Source code for galaxy.tool_util.deps.conda_compat

"""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 os
from import Hashable

import yaml

    from conda_build.metadata import MetaData
except ImportError:
    MetaData = None

    from anaconda_verify.recipe import (
except ImportError:
    render_jinja2 = None
    parse = None

class _Memoized:
    def __init__(self, func):
        self.func = func
        self.cache = {}

    def __call__(self, *args):
        if not isinstance(args, 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]
            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."""
        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)

def yamlize(data):
    res = yaml.safe_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

[docs]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 = if b"{{" in data: data = render_jinja2(recipe_dir) meta = parse(data, None) return meta
class _MetaData: 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", )