mvdbeek

Recovering hifiasm job

Situation

Job failed on first run, rerun with "replace dataset collection elements" selected. Discovered output dataset collection elements were added to original collection, while new output dataset collection is not populated. This probably makes the job ineligible for the job cache / job search.

Collections and IDs

mvdbeek

#!/usr/bin/env python3
"""
Benchmarking script for Galaxy API endpoints performance testing.

This script creates a test history with a configurable list:list collection,
then benchmarks two API endpoints:
1. /api/histories/{history_id}/contents
2. /api/dataset_collections/{hdca_id}/contents/{collection_id}
"""

mvdbeek

library(GBCC.mcm)
library(SummarizedExperiment)
library(SpatialFeatureExperiment)
x = GBCC.mcm::process_mcmicro("input.h5ad")
expr_matrix <- assay(x, "X")
expr_df <- as.data.frame(t(expr_matrix))  # Transpose so cells are rows
# Get cell metadata
metadata <- as.data.frame(colData(x))
# Get spatial coordinates
coords <- as.data.frame(spatialCoords(x))

mvdbeek

EXPLAIN (ANALYZE, COSTS, VERBOSE, BUFFERS, FORMAT JSON) SELECT 
  filtered_jobs_subquery.job_id, 
  filtered_jobs_subquery."reference_genome|history_item_152775960", 
  filtered_jobs_subquery."library|input_1_152726579" 
FROM 
  (
    SELECT 
      job_ids_subquery.job_id AS job_id, 
      job_ids_subquery."reference_genome|history_item_152775960" AS "reference_genome|history_item_152775960", 
      job_ids_subquery."library|input_1_152726579" AS "library|input_1_152726579" 

mvdbeek

diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py
new file mode 100644
index 00000000000..a449de1b6d7
--- /dev/null
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/0c681a59dce1_add_on_delete_to_fkey_on_event_session_.py
@@ -0,0 +1,40 @@
+"""Add on-delete to fkey on event.session_id
+
+Revision ID: 0c681a59dce1
+Revises: 24feca8a6a5a

mvdbeek

{
  "$defs": {
    "CollectionElementCollectionRequestUri": {
      "additionalProperties": false,
      "properties": {
        "class": {
          "const": "Collection",
          "title": "Class",
          "type": "string"
        },

mvdbeek

workflows:
- trs_id: '#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.2'
  workflow_categories:
  - ASSEMBLY
  workflow_name: Genome assembly with Flye
  workflow_description: Assemble long reads with Flye, then view assembly statistics
    and assembly graph
  ploidy: any
  parameters:
    Input sequence reads:

mvdbeek

[
  {
    "version": 1.2,
    "workflows": [
      {
        "name": "main",
        "subclass": "Galaxy",
        "publish": true,
        "primaryDescriptorPath": "/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga",
        "testParameterFiles": [

mvdbeek

{"$defs": {"CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RootModel_List_Union_Annotated_Union_has_line_model__has_line_matching_model__has_n_lines_model__has_text_model__has_text_matching_model__not_has_text_model__has_n_columns_model__attribute_is_model__attribute_matches_model__element_text_model__element_text_is_model__element_text_matches_model__has_element_with_path_model__has_n_elements_with_path_model__is_valid_xml_model__xml_element_model__has_json_property_with_text_model__has_json_property_with_value_model__has_h5_attribute_model__has_h5_keys_model__has_archive_member_model__has_size_model__has_image_center_of_mass_model__has_image_channels_model__has

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 \" > [email protected]\" has incorrect peer dependency \"webpack@^3.1.0\".\nwarning \"@h5web/app > @h5web/lib > [email protected]\" has incorrect peer dependency \"react@^16.3.0 || ^17.0.0\".\nwarning \"@h5web/app > @react-three/fiber > [email protected]\" 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