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Feat/base peregrine #110

Merged
merged 20 commits into from
Mar 20, 2019
Merged

Feat/base peregrine #110

merged 20 commits into from
Mar 20, 2019

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stevencui729
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@stevencui729 stevencui729 commented Feb 20, 2019 •
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Peregrine update for building with the new python2 base image in cloud-automation

New Features

Breaking Changes

  • removed redundant building steps

Bug Fixes

Improvements

Dependency updates

  • removed scipy, unnecessary

Deployment changes

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Jenkins Build 3 : time taken 1 hr 0 min
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Jenkins Build 6 : time taken 1 hr 6 min
Check the https://jenkins.planx-pla.net/job/perf-peregrine/job/PR-110/6/display/redirect

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Jenkins Build 7 : time taken 32 min
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Jenkins Build 8 : time taken 1 hr 49 min
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Jenkins Build 1 : time taken 20 min
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Jenkins Build 2 : time taken 1 min 6 sec
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Jenkins Build 3 : time taken 8 min 0 sec
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Jenkins Build 4 : time taken 50 min
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Jenkins Build 5 : time taken 58 min
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Jenkins Build 6 : time taken 1 hr 1 min
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Jenkins Build 7 : time taken 32 min
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Test results:
Passed: 109, Failed: 0, Skipped: 0

Test Time (PR) Time (master) Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot 0.461 0.379 0.08
@ExportPerformanceTests @performance: Export all nodes of type: experiment 0.672 0.499 0.17
@ExportPerformanceTests @performance: Export all nodes of type: read_group_qc 0.138 0.098 0.04
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot 0.195 0.153 0.04
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case 0.258 0.219 0.04
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group 0.099 0.069 0.03
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc 0.077 0.069 0.01
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample 0.121 0.093 0.03
@QueryPerformanceTests @performance: Executing bottomUp query # 1 0.665 0.599 0.07
@QueryPerformanceTests @performance: Executing bottomUp query # 2 0.601 0.494 0.11
@QueryPerformanceTests @performance: Executing bottomUp query # 3 0.489 0.463 0.03
@QueryPerformanceTests @performance: Executing bottomUp query # 4 0.434 0.374 0.06
@QueryPerformanceTests @performance: Executing topDown query # 2 0.123 0.1 0.02
@QueryPerformanceTests @performance: Executing topDown query # 5 0.431 0.315 0.12
@QueryPerformanceTests @performance: Executing topDown query # 6 0.588 0.485 0.10
@QueryPerformanceTests @performance: Executing topDown query # 7 0.621 0.501 0.12
@SubmissionPerformanceTests @performance: Submission acknowledgement 10 0.398 0.307 0.09
@SubmissionPerformanceTests @performance: Submission acknowledgement 100 2.592 1.689 0.90
@SubmissionPerformanceTests @performance: Submission acknowledgement 1000 23.268 18.883 4.39
@SubmissionPerformanceTests @performance: Submission aliquot 10 0.541 0.364 0.18
@SubmissionPerformanceTests @performance: Submission aliquot 100 3.216 2.899 0.32
@SubmissionPerformanceTests @performance: Submission aliquot 1000 24.195 18.669 5.53
@SubmissionPerformanceTests @performance: Submission case 100 2.893 1.808 1.08
@SubmissionPerformanceTests @performance: Submission case 1000 24.542 20.019 4.52
@SubmissionPerformanceTests @performance: Submission clinical_test 10 0.44 0.345 0.09
@SubmissionPerformanceTests @performance: Submission clinical_test 100 2.851 2.261 0.59
@SubmissionPerformanceTests @performance: Submission clinical_test 1000 29.699 21.369 8.33
@SubmissionPerformanceTests @performance: Submission core_metadata_collection 100 2.79 2.101 0.69
@SubmissionPerformanceTests @performance: Submission core_metadata_collection 1000 23.83 22.514 1.32
@SubmissionPerformanceTests @performance: Submission demographic 100 2.469 2.14 0.33
@SubmissionPerformanceTests @performance: Submission demographic 1000 30.014 19.966 10.05
@SubmissionPerformanceTests @performance: Submission diagnosis 10 0.528 0.292 0.24
@SubmissionPerformanceTests @performance: Submission diagnosis 100 3.149 2.201 0.95
@SubmissionPerformanceTests @performance: Submission diagnosis 1000 30.189 23.139 7.05
@SubmissionPerformanceTests @performance: Submission experiment 10 0.43 0.334 0.10
@SubmissionPerformanceTests @performance: Submission experiment 100 2.8 2.223 0.58
@SubmissionPerformanceTests @performance: Submission experiment 1000 24.898 20.436 4.46
@SubmissionPerformanceTests @performance: Submission exposure 10 0.45 0.28 0.17
@SubmissionPerformanceTests @performance: Submission exposure 100 2.782 2.294 0.49
@SubmissionPerformanceTests @performance: Submission exposure 1000 25.183 19.97 5.21
@SubmissionPerformanceTests @performance: Submission family_history 10 0.38 0.305 0.07
@SubmissionPerformanceTests @performance: Submission family_history 100 2.431 2.045 0.39
@SubmissionPerformanceTests @performance: Submission family_history 1000 26.381 18.965 7.42
@SubmissionPerformanceTests @performance: Submission keyword 100 2.358 1.894 0.46
@SubmissionPerformanceTests @performance: Submission keyword 1000 25.124 18.301 6.82
@SubmissionPerformanceTests @performance: Submission publication 10 0.4 0.269 0.13
@SubmissionPerformanceTests @performance: Submission publication 100 2.375 1.746 0.63
@SubmissionPerformanceTests @performance: Submission publication 1000 25.972 18.766 7.21
@SubmissionPerformanceTests @performance: Submission read_group 10 0.474 0.318 0.16
@SubmissionPerformanceTests @performance: Submission read_group 100 3.27 2.29 0.98
@SubmissionPerformanceTests @performance: Submission read_group 1000 28.498 22.004 6.49
@SubmissionPerformanceTests @performance: Submission read_group_qc 10 0.578 0.448 0.13
@SubmissionPerformanceTests @performance: Submission read_group_qc 100 4.18 3.601 0.58
@SubmissionPerformanceTests @performance: Submission read_group_qc 1000 27.863 17.59 10.27
@SubmissionPerformanceTests @performance: Submission sample 100 3.097 2.499 0.60
@SubmissionPerformanceTests @performance: Submission sample 1000 29.532 23.001 6.53
@SubmissionPerformanceTests @performance: Submission slide 100 2.698 2.477 0.22
@SubmissionPerformanceTests @performance: Submission slide 1000 27.05 21.579 5.47
@SubmissionPerformanceTests @performance: Submission slide_count 10 0.56 0.376 0.18
@SubmissionPerformanceTests @performance: Submission slide_count 100 3.077 1.869 1.21
@SubmissionPerformanceTests @performance: Submission slide_count 1000 28.191 20.161 8.03
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 10 1.909 1.807 0.10
@SubmissionPerformanceTests @performance: Submission submitted_methylation 10 2.724 2.173 0.55
@SubmissionPerformanceTests @performance: Submission treatment 10 0.403 0.306 0.10
@SubmissionPerformanceTests @performance: Submission treatment 100 2.437 2.214 0.22
@SubmissionPerformanceTests @performance: Submission treatment 1000 24.842 19.318 5.52

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Jenkins Build 8 : time taken 1 hr 1 min
Check the https://jenkins.planx-pla.net/job/perf-peregrine/job/PR-110/8/display/redirect

Test results:
Passed: 109, Failed: 0, Skipped: 0

Test Time (PR) Time (master) Diff
@QueryPerformanceTests @performance: Executing bottomUp query # 2 0.72 0.494 0.23
@QueryPerformanceTests @performance: Executing bottomUp query # 3 0.623 0.463 0.16
@QueryPerformanceTests @performance: Executing topDown query # 2 0.123 0.1 0.02
@QueryPerformanceTests @performance: Executing topDown query # 5 0.365 0.315 0.05
@QueryPerformanceTests @performance: Executing topDown query # 6 0.773 0.485 0.29
@QueryPerformanceTests @performance: Executing topDown query # 7 0.646 0.501 0.15
@SubmissionPerformanceTests @performance: Submission acknowledgement 10 0.377 0.307 0.07
@SubmissionPerformanceTests @performance: Submission acknowledgement 100 2.228 1.689 0.54
@SubmissionPerformanceTests @performance: Submission aligned_reads_index 10 2.042 1.908 0.13
@SubmissionPerformanceTests @performance: Submission aliquot 1000 20.149 18.669 1.48
@SubmissionPerformanceTests @performance: Submission case 100 1.9 1.808 0.09
@SubmissionPerformanceTests @performance: Submission case 1000 21.226 20.019 1.21
@SubmissionPerformanceTests @performance: Submission clinical_test 10 0.427 0.345 0.08
@SubmissionPerformanceTests @performance: Submission clinical_test 1000 23.688 21.369 2.32
@SubmissionPerformanceTests @performance: Submission demographic 1000 22.73 19.966 2.76
@SubmissionPerformanceTests @performance: Submission diagnosis 10 0.336 0.292 0.04
@SubmissionPerformanceTests @performance: Submission diagnosis 100 2.345 2.201 0.14
@SubmissionPerformanceTests @performance: Submission experimental_metadata 10 2.191 2.001 0.19
@SubmissionPerformanceTests @performance: Submission exposure 10 0.298 0.28 0.02
@SubmissionPerformanceTests @performance: Submission family_history 10 0.529 0.305 0.22
@SubmissionPerformanceTests @performance: Submission family_history 1000 20.67 18.965 1.70
@SubmissionPerformanceTests @performance: Submission keyword 100 2.072 1.894 0.18
@SubmissionPerformanceTests @performance: Submission keyword 1000 19.747 18.301 1.45
@SubmissionPerformanceTests @performance: Submission publication 10 0.297 0.269 0.03
@SubmissionPerformanceTests @performance: Submission publication 100 1.955 1.746 0.21
@SubmissionPerformanceTests @performance: Submission publication 1000 20.153 18.766 1.39
@SubmissionPerformanceTests @performance: Submission read_group 10 0.344 0.318 0.03
@SubmissionPerformanceTests @performance: Submission read_group_qc 1000 19.988 17.59 2.40
@SubmissionPerformanceTests @performance: Submission slide 1000 23.589 21.579 2.01
@SubmissionPerformanceTests @performance: Submission slide_count 100 2.05 1.869 0.18
@SubmissionPerformanceTests @performance: Submission slide_count 1000 22.156 20.161 2.00
@SubmissionPerformanceTests @performance: Submission treatment 1000 21.494 19.318 2.18

fantix
fantix approved these changes Mar 20, 2019
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This looks good to me

@stevencui729 stevencui729 merged commit 365d957 into master Mar 20, 2019
@stevencui729 stevencui729 deleted the feat/base-peregrine branch March 20, 2019 19:21
@PlanXCyborg PlanXCyborg mentioned this pull request Oct 21, 2022
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@fantix fantix fantix approved these changes

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@stevencui729 @PlanXCyborg @fantix