represents a container of tool references.""" - __metaclass__ = ABCMeta - @abstractmethod def parse_items(self): """Return a list of ToolConfItem describing source.""" @@ -45,7 +44,7 @@ class XmlToolConfSource(ToolConfSource): return self.root.get('tool_path') def parse_items(self): - return map(ensure_tool_conf_item, self.root.getchildren()) + return [ensure_tool_conf_item(_) for _ in self.root.getchildren()] def is_shed_tool_conf(self): has_tool_path = self.parse_tool_path() is not None @@ -67,7 +66,7 @@ class YamlToolConfSource(ToolConfSource): return self.as_dict.get('tool_path') def parse_items(self): - return map(ToolConfItem.from_dict, self.as_dict.get('items')) + return [ToolConfItem.from_dict(_) for _ in self.as_dict.get('items')] def parse_monitor(self): return self.as_dict.get('monitor', DEFAULT_MONITOR) @@ -94,7 +93,7 @@ class ToolConfItem(object): del as_dict['type'] attributes = as_dict if type == 'section': - items = map(cls.from_dict, as_dict['items']) + items = [cls.from_dict(_) for _ in as_dict['items']] del as_dict['items'] item = ToolConfSection(attributes, items) else: @@ -141,18 +140,18 @@ def ensure_tool_conf_item(xml_or_item): if type != "section": return ToolConfItem(type, attributes, elem) else: - items = map(ensure_tool_conf_item, elem.getchildren()) + items = [ensure_tool_conf_item(_) for _ in elem.getchildren()] return ToolConfSection(attributes, items, elem=elem) def get_toolbox_parser(config_filename): - is_yaml = any(map(lambda e: config_filename.endswith(e), [".yml", ".yaml", ".json"])) + is_yaml = any(config_filename.endswith(e) for e in [".yml", ".yaml", ".json"]) if is_yaml: return YamlToolConfSource(config_filename) else: return XmlToolConfSource(config_filename) -__all__ = [ +__all__ = ( "get_toolbox_parser", "ensure_tool_conf_item", -] +) diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index 4b3a3bc9289..4f47835fd76 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -371,4 +371,4 @@ def __cleanup_param_values( inputs, values ): cleanup( "", inputs, values ) return associations -__all__ = [ summarize, extract_workflow ] +__all__ = ( 'summarize', 'extract_workflow' ) diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index 8b99cf75e95..6061254f58c 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -1,15 +1,13 @@ +import logging import uuid -from galaxy import model -from galaxy import util - -from galaxy.util.odict import odict +from galaxy import model, util from galaxy.util import ExecutionTimer +from galaxy.util.odict import odict from galaxy.workflow import modules -from galaxy.workflow.run_request import WorkflowRunConfig -from galaxy.workflow.run_request import workflow_run_config_to_request +from galaxy.workflow.run_request import (workflow_run_config_to_request, + WorkflowRunConfig) -import logging log = logging.getLogger( __name__ ) @@ -253,7 +251,7 @@ class WorkflowProgress( object ): self.module_injector.inject( step ) if step_id not in step_states: template = "Workflow invocation [%s] has no step state for step id [%s]. States ids are %s." - message = template % (self.workflow_invocation.id, step_id, step_states.keys()) + message = template % (self.workflow_invocation.id, step_id, list(step_states.keys())) raise Exception(message) runtime_state = step_states[ step_id ].value step.state = step.module.recover_runtime_state( runtime_state ) @@ -399,4 +397,4 @@ class WorkflowProgress( object ): except modules.DelayedWorkflowEvaluation: self.mark_step_outputs_delayed( step ) -__all__ = [ invoke, WorkflowRunConfig ] +__all__ = ( 'invoke', 'WorkflowRunConfig' ) diff --git a/lib/galaxy/workflow/schedulers/core.py b/lib/galaxy/workflow/schedulers/core.py index 7a111a7cab1..e513a258ed9 100644 --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -1,14 +1,13 @@ """ The class defines the stock Galaxy workflow scheduling plugin - currently it simply schedules the whole workflow up front when offered. """ -from ..schedulers import ActiveWorkflowSchedulingPlugin +import logging from galaxy.work import context +from galaxy.workflow import run, run_request -from galaxy.workflow import run -from galaxy.workflow import run_request +from ..schedulers import ActiveWorkflowSchedulingPlugin -import logging log = logging.getLogger( __name__ ) @@ -43,4 +42,4 @@ class CoreWorkflowSchedulingPlugin( ActiveWorkflowSchedulingPlugin ): workflow_invocation=workflow_invocation, ) -__all__ = [ 'CoreWorkflowSchedulingPlugin' ] +__all__ = ( 'CoreWorkflowSchedulingPlugin', ) diff --git a/test/api/workflows_format_2/__init__.py b/test/api/workflows_format_2/__init__.py index e680a3db612..c5e73c59a2d 100644 --- a/test/api/workflows_format_2/__init__.py +++ b/test/api/workflows_format_2/__init__.py @@ -5,7 +5,7 @@ from .interface import ImporterGalaxyInterface from .main import convert_and_import_workflow -__all__ = [ +__all__ = ( 'convert_and_import_workflow', 'ImporterGalaxyInterface', -] +) diff --git a/test/api/workflows_format_2/converter.py b/test/api/workflows_format_2/converter.py index 61ef54e6685..05a9a319c49 100644 --- a/test/api/workflows_format_2/converter.py +++ b/test/api/workflows_format_2/converter.py @@ -512,7 +512,7 @@ def main(argv): if __name__ == "__main__": main(sys.argv) -__all__ = [ +__all__ = ( 'yaml_to_workflow', 'python_to_workflow', -] +) diff --git a/test/api/workflows_format_2/main.py b/test/api/workflows_format_2/main.py index e147c52ec23..0a79382ea5e 100644 --- a/test/api/workflows_format_2/main.py +++ b/test/api/workflows_format_2/main.py @@ -36,6 +36,6 @@ def convert_and_import_workflow(has_workflow, **kwds): import_kwds["publish"] = True return galaxy_interface.import_workflow(workflow, **import_kwds) -__all__ = [ +__all__ = ( 'convert_and_import_workflow', -] +) diff --git a/test/base/driver_util.py b/test/base/driver_util.py index 977a88a3d0a..0b2e8b5585b 100644 --- a/test/base/driver_util.py +++ b/test/base/driver_util.py @@ -692,7 +692,7 @@ def drive_test(test_driver_class): sys.exit(test_driver_class().run()) -__all__ = [ +__all__ = ( "copy_database_template", "build_logger", "drive_test", @@ -705,4 +705,4 @@ __all__ = [ "setup_galaxy_config", "TestDriver", "wait_for_http_server", -] +) diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py index a3d2528ed5d..51f23cb4ccc 100644 --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -3,22 +3,22 @@ tool evaluation. Such extensive "fixtures" are something of an anti-pattern so use of this should be limitted to tests of very 'extensive' classes. """ -from collections import defaultdict import os.path -import tempfile import shutil import string +import tempfile +from collections import defaultdict -from galaxy.util.bunch import Bunch -from galaxy.web.security import SecurityHelper +import galaxy.datatypes.registry import galaxy.model +from galaxy.jobs import NoopQueue from galaxy.model import mapping from galaxy.tools import Tool -from galaxy.util.dbkeys import GenomeBuilds -from galaxy.jobs import NoopQueue -from galaxy.tools.parser import get_tool_source from galaxy.tools.deps.containers import NullContainerFinder -import galaxy.datatypes.registry +from galaxy.tools.parser import get_tool_source +from galaxy.util.bunch import Bunch +from galaxy.util.dbkeys import GenomeBuilds +from galaxy.web.security import SecurityHelper datatypes_registry = galaxy.datatypes.registry.Registry() datatypes_registry.load_datatypes() @@ -207,4 +207,4 @@ class MockQuery(object): return self.class_objects.get(id, None) -__all__ = [ UsesApp ] +__all__ = ( 'UsesApp', ) diff --git a/test/unit/unittest_utils/utility.py b/test/unit/unittest_utils/utility.py index 3341ee3879b..465fd4c42c9 100644 --- a/test/unit/unittest_utils/utility.py +++ b/test/unit/unittest_utils/utility.py @@ -4,12 +4,7 @@ Unit test utilities. import os import sys import textwrap - -from sys import version_info -if version_info < (2, 7): - import unittest2 as unittest -else: - import unittest as unittest +import unittest # ============================================================================= @@ -45,10 +40,10 @@ def clean_multiline_string( multiline_string, sep='\n' ): sys.path[1:1] = [ get_galaxy_libpath(), get_unittest_utils_path() ] -__all__ = [ +__all__ = ( "clean_multiline_string", "get_unittest_utils_path", "get_galaxy_root", "get_galaxy_libpath", "unittest", -] +) From bb4428896839898fb5d0c9b88ae18fc9b705a27b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 13 Oct 2016 09:54:55 -0400 Subject: [PATCH 21/32] Failthrough to using imghdr when PIL does not detect an image correctly. Some misc cleanup, avoiding use of system functions as variable names, etc. --- lib/galaxy/datatypes/images.py | 8 --- lib/galaxy/datatypes/util/image_util.py | 71 ++++++++++++------------- lib/galaxy/util/checkers.py | 23 ++------ tools/data_source/upload.py | 8 +-- 4 files changed, 39 insertions(+), 71 deletions(-) diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index 6832790e842..fe5f87b18fc 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -12,14 +12,6 @@ from galaxy.datatypes.util.image_util import check_image_type from galaxy.util import nice_size from . import data -try: - import Image as PIL -except ImportError: - try: - from PIL import Image as PIL - except: - PIL = None - log = logging.getLogger(__name__) # TODO: Uploading image files of various types is supported in Galaxy, but on diff --git a/lib/galaxy/datatypes/util/image_util.py b/lib/galaxy/datatypes/util/image_util.py