view env/lib/python3.9/site-packages/planemo/ @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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"""Utilities to help linting various targets."""
from __future__ import absolute_import

import os

import requests
from galaxy.tool_util.lint import LintContext
from six.moves.urllib.request import urlopen

from import error
from planemo.shed import find_urls_for_xml
from planemo.xml import validation

def build_lint_args(ctx, **kwds):
    """Handle common report, error, and skip linting arguments."""
    report_level = kwds.get("report_level", "all")
    fail_level = kwds.get("fail_level", "warn")
    skip = kwds.get("skip", None)
    if skip is None:
        skip = ctx.global_config.get("lint_skip", "")
        if isinstance(skip, list):
            skip = ",".join(skip)

    skip_types = [s.strip() for s in skip.split(",")]
    lint_args = dict(
    return lint_args

def setup_lint(ctx, **kwds):
    """Prepare lint_args and lint_ctx to begin linting a target."""
    lint_args = kwds.get("lint_args", None) or build_lint_args(ctx, **kwds)
    lint_ctx = LintContext(lint_args["level"])
    return lint_args, lint_ctx

def handle_lint_complete(lint_ctx, lint_args, failed=False):
    """Complete linting of a target and decide exit code."""
    if not failed:
        failed = lint_ctx.failed(lint_args["fail_level"])
    if failed:
        error("Failed linting")
    return 1 if failed else 0

def lint_dois(tool_xml, lint_ctx):
    """Find referenced DOIs and check they have valid with"""
    dois = find_dois_for_xml(tool_xml)
    for publication in dois:
        is_doi(publication, lint_ctx)

def find_dois_for_xml(tool_xml):
    dois = []
    for element in tool_xml.getroot().findall("citations"):
        for citation in list(element):
            if citation.tag == 'citation' and citation.attrib.get('type', '') == 'doi':
    return dois

def is_doi(publication_id, lint_ctx):
    """Check if dx.doi knows about the ``publication_id``."""
    base_url = ""
    if publication_id is None:
        lint_ctx.error('Empty DOI citation')
    publication_id = publication_id.strip()
    doiless_publication_id = publication_id.split("doi:", 1)[-1]
    if not doiless_publication_id:
        lint_ctx.error('Empty DOI citation')
    url = "%s/%s" % (base_url, doiless_publication_id)
    r = requests.get(url)
    if r.status_code == 200:
        if publication_id != doiless_publication_id:
            lint_ctx.error("%s is valid, but Galaxy expects DOI without 'doi:' prefix" % publication_id)
  "%s is a valid DOI" % publication_id)
    elif r.status_code == 404:
        lint_ctx.error("%s is not a valid DOI" % publication_id)
        lint_ctx.warn("dx.doi returned unexpected status code %d" % r.status_code)

def lint_xsd(lint_ctx, schema_path, path):
    """Lint XML at specified path with supplied schema."""
    name = lint_ctx.object_name or os.path.basename(path)
    validator = validation.get_validator(require=True)
    validation_result = validator.validate(schema_path, path)
    if not validation_result.passed:
        msg = "Invalid XML found in file: %s. Errors [%s]"
        msg = msg % (name, validation_result.output)
    else:"File validates against XML schema.")

def lint_urls(root, lint_ctx):
    """Find referenced URLs and verify they are valid."""
    urls, docs = find_urls_for_xml(root)

    # This is from Google Chome on macOS, current at time of writing:
    BROWSER_USER_AGENT = "Mozilla/5.0 (Macintosh; Intel Mac OS X 11_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/87.0.4280.141 Safari/537.36"

    def validate_url(url, lint_ctx, user_agent=None):
        is_valid = True
        if url.startswith('http://') or url.startswith('https://'):
            if user_agent:
                headers = {"User-Agent": user_agent, 'Accept': '*/*'}
                headers = None
            r = None
                r = requests.get(url, headers=headers, stream=True)
            except Exception as e:
                if r is not None and r.status_code == 429:
                    # too many requests
                if r is not None and r.status_code == 403 and 'cloudflare' in r.text:
                    # CloudFlare protection block
                    is_valid = False
                    lint_ctx.error("Error '%s' accessing %s" % (e, url))
                with urlopen(url) as handle:
            except Exception as e:
                is_valid = False
                lint_ctx.error("Error '%s' accessing %s" % (e, url))
        if is_valid:
  "URL OK %s" % url)

    for url in urls:
        validate_url(url, lint_ctx)
    for url in docs:
        validate_url(url, lint_ctx, BROWSER_USER_AGENT)

__all__ = (