mvdbeek

changed: [cvmfs0-psu1.galaxyproject.org] => (item=client)
failed: [cvmfs0-psu1.galaxyproject.org] (item=plugins) => {"ansible_loop_var": "item", "changed": true, "cmd": ["yarn", "run", "gulp", "plugins"], "delta": "0:09:31.824149", "end": "2024-06-21 15:56:11.744263", "item": "plugins", "msg": "non-zero return code", "rc": 1, "start": "2024-06-21 15:46:39.920114", "stderr": "warning \" > extract-text-webpack-plugin@3.0.2\" has incorrect peer dependency \"webpack@^3.1.0\".\nwarning \"@h5web/app > @h5web/lib > react-aria-menubutton@7.0.3\" has incorrect peer dependency \"react@^16.3.0 || ^17.0.0\".\nwarning \"@h5web/app > @react-three/fiber > react-reconciler@0.26.2\" has incorrect peer dependency \"react@^17.0.2\".\nBrowserslist: caniuse-lite is outdated. Please run:\n  npx update-browserslist-db@latest\n  Why you should do it regularly: https://github.com/browserslist/update-db#readme\nBrowserslist: caniuse-lite is outdated. Please run:\n  npx update-browserslist-db@latest\n  Why you should do it regularly: h

mvdbeek

import json
import subprocess
import time

from requests import Session

from galaxy.tool_util.deps.mulled.util import quay_versions
from galaxy.tool_util.deps.mulled.util import _get_namespace

mvdbeek

# Run from galaxy root with PYTHONPATH=lib GALAXY_CONFIG_FILE=config/galaxy.yml  python example.py
import os

from scripts.db_shell import config
from galaxy.celery import get_galaxy_app
from galaxy.managers.api_keys import ApiKeyManager

EMAIL = "abc@abc.com"

os.environ["GALAXY_CONFIG_FILE"] = os.environ.get("GALAXY_CONFIG_FILE", config["config_file"])

mvdbeek

BEGIN;

-- Clean up pgcleanup table
DELETE FROM cleanup_event_history_association WHERE cleanup_event_history_association.history_id IN (SELECT id FROM history WHERE history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 100);
-- Clean up audit table
DELETE FROM history_audit WHERE history_audit.history_id IN (select id from history where history.user_id is null and history.hid_counter = 1 ORDER BY history.update_time LIMIT 100);
-- Cleanup galaxy_session_to_history
DELETE FROM galaxy_session_to_history WHERE galaxy_session_to_history.session_id IN (SELECT galaxy_session.id FROM galaxy_session WHERE galaxy_session.current_history_id IN (SELECT history.id FROM history WHERE history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 100));
-- Clean up galaxy_session
DELETE FROM galaxy_session WHERE galaxy_session.current_history_id IN (select id from history where history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 10

mvdbeek

Hmm, those tests are passing, but if you look at the logs it appears that some functionality is actually broken ?

```
================================================================ test session starts =================================================================
platform darwin -- Python 3.11.7, pytest-7.4.4, pluggy-1.4.0 -- /Users/mvandenb/src/galaxy/.venv/bin/python3.11
cachedir: .pytest_cache
metadata: {'Python': '3.11.7', 'Platform': 'macOS-14.1.1-arm64-arm-64bit', 'Packages': {'pytest': '7.4.4', 'pluggy': '1.4.0'}, 'Plugins': {'cwltest': '2.4.20240129145612', 'asyncio': '0.23.5', 'postgresql': '5.1.0', 'instafail': '0.5.0', 'shard': '0.1.2', 'html': '4.1.1', 'json-report': '1.5.0', 'pytest_httpserver': '1.0.9', 'metadata': '3.1.1', 'cov': '4.1.0', 'playwright': '0.4.4', 'mock': '3.12.0', 'base-url': '2.1.0', 'anyio': '4.2.0', 'celery': '0.0.0'}, 'Base URL': ''}
rootdir: /Users/mvandenb/src/galaxy
configfile: pytest.ini
plugins: cwltest-2.4.20240129145612, asyncio-0.23.5, postgresql-5.1.0, instafai

mvdbeek

❯ python setup.py bdist_wheel
requirement found install_requires requests<=2.31.0,>=2.25.1
requirement found install_requires urllib3~=1.26.18
requirement found install_requires dogpile.cache~=1.2.2
requirement found install_requires tabulate~=0.9.0
requirement found install_requires jsonschema~=4.20.0
requirement found install_requires paramiko~=3.4.0
requirement found kerberos kerberos~=1.3.1
requirement found kerberos pykerberos~=1.2.4
requirement found kerberos requests-kerberos>=0.14.0

mvdbeek

# VGP Kmer profiling and mitogenome report

Time workflow was run:

```galaxy
invocation_time()
```


## GenomeScope results

mvdbeek

{
  "$defs": {
    "AssertAttributeIs": {
      "additionalProperties": false,
      "properties": {
        "path": {
          "description": "Path to check for. Valid paths are the simplified subsets of XPath implemented by lxml.etree; https://lxml.de/xpathxslt.html for more information.",
          "title": "Path",
          "type": "string"
        },

mvdbeek

<tool id="select_from_ucsc" name="select_from_ucsc" version="0.1.0" profile="23.1">
    <command><![CDATA[
echo '$url_param_value_postprocessed' > '$param_value_postprocessed'
    ]]></command>
    <inputs>
        <param name="url_param_value_postprocessed" type="select" multiple="true">
            <options from_url="https://api.genome.ucsc.edu/list/ucscGenomes">
                <postprocess_expression type="ecma5.1"><![CDATA[
                    $( Object.entries(inputs.ucscGenomes).map(([key, item]) => [`${item.description} (${item.organism})`, key]) )
                ]]></postprocess_expression>

mvdbeek

Test Results (powered by Planemo)

Test Summary