index 1d825b80111..89c397d407e 100644 --- a/lib/galaxy/datatypes/util/image_util.py +++ b/lib/galaxy/datatypes/util/image_util.py @@ -13,66 +13,63 @@ except ImportError: log = logging.getLogger(__name__) -def image_type( filename, image=None ): - format = '' +def image_type( filename ): + fmt = None if PIL is not None: - if image is not None: - format = image.format - else: - try: - im = PIL.open( filename ) - format = im.format - im.close() - except: - return False + try: + im = PIL.open( filename ) + fmt = im.format + im.close() + except: + # We continue to try with imghdr, so this is a rare case of an + # exception we expect to happen frequently, so we're not logging + pass + if not fmt: + fmt = imghdr.what( filename ) + if fmt: + return fmt.upper() else: - format = imghdr.what( filename ) - if format is not None: - format = format.upper() - else: - return False - return format + return False def check_image_type( filename, types, image=None ): - format = image_type( filename, image ) - # First check if we can use PIL - if format in types: + fmt = image_type( filename, image ) + if fmt in types: return True return False -def get_image_ext( file_path, image ): +def get_image_ext( file_path ): # determine ext - format = image_type( file_path, image ) - if format in [ 'JPG', 'JPEG' ]: + fmt = image_type( file_path ) + if fmt in [ 'JPG', 'JPEG' ]: return 'jpg' - if format == 'PNG': + if fmt == 'PNG': return 'png' - if format == 'TIFF': + if fmt == 'TIFF': return 'tiff' - if format == 'BMP': + if fmt == 'BMP': return 'bmp' - if format == 'GIF': + if fmt == 'GIF': return 'gif' - if format == 'IM': + if fmt == 'IM': return 'im' - if format == 'PCD': + if fmt == 'PCD': return 'pcd' - if format == 'PCX': + if fmt == 'PCX': return 'pcx' - if format == 'PPM': + if fmt == 'PPM': return 'ppm' - if format == 'PSD': + if fmt == 'PSD': return 'psd' - if format == 'XBM': + if fmt == 'XBM': return 'xbm' - if format == 'XPM': + if fmt == 'XPM': return 'xpm' - if format == 'RGB': + if fmt == 'RGB': return 'rgb' - if format == 'PBM': + if fmt == 'PBM': return 'pbm' - if format == 'PGM': + if fmt == 'PGM': return 'pgm' return None diff --git a/lib/galaxy/util/checkers.py b/lib/galaxy/util/checkers.py index 9cf66ea7c51..6d187b5dad8 100644 --- a/lib/galaxy/util/checkers.py +++ b/lib/galaxy/util/checkers.py @@ -10,28 +10,11 @@ from galaxy import util HTML_CHECK_LINES = 100 -try: - import Image as PIL -except ImportError: - try: - from PIL import Image as PIL - except: - PIL = None - def check_image( file_path ): - if PIL is not None: - try: - im = PIL.open( file_path ) - except: - return False - if im: - return im - return False - else: - if imghdr.what( file_path ) is not None: - return True - return False + if imghdr.what( file_path ) is not None: + return True + return False def check_html( file_path, chunk=None ): diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index a123aa327f2..f725cf19782 100644 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -116,12 +116,8 @@ def add_file( dataset, registry, json_file, output_path ): except UnicodeDecodeError as e: dataset.is_multi_byte = False # Is dataset an image? - image = check_image( dataset.path ) - if image: - if not PIL: - image = None - # get_image_ext() returns None if nor a supported Image type - ext = get_image_ext( dataset.path, image ) + if check_image( dataset.path ): + ext = get_image_ext( dataset.path ) data_type = ext # Is dataset content multi-byte? elif dataset.is_multi_byte: From cb6e25278c4a59d4ea2edd9ce5e9c757b1ebf7f8 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 13 Oct 2016 10:25:18 -0400 Subject: [PATCH 22/32] Refactoring, because it was bugging me. --- lib/galaxy/datatypes/images.py | 2 +- lib/galaxy/datatypes/sequence.py | 2 +- lib/galaxy/util/checkers.py | 15 ++++++++------- lib/galaxy/{datatypes => }/util/image_util.py | 0 tools/data_source/upload.py | 16 +++++----------- 5 files changed, 15 insertions(+), 20 deletions(-) rename lib/galaxy/{datatypes => }/util/image_util.py (100%) diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index fe5f87b18fc..f3858ccc68e 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -8,8 +8,8 @@ from six.moves.urllib.parse import quote_plus from galaxy.datatypes.binary import Binary from galaxy.datatypes.sniff import get_headers from galaxy.datatypes.text import Html as HtmlFromText -from galaxy.datatypes.util.image_util import check_image_type from galaxy.util import nice_size +from galaxy.util.image_util import check_image_type from . import data log = logging.getLogger(__name__) diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index 1b4619d731e..a6d67f2af32 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -15,9 +15,9 @@ from six import PY3 from galaxy import util from galaxy.datatypes import metadata from galaxy.util.checkers import is_gzip +from galaxy.util.image_util import check_image_type from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.sniff import get_headers -from galaxy.datatypes.util.image_util import check_image_type from galaxy.util import nice_size from . import data diff --git a/lib/galaxy/util/checkers.py b/lib/galaxy/util/checkers.py index 6d187b5dad8..daf8866424b 100644 --- a/lib/galaxy/util/checkers.py +++ b/lib/galaxy/util/checkers.py @@ -1,22 +1,16 @@ import bz2 import gzip -import imghdr import re import zipfile from six import StringIO from galaxy import util +from galaxy.util.image_util import image_type HTML_CHECK_LINES = 100 -def check_image( file_path ): - if imghdr.what( file_path ) is not None: - return True - return False - - def check_html( file_path, chunk=None ): if chunk is None: temp = open( file_path, "U" ) @@ -126,6 +120,13 @@ def is_gzip( file_path ): return is_gzipped +def check_image( file_path ): + """ Simple wrapper around image_type to yield a True/False verdict """ + if image_type( file_path ): + return True + return False + + __all__ = [ 'check_binary', 'check_bz2', diff --git a/lib/galaxy/datatypes/util/image_util.py b/lib/galaxy/util/image_util.py similarity index 100% rename from lib/galaxy/datatypes/util/image_util.py rename to lib/galaxy/util/image_util.py diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index f725cf19782..85355c3eb3b 100644 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -20,17 +20,10 @@ from galaxy import util from galaxy.datatypes import sniff from galaxy.datatypes.binary import Binary from galaxy.datatypes.registry import Registry -from galaxy.datatypes.util.image_util import get_image_ext from galaxy.util import multi_byte -from galaxy.util.checkers import check_binary, check_bz2, check_gzip, check_html, check_image, check_zip +from galaxy.util.checkers import check_binary, check_bz2, check_gzip, check_html, check_zip +from galaxy.util.image_util import get_image_ext -try: - import Image as PIL -except ImportError: - try: - from PIL import Image as PIL - except: - PIL = None try: import bz2 @@ -116,8 +109,9 @@ def add_file( dataset, registry, json_file, output_path ): except UnicodeDecodeError as e: dataset.is_multi_byte = False # Is dataset an image? - if check_image( dataset.path ): - ext = get_image_ext( dataset.path ) + i_ext = get_image_ext( dataset.path ) + if i_ext: + ext = i_ext data_type = ext # Is dataset content multi-byte? elif dataset.is_multi_byte: From ba07956117e5e4527fa5d2837da2c267f6ab981d Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Thu, 13 Oct 2016 10:40:40 -0400 Subject: [PATCH 23/32] Fix tabular filtering tool broken in #2983 --- tools/stats/filtering.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py index 94640ef61ec..c6781e3b598 100644 --- a/tools/stats/filtering.py +++ b/tools/stats/filtering.py @@ -219,7 +219,7 @@ for i, line in enumerate( open( in_fname ) ): if i < num_header_lines: lines_kept += 1 - print >> out, line + print( line, file=out ) continue if not line or line.startswith( '#' ): @@ -230,7 +230,7 @@ for i, line in enumerate( open( in_fname ) ): %s if %s: lines_kept += 1 - print >> out, line + print( line, file=out ) except: invalid_lines += 1 if not invalid_line: From 5d294ea7d3a14561a15c30f3527dfcd21d517369 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Thu, 13 Oct 2016 10:54:41 -0400 Subject: [PATCH 24/32] Fix GFF attribute filtering tool broken in #2983 --- tools/filters/gff/gff_filter_by_attribute.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py index 7d5051dfd9e..452e812e895 100644 --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -125,9 +125,9 @@ for i, line in enumerate( open( in_fname ) ): %s if %s: lines_kept += 1 - print >> out, line + print( line, file=out ) except Exception as e: - print e + print ( e ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 From 32bc17cdaa636ba0ba2a97a372b37d518cdd6390 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Thu, 13 Oct 2016 11:08:18 -0400 Subject: [PATCH 25/32] Whitespace fix --- tools/filters/gff/gff_filter_by_attribute.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py index 452e812e895..a731df826b5 100644 --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -127,7 +127,7 @@ for i, line in enumerate( open( in_fname ) ): lines_kept += 1 print( line, file=out ) except Exception as e: - print ( e ) + print( e ) skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 From b6d4473aa0975f88b2d2cf8aa1372aecfc92919b Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Thu, 13 Oct 2016 11:19:37 -0400 Subject: [PATCH 26/32] Fix for displaying parameters to the user, that have a False value. Previously, e.g. an integer with a value of 0 would display "Not available.". --- lib/galaxy/tools/parameters/basic.