Unverified Commit afe9ddb4 authored by mvdbeek's avatar mvdbeek
Browse files

Use resource consistently

parent fed7f6ab

lib/galaxy/tool_util/cwl/parser.py

+2 −17
Original line number Diff line number Diff line
@@ -459,23 +459,8 @@ class CommandLineToolProxy(ToolProxy): 
                    requirements.append((package["package"], first_version))

        return requirements



    def resource_requirements(self) -> List[Dict[str, Union[int, float, str]]]:

        cwl_to_galaxy = {

            "coresMin": "cores_min",

            "coresMax": "cores_max",

            "ramMin": "ram_min",

            "ramMax": "ram_max",

            "tmpdirMin": "tmpdir_min",

            "tmpdirMax": "tmpdir_max",

        }

        cwl_key_set = set(cwl_to_galaxy.keys())

        rr = []

        for r in self._tool.tool.get("requirements", []):

            if r["class"] == "ResourceRequirement":

                for key in cwl_key_set.intersection(set(r.keys())):

                    galaxy_key = cwl_to_galaxy[key]

                    rr.append({galaxy_key: r[key]})

        return rr

    def resource_requirements(self):

        return [r for r in self.requirements if r["class"] == "ResourceRequirement"]



    @property

    def requirements(self):

lib/galaxy/tool_util/deps/requirements.py

+30 −4
Original line number Diff line number Diff line 
import copy

from typing import (

    Callable,

    cast,

    Dict,

    List,

    Optional,

    Union,

)
@@ -262,20 +264,44 @@ class ResourceRequirement: 
        return float(self.value_or_expression)





def resource_requirements_from_list(requirements) -> List[ResourceRequirement]:

    cwl_to_galaxy = {

        "coresMin": "cores_min",

        "coresMax": "cores_max",

        "ramMin": "ram_min",

        "ramMax": "ram_max",

        "tmpdirMin": "tmpdir_min",

        "tmpdirMax": "tmpdir_max",

    }

    rr = []

    for r in requirements:

        if r.get("class") == "ResourceRequirement":

            valid_key_set = set(cwl_to_galaxy.keys())

        elif r.get("type") == "resource":

            valid_key_set = set(cwl_to_galaxy.values())

        else:

            continue

        for key in valid_key_set.intersection(set(r.keys())):

            value = r[key]

            key = cast(ResourceType, cwl_to_galaxy.get(key, key))

            rr.append(ResourceRequirement(value_or_expression=value, resource_type=key))

    return rr





def parse_requirements_from_dict(root_dict):

    requirements = root_dict.get("requirements", [])

    resource_requirements = root_dict.get("resource_requirements", [])

    resource_requirements = resource_requirements_from_list(requirements)

    containers = root_dict.get("containers", [])

    return (

        ToolRequirements.from_list(requirements),

        [ContainerDescription.from_dict(c) for c in containers],

        [ResourceRequirement.from_dict(r) for r in resource_requirements],

        resource_requirements,

    )





def parse_requirements_from_xml(xml_root, parse_resources=False):

    """

    Parses requirement, containers and optionally resource_requirements from Xml tree.

    Parses requirements, containers and optionally resource requirements from Xml tree.



    >>> from galaxy.util import parse_xml_string

    >>> def load_requirements(contents, parse_resources=False):
@@ -317,7 +343,7 @@ def parse_requirements_from_xml(xml_root, parse_resources=False): 


    containers = [container_from_element(c) for c in container_elems]

    if parse_resources:

        resource_elems = requirements_elem.findall("resource_requirement") if requirements_elem else []

        resource_elems = requirements_elem.findall("resource") if requirements_elem else []

        resources = [resource_from_element(r) for r in resource_elems]

        return requirements, containers, resources

test/unit/tool_util/test_parsing.py

+3 −3
Original line number Diff line number Diff line
@@ -30,7 +30,7 @@ TOOL_XML_1 = """ 
    <requirements>

        <container type="docker">mycool/bwa</container>

        <requirement type="package" version="1.0">bwa</requirement>

        <resource_requirement type="cores_min">1</resource_requirement>

        <resource type="cores_min">1</resource>

    </requirements>

    <outputs>

        <data name="out1" format="bam" from_work_dir="out1.bam" />
@@ -119,12 +119,12 @@ command: "bowtie_wrapper.pl --map-the-stuff" 
interpreter: "perl"

runtime_version:

  command: "bowtie --version"

resource_requirements:

  - cores_min: 1

requirements:

  - type: package

    name: bwa

    version: 1.0.1

  - type: resource

    cores_min: 1

containers:

  - type: docker

    identifier: "awesome/bowtie"