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1
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(venv)radhika@shell.9tee4:~/cwl/common-workflow-language$ cat arv-run.sh
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2
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#!/bin/sh
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3
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exec arvados-cwl-runner --compute-checksum --api containers "$@"
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4
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5
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(venv)radhika@shell.9tee4:~/cwl/common-workflow-language$ ./run_test.sh RUNNER=./arv-run.sh
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6
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--- Running conformance test v1.0 on /home/radhika/cwl/common-workflow-language/arv-run.sh ---
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7
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/home/radhika/venv/bin/arvados-cwl-runner 1.0.20160728182727, arvados-python-client 0.1.20160721023501, cwltool 1.0.20160726135535
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8
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Test [6/73] Workflow or tool uses unsupported feature:
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9
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Generate files not supported
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10
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Test [10/73] Workflow or tool uses unsupported feature:
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11
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Stderr redirection currently not suppported
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12
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Test [11/73] Workflow or tool uses unsupported feature:
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13
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Stderr redirection currently not suppported
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14
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Test [12/73] Workflow or tool uses unsupported feature:
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15
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Stderr redirection currently not suppported
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16
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Test [13/73] Workflow or tool uses unsupported feature:
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17
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Stdin redirection currently not suppported
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18
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Test [18/73] Workflow or tool uses unsupported feature:
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19
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Stdin redirection currently not suppported
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20
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Test [21/73] 2016-08-03 14:30:39 arvados.cwl-runner[8889] ERROR: While getting final output object: No JSON object could be decoded
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21
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2016-08-03 14:30:39 arvados.cwl-runner[8889] WARNING: Overall process status is UnsupportedRequirement
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22
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Workflow or tool uses unsupported feature:
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23
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Check log for details.
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24
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Test [35/73] 2016-08-03 14:54:15 arvados.cwl-runner[11710] ERROR: While getting final output object: No JSON object could be decoded
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25
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2016-08-03 14:54:15 arvados.cwl-runner[11710] WARNING: Overall process status is UnsupportedRequirement
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26
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Workflow or tool uses unsupported feature:
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27
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Check log for details.
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28
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Test [36/73] Test failed: /home/radhika/cwl/common-workflow-language/arv-run.sh --outdir=/tmp/tmpc3berE --quiet v1.0/env-wf1.cwl v1.0/env-job.json
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29
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Test requirement priority
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30
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expected output object {
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"out": {
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"checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",
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33
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"class": "File",
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"location": "out",
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35
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"size": 15
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36
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}
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37
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}
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38
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got {
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39
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"out": {
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40
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"basename": "out",
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41
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"class": "File",
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"location": "keep:e44c7b6c572a790cda32c3b8ff288222+47/out",
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43
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"size": 15
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44
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}
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45
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}
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46
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Compare failure expected {
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47
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"checksum": "sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519",
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48
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"class": "File",
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49
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"size": 15
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50
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}
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51
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got {
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52
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"class": "File",
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53
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"size": 15
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54
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}
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55
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Test [37/73] Test failed: /home/radhika/cwl/common-workflow-language/arv-run.sh --outdir=/tmp/tmp7Rbd_j --quiet v1.0/env-wf2.cwl v1.0/env-job.json
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56
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Test requirements override hints
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57
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expected output object {
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58
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"out": {
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59
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"checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",
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60
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"class": "File",
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61
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"location": "out",
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62
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"size": 9
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63
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}
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64
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}
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65
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got {
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"out": {
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"basename": "out",
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68
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"class": "File",
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69
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"location": "keep:6b537bf2bb97bd4f5b14686b2f5457cd+45/out",
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70
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"size": 9
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71
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}
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72
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}
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73
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Compare failure expected {
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74
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"checksum": "sha1$cdc1e84968261d6a7575b5305945471f8be199b6",
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75
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"class": "File",
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76
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"size": 9
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77
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}
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78
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got {
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79
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"class": "File",
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80
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"size": 9
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81
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}
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82
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Test [38/73] 2016-08-03 14:59:04 arvados.cwl-runner[12192] ERROR: While getting final output object: No JSON object could be decoded
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83
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2016-08-03 14:59:04 arvados.cwl-runner[12192] WARNING: Overall process status is UnsupportedRequirement
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84
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Workflow or tool uses unsupported feature:
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85
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Check log for details.