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 236c6616115..ddb50cecc16 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -151,7 +151,7 @@ class ToolParameter( object, Dictifiable ): Convert a value to a text representation suitable for displaying to the user """ - if value: + if value is not None: return unicodify( value ) return "Not available." From ed263bf8a52b37199cc7822126598a75a9984335 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 13 Oct 2016 12:07:25 -0400 Subject: [PATCH 27/32] import order. --- lib/galaxy/util/image_util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/util/image_util.py b/lib/galaxy/util/image_util.py index 89c397d407e..9430d2eb5fb 100644 --- a/lib/galaxy/util/image_util.py +++ b/lib/galaxy/util/image_util.py @@ -1,6 +1,6 @@ """Provides utilities for working with image files.""" -import logging import imghdr +import logging try: import Image as PIL From 4bc429776853239961c45c9656c69b3be0ae01bc Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 13 Oct 2016 12:09:18 -0400 Subject: [PATCH 28/32] Simplify, strip out passing of image. --- lib/galaxy/util/image_util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/util/image_util.py b/lib/galaxy/util/image_util.py index 9430d2eb5fb..a54043bfc31 100644 --- a/lib/galaxy/util/image_util.py +++ b/lib/galaxy/util/image_util.py @@ -32,8 +32,8 @@ def image_type( filename ): return False -def check_image_type( filename, types, image=None ): - fmt = image_type( filename, image ) +def check_image_type( filename, types ): + fmt = image_type( filename ) if fmt in types: return True return False From 6c17d1a823b4367b93fff61d7f2fbed23dc5de3b Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Thu, 13 Oct 2016 16:21:12 +0000 Subject: [PATCH 29/32] Remove outdated warning After digging through the code I am not finding evidence that this was ever possible to do, at least not since sometime pre-2010. --- config/galaxy.ini.sample | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 3062bd1d9d4..a2a4bfac44f 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -886,8 +886,7 @@ use_interactive = True # Galaxy encodes various internal values when these values will be output in # some format (for example, in a URL or cookie). You should set a key to be # used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. +# string. # One simple way to generate a value for this is with the shell command: # python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' ' #id_secret = USING THE DEFAULT IS NOT SECURE! From f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 Mon Sep 17 00:00:00 2001 From: Dave B Date: Thu, 13 Oct 2016 12:42:54 -0400 Subject: [PATCH 30/32] Fix downloading tool tarball with boolean test input values. --- lib/galaxy/tools/__init__.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 8b965d48f59..bddd0a0292f 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1538,9 +1538,10 @@ class Tool( object, Dictifiable ): # Add input file tuples to the list. for input in test.inputs: for input_value in test.inputs[ input ]: - input_path = os.path.abspath( os.path.join( 'test-data', input_value ) ) + input_filename = str( input_value ) + input_path = os.path.abspath( os.path.join( 'test-data', input_filename ) ) if os.path.exists( input_path ): - td_tup = ( input_path, os.path.join( 'test-data', input_value ) ) + td_tup = ( input_path, os.path.join( 'test-data', input_filename ) ) tarball_files.append( td_tup ) # And add output file tuples to the list. for label, filename, _ in test.outputs: From 36134bca694c9dc6b2584fb661dfbce4ddb793e6 Mon Sep 17 00:00:00 2001 From: Scott Szakonyi Date: Thu, 6 Oct 2016 15:17:30 -0400 Subject: [PATCH 31/32] Added code to adjust top setting of tool search if messagebox is visible, issue 2907 --- client/galaxy/scripts/mvc/tool/tools.js | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js index 710b0230ec2..12323a58cc7 100644 --- a/client/galaxy/scripts/mvc/tool/tools.js +++ b/client/galaxy/scripts/mvc/tool/tools.js @@ -633,6 +633,12 @@ var ToolSearchView = Backbone.View.extend({ if (!this.model.is_visible()) { this.$el.hide(); } + + // Adjust top for issue 2907 depending on whether the messagebox is visible. + if ($("#messagebox").is(":visible")) { + this.$el.css("top","95px"); + } + this.$el.find('[title]').tooltip(); return this; }, From 6312d8052b9668a03b3bb25ea02b9d42ac32de6d Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 14 Oct 2016 09:43:41 -0400 Subject: [PATCH 32/32] Rebuild cilent. --- client/galaxy/scripts/mvc/tool/tools.js | 2 +- static/maps/mvc/tool/tools.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 25 ++++++++------- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 32 +++++++++---------- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/mvc/tool/tools.js | 2 +- 7 files changed, 34 insertions(+), 33 deletions(-) diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js index 12323a58cc7..8de4925a705 100644 --- a/client/galaxy/scripts/mvc/tool/tools.js +++ b/client/galaxy/scripts/mvc/tool/tools.js @@ -638,7 +638,7 @@ var ToolSearchView = Backbone.View.extend({ if ($("#messagebox").is(":visible")) { this.$el.css("top","95px"); } - + this.$el.find('[title]').tooltip(); return this; }, diff --git a/static/maps/mvc/tool/tools.js.map b/static/maps/mvc/tool/tools.js.map index 379f959a153..581ef5cbe13 100644 --- a/static/maps/mvc/tool/tools.js.map +++ b/static/maps/mvc/tool/tools.js.map @@ -1 +1 @@ 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").append(this.$button=a("
").append(this.$icon=a("")).append(this.$title=a("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(e){var e=this.model.attributes;this.$el.removeClass().addClass(e.cls).addClass(e.disabled&&"disabled").attr("disabled",e.disabled).attr("id",e.id).css("float",e.floating).off("click").on("click",function(){a(".tooltip").hide(),!e.disabled&&e.onclick&&e.onclick()}),this.$button.addClass("button").tooltip({title:e.tooltip,placement:"bottom"}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right")}}),r=t.extend({$menu:null,initialize:function(e){this.model=e&&e.model||new o.Model({id:"",title:"",floating:"right",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(e),this.setElement(a("
").append(this.$root=a("
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","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
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","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',n("This collection has been deleted"),"
","<% } %>"])}),t=i.wrapTemplate(['
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','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection"),a=i.wrapTemplate(['
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"],"collection");return o.extend({},s.prototype.templates,{warnings:e,titleBar:t,subtitle:a})}();var d=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),l.prototype.initialize.call(this,e)},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCEListItemView("+e+")"}});d.prototype.templates=function(){var e=i.wrapTemplate(['
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','<%- element.element_identifier %>',"
",'
',"
"],"element");return o.extend({},l.prototype.templates,{titleBar:e})}();var h=t.DatasetListItemView.extend({className:t.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),t.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return o.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(70),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return o.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=a.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),c=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:o.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),constructor:function(e,t){this.debug(" DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},"delete":function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),g=h.extend(t.mixin(n,{constructor:function(e,t){this.debug(" NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),f=l.extend({model:g,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug(" NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=f.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug(" NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=f.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(39),i(12),i(6),i(8),i(87),i(5),i(84)],s=function(e,t,i,n,s,c){"use strict";function d(e){var t=e.toJSON(),i=f(t,{creationFn:function(t,i){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i)}});return i}var h="collections",u=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the 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creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;a.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset"!==e.history_content_type?c("is not a dataset"):e.state!==t.OK?c(a.contains(t.NOT_READY_STATES,e.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):e.deleted||e.purged?c("has been deleted or purged"):null},_mangleDuplicateNames:function(){var e=900,t=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+t+")",t+=1,t>=e)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,n=l("
