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Source code for galaxy.tool_util.parser.cwl

import logging
import math
import os

from galaxy.tool_util.cwl.parser import tool_proxy
from galaxy.tool_util.deps import requirements
from .interface import (
    PageSource,
    PagesSource,
    ToolSource,
)
from .output_actions import ToolOutputActionGroup
from .output_objects import ToolOutput
from .stdio import (
    StdioErrorLevel,
    ToolStdioExitCode,
)
from .yaml import YamlInputSource

log = logging.getLogger(__name__)


[docs]class CwlToolSource(ToolSource): language = "yaml"
[docs] def __init__(self, tool_file, strict_cwl_validation=True, tool_id=None, tool_proxy=None): self._cwl_tool_file = tool_file self._id = tool_id or os.path.splitext(os.path.basename(tool_file))[0] self._tool_proxy = tool_proxy self._source_path = tool_file self._strict_cwl_validation = strict_cwl_validation
@property def source_path(self): return self._source_path @property def tool_proxy(self): if self._tool_proxy is None: self._tool_proxy = tool_proxy(self._source_path, strict_cwl_validation=self._strict_cwl_validation) return self._tool_proxy
[docs] def parse_tool_type(self): return "cwl"
[docs] def parse_id(self): return self._id
[docs] def parse_name(self): return self.tool_proxy.label() or self.parse_id()
[docs] def parse_command(self): return "$__cwl_command"
[docs] def parse_environment_variables(self): environment_variables = [] # TODO: Is this even possible from here, should instead this be moved # into the job. # for environment_variable_el in environment_variables_el.findall("environment_variable"): # definition = { # "name": environment_variable_el.get("name"), # "template": environment_variable_el.text, # } # environment_variables.append( # definition # ) return environment_variables
[docs] def parse_edam_operations(self): return []
[docs] def parse_edam_topics(self): return []
[docs] def parse_help(self): return self.tool_proxy.doc()
[docs] def parse_sanitize(self): return False
[docs] def parse_strict_shell(self): return True
[docs] def parse_stdio(self): # TODO: remove duplication with YAML # New format - starting out just using exit code. exit_code_lower = ToolStdioExitCode() exit_code_lower.range_start = -math.inf exit_code_lower.range_end = -1 exit_code_lower.error_level = StdioErrorLevel.FATAL exit_code_high = ToolStdioExitCode() exit_code_high.range_start = 1 exit_code_high.range_end = math.inf exit_code_lower.error_level = StdioErrorLevel.FATAL return [exit_code_lower, exit_code_high], []
[docs] def parse_interpreter(self): return None
[docs] def parse_version(self): return "0.0.1"
[docs] def parse_description(self): return self.tool_proxy.description()
[docs] def parse_interactivetool(self): return []
[docs] def parse_input_pages(self): page_source = CwlPageSource(self.tool_proxy) return PagesSource([page_source])
[docs] def parse_outputs(self, tool): output_instances = self.tool_proxy.output_instances() outputs = {} output_defs = [] for output_instance in output_instances: output_defs.append(self._parse_output(tool, output_instance)) # TODO: parse outputs collections for output_def in output_defs: outputs[output_def.name] = output_def return outputs, {}
def _parse_output(self, tool, output_instance): name = output_instance.name # TODO: handle filters, actions, change_format output = ToolOutput(name) if "File" in output_instance.output_data_type: output.format = "_sniff_" else: output.format = "expression.json" output.change_format = [] output.format_source = None output.metadata_source = "" output.parent = None output.label = None output.count = None output.filters = [] output.tool = tool output.hidden = "" output.dataset_collector_descriptions = [] output.actions = ToolOutputActionGroup(output, None) return output
[docs] def parse_requirements_and_containers(self): containers = [] docker_identifier = self.tool_proxy.docker_identifier() if docker_identifier: containers.append({"type": "docker", "identifier": docker_identifier}) software_requirements = self.tool_proxy.software_requirements() resource_requirements = self.tool_proxy.resource_requirements() return requirements.parse_requirements_from_lists( software_requirements=[{"name": r[0], "version": r[1], "type": "package"} for r in software_requirements], containers=containers, resource_requirements=resource_requirements, )
[docs] def parse_profile(self): return "16.04"
[docs] def parse_license(self): return None
[docs] def parse_python_template_version(self): return "3.5"
class CwlPageSource(PageSource): def __init__(self, tool_proxy): cwl_instances = tool_proxy.input_instances() self._input_list = list(map(self._to_input_source, cwl_instances)) def _to_input_source(self, input_instance): as_dict = input_instance.to_dict() return YamlInputSource(as_dict) def parse_input_sources(self): return self._input_list __all__ = ( "CwlToolSource", "tool_proxy", )