Today's sync bug #970
Description
$ nf-core --log-file sync_log_dualrnaseq.txt sync nf-core/dualrnaseq --from-branch dev --pull-request --username nf-core-bot --repository nf-core/dualrnaseq
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nf-core/tools version 1.13.3
INFO Pipeline directory: sync.py:86
/home/runner/work/tools/tools/nf-core/dualrnaseq
INFO Using branch 'dev' to fetch workflow variables sync.py:88
INFO Will attempt to automatically create a pull request sync.py:90
INFO Original pipeline repository branch is 'dev' sync.py:142
INFO Deleting all files in 'TEMPLATE' branch sync.py:198
INFO Making a new template pipeline using pipeline variables sync.py:216
INFO Committed changes to 'TEMPLATE' branch sync.py:242
INFO Pushing TEMPLATE branch to remote: 'dualrnaseq' sync.py:252
INFO Checking out merge base branch sync.py:280
'nf-core-template-merge-1.13.3'
INFO Pushing 'nf-core-template-merge-1.13.3' branch to remote sync.py:288
INFO Submitting a pull request via the GitHub API sync.py:301
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /opt/hostedtoolcache/Python/3.8.8/x64/bin/nf-core:8 in <module> │
│ │
│ 7 │ sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) │
│ ❱ 8 │ sys.exit(run_nf_core()) │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/nf_core/__ │
│ main__.py:57 in run_nf_core │
│ │
│ 56 │ # Lanch the click cli │
│ ❱ 57 │ nf_core_cli() │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/click/core │
│ .py:829 in __call__ │
│ │
│ 828 │ │ """Alias for :meth:`main`.""" │
│ ❱ 829 │ │ return self.main(*args, **kwargs) │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/click/core │
│ .py:782 in main │
│ │
│ 781 │ │ │ │ with self.make_context(prog_name, args, **extra) as c │
│ ❱ 782 │ │ │ │ │ rv = self.invoke(ctx) │
│ 783 │ │ │ │ │ if not standalone_mode: │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/click/core │
│ .py:1259 in invoke │
│ │
│ 1258 │ │ │ │ with sub_ctx: │
│ ❱ 1259 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/click/core │
│ .py:1066 in invoke │
│ │
│ 1065 │ │ if self.callback is not None: │
│ ❱ 1066 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/click/core │
│ .py:610 in invoke │
│ │
│ 609 │ │ │ with ctx: │
│ ❱ 610 │ │ │ │ return callback(*args, **kwargs) │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/nf_core/__ │
│ main__.py:664 in sync │
│ │
│ 663 │ try: │
│ ❱ 664 │ │ sync_obj.sync() │
│ 665 │ except (nf_core.sync.SyncException, nf_core.sync.PullRequestExcept │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/nf_core/sy │
│ nc.py:113 in sync │
│ │
│ 112 │ │ │ │ self.push_merge_branch() │
│ ❱ 113 │ │ │ │ self.make_pull_request() │
│ 114 │ │ │ │ self.close_open_template_merge_prs() │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/site-packages/nf_core/sy │
│ nc.py:349 in make_pull_request │
│ │
│ 348 │ │ │ │ log.debug(f"GitHub API PR failed with 403 │
│ error:\n{returned_data_prettyprint}\n\n{r.headers}") │
│ ❱ 349 │ │ │ │ wait_time = float(re.sub("[^0-9]", "", r.headers.get(" │
│ 30))) │
│ 350 │ │ │ │ log.warning(f"Got 403 code - probably the abuse protec │
│ after {wait_time} seconds..") │
│ │
│ /opt/hostedtoolcache/Python/3.8.8/x64/lib/python3.8/re.py:210 in sub │
│ │
│ 209 │ a replacement string to be used.""" │
│ ❱ 210 │ return _compile(pattern, flags).sub(repl, string, count) │
╰──────────────────────────────────────────────────────────────────────────────╯
TypeError: expected string or bytes-like object
Error: Process completed with exit code 1.Verbose log:
[2021-03-25 18:17:33,223] nf_core.sync [INFO ] Submitting a pull request via the GitHub API
[2021-03-25 18:17:33,577] nf_core.sync [DEBUG ] GitHub API PR failed with 403 error:
{
"message": "You have triggered an abuse detection mechanism and have been temporarily blocked from content creation. Please retry your request again later.",
"documentation_url": "https://docs.github.com/overview/resources-in-the-rest-api#abuse-rate-limits"
}
{'Server': 'GitHub.com', 'Date': 'Thu, 25 Mar 2021 18:17:33 GMT', 'Content-Type': 'application/json; charset=utf-8', 'Transfer-Encoding': 'chunked', 'X-OAuth-Scopes': 'repo, workflow', 'X-Accepted-OAuth-Scopes': '', 'X-GitHub-Media-Type': 'github.v3; format=json', 'X-RateLimit-Limit': '5000', 'X-RateLimit-Remaining': '4513', 'X-RateLimit-Reset': '1616696995', 'X-RateLimit-Used': '487', 'Access-Control-Expose-Headers': 'ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Used, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type, Deprecation, Sunset', 'Access-Control-Allow-Origin': '*', 'Strict-Transport-Security': 'max-age=31536000; includeSubdomains; preload', 'X-Frame-Options': 'deny', 'X-Content-Type-Options': 'nosniff', 'X-XSS-Protection': '0', 'Referrer-Policy': 'origin-when-cross-origin, strict-origin-when-cross-origin', 'Content-Security-Policy': "default-src 'none'", 'Vary': 'Accept-Encoding, Accept, X-Requested-With', 'Content-Encoding': 'gzip', 'X-GitHub-Request-Id': '0480:6787:124C0:36C3E:605CD3BD'}
So looks like I messed up the new regex code in the abuse mechanism loop. I probably should have written a pytest for it.. 🙄