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":content+=": "+n}t._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(e){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(e){e.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(e){e.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(e){e.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(e,t){t=t||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(t).show().find(".alert-message").html(e)},_hideAlert:function(e){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(e){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(e){e.preventDefault();var t=this.$list();this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestElement(e.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=r('
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','
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','',c("More help"),"",'
','',c("Less"),"","
","
",'
','','',"
"].join("")),middle:a.template(['
','',c("Start over"),"",'',c("Clear selected"),"","
",'
',"
"].join("")),footer:a.template(['
','
','','
',c("Name"),":
","
","
",'
','
','",'
','",'","
","
",'
','","
","
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","
    ","
  • ",c(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
    • ","
  • ",c(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
    • ","
  • ",c(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
    • ","
  • ",c(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
    • ","
  • ",c(['Click the "Cancel" button to exit the interface.'].join("")),"
    • ","

","

",c(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

"].join("")),invalidElements:a.template([c("The following selections could not be included due to problems:"),"
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  • <%- problem.element.name %>: <%- problem.text %>
    • ","<% }); %>
"].join("")),noElementsLeft:a.template(['
  • ',c("No elements left! "),c("Would you like to "),'',c("start over"),"?","
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    ','
    ','',"<% if( _.size( problems ) ){ %>",c("The following selections could not be included due to problems"),":","
      <% _.each( problems, function( problem ){ %>","
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    ","<% } else if( _.size( elements ) < 1 ){ %>",c("No datasets were selected"),".","<% } %>","
    ",c("At least one element is needed for the collection"),". ",c("You may need to "),'',c("cancel")," ",c("and reselect new elements"),".","    ","
    ","
    ",'
    ','
    ','
    ','","
    ","
    ","
    "].join(""))},toString:function(){return"ListCollectionCreator"}}),g=function(e,t,i){var s,o=l.Deferred(),r=Galaxy.modal||new n.View;return t=a.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),s=new i(t),r.show({title:t.title||c("Create a collection"),body:s.$el,width:"80%",height:"100%",closing_events:!0}),s.render(),window._collectionCreator=s,o},f=function(e,t){return t=t||{},t.title=c("Create a collection from a list of datasets"),g(e,t,p)};return{DatasetCollectionElementView:u,ListCollectionCreator:p,collectionCreatorModal:g,listCollectionCreatorModal:f,createListCollection:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(42),i(12),i(22),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var c="dataset",d=e.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger), -this.log(this+".initialize:",e),d.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t,i){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):o.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){a.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===t.NOT_VIEWABLE||e===t.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(e===t.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(e===t.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),e.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===t.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var e=d.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=r('
    '),i=e.model.toJSON();return l.each(e.templates.detailMessages,function(n){t.append(r(n(i,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case t.NOT_VIEWABLE:return[];case t.OK:case t.FAILED_METADATA:case t.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return r(['
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    "].join("\n"))},events:l.extend(l.clone(d.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetListItemView("+e+")"}});return h.prototype.templates=function(){var e=l.extend({},d.prototype.templates.warnings,{failed_metadata:n.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','
    ',s("An error occurred setting the metadata for this dataset"),"
    ","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'
    ',s("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'
    ',s("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',s("This dataset has been deleted"),"
    ","<% } %>"])}),i=n.wrapTemplate(['
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    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
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    ',"<% } %>","<% } %>","
    "],"dataset"),o=n.wrapTemplate(['
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    ',s("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),a={};a[t.OK]=a[t.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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    ','",'<%- dataset.file_ext %>',"
    ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
    ','",'',"<%- dataset.metadata_dbkey %>","","
    ","<% } %>","<% if( dataset.misc_info ){ %>",'
    ','<%- dataset.misc_info %>',"
    ","<% } %>"],"dataset"),a[t.NEW]=n.wrapTemplate(["
    ",s("This is a new dataset and not all of its data are available yet"),"
    "],"dataset"),a[t.NOT_VIEWABLE]=n.wrapTemplate(["
    ",s("You do not have permission to view this dataset"),"
    "],"dataset"),a[t.DISCARDED]=n.wrapTemplate(["
    ",s("The job creating this dataset was cancelled before completion"),"
    "],"dataset"),a[t.QUEUED]=n.wrapTemplate(["
    ",s("This job is waiting to run"),"
    "],"dataset"),a[t.RUNNING]=n.wrapTemplate(["
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    "],"dataset"),a[t.UPLOAD]=n.wrapTemplate(["
    ",s("This dataset is currently uploading"),"
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    ",s("Metadata is being auto-detected"),"
    "],"dataset"),a[t.PAUSED]=n.wrapTemplate(["
    ",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
    "],"dataset"),a[t.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","
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    ","<% } %>",'',s("An error occurred with this dataset"),":",'
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    '],"dataset"),a[t.EMPTY]=n.wrapTemplate(["
    ",s("No data"),": <%- dataset.misc_blurb %>
    "],"dataset"),a.unknown=n.wrapTemplate(['
    Error: unknown dataset state: "<%- dataset.state %>"
    '],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'
    ',s("The job creating this dataset has been resubmitted"),"
    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
    ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:e,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4)],s=function(e){var t=o.Model.extend({initialize:function(e){this.app=e},checksum:function(){var e="",t=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=t.app.field_list[i];n&&(e+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),e},create:function(){function e(e,t,i){n.flat_dict[e]=t,o[e]=i,n.app.element_list[t]&&n.app.element_list[t].$el.attr("tour_id",e)}function t(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);-1!=g&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(e,t){return e-t});var a=0;for(var f in h)t(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();e(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&t(c,o[l.id+"-section-"+v]);break;case"section":t(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),e(c,l.id,m),l.payload))for(var y in l.payload)e(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},t("",s),o},match:function(e){return this.flat_dict&&this.flat_dict[e]},matchCase:function(e,t){return i(e,t)},matchModel:function(e,t){var i=this;n(e.inputs,function(e,n){i.flat_dict[n]&&t(e,i.flat_dict[n])})},matchResponse:function(e){function t(e,s){if("string"==typeof s){var o=n.flat_dict[e];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==e){var l="|";s instanceof Array&&(l="_"),r=e+l+r}t(r,s[a])}}var i={},n=this;return t("",e),i},_iterate:function(e,t){var i=this,n=a(e).children();n.each(function(){var e=this,n=a(e).attr("id");if(a(e).hasClass("section-row")){var s=i.app.input_list[n];t[n]=s&&{input:s}||{},i._iterate(e,t[n])}else i._iterate(e,t)})}}),i=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},n=function(e,t,s,o){o=a.extend(!0,{},o),r.each(e,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var l in e){var c=e[l];c.name=c.name||l;var d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":r.each(c.cache,function(e,i){n(e,t,d+"_"+i,o)});break;case"conditional":if(c.test_param){t(c.test_param,d+"|"+c.test_param.name,o);var h=i(c,c.test_param.value);-1!=h?n(c.cases[h].inputs,t,d,o):Galaxy.emit.debug("form-data::visitInputs() - 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    ").addClass("ui-form-element").append(o("
