Source code for planemo.lint

"""Utilities to help linting various targets."""

import os
from urllib.request import urlopen

import requests
from galaxy.tool_util.lint import LintContext

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

[docs] 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( level=report_level, fail_level=fail_level, skip_types=skip_types, ) 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(level=lint_args["level"], skip_types=lint_args["skip_types"]) return lint_args, lint_ctx
[docs] 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
[docs] 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": dois.append(citation.text) 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") return 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") return url = f"{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) else:"%s is a valid DOI" % publication_id) elif r.status_code == 404: lint_ctx.error("%s is not a valid DOI" % publication_id) else: lint_ctx.warn("dx.doi returned unexpected status code %d" % r.status_code)
[docs] 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) lint_ctx.error(msg) else:"File validates against XML schema.")
[docs] 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": "*/*"} else: headers = None r = None try: r = requests.get(url, headers=headers, stream=True) r.raise_for_status() next(r.iter_content(1000)) except Exception as e: if r is not None and r.status_code == 429: # too many requests pass if r is not None and r.status_code in [403, 503] and "cloudflare" in r.text: # CloudFlare protection block pass else: is_valid = False lint_ctx.error(f"Error '{e}' accessing {url}") else: try: with urlopen(url) as handle: except Exception as e: is_valid = False lint_ctx.error(f"Error '{e}' accessing {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__ = ( "build_lint_args", "handle_lint_complete", "lint_dois", "lint_urls", "lint_xsd", )