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

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