    ").addClass("ui-form-error ui-error").append(o("").addClass("fa fa-arrow-down")).append(o("").addClass("ui-form-error-text"))).append(o("
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    ").addClass("ui-form-field").append(o("").addClass("ui-form-info")).append(o("
    ").addClass("ui-form-backdrop"))).append(o("
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    ").append(this.$list=a("
    ")).append(a("
    ").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var n=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),s=new t.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:n}});s.append(e.$el),s.$el.addClass("section-row").hide(),this.list[e.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){return this.list[e]?(this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(e){e.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(4),i(7),i(9),i(36),i(34),i(35)],s=function(e,t,i,n,s,c){var d=o.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new c,this.setElement(a("
    ")),this.render()},render:function(){var e=this;this.$el.empty(),r.each(this.inputs,function(t){e.add(t)})},add:function(t){var i=l.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.options.sustain_conditionals&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var o=e.cases[s],a=t.$("#"+e.id+"-section-"+s),r=!1;for(var l in o.inputs)if(!o.inputs[l].hidden){r=!0;break}s==n&&r?a.fadeIn("fast"):a.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new d(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+o++,s=new d(i.app,{inputs:t});a.add({id:n,$el:s.$el,ondel:function(){a.del(n),i.app.trigger("change")}})}for(var i=this,o=0,a=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),l=r.size(e.cache),c=0;cc?e.cache[c]:e.inputs);this.app.options.sustain_repeats&&a.hideOptions();var h=new s(this.app,{label:e.title||e.name,help:e.help,field:a});this._append(h.$el,e.id)},_addSection:function(e){var t=new i.View({title:e.title||e.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!e.expanded});t.append(new d(this.app,{inputs:e.inputs}).$el),t.append(a("
    ").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var o=new s(this.app,{name:e.name,label:e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,field:n});return this.app.element_list[i]=o,this._append(o.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});return{View:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(37),i(33)],s=function(e,t,i,n,s){return o.View.extend({initialize:function(t){this.options=e.merge(t,{initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0}),this.setElement("
    "),this.render()},update:function(e){var t=this;this.data.matchModel(e,function(e,i){var n=t.input_list[i];if(n&&n.options&&!a.isEqual(n.options,e.options)){n.options=e.options;var s=t.field_list[i];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in e.options){var l=e.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+i)}}})},wait:function(e){for(var t in this.input_list){var i=this.field_list[t],n=this.input_list[t];n.is_dynamic&&i.wait&&i.unwait&&i[e?"wait":"unwait"]()}},highlight:function(e,t,i){var n=this.element_list[e];if(n&&(n.error(t||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",e),!i)){var s=this.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(r(this).css("overflow"))}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-120},500)}},errors:function(e){if(this.trigger("reset"),e&&e.errors){var t=this.data.matchResponse(e.errors);for(var i in this.element_list){this.element_list[i];t[i]&&this.highlight(i,t[i],!0)}}},render:function(){var e=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var t=this.data.checksum();return this.on("change",function(i){var n=e.input_list[i];if(!n||n.refresh_on_change||e.options.always_refresh){var s=e.data.checksum();s!=t&&(t=s,e.options.onchange&&e.options.onchange())}}),this.on("reset",function(){a.each(e.element_list,function(e){e.reset()})}),this},_renderForm:function(){r(".tooltip").remove(),this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),this.portlet=new t.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.options.inputs&&this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(30),i(74),i(5)],s=function(e,t,i){"use strict";function n(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}var s=t.HistoryContentMixin,a=e.ListDatasetCollection,r=e.PairDatasetCollection,l=e.ListPairedDatasetCollection,c=e.ListOfListsDatasetCollection,d=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(a.prototype.save),toString:function(){return"History"+a.prototype.toString.call(this)}}),h=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),u=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),p=c.extend(s).extend({defaults:o.extend(o.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(67),i(72),i(39),i(41),i(6),i(129)],s=function(e,t,i,n,s,l){"use strict";var c=e.PaginatedCollection,d=c.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(e,n){if("dataset"===e.history_content_type)return new t.HistoryDatasetAssociation(e,n);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new i.HistoryListDatasetCollection(e,n);case"paired":return new i.HistoryPairDatasetCollection(e,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(e,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(e,n)}var s="Unknown collection_type: "+e.collection_type;return console.warn(s,e),{validationError:s}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},c.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){return this.historyId?(this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this):void 0},comparators:o.extend(o.clone(c.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(o.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,o.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(o.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},o.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();o.isEmpty(t.expandedIds)||(e.details=o.values(t.expandedIds).join(","))}return c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return o.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=o.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=o.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var o=i.get(t[n]);return o?e.concat(o):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){ -return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=o.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var a=o.extend(o.clone(e),{view:"summary",keys:c,limit:r,offset:t,reset:0===t,remove:!1});o.defer(function(){s.fetch.call(s,a).fail(n.reject).done(function(e){n.notify(e,r,t),e.length!==r?(s.allFetched=!0,n.resolve(e,r,t)):i(t+r)})})}e=e||{};var n=a.Deferred(),s=this,r=e.limitPerCall||s.limitPerProgressiveFetch,l=t.HistoryDatasetAssociation.prototype.searchAttributes,c=l.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(e)&&e.id&&o.contains(t,e.model_class)},copy:function(e){var t,i,n;o.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=a.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,o,a){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:t,source:n})});return r},createHDCA:function(e,t,i,n){var s=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,element_identifiers:e});return s.save(n)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return o.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=r.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(o){n=[i(6)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return o.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return o.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){return o.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return o.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(e,t){"use strict";var i="list",n=o.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=a('
    '),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(a(n(i,e)))}),t},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i?!0:(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=e.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=e.wrapTemplate(['
    ']),o=e.wrapTemplate(['
