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

mvdbeek

/slurm/uid_527616/job_25273497/step_batch:
memory.use_hierarchy: 1
memory.kmem.tcp.usage_in_bytes: 0
memory.soft_limit_in_bytes: 128849018880
memory.move_charge_at_immigrate: 0
memory.memsw.failcnt: 0
memory.kmem.tcp.max_usage_in_bytes: 0
memory.max_usage_in_bytes: 144314368
memory.oom_control: oom_kill_disable 0
	under_oom 0

mvdbeek

In [2]: import urllib

In [3]: urllib.parse.parse_qs('tool_id=ucsc_table_direct1&URL=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTables&hguid=1587314780_KBXslDDpain7o5EBARpPf
   ...: 3nJ1NbE&db=hg38&org=Human&hgta_table=knownGene&hgta_track=knownGene&hgta_regionType=range&hgta_outputType=bed&position=chr2%3A25%2C160%2C915-2
   ...: 5%2C168%2C903&hgsid=1708063580_QD5ONXCqxp8H5TlaKJtczZ2cy5pQ&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_knownGene&hgta_ctDesc=table
   ...: +browser+query+on+knownGene&hgta_ctVis=pack&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbExonBases=0&fbIntronBases=0&fbDownBases=200&hgta_doGetBed
   ...: =get+BED&hgta_doGalaxyQuery=Send+query+to+Galaxy')
Out[3]:
{'tool_id': ['ucsc_table_direct1'],
 'URL': ['http://genome.ucsc.edu/cgi-bin/hgTables'],

mvdbeek

Convert characters1
Cut1
Paste1
__EXTRACT_DATASET__
__SORTLIST__
addValue
cat1
export_remote
param_value_from_file
sort1