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Merge branch 'release_20.09' into release_21.01

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This commit is contained in:
Nicola Soranzo
2021-01-20 18:15:49 +00:00
parent da0d41f0dd a271d2419c
commit 72c08ccaad
6 changed files with 61 additions and 42 deletions
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client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue
+3 -3
View File
@@ -46,7 +46,7 @@
from History</a
>
<a
v-if="user_library_import_dir"
v-if="user_library_import_dir_available"
class="dropdown-item cursor-pointer"
@click="addDatasets('userdir')"
>
@@ -203,7 +203,7 @@ export default {
data() {
return {
is_admin: false,
user_library_import_dir: false,
user_library_import_dir_available: false,
library_import_dir: false,
allow_library_path_paste: false,
list_genomes: [],
@@ -225,7 +225,7 @@ export default {
const Galaxy = getGalaxyInstance();
this.services = new Services();
this.is_admin = Galaxy.user.attributes.is_admin;
this.user_library_import_dir = Galaxy.config.user_library_import_dir;
this.user_library_import_dir_available = Galaxy.config.user_library_import_dir_available;
this.library_import_dir = Galaxy.config.library_import_dir;
this.allow_library_path_paste = Galaxy.config.allow_library_path_paste;
client/src/components/LibraryFolder/TopToolbar/add-datasets.js
+1
View File
@@ -411,6 +411,7 @@ var AddDatasets = Backbone.View.extend({
if (typeof response.responseJSON !== "undefined") {
if (response.responseJSON.err_code === 404001) {
Toast.warning(response.responseJSON.err_msg);
getGalaxyInstance().modal.hide();
} else {
Toast.error(response.responseJSON.err_msg);
}
lib/galaxy/managers/configuration.py
+1
View File
@@ -108,6 +108,7 @@ class ConfigSerializer(base.ModelSerializer):
'file_sources_configured' : lambda config, key, **context: self.app.file_sources.custom_sources_configured,
'upload_from_form_button' : _use_config,
'release_doc_base_url' : _use_config,
'user_library_import_dir_available' : lambda config, key, **context: bool(config.get('user_library_import_dir')),
}
lib/galaxy/tool_util/deps/container_resolvers/mulled.py
+49 -32
View File
@@ -6,6 +6,7 @@ import subprocess
from typing import NamedTuple, Optional
from galaxy.util import (
safe_makedirs,
string_as_bool,
unicodify,
which,
@@ -335,37 +336,49 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
return name
class DockerContainerResolver(ContainerResolver):
class CliContainerResolver(ContainerResolver):
container_type = 'docker'
cli = 'docker'
def __init__(self, *args, **kwargs):
self._docker_cli_available = bool(which('docker'))
self._cli_available = bool(which(self.cli))
super().__init__(*args, **kwargs)
@property
def docker_cli_available(self):
return self._docker_cli_available
def cli_available(self):
return self._cli_available
@docker_cli_available.setter
def docker_cli_available(self, value):
@cli_available.setter
def cli_available(self, value):
if not value:
log.info('Docker CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes.')
self._docker_cli_available = value
log.info('{} CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes.'.format(self.cli))
self._cli_available = value
class CachedMulledDockerContainerResolver(DockerContainerResolver):
class SingularityCliContainerResolver(CliContainerResolver):
container_type = 'singularity'
cli = 'singularity'
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.cache_directory = kwargs.get("cache_directory", os.path.join(kwargs['app_info'].container_image_cache_path, "singularity", "mulled"))
safe_makedirs(self.cache_directory)
class CachedMulledDockerContainerResolver(CliContainerResolver):
resolver_type = "cached_mulled"
shell = '/bin/bash'
def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", **kwds):
super().__init__(app_info)
super().__init__(app_info=app_info, **kwds)
self.namespace = namespace
self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info, **kwds):
if not self.docker_cli_available or tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
if not self.cli_available or tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
return None
targets = mulled_targets(tool_info)
@@ -376,15 +389,13 @@ class CachedMulledDockerContainerResolver(DockerContainerResolver):
return "CachedMulledDockerContainerResolver[namespace=%s]" % self.namespace
class CachedMulledSingularityContainerResolver(ContainerResolver):
class CachedMulledSingularityContainerResolver(SingularityCliContainerResolver):
resolver_type = "cached_mulled_singularity"
container_type = "singularity"
shell = '/bin/bash'
def __init__(self, app_info=None, hash_func="v2", **kwds):
super().__init__(app_info)
self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
super().__init__(app_info=app_info, **kwds)
self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info, **kwds):
@@ -398,7 +409,7 @@ class CachedMulledSingularityContainerResolver(ContainerResolver):
return "CachedMulledSingularityContainerResolver[cache_directory=%s]" % self.cache_directory
class MulledDockerContainerResolver(DockerContainerResolver):
class MulledDockerContainerResolver(CliContainerResolver):
"""Look for mulled images matching tool dependencies."""