    ']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return c.prototype.templates=function(){var t=e.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(4),i(55),i(7),i(38),i(17),i(28)],s=function(e,t,i,n,s,r){return n.extend({initialize:function(e){var i=this;n.prototype.initialize.call(this,e),this.deferred=new t,e.inputs?this._buildForm(e):this.deferred.execute(function(t){i._buildModel(t,e,!0)}),e.listen_to_history&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){this.refresh()}),this.$el.on("remove",function(){i.remove()})},refresh:function(){var e=this;e.deferred.reset(),this.deferred.execute(function(t){e._updateModel(t)})},remove:function(){var e=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(e),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(t){var i=this;this.options=e.merge(t,this.options),this.options=e.merge({icon:t.icon,title:""+t.name+" "+t.description+" (Galaxy Version "+t.version+")",operations:!this.options.hide_operations&&this._operations(),onchange:function(){i.refresh()}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(t,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),e.get({url:r,data:l,success:function(e){return e=e.tool_model||e,e.display?(a._buildForm(e),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",e),void t.resolve()):void(window.location=Galaxy.root)},error:function(e,n){var s=e&&e.err_msg||"Uncaught error.";401==n?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+a.options.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",e),t.reject()}})},_updateModel:function(t){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),e.request({type:"POST",url:n,data:s,success:function(e){i.update(e.tool_model||e),i.options.update&&i.options.update(e),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",e),t.reject()}})},_operations:function(){var e=this,t=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!t.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!t.sustain_version&&t.versions&&t.versions.length>1)for(var s in t.versions){var o=t.versions[s];o!=t.version&&n.addMenu({title:"Switch to "+o,version:o,icon:"fa-cube",onclick:function(){var i=t.id.replace(t.version,this.version),n=this.version;e.deferred.reset(),e.deferred.execute(function(t){e._buildModel(t,{id:i,version:n})})}})}else n.$el.hide();var a=new i.ButtonMenu({icon:"fa-caret-down",title:!t.narrow&&"Options"||null,tooltip:"View available options"});return t.biostar_url&&(a.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}}),a.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/local/search/page/?q="+t.name)}})),a.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+t.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&a.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+t.id+"/download"}}),t.requirements&&t.requirements.length>0&&a.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){!this.visible||e.portlet.collapsed?(this.visible=!0,e.portlet.expand(),e.message.update({persistent:!0,message:e._templateRequirements(t),status:"info"})):(this.visible=!1,e.message.update({message:""}))}}),t.sharable_url&&a.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(t.sharable_url)}}),{menu:a,versions:n}},_footer:function(){var e=this.options,t=o("
    ").append(this._templateHelp(e));if(e.citations){var i=o("
    "),n=new s.ToolCitationCollection;n.tool_id=e.id;var a=new r.CitationListView({el:i,collection:n});a.render(),n.fetch(),t.append(i)}return t},_templateHelp:function(e){var t=o("
    ").addClass("ui-form-help").append(e.help);return t.find("a").attr("target","_blank"),t},_templateRequirements:function(e){var t=e.requirements.length;if(t>0){var i="This tool requires ";a.each(e.requirements,function(e,n){i+=e.name+(e.version?" (Version "+e.version+")":"")+(t-2>n?", ":n==t-2?" and ":"")});var n=o("").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return o("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(2),i(16),i(11),i(18)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=r.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});r.subModelTypes={integer:d,"float":h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new l(e.map(t.inputs,function(e){var t=r.subModelTypes[e.type]||r;return new t(e)})))},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return-1!==e.indexOf(t.get("type"))});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new o.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return-1!==e.indexOf(t,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return a.when(r.go()).then(function(e){o.resolve(new i.DatasetCollection(e))}),o}});e.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof f?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length");e.append(S.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault();var t=new n.View({id:i.model.id,version:i.model.get("version")});t.deferred.execute(function(){Galaxy.app.display(t)})})}return this.$el.append(e),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new w({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof f){var n=new b({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new w({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof f){var s=new b({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=a(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
    ','<%- name %>',"
    ",'
    '+e.content+"
    "}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(i){n=[],s=function(){var e=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),t=i.Collection.extend({model:e});return{Model:e,Collection:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},,function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){return o.Model.extend({initialize:function(){this.active={},this.last=null},execute:function(t){var i=this,n=e.uid(),s=t.length>0;this.active[n]=!0;var o=a.Deferred();o.promise().always(function(){delete i.active[n],s&&Galaxy.emit.debug("deferred::execute()",this.state().charAt(0).toUpperCase()+this.state().slice(1)+" "+n)}),a.when(this.last).always(function(){i.active[n]?(s&&Galaxy.emit.debug("deferred::execute()","Running "+n),t(o),!s&&o.resolve()):o.reject()}),this.last=o.promise()},reset:function(){Galaxy.emit.debug("deferred::execute()","Reset");for(var e in this.active)this.active[e]=!1},ready:function(){return a.isEmptyObject(this.active)}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},,,,,,,,,,,function(e,t,i){var n,s;(function(o,a){n=[i(6),i(5),i(15)],s=function(e,t){var i=o.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'
    ',a.escape(e),"
    "].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(o){n=[i(2),i(3),i(6)],s=function(e,t,i){"use strict";var n=t.Collection.extend({initialize:function(e,i){t.Collection.prototype.initialize.call(this,e,i),this.setOrder(i.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),t.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(t){t=e.clone(t)||{};var i=this;t.traditional=!0,t.data=t.data||i._buildFetchData(t);var n=this._buildFetchFilters(t);return e.isEmpty(n)||e.extend(t.data,this._fetchFiltersToAjaxData(n)),t},_buildFetchData:function(t){var i={};return this.order&&(i.order=this.order),e.defaults(e.pick(t,this._fetchParams),i)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(t){return e.clone(t.filters||{})},_fetchFiltersToAjaxData:function(t){var i={q:[],qv:[]};return e.each(t,function(e,t){void 0!==e&&""!==e&&(e===!0&&(e="True"),e===!1&&(e="False"),null===e&&(e="None"),i.q.push(t),i.qv.push(e))}),i},reset:function(e,i){return this.allFetched=!1,t.Collection.prototype.reset.call(this,e,i)},order:null,comparators:{update_time:i.buildComparator("update_time",{ascending:!1}),"update_time-asc":i.buildComparator("update_time",{ascending:!0}),create_time:i.buildComparator("create_time",{ascending:!1}),"create_time-asc":i.buildComparator("create_time",{ascending:!0})},setOrder:function(t,i){i=i||{};var n=this,s=n.comparators[t];if(e.isUndefined(s))throw new Error("unknown order: "+t);if(s!==n.comparator){n.order;return n.order=t,n.comparator=s,i.silent||n.trigger("changed-order",i),n}}}),s=n.extend({limitPerPage:500,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(t,i){var n=this;return t=n.constrainPageNum(t),n.currentPage=t,i=e.defaults(i||{},n.getPageLimitOffset(t)),n.trigger("fetching-more"),n.fetch(i).always(function(){n.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),a=n.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,n.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(t){return t=t?e.clone(t):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(e.defaults(t,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){t=e.clone(t||{});var i=this;if(!t.reset&&i.allFetched)return o.when();t.offset=t.reset?0:t.offset||i.lastFetched;var n=t.limit=t.limit||i.limitPerFetch||null;return i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(t){var s=e.isArray(t)?t.length:0;i.lastFetched+=s,(!n||n>s)&&(i.allFetched=!0,i.trigger("all-fetched",this))})},fetchAll:function(t){t=t||{};var i=this;return t=e.pick(t,"silent"),t.filters={},i.fetch(t).done(function(e){i.allFetched=!0,i.trigger("all-fetched",i)})}});return{ControlledFetchCollection:n,PaginatedCollection:s,InfinitelyScrollingCollection:a}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1))},function(e,t,i){var n,s;(function(o){n=[i(76),i(30),i(29),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var a="collections",r=e.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(e){r.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout"},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(e){var t=r.prototype._getItemViewOptions.call(this,e);return o.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return r.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var e=n.wrapTemplate(['
    ','
    ','','',s("Back to "),"<%- view.parentName %>","","
    ",'
    ','
    <%- collection.name || collection.element_identifier %>
    ','
    ','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',s("a list of dataset lists"),"<% } %>","
    ","
    ","