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86
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Test [39/73] Test failed: /home/radhika/cwl/common-workflow-language/arv-run.sh --outdir=/tmp/tmpzrhPwi --quiet v1.0/revsort.cwl v1.0/revsort-job.json
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87
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Test sample workflows from the specification
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88
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expected output object {
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89
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"output": {
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90
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"checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",
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91
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"class": "File",
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92
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"location": "output.txt",
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93
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"size": 1111
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94
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}
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95
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}
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96
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got {
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97
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"output": {
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98
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"basename": "output.txt",
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99
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"class": "File",
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100
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"location": "keep:ed7aa65105811db1a01b2c5b3c001de9+58/output.txt",
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101
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"size": 1111
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102
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}
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103
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}
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104
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Compare failure expected {
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105
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"checksum": "sha1$b9214658cc453331b62c2282b772a5c063dbd284",
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106
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"class": "File",
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107
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"size": 1111
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108
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}
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109
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got {
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110
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"class": "File",
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111
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"size": 1111
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112
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}
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113
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Test [40/73]
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114
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115
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116
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Test [41/73] 2016-08-03 15:03:38 arvados.cwl-runner[12891] ERROR: While getting final output object: No JSON object could be decoded
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117
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2016-08-03 15:03:38 arvados.cwl-runner[12891] WARNING: Overall process status is UnsupportedRequirement
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118
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Workflow or tool uses unsupported feature:
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119
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Check log for details.
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120
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Test [42/73] Workflow or tool uses unsupported feature:
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121
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Generate files not supported
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122
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Test [45/73] Test failed: /home/radhika/cwl/common-workflow-language/arv-run.sh --outdir=/tmp/tmptdNybC --quiet v1.0/schemadef-wf.cwl v1.0/schemadef-job.json
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123
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Test SchemaDefRequirement definition used in workflow parameter
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124
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125
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expected output object {
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126
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"output": {
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127
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"checksum": "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e",
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128
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"class": "File",
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129
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"location": "output.txt",
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130
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"size": 12
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131
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}
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132
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}
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133
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got {
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134
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"output": {
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135
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"basename": "output.txt",
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136
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"class": "File",
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137
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"location": "keep:0615107d3b762bf17891133ceac58423+54/output.txt",
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138
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"size": 12
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139
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}
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140
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}
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141
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Compare failure expected {
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142
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"checksum": "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e",
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143
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"class": "File",
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144
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"size": 12
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145
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}
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146
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got {
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147
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"class": "File",
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148
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"size": 12
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149
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}
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150
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Test [46/73]
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151
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152
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Test [50/73]
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153
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154
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Test [53/73] 2016-08-03 15:19:07 arvados.cwl-runner[23331] ERROR: While getting final output object: No JSON object could be decoded 2016-08-03 15:19:07 arvados.cwl-runner[23331] WARNING: Overall process status is UnsupportedRequirement
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155
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Workflow or tool uses unsupported feature:
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156
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Check log for details.
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157
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Test [64/73] Test failed: /home/radhika/cwl/common-workflow-language/arv-run.sh --outdir=/tmp/tmp9HP57r --quiet 'v1.0/conflict-wf.cwl#collision' v1.0/conflict-job.json
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158
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Test workflow two input files with same name.
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159
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expected output object {
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160
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"fileout": {
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161
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"checksum": "sha1$a2d8d6e7b28295dc9977dc3bdb652ddd480995f0",
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162
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"class": "File",
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163
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"location": "out.txt",
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164
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"size": 25
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165
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}
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166
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}
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167
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got {
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168
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"fileout": {
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169
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"basename": "out.txt",
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170
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"class": "File",
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171
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"location": "keep:0e8e4042f19c03f0da52b90c2466e56c+51/out.txt",
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172
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"size": 25
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173
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}
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174
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}
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175
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Compare failure expected {
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176
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"checksum": "sha1$a2d8d6e7b28295dc9977dc3bdb652ddd480995f0",
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177
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"class": "File",
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178
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"size": 25
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179
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}
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180
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got {
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181
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"class": "File",
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182
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"size": 25
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183
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}
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184
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Test [69/73] Workflow or tool uses unsupported feature:
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185
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Generate files not supported
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186
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Test [70/73] Workflow or tool uses unsupported feature:
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187
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Generate files not supported
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188
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Test [72/73] Workflow or tool uses unsupported feature:
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189
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Generate files not supported
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190
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Test [73/73] 5 failures, 15 unsupported features
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191
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192
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1 tool tests failed
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193
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