CI
04a5851ff8
Build pipeline: viash-hub.biobox.main-tb4cv
Source commit: 7158daa5f6
Source message: Fix bases2fastq component, update to latest practices (#190)
* wip updates
* refactor component
* assume bases2fastq follows semver
* fix version command
* add entry to changelog
* move to minor changes
126 lines
4.0 KiB
Bash
126 lines
4.0 KiB
Bash
#!/bin/bash
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## VIASH START
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## VIASH END
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# Source the centralized test helpers
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source "$meta_resources_dir/test_helpers.sh"
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# Initialize test environment with strict error handling
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setup_test_env
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#############################################
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# Test execution with centralized functions
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#############################################
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log "Starting tests for $meta_name"
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# Create test directory
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test_dir="$meta_temp_dir/test_data"
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mkdir -p "$test_dir"
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# Create test BED file with data for grouping
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log "Creating test BED data..."
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cat > "$test_dir/test.bed" << 'EOF'
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chr1 100 200 feature1 10 +
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chr1 300 400 feature2 20 +
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chr1 500 600 feature3 30 +
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chr2 100 200 feature4 15 -
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chr2 300 400 feature5 25 -
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chr3 100 200 feature6 35 +
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EOF
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# --- Test Case 1: Basic grouping by column 1 (chromosome) with sum operation ---
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log "Starting TEST 1: Basic grouping by chromosome with sum"
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log "Executing $meta_name with basic grouping..."
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"$meta_executable" \
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--input "$test_dir/test.bed" \
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--groupby 1 \
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--column 5 \
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--operation sum \
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--output "$meta_temp_dir/output1.txt"
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log "Validating TEST 1 outputs..."
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check_file_exists "$meta_temp_dir/output1.txt" "grouped output file"
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check_file_not_empty "$meta_temp_dir/output1.txt" "grouped output file"
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check_file_contains "$meta_temp_dir/output1.txt" "chr1"
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check_file_contains "$meta_temp_dir/output1.txt" "chr2"
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check_file_contains "$meta_temp_dir/output1.txt" "chr3"
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log "✅ TEST 1 completed successfully"
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# --- Test Case 2: Group by multiple columns with mean operation ---
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log "Starting TEST 2: Group by chromosome and strand with mean"
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log "Executing $meta_name with multiple column grouping..."
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"$meta_executable" \
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--input "$test_dir/test.bed" \
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--groupby 1,6 \
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--column 5 \
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--operation mean \
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--output "$meta_temp_dir/output2.txt"
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log "Validating TEST 2 outputs..."
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check_file_exists "$meta_temp_dir/output2.txt" "multi-column grouped output"
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check_file_not_empty "$meta_temp_dir/output2.txt" "multi-column grouped output"
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check_file_contains "$meta_temp_dir/output2.txt" "chr1"
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check_file_contains "$meta_temp_dir/output2.txt" "+"
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check_file_contains "$meta_temp_dir/output2.txt" "-"
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log "✅ TEST 2 completed successfully"
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# --- Test Case 3: Count operation ---
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log "Starting TEST 3: Group by chromosome with count operation"
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log "Executing $meta_name with count operation..."
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"$meta_executable" \
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--input "$test_dir/test.bed" \
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--groupby 1 \
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--column 5 \
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--operation count \
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--output "$meta_temp_dir/output3.txt"
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log "Validating TEST 3 outputs..."
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check_file_exists "$meta_temp_dir/output3.txt" "count output file"
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check_file_not_empty "$meta_temp_dir/output3.txt" "count output file"
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# chr1 should have 3 features, chr2 should have 2, chr3 should have 1
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check_file_contains "$meta_temp_dir/output3.txt" "3"
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check_file_contains "$meta_temp_dir/output3.txt" "2"
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check_file_contains "$meta_temp_dir/output3.txt" "1"
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log "✅ TEST 3 completed successfully"
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# --- Test Case 4: Min/Max operations ---
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log "Starting TEST 4: Group by chromosome with min operation"
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log "Executing $meta_name with min operation..."
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"$meta_executable" \
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--input "$test_dir/test.bed" \
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--groupby 1 \
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--column 5 \
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--operation min \
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--output "$meta_temp_dir/output4.txt"
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log "Validating TEST 4 outputs..."
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check_file_exists "$meta_temp_dir/output4.txt" "min output file"
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check_file_not_empty "$meta_temp_dir/output4.txt" "min output file"
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log "✅ TEST 4 completed successfully"
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# --- Test Case 5: Full output with additional options ---
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log "Starting TEST 5: Group with full output and header"
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log "Executing $meta_name with full output options..."
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"$meta_executable" \
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--input "$test_dir/test.bed" \
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--groupby 1 \
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--column 5 \
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--operation sum \
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--full \
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--output "$meta_temp_dir/output5.txt"
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log "Validating TEST 5 outputs..."
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check_file_exists "$meta_temp_dir/output5.txt" "full output file"
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check_file_not_empty "$meta_temp_dir/output5.txt" "full output file"
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# Full output should include more columns from original data
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log "✅ TEST 5 completed successfully"
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log "🎉 All tests completed successfully for $meta_name!"
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