    "],"collection");return o.extend(o.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(12),i(32),i(77),i(66),i(22),i(6),i(5)],s=function(e,t,n,s,r,l,c){"use strict";var d=t.DatasetListItemView,h=d.extend({initialize:function(e){d.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return r({title:c(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model["delete"]()}})},_renderDetails:function(){var t=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderSecondaryActions:function(){var t=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return t.concat([this._renderRerunButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");return this.model.get("rerunnable")?r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),!function(){var t=[i(18)];(function(t){var i=new t.View({job_id:e});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,t)}()}}):void 0},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(e))return null;if(!o.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=a(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=a('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(c("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return h.prototype.templates=function(){var e=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
    ',c("An error occurred setting the metadata for this dataset"),'
    ',c("Set it manually or retry auto-detection"),"","
    ","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
    ',c("This dataset has been deleted"),'
    ',c("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
    ',c("Permanently remove it from disk"),"","<% } %>","
    ","<% } %>"],"dataset")}),t=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
    ','','',"",'","
    ","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:e,visualizations:t})}(),{DatasetListItemEdit:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(12),i(6),i(5)],s=function(e,t,i){"use strict";var n="dataset",s=t.SearchableModelMixin,l=o.Model.extend(t.LoggableMixin).extend(t.mixin(s,{_logNamespace:n,defaults:{state:e.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(t,i){this.debug(this+"(Dataset).initialize",t,i),this.get("accessible")||this.set("state",e.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/"+e+"/edit",download:"datasets/"+e+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return a.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return a.extend(e,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var t=a.contains(e.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||t},hasDetails:function(){return this.get("accessible")?this.has("annotation"):!0},hasData:function(){return this.get("file_size")>0},fetch:function(e){var t=this;return o.Model.prototype.fetch.call(this,e).always(function(){t._generateUrls()})},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},save:function(e,t){return t=t||{},t.wait=a.isUndefined(t.wait)?!0:t.wait,o.Model.prototype.save.call(this,e,t)},"delete":function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return r.when();e=e||{},e.url=this.urls.purge;var t=this,n=r.ajax(e);return n.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf(r)&&(a=r), -n.responseText=a,t.trigger("error",t,n,e,i(a),{error:a})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),c=o.Collection.extend(t.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=e.call(a,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:a})}),l.always(function(e){s.push(e),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(32),i(6),i(5)],s=function(e,t,i){"use strict";var n=e.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(e,t){n.prototype.initialize.call(this,e,t)},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemView("+e+")"}});return s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','','
    ','<%- dataset.hid %> ','<%- dataset.name %>',"
    ","
    "],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:t.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',i("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:e,warnings:s})}(),{HDAListItemView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(70),i(74),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetAssociation,a=t.HistoryContentMixin,r=s.extend(i.mixin(a,{defaults:o.extend({},s.prototype.defaults,a.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));return{HistoryDatasetAssociation:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(12),i(29),i(68),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var a=t.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:populated change:visible":function(e,t){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView;case"list:list":return i.ListOfListsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(t){a.prototype._swapNewRender.call(this,t);var i=this.model.get("populated")?e.OK:e.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDCAListItemView("+e+")"}});return r.prototype.templates=function(){var e=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'
    ',s("This collection has been hidden"),"
    ","<% } %>"],"collection")}),t=n.wrapTemplate(['
    ','','
    ','<%- collection.hid %> ','<%- collection.name %>',"
    ",'
    ',"
    "],"collection");return o.extend({},a.prototype.templates,{warnings:e,titleBar:t})}(),{HDCAListItemView:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o){n=[i(12),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return e},hide:function(e){return this.get("visible")?this.save({visible:!1},e):o.when()},unhide:function(e){return this.get("visible")?o.when():this.save({visible:!0},e)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};return{HistoryContentMixin:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(40),i(41),i(67),i(4),i(6),i(5)],s=function(e,t,i,n,s,c){"use strict";var d=o.Model.extend(s.LoggableMixin).extend(s.mixin(s.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:e.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,a.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?n.bytesToString(e,!0,2):c("(empty)")},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(e){return"nice_size"===e?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return Galaxy&&Galaxy.user?Galaxy.user.isAnonymous()||Galaxy.user.id!==this.get("user_id")?!1:!0:!1},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:l.param({keys:e.join(",")})})},refresh:function(e){e=e||{};var t=this,i=t.lastUpdateTime;this.contents.allFetched=!1;var n=0!==t.contents.currentPage?function(){return t.contents.fetchPage(0)}:function(){return t.contents.fetchUpdated(i)};return n().done(function(i,n,s){var o;try{o=new Date(s.getResponseHeader("Date"))}catch(a){}t.lastUpdateTime=o||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){function t(){n.clearUpdateTimeout(),n.updateTimeoutId=setTimeout(function(){n.refresh(e)},i)}e=e||{};var i=this.UPDATE_DELAY,n=this;if(n.id){var s=this.numOfUnfinishedShownContents();s>0?t():n._fetchContentRelatedAttributes().done(function(e){n.numOfUnfinishedJobs()>0?t():n.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?a.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?a.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):a.when()},copy:function(e,t,i){if(e=void 0!==e?e:!0,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};e&&(n.current=!0),t&&(n.name=t),i||(n.all_datasets=!1),n.view="dev-detailed";var s=this,o=a.post(this.urlRoot,n);return e?o.then(function(e){var t=new d(e);return t.setAsCurrent().done(function(){s.trigger("copied",s,e)})}):o.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=a.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),h=i.InfinitelyScrollingCollection,u=h.extend(s.LoggableMixin).extend({_logNamespace:"history",model:d,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),h.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new d(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return r.extend(h.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=h.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),r.defaults(t,i)},fetchFirst:function(e){var t=this,i=l.when();return this.currentHistoryId&&(i=h.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:r.extend(r.clone(h.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),size:s.buildComparator("size",{ascending:!1}),"size-asc":s.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return h.prototype.sort.call(this,r.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,n){var s=this,o=a.getJSON(Galaxy.root+"history/create_new_current");return o.done(function(e){s.setCurrent(new d(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});return{History:d,HistoryCollection:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(42),i(127),i(6),i(5),i(85)],s=function(e,t,i,n){"use strict";var s="list",l=o.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:e.ListItemView,collectionClass:o.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:n("This list is empty"),noneFoundMsg:n("No matching items found"),searchPlaceholder:n("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=a.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0!==e.selecting?e.selecting:!0,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(a.first(i.added),e,t):1===i.removed.length?this.removeItemView(a.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=a.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=r(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=r(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),r(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var s=r(['
    ','",'","
    "].join("")),o=i.map(function(e){var t=['
  • ',e.html,"
    • "].join("");return r(t).click(function(t){return t.preventDefault(),e.func(t)})});return s.find("ul").append(o),t.replaceWith(s),s},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){var i=t._createItemView(e);return i}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(a.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return a.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=a.extend(this._getItemViewOptions(e),{model:e}),n=new t(i);return this._setUpItemViewListeners(n),n},_destroyItemView:function(e){this.stopListening(e),this.views=a.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:a.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){a.each(this.views,function(e){e.expand()})},collapseAll:function(){a.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(-1!==s){var o=n._createItemView(e);return r(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,s),e()}]),o}},_attachView:function(e,t,i){i=a.isUndefined(i)?!0:i,t=t||0;var n=this;return n.views.splice(t,0,e),n._insertIntoListAt(t,n._renderItemView$el(e).hide()),n.trigger("view:attached",e),i?e.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")}):(e.$el.show(),n.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var n=this,s=a.find(n.views,function(t){return t.model===e});return s?(n.views=a.without(n.views,s),n.trigger("view:removed",s),r({}).queue("fx",[function(e){s.$el.fadeOut(n.fxSpeed,e)},function(e){s.remove(),n.trigger("view:removed:rendered"),n.views.length?e():n._renderEmptyMessage().fadeIn(n.fxSpeed,e)}]),s):void 0},viewFromModelId:function(e){return a.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return a.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:n>i?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(e){return e.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:a.bind(this._firstSearch,this),onsearch:a.bind(this.searchItems,this),onclear:a.bind(this.clearSearch,this)}),e},_firstSearch:function(e){return this.log("onFirstSearch",e),this.searchItems(e)},searchItems:function(e,t){if(this.log("searchItems",e,this.searchFor,t),!t&&this.searchFor===e)return this;this.searchFor=e,this.renderItems(),this.trigger("search:searching",e,this);var i=this.$("> .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,a.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,a.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){a.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,a.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return a.each(i,function(e){e.select()}),i},getSelectedViews:function(){return a.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(a.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,i,n){this.debug("_showLoadingIndicator",this.indicator,e,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new t(this.$el),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(e,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return e?this:this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var e=i.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),t=i.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:e,controls:t}}();var c=l.extend({modelCollectionKey:"contents",initialize:function(e){l.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting?e.selecting:!1,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=r(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});return c.prototype.templates=function(){var e=i.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return a.extend(a.clone(l.prototype.templates),{controls:e})}(),{ListPanel:l,ModelListPanel:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(6),i(5)],s=function(e,t){var i=o.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(e){this.listenTo(this.model,"change:tags",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_template:function(){return['",''].join("")},tagsToCSV:function(){var e=this.model.get("tags");return!a.isArray(e)||a.isEmpty(e)?"":e.map(function(e){return a.escape(e)}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.user.get("tags_used")},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){e.model.save({tags:t.val},{silent:!0}),t.added&&e._addNewTagToTagsUsed(t.added.text+"")})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");a.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(5)],s=function(e){"use strict";function t(t,i,n){return Galaxy.modal.show({title:i,body:t,closing_events:!0,buttons:{Ok:function(){Galaxy.modal.hide()}}}),Galaxy.modal.$el.addClass("error-modal"),n&&(Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove(),o("
    ").addClass("error-details").hide().appendTo(Galaxy.modal.$(".modal-content")).append([o("

    ").text(h),o("

    ").text(JSON.stringify(n,null,"  "))]),o('").appendTo(Galaxy.modal.$(".buttons")).click(function(){Galaxy.modal.$(".error-details").toggle()})),Galaxy.modal}function i(i,n,s){if(i){if(i=e(i),n=e(n)||e("Error:"),window.Galaxy&&Galaxy.modal)return t(i,n,s);alert(n+"\n\n"+i),console.log("error details:",JSON.stringify(s))}}function n(){return i(e("You appear to be offline. Please check your connection and try again."),e("Offline?"))}function s(){return i(e("Galaxy is currently unreachable. Please try again in a few minutes.")+" "+c,e("Cannot connect to Galaxy"))}function r(t,n,s,o,a){o=o||d,o+=" "+c,a=a||e("An error occurred");var r=l(t,n,s);return i(o,a,r)}function l(e,t,i){return{raven:a.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:a.result(Galaxy.config,"version_major"),xhr:a.omit(t,a.functions(t)),options:a.omit(i,"xhr"),url:a.result(Galaxy.lastAjax,"url"),data:a.result(Galaxy.lastAjax,"data"),model:a.result(e,"toJSON",e+""),user:a.omit(a.result(Galaxy.user,"toJSON"),"email")}}var c=e("Please contact a Galaxy administrator if the problem persists."),d=e("An error occurred while updating information with the server."),h=e("The following information can assist the developers in finding the source of the error:");return{errorModal:i,offlineErrorModal:n,badGatewayErrorModal:s,ajaxErrorModal:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(i,o,a,r){n=[],s=function(){var e=i.View.extend({initialize:function(e,t){this.$button=e,this.$button.length||(this.$button=o("
    ")),this.options=t||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(e){return o(".popmenu-wrapper").remove(),i._renderAndShow(e),!1})},_renderAndShow:function(e){this.render(),this.$el.appendTo("body").css(this._getShownPosition(e)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var e=this;this.$el.find("li").each(function(t,i){var n=e.options[t];n.func&&o(this).children("a.popupmenu-option").click(function(t){n.func.call(e,t,n),t.preventDefault()})})}return this},template:function(e,t){return['"].join("")},_templateOptions:function(e){return e.length?a.map(e,function(e){if(e.divider)return'
  • ';if(e.header)return['
  • ',e.html,"
    • "].join("");var t=e.href||"javascript:void(0);",i=e.target?' target="'+e.target+'"':"",n=e.checked?'':"";return['
  • ",n,e.html,"
    • "].join("")}).join(""):"
  • (no options)
    • "},_getShownPosition:function(e){var t=this.$el.width(),i=e.pageX-t/2;return i=Math.min(i,o(document).scrollLeft()+o(window).width()-t-5),i=Math.max(i,o(document).scrollLeft()+5),{top:e.pageY,left:i}},_setUpCloseBehavior:function(){function e(e){if(o(document).off("click.close_popup"),window&&window.parent!==window)try{o(window.parent.document).off("click.close_popup")}catch(i){}else try{o("iframe#galaxy_main").contents().off("click.close_popup")}catch(i){}t.remove()}var t=this;if(o("html").one("click.close_popup",e),window&&window.parent!==window)try{o(window.parent.document).find("html").one("click.close_popup",e)}catch(i){}else try{o("iframe#galaxy_main").contents().one("click.close_popup",e)}catch(i){}},addItem:function(e,t){return t=t>=0?t:this.options.length,this.options.splice(t,0,e),this},removeItem:function(e){return e>=0&&this.options.splice(e,1),this},findIndexByHtml:function(e){for(var t=0;t0){this.$(".upload-ftp-content").html(a(this._templateTable()));var i=0;for(index in t)this.rows.push(this._add(t[index])),i+=t[index].size;if(this.$(".upload-ftp-number").html(t.length+" files"),this.$(".upload-ftp-disk").html(e.bytesToString(i,!0)),this.collection){var n=this;this.$("._has_collection").show(),this.$select_all=this.$(".upload-selectall").addClass(this.options.class_add),this.$select_all.on("click",function(){var e=n.$select_all.hasClass(n.options.class_add);for(index in t){var i=t[index],s=n._find(i);(!s&&e||s&&!e)&&n.rows[index].trigger("click")}}),this._refresh()}}else this.$(".upload-ftp-content").html(a(this._templateInfo()));this.$(".upload-ftp-wait").hide()},_add:function(e){var t=this,i=a(this._templateRow(e)),n=i.find(".icon");return this.$("tbody").append(i),this.collection?(n.addClass(this._find(e)?this.options.class_remove:this.options.class_add),i.on("click",function(){var i=t._find(e);n.removeClass(),i?(t.options.onremove(i),n.addClass(t.options.class_add)):(t.options.onadd(e),n.addClass(t.options.class_remove)),t._refresh()})):i.on("click",function(){t.options.onchange(e)}),i},_refresh:function(){var e=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),0==e.length?this.$select_all.addClass(this.options.class_add):this.$select_all.addClass(e.length==this.rows.length?this.options.class_remove:this.options.class_partial)},_find:function(e){var t=this.collection.findWhere({file_path:e.path,file_mode:"ftp",enabled:!0});return t&&t.get("id")},_templateRow:function(t){return'
    '+t.path+''+e.bytesToString(t.size)+''+t.ctime+""},_templateTable:function(){return'Available files:   
    NameSizeCreated
    '},_templateInfo:function(){return'
    Your FTP directory does not contain any files.
    '},_template:function(){return'