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Polish help and error messages related to optional dependency on galaxy-lib. #459

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Merged
merged 1 commit into from
Jul 9, 2017
Merged

Polish help and error messages related to optional dependency on galaxy-lib. #459

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25 changes: 16 additions & 9 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
relocateOutputs, scandeps, shortname, use_custom_schema,
use_standard_schema)
from .resolver import ga4gh_tool_registries, tool_resolver
from .software_requirements import DependenciesConfiguration, get_container_from_software_requirements
from .software_requirements import DependenciesConfiguration, get_container_from_software_requirements, SOFTWARE_REQUIREMENTS_ENABLED
from .stdfsaccess import StdFsAccess
from .update import ALLUPDATES, UPDATES

Expand Down Expand Up @@ -153,14 +153,21 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
exgroup.add_argument("--debug", action="store_true", help="Print even more logging")

# help="Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=argparse.SUPPRESS)
# help="Defaut root directory used by dependency resolvers configuration."
parser.add_argument("--beta-dependencies-directory", default=None, help=argparse.SUPPRESS)
# help="Use biocontainers for tools without an explicitly annotated Docker container."
parser.add_argument("--beta-use-biocontainers", default=None, help=argparse.SUPPRESS, action="store_true")
# help="Short cut to use Conda to resolve 'SoftwareRequirement' packages."
parser.add_argument("--beta-conda-dependencies", default=None, help=argparse.SUPPRESS, action="store_true")
dependency_resolvers_configuration_help = argparse.SUPPRESS
dependencies_directory_help = argparse.SUPPRESS
use_biocontainers_help = argparse.SUPPRESS
conda_dependencies = argparse.SUPPRESS

if SOFTWARE_REQUIREMENTS_ENABLED:
dependency_resolvers_configuration_help = "Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system."
dependencies_directory_help = "Defaut root directory used by dependency resolvers configuration."
use_biocontainers_help = "Use biocontainers for tools without an explicitly annotated Docker container."
conda_dependencies = "Short cut to use Conda to resolve 'SoftwareRequirement' packages."

parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=dependency_resolvers_configuration_help)
parser.add_argument("--beta-dependencies-directory", default=None, help=dependencies_directory_help)
parser.add_argument("--beta-use-biocontainers", default=None, help=use_biocontainers_help, action="store_true")
parser.add_argument("--beta-conda-dependencies", default=None, help=conda_dependencies, action="store_true")

parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")

Expand Down
17 changes: 10 additions & 7 deletions cwltool/software_requirements.py
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Expand Up @@ -22,6 +22,7 @@

from .utils import get_feature

SOFTWARE_REQUIREMENTS_ENABLED = deps is not None

COMMAND_WITH_DEPENDENCIES_TEMPLATE = string.Template("""#!/bin/bash
$handle_dependencies
Expand Down Expand Up @@ -60,8 +61,7 @@ def config_dict(self):

def build_job_script(self, builder, command):
# type: (Any, List[str]) -> Text
if deps is None:
raise Exception("galaxy-lib not found")
ensure_galaxy_lib_available()
tool_dependency_manager = deps.build_dependency_manager(self) # type: deps.DependencyManager
dependencies = get_dependencies(builder)
handle_dependencies = "" # str
Expand Down Expand Up @@ -99,11 +99,8 @@ def get_dependencies(builder):

def get_container_from_software_requirements(args, builder):
if args.beta_use_biocontainers:
try:
from galaxy.tools.deps.containers import ContainerRegistry, AppInfo, ToolInfo, DOCKER_CONTAINER_TYPE
except ImportError:
raise Exception("Optional requirement galaxy-lib not found, it is required for this configuration.")

ensure_galaxy_lib_available()
from galaxy.tools.deps.containers import ContainerRegistry, AppInfo, ToolInfo, DOCKER_CONTAINER_TYPE
app_info = AppInfo(
involucro_auto_init=True,
enable_beta_mulled_containers=True,
Expand All @@ -117,3 +114,9 @@ def get_container_from_software_requirements(args, builder):
return container_description.identifier

return None


def ensure_galaxy_lib_available():
# type: () -> None
if not SOFTWARE_REQUIREMENTS_ENABLED:
raise Exception("Optional Python library galaxy-lib not available, it is required for this configuration.")