resolver_type = "mulled"
@@ -406,7 +417,7 @@ class MulledDockerContainerResolver(DockerContainerResolver):
protocol: Optional[str] = None
def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
super().__init__(app_info)
super().__init__(app_info=app_info, **kwds)
self.namespace = namespace
self.hash_func = hash_func
self.auto_install = string_as_bool(auto_install)
@@ -421,10 +432,14 @@ class MulledDockerContainerResolver(DockerContainerResolver):
return None
def pull(self, container):
if self.docker_cli_available:
if self.cli_available:
command = container.build_pull_command()
shell(command)
@property
def can_list_containers(self):
return self.cli_available
def resolve(self, enabled_container_types, tool_info, install=False, session=None, **kwds):
resolution_cache = kwds.get("resolution_cache")
if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
@@ -444,7 +459,7 @@ class MulledDockerContainerResolver(DockerContainerResolver):
type=self.container_type,
shell=self.shell,
)
if self.docker_cli_available:
if self.can_list_containers:
if install and not self.cached_container_description(
targets,
namespace=self.namespace,
@@ -468,22 +483,20 @@ class MulledDockerContainerResolver(DockerContainerResolver):
namespace=self.namespace,
hash_func=self.hash_func,
resolution_cache=resolution_cache,
)
) or container_description
return container_description
def __str__(self):
return "MulledDockerContainerResolver[namespace=%s]" % self.namespace
class MulledSingularityContainerResolver(MulledDockerContainerResolver):
class MulledSingularityContainerResolver(SingularityCliContainerResolver, MulledDockerContainerResolver):
resolver_type = "mulled_singularity"
container_type = "singularity"
protocol = 'docker://'
def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
super().__init__(app_info)
self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
super().__init__(app_info=app_info, **kwds)
self.namespace = namespace
self.hash_func = hash_func
self.auto_install = string_as_bool(auto_install)
@@ -493,15 +506,21 @@ class MulledSingularityContainerResolver(MulledDockerContainerResolver):
cache_directory=self.cache_directory,
hash_func=hash_func)
@property
def can_list_containers(self):
# Only needs access to path, doesn't require CLI
return True
def pull(self, container):
cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory, namespace=self.namespace)
shell(cmds=cmds)
if self.cli_available:
cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory, namespace=self.namespace)
shell(cmds=cmds)
def __str__(self):
return "MulledSingularityContainerResolver[namespace=%s]" % self.namespace
class BuildMulledDockerContainerResolver(DockerContainerResolver):
class BuildMulledDockerContainerResolver(CliContainerResolver):
"""Build for Docker mulled images matching tool dependencies."""
resolver_type = "build_mulled"
@@ -509,7 +528,7 @@ class BuildMulledDockerContainerResolver(DockerContainerResolver):
builds_on_resolution = True
def __init__(self, app_info=None, namespace="local", hash_func="v2", auto_install=True, **kwds):
super().__init__(app_info)
super().__init__(app_info=app_info, **kwds)
self._involucro_context_kwds = {
'involucro_bin': self._get_config_option("involucro_path", None)
}
@@ -548,20 +567,18 @@ class BuildMulledDockerContainerResolver(DockerContainerResolver):
return "BuildDockerContainerResolver[namespace=%s]" % self.namespace
class BuildMulledSingularityContainerResolver(ContainerResolver):
class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
"""Build for Singularity mulled images matching tool dependencies."""
resolver_type = "build_mulled_singularity"
container_type = "singularity"
shell = '/bin/bash'
builds_on_resolution = True
def __init__(self, app_info=None, hash_func="v2", auto_install=True, **kwds):
super().__init__(app_info)
super().__init__(app_info=app_info, **kwds)
self._involucro_context_kwds = {
'involucro_bin': self._get_config_option("involucro_path", None)
}
self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
self.hash_func = hash_func
self.auto_install = string_as_bool(auto_install)
self._mulled_kwds = {
lib/galaxy/tool_util/deps/containers.py
+1 -1
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@@ -226,7 +226,7 @@ class ContainerRegistry:
# BuildMulledDockerContainerResolver and BuildMulledSingularityContainerResolver both need the docker daemon to build images.
# If docker is not available, we don't load them.
build_mulled_docker_container_resolver = BuildMulledDockerContainerResolver(self.app_info)
if build_mulled_docker_container_resolver.docker_cli_available:
if build_mulled_docker_container_resolver.cli_available:
default_resolvers.extend([
build_mulled_docker_container_resolver,
BuildMulledSingularityContainerResolver(self.app_info),
test/unit/tool_util/test_container_resolution.py
+6 -6
View File
@@ -11,26 +11,26 @@ from galaxy.tool_util.deps.requirements import ToolRequirement
def test_docker_container_resolver_detects_docker_cli_absent(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
resolver = CachedMulledDockerContainerResolver()
assert resolver.docker_cli_available is False
assert resolver._cli_available is False
def test_docker_container_resolver_detects_docker_cli(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled', return_value='/bin/docker')
resolver = CachedMulledDockerContainerResolver()
assert resolver.docker_cli_available
assert resolver.cli_available
def test_cached_docker_container_docker_cli_absent_resolve(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
resolver = CachedMulledDockerContainerResolver()
assert resolver.docker_cli_available is False
assert resolver.cli_available is False
assert resolver.resolve(enabled_container_types=[], tool_info={}) is None
def test_docker_container_docker_cli_absent_resolve(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
resolver = MulledDockerContainerResolver()
assert resolver.docker_cli_available is False
assert resolver.cli_available is False
requirement = ToolRequirement(name="samtools", version="1.10", type="package")
tool_info = ToolInfo(requirements=[requirement])
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
@@ -42,12 +42,12 @@ def test_docker_container_docker_cli_absent_resolve(mocker):
def test_docker_container_docker_cli_exception_resolve(mocker):
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value='/bin/docker')
resolver = MulledDockerContainerResolver()
assert resolver.docker_cli_available is True
assert resolver.cli_available is True
requirement = ToolRequirement(name="samtools", version="1.10", type="package")
tool_info = ToolInfo(requirements=[requirement])
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.docker_cached_container_description', side_effect=CalledProcessError(1, 'bla'))
container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info, install=True)
assert resolver.docker_cli_available is True
assert resolver.cli_available is True
assert container_description.type == 'docker'
assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'