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Update Dockerfile #276

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Update Dockerfile #276

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Avantol13
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New Features

Breaking Changes

Bug Fixes

  • Python base image has uwsgi configuration for timeout to return valid JSON now

Improvements

Dependency updates

Deployment changes

@PlanXCyborg
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Jenkins Build 2 : time taken 1 hr 6 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-276/2/display/redirect

Test results:
Passed: 107, Failed: 2, Skipped: 0

Test Time (PR) Time (master) Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot 0.28 0.067 0.21
@ExportPerformanceTests @performance: Export all nodes of type: case 0.208 0.07 0.14
@ExportPerformanceTests @performance: Export all nodes of type: experiment 0.335 0.096 0.24
@ExportPerformanceTests @performance: Export all nodes of type: program 0.058 0.049 0.01
@ExportPerformanceTests @performance: Export all nodes of type: project 0.051 0.043 0.01
@ExportPerformanceTests @performance: Export all nodes of type: read_group 0.545 0.114 0.43
@ExportPerformanceTests @performance: Export all nodes of type: read_group_qc 0.111 0.099 0.01
@ExportPerformanceTests @performance: Export all nodes of type: sample 0.434 0.084 0.35
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot 0.283 0.205 0.08
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case 0.259 0.234 0.03
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment 0.225 0.213 0.01
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc 0.065 0.056 0.01
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample 0.159 0.13 0.03
@QueryPerformanceTests @performance: Executing bottomUp query # 0 0.694 0.588 0.11
@QueryPerformanceTests @performance: Executing bottomUp query # 1 0.568 0.478 0.09
@QueryPerformanceTests @performance: Executing bottomUp query # 2 0.574 0.446 0.13
@QueryPerformanceTests @performance: Executing bottomUp query # 3 0.434 0.366 0.07
@QueryPerformanceTests @performance: Executing bottomUp query # 5 0.254 0.228 0.03
@QueryPerformanceTests @performance: Executing topDown query # 0 0.056 0.046 0.01
@QueryPerformanceTests @performance: Executing topDown query # 1 0.083 0.07 0.01
@QueryPerformanceTests @performance: Executing topDown query # 2 0.095 0.088 0.01
@QueryPerformanceTests @performance: Executing topDown query # 3 0.174 0.152 0.02
@QueryPerformanceTests @performance: Executing topDown query # 4 0.271 0.228 0.04
@QueryPerformanceTests @performance: Executing topDown query # 5 0.363 0.301 0.06
@QueryPerformanceTests @performance: Executing topDown query # 6 0.57 0.417 0.15
@QueryPerformanceTests @performance: Executing topDown query # 7 0.587 0.48 0.11
@SubmissionPerformanceTests @performance: Submission acknowledgement 10 0.361 0.325 0.04
@SubmissionPerformanceTests @performance: Submission acknowledgement 100 2.593 2.146 0.45
@SubmissionPerformanceTests @performance: Submission acknowledgement 1000 25.606 21.467 4.14
@SubmissionPerformanceTests @performance: Submission aliquot 10 0.393 0.357 0.04
@SubmissionPerformanceTests @performance: Submission aliquot 1000 25.592 12.707 12.88
@SubmissionPerformanceTests @performance: Submission clinical_test 10 0.395 0.368 0.03
@SubmissionPerformanceTests @performance: Submission clinical_test 100 2.78 2.533 0.25
@SubmissionPerformanceTests @performance: Submission clinical_test 1000 31.665 13.157 18.51
@SubmissionPerformanceTests @performance: Submission core_metadata_collection 10 1.762 0.914 0.85
@SubmissionPerformanceTests @performance: Submission core_metadata_collection 1000 25.918 23.058 2.86
@SubmissionPerformanceTests @performance: Submission demographic 1000 28.561 12.126 16.44
@SubmissionPerformanceTests @performance: Submission diagnosis 10 0.493 0.375 0.12
@SubmissionPerformanceTests @performance: Submission diagnosis 100 3.226 2.688 0.54
@SubmissionPerformanceTests @performance: Submission diagnosis 1000 64.026 16.018 48.01
@SubmissionPerformanceTests @performance: Submission experimental_metadata 10 1.704 1.555 0.15
@SubmissionPerformanceTests @performance: Submission experimental_metadata 100 15.694 14.655 1.04
@SubmissionPerformanceTests @performance: Submission exposure 1000 25.423 13.04 12.38
@SubmissionPerformanceTests @performance: Submission family_history 10 0.366 0.338 0.03
@SubmissionPerformanceTests @performance: Submission family_history 1000 25.581 12.111 13.47
@SubmissionPerformanceTests @performance: Submission keyword 10 0.355 0.332 0.02
@SubmissionPerformanceTests @performance: Submission keyword 100 2.365 2.142 0.22
@SubmissionPerformanceTests @performance: Submission keyword 1000 23.929 21.424 2.51
@SubmissionPerformanceTests @performance: Submission publication 10 0.411 0.327 0.08
@SubmissionPerformanceTests @performance: Submission publication 100 2.374 2.194 0.18
@SubmissionPerformanceTests @performance: Submission publication 1000 25.553 21.237 4.32
@SubmissionPerformanceTests @performance: Submission read_group 100 2.753 2.474 0.28
@SubmissionPerformanceTests @performance: Submission read_group 1000 34.644 14.586 20.06
@SubmissionPerformanceTests @performance: Submission read_group_qc 10 0.52 0.481 0.04
@SubmissionPerformanceTests @performance: Submission sample 100 2.787 0.4 2.39
@SubmissionPerformanceTests @performance: Submission sample 1000 28.24 3.651 24.59
@SubmissionPerformanceTests @performance: Submission slide 100 2.728 0.369 2.36
@SubmissionPerformanceTests @performance: Submission slide 1000 27.164 3.414 23.75
@SubmissionPerformanceTests @performance: Submission slide_count 100 2.491 0.356 2.13
@SubmissionPerformanceTests @performance: Submission slide_count 1000 26.044 2.823 23.22
@SubmissionPerformanceTests @performance: Submission slide_image 100 14.873 1.577 13.30
@SubmissionPerformanceTests @performance: Submission slide_image 1000 44.988 14.299 30.69
@SubmissionPerformanceTests @performance: Submission submitted_aligned_reads 100 15.484 1.698 13.79
@SubmissionPerformanceTests @performance: Submission submitted_aligned_reads 1000 45.06 15.64 29.42
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 100 15.114 1.609 13.51
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 1000 45.153 14.46 30.69
@SubmissionPerformanceTests @performance: Submission submitted_methylation 100 15.35 1.654 13.70
@SubmissionPerformanceTests @performance: Submission submitted_methylation 1000 44.698 14.876 29.82
@SubmissionPerformanceTests @performance: Submission submitted_somatic_mutation 100 15.366 1.55 13.82
@SubmissionPerformanceTests @performance: Submission submitted_somatic_mutation 1000 45.005 14.17 30.84
@SubmissionPerformanceTests @performance: Submission submitted_unaligned_reads 100 15.311 1.632 13.68
@SubmissionPerformanceTests @performance: Submission treatment 1000 19.887 0.34 19.55

@PlanXCyborg
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Jenkins Build 3 : time taken 1 hr 7 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-276/3/display/redirect

Test results:
Passed: 108, Failed: 1, Skipped: 0

Test Time (PR) Time (master) Diff
@ExportPerformanceTests @performance: Export all nodes of type: aliquot 0.222 0.067 0.16
@ExportPerformanceTests @performance: Export all nodes of type: case 0.188 0.07 0.12
@ExportPerformanceTests @performance: Export all nodes of type: experiment 0.262 0.096 0.17
@ExportPerformanceTests @performance: Export all nodes of type: program 0.065 0.049 0.02
@ExportPerformanceTests @performance: Export all nodes of type: read_group 0.397 0.114 0.28
@ExportPerformanceTests @performance: Export all nodes of type: sample 0.332 0.084 0.25
@QueryPerformanceTests @performance: Executing bottomUp query # 0 0.786 0.588 0.20
@QueryPerformanceTests @performance: Executing bottomUp query # 1 0.595 0.478 0.12
@QueryPerformanceTests @performance: Executing bottomUp query # 2 0.796 0.446 0.35
@QueryPerformanceTests @performance: Executing bottomUp query # 3 0.505 0.366 0.14
@QueryPerformanceTests @performance: Executing bottomUp query # 4 0.46 0.39 0.07
@QueryPerformanceTests @performance: Executing bottomUp query # 5 0.372 0.228 0.14
@QueryPerformanceTests @performance: Executing bottomUp query # 6 0.262 0.174 0.09
@QueryPerformanceTests @performance: Executing bottomUp query # 7 0.156 0.128 0.03
@QueryPerformanceTests @performance: Executing topDown query # 0 0.125 0.046 0.08
@QueryPerformanceTests @performance: Executing topDown query # 1 0.138 0.07 0.07
@QueryPerformanceTests @performance: Executing topDown query # 2 0.175 0.088 0.09
@QueryPerformanceTests @performance: Executing topDown query # 3 0.267 0.152 0.11
@QueryPerformanceTests @performance: Executing topDown query # 4 0.484 0.228 0.26
@QueryPerformanceTests @performance: Executing topDown query # 5 0.473 0.301 0.17
@QueryPerformanceTests @performance: Executing topDown query # 6 0.502 0.417 0.08
@QueryPerformanceTests @performance: Executing topDown query # 7 0.601 0.48 0.12
@SubmissionPerformanceTests @performance: Submission aligned_reads_index 10 1.671 1.585 0.09
@SubmissionPerformanceTests @performance: Submission aliquot 1000 18.689 12.707 5.98
@SubmissionPerformanceTests @performance: Submission clinical_test 1000 20.866 13.157 7.71
@SubmissionPerformanceTests @performance: Submission demographic 1000 20.329 12.126 8.20
@SubmissionPerformanceTests @performance: Submission diagnosis 1000 21.672 16.018 5.65
@SubmissionPerformanceTests @performance: Submission experimental_metadata 10 1.868 1.555 0.31
@SubmissionPerformanceTests @performance: Submission experimental_metadata 100 15.527 14.655 0.87
@SubmissionPerformanceTests @performance: Submission exposure 1000 19.16 13.04 6.12
@SubmissionPerformanceTests @performance: Submission family_history 1000 18.418 12.111 6.31
@SubmissionPerformanceTests @performance: Submission publication 10 0.363 0.327 0.04
@SubmissionPerformanceTests @performance: Submission read_group 1000 20.722 14.586 6.14
@SubmissionPerformanceTests @performance: Submission read_group_qc 1000 17.911 16.372 1.54
@SubmissionPerformanceTests @performance: Submission slide 100 1.806 0.369 1.44
@SubmissionPerformanceTests @performance: Submission slide 1000 11.48 3.414 8.07
@SubmissionPerformanceTests @performance: Submission slide_count 100 1.792 0.356 1.44
@SubmissionPerformanceTests @performance: Submission slide_count 1000 10.13 2.823 7.31
@SubmissionPerformanceTests @performance: Submission slide_image 100 14.773 1.577 13.20
@SubmissionPerformanceTests @performance: Submission slide_image 1000 45.139 14.299 30.84
@SubmissionPerformanceTests @performance: Submission submitted_aligned_reads 100 14.778 1.698 13.08
@SubmissionPerformanceTests @performance: Submission submitted_aligned_reads 1000 45.07 15.64 29.43
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 100 14.539 1.609 12.93
@SubmissionPerformanceTests @performance: Submission submitted_copy_number 1000 45.157 14.46 30.70
@SubmissionPerformanceTests @performance: Submission submitted_methylation 100 15.305 1.654 13.65
@SubmissionPerformanceTests @performance: Submission submitted_methylation 1000 44.95 14.876 30.07
@SubmissionPerformanceTests @performance: Submission submitted_somatic_mutation 100 14.288 1.55 12.74
@SubmissionPerformanceTests @performance: Submission submitted_somatic_mutation 1000 45.107 14.17 30.94
@SubmissionPerformanceTests @performance: Submission submitted_unaligned_reads 100 15.405 1.632 13.77
@SubmissionPerformanceTests @performance: Submission submitted_unaligned_reads 1000 45.022 17.244 27.78
@SubmissionPerformanceTests @performance: Submission treatment 100 1.932 0.34 1.59
@SubmissionPerformanceTests @performance: Submission treatment 1000 19.71 2.521 17.19

@PlanXCyborg
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Jenkins Build 4 : time taken 58 min
Check the https://jenkins.planx-pla.net/job/perf-sheepdog/job/PR-276/4/display/redirect

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

Test Time (PR) Time (master) Diff
@ExportPerformanceTests @performance: Export all nodes of type: experiment 0.318 0.261 0.06
@ExportPerformanceTests @performance: Export all nodes of type: project 0.071 0.042 0.03
@ExportPerformanceTests @performance: Export all nodes of type: read_group_qc 0.104 0.084 0.02
@ExportPerformanceTests @performance: Export all nodes of type: sample 0.429 0.359 0.07
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: aliquot 0.211 0.146 0.06
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: case 0.31 0.214 0.10
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: experiment 0.238 0.174 0.06
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group 0.106 0.064 0.04
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: read_group_qc 0.064 0.056 0.01
@ExportPerformanceTests @performance: Exporting a record by ID on nodes of type: sample 0.106 0.094 0.01
@SubmissionPerformanceTests @performance: Submission acknowledgement 100 2.47 2.238 0.23
@SubmissionPerformanceTests @performance: Submission acknowledgement 1000 27.055 24.028 3.03
@SubmissionPerformanceTests @performance: Submission aliquot 1000 45.361 32.058 13.30
@SubmissionPerformanceTests @performance: Submission case 100 2.731 2.235 0.50
@SubmissionPerformanceTests @performance: Submission core_metadata_collection 10 1.729 1.586 0.14
@SubmissionPerformanceTests @performance: Submission demographic 100 2.991 2.254 0.74
@SubmissionPerformanceTests @performance: Submission demographic 1000 30.831 26.739 4.09
@SubmissionPerformanceTests @performance: Submission diagnosis 100 2.969 2.593 0.38
@SubmissionPerformanceTests @performance: Submission diagnosis 1000 91.961 28.558 63.40
@SubmissionPerformanceTests @performance: Submission experiment 1000 28.167 24.51 3.66
@SubmissionPerformanceTests @performance: Submission exposure 100 3.07 2.169 0.90
@SubmissionPerformanceTests @performance: Submission family_history 100 2.988 2.018 0.97
@SubmissionPerformanceTests @performance: Submission family_history 1000 26.426 22.378 4.05
@SubmissionPerformanceTests @performance: Submission keyword 10 0.361 0.342 0.02
@SubmissionPerformanceTests @performance: Submission keyword 100 2.773 1.94 0.83
@SubmissionPerformanceTests @performance: Submission publication 10 0.387 0.339 0.05
@SubmissionPerformanceTests @performance: Submission publication 100 2.399 2.01 0.39
@SubmissionPerformanceTests @performance: Submission publication 1000 25.991 19.284 6.71
@SubmissionPerformanceTests @performance: Submission read_group 10 0.4 0.349 0.05
@SubmissionPerformanceTests @performance: Submission read_group 100 2.731 2.435 0.30
@SubmissionPerformanceTests @performance: Submission read_group_qc 10 0.574 0.529 0.05
@SubmissionPerformanceTests @performance: Submission read_group_qc 100 4.018 3.603 0.42
@SubmissionPerformanceTests @performance: Submission sample 10 0.598 0.4 0.20
@SubmissionPerformanceTests @performance: Submission sample 1000 33.477 27.565 5.91
@SubmissionPerformanceTests @performance: Submission slide 10 0.432 0.379 0.05
@SubmissionPerformanceTests @performance: Submission slide 100 2.97 2.763 0.21
@SubmissionPerformanceTests @performance: Submission slide_count 10 0.378 0.352 0.03
@SubmissionPerformanceTests @performance: Submission slide_count 1000 28.818 23.338 5.48
@SubmissionPerformanceTests @performance: Submission submitted_methylation 10 2.243 1.974 0.27
@SubmissionPerformanceTests @performance: Submission treatment 10 0.432 0.411 0.02
@SubmissionPerformanceTests @performance: Submission treatment 100 2.777 2.633 0.14

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@frickjack frickjack frickjack approved these changes

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@Avantol13 @PlanXCyborg